From 2e3a141cdb752e65f8ec49d87d53ecc127e43be2 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Tue, 15 Nov 2022 09:46:37 -0500 Subject: [PATCH 01/60] original xlsx, partially tidied txt --- .../TermsUpdated_organicmatterextraction.txt | 66 ++++++++++++++++++ .../TermsUpdated_organicmatterextraction.xlsx | Bin 0 -> 18161 bytes 2 files changed, 66 insertions(+) create mode 100644 assets/TermsUpdated_organicmatterextraction.txt create mode 100644 assets/TermsUpdated_organicmatterextraction.xlsx diff --git a/assets/TermsUpdated_organicmatterextraction.txt b/assets/TermsUpdated_organicmatterextraction.txt new file mode 100644 index 0000000000..2c85c87d47 --- /dev/null +++ b/assets/TermsUpdated_organicmatterextraction.txt @@ -0,0 +1,66 @@ +class is_a Slot Replaced Origin additional mapped slots aliases comments slot_uri Link description Notes / commends +class is_a slot ignore ignore ignore comments slot_uri ignore ignore ignore +FiltrationActivity separation_method funnel CHMO: Chemical Method Ontology http://purl.obolibrary.org/obo/CHMO_0000999 https://www.ebi.ac.uk/ols/ontologies/chmo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0000999&lang=en&viewMode=All&siblings=false A method that results in the separation of two or more components according to some property. +AcidificationActivity concentration "EDAM : Bioinformatics operations, data types, formats, identifiers and topics" "The URI corresponding to the Link is http://edamontology.org/data_2140, but that is for ""Concentration""" https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_2140 The concentration of a chemical compound. +AcidificationActivity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the acidification +Aliquot source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the weighing activity +AnalyteStorage Activity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the weighing activity +Extraction source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the extraction activity +FiltrationActivity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the extraction activity +AcidificationActivity acid IUPAC Gold Book https://goldbook.iupac.org/terms/view/A00071 A molecular entity or chemical species capable of donating a hydron (proton) (see Brnsted acid) or capable of forming a covalent bond with an electron pair (see Lewis acid). +AcidificationActivity unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 "Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols." general unit term for values that don't have something more specific +AnalyteStorage celsius_temperature temperature & unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/C00928 "Thermodynamic temperature minus 273.15 K, invariably expressed in the SI unit degree Celsius (_C) which is equal to the kelvin. Sometimes the misnomer centigrade temperature is used for Celsius temperature." +Extraction extractant solvent IUPAC Gold Book https://goldbook.iupac.org/terms/view/E02299 The active component(s) primarily responsible for transfer of a solute from one phase to the other. +Extraction mixing shaker IUPAC Gold Book https://goldbook.iupac.org/terms/view/M03945 "The combining of components, particles or layers into a more homogeneous state. The mixing may be achieved manually or mechanically by shifting the material with stirrers or pumps or by revolving or shaking the container. The process must not permit segregation of particles of different size or properties. Homogeneity may be considered to have been achieved in a practical sense when the sampling error of the processed portion is negligible compared to the total error of the measurement system." +Extraction unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 "Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols." general unit term for values that don't have something more specific +FiltrationActivity conditioning IUPAC Gold Book https://goldbook.iupac.org/terms/view/C01242 Preliminary treatment of either phase with a suitable solution of the other phase (in the absence of main extractable solute(s)) so that when the subsequent equilibration is carried out changes in the (volume) phase ratio or in the concentrations of other components are minimized. synonomous with pre-equilibrium +FiltrationActivity filter IUPAC Gold Book https://goldbook.iupac.org/terms/view/F02384 "A porous material on which solid particles present in air or other fluid which flows through it are largely caught and retained. Filters are made with a variety of materials: cellulose and derivatives, glass fibre, ceramic, synthetic plastics and fibres. Filters may be naturally porous or be made so by mechanical or other means. Membrane/ceramic filters are prepared with highly controlled pore size in a sheet of suitable material such as polyfluoroethylene, polycarbonate or cellulose esters. Nylon mesh is sometimes used for reinforcement. The pores constitute 8085% of the filter volume commonly and several pore sizes are available for air sampling (0.45_0.8 _m are commonly employed)." +FiltrationActivity unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 "Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols." +FiltrationActivity Activity filtration-activity IUPAC Gold Book https://goldbook.iupac.org/terms/view/F02388 "The process of segregation of phases; e.g. the separation of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium." +PhaseSeparation unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 "Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols." general unit term for values that don't have something more specific +PhaseSeparation unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 "Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols." general unit term for values that don't have something more specific +PhaseSeparation value speed IUPAC Gold Book https://goldbook.iupac.org/terms/view/V06593 Magnitude of a particular quantity generally expressed as a unit of measurement multiplied by a number. +PhaseSeparation Activity centrifugation-activity IUPAC Gold Book https://goldbook.iupac.org/terms/view/P04534 The process by which a single solid (liquid) phase separates into two or more new phases. +AcidificationActivity volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." +Aliquot volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." +AnalyticalSample volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." +Extraction sample_volume volume Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000005&jump_to_nav=true " +Total volume of solution used." +Extraction volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." +Extraction Activity dissolution-activity Mass Spectrometry Ontology solvent extraction (IUPAC GOLD book) https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0302884&jump_to_nav=true " +A material separation in which a desired component of an input material is separated from the remainder" +FiltrationActivity volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." +AcidificationActivity analyte_id id National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id" Unique identifier for the analytical sample resulting from the extraction activity Not directly taken from proteomic data commons +Aliquot analyte_id id National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id" Unique identifier for the analytical sample resulting from the Weighing Activity Not directly taken from proteomic data commons +Aliquot starting_amount weight National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Protocol Mass with units Terms required units are the best / could be incorrect. See notes +Aliquot MaterialEntity weighing-activity National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Aliquot "Pertaining to a portion of the whole; any one of two or more samples of something, of the same volume or weight." +AnalyteStorage analyte_id id National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id" Unique identifier for the analytical sample resulting from the Weighing Activity Not directly taken from proteomic data commons +AnalyteStorage analyte_volume volume National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in" The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. +AnalyticalSample analyte_id id National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id" Unique identifier for the analytical sample resulting from the Weighing Activity Not directly taken from proteomic data commons +AnalyticalSample analyte_volume volume National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in" The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. +AnalyticalSample MaterialEntity National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte "A liquid bulk product produced according to specified lab protocols, from a sample or analyte, intended for further analysis." +Extraction analyte_id id National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id" Unique identifier for the analytical sample resulting from the extraction activity Not directly taken from proteomic data commons +Extraction concentration National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,concentration,-Numeric%20value%20that" "Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter." +FiltrationActivity analyte_id id National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id" Unique identifier for the analytical sample resulting from the extraction activity Not directly taken from proteomic data commons +FiltrationActivity analyte_volume volume National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in" The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. +AcidificationActivity volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. +Aliquot volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. +AnalyticalSample volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. +Extraction duration time National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25330&jump_to_nav=true " +The period of time during which something continues." +Extraction speed National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C41146&jump_to_nav=true A scalar measure of the rate of movement of the object expressed either as the distance travelled divided by the time taken (average speed) or the rate of change of position with respect to time at a particular point (instantaneous speed). +Extraction volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. +FiltrationActivity volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. +PhaseSeparation duration time National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25330&jump_to_nav=true " +The period of time during which something continues." +AcidificationActivity pH NCIT: NCI Thesaurus OBO Edition https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C45997 "Quantity of dimension one used to express on a scale from 0 to 14 the amount-of-substance concentration of hydrogen ion of dilute aqueous solution, calculated as the logarithm of the reciprocal of hydrogen-ion concentration in gram atoms per liter." +FiltrationActivity material_pore_size numeric_value NCIT: NCI Thesaurus OBO Edition https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C112332 A quantitative or qualitative measurement of the physical dimensions of the pores in a material. +PhaseSeparation material_component_separation type OBI https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0600014&lang=en&viewMode=All&siblings=true a material processing in which components of an input material become segregated in space centrifugation is a sub-ontology of this term and is the method we'll use (https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0302886&lang=en&viewMode=All&siblings=true) +AcidificationActivity Activity acidification-activity Activity of modifying the pH of a sample or solution via addition of some acid. No ontology term found +Aliquot container_type contanier The vessel the sample was stored and extracted in No ontology term found +AnalyticalSample container_type contanier The vessel the sample was stored and extracted in No ontology term found +Extraction container_type contanier The vessel the sample was stored and extracted in No ontology term found +FiltrationActivity conditioning_volume The volume of solvent used to condition the filter in milliliters ? Is that it? 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Miller" Date: Wed, 16 Nov 2022 12:07:34 -0500 Subject: [PATCH 02/60] TermsUpdated_organicmatterextraction sheet compiles needs work; lots of ignores --- Makefile | 7 +- .../TermsUpdated_organicmatterextraction.tsv | 66 +++++++++++++++++++ .../TermsUpdated_organicmatterextraction.txt | 66 ------------------- pyproject.toml | 1 + 4 files changed, 73 insertions(+), 67 deletions(-) create mode 100644 assets/TermsUpdated_organicmatterextraction.tsv delete mode 100644 assets/TermsUpdated_organicmatterextraction.txt diff --git a/Makefile b/Makefile index cdccc3fa63..53a77e6ef6 100644 --- a/Makefile +++ b/Makefile @@ -331,4 +331,9 @@ from_mongo_cleanup: rm -rf assets/from_mongodb.yaml rm -rf assets/from_mongodb_updated.json -from_mongo_all: from_mongo_cleanup validate_vs_3_2_0 validate_vs_current \ No newline at end of file +from_mongo_all: from_mongo_cleanup validate_vs_3_2_0 validate_vs_current + +target/TermsUpdated_organicmatterextraction.yaml: assets/TermsUpdated_organicmatterextraction.tsv + $(RUN) sheets2linkml \ + --name TermsUpdated_organicmatterextraction \ + --output $@ $^ \ No newline at end of file diff --git a/assets/TermsUpdated_organicmatterextraction.tsv b/assets/TermsUpdated_organicmatterextraction.tsv new file mode 100644 index 0000000000..5c52bb55f9 --- /dev/null +++ b/assets/TermsUpdated_organicmatterextraction.tsv @@ -0,0 +1,66 @@ +class is_a Slot range Replaced Origin additional mapped slots aliases comments slot_uri Link description Notes / commends +> class is_a slot range ignore ignore ignore aliases comments slot_uri ignore ignore ignore +AcidificationActivity acid IUPAC Gold Book https://goldbook.iupac.org/terms/view/A00071 A molecular entity or chemical species capable of donating a hydron (proton) (see Br�nsted acid) or capable of forming a covalent bond with an electron pair (see Lewis acid). +AcidificationActivity analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the extraction activity +AcidificationActivity concentration EDAM : Bioinformatics operations, data types, formats, identifiers and topics "The URI corresponding to the Link is http://edamontology.org/data_2140, but that is for ""Concentration""" https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_2140 The concentration of a chemical compound. +AcidificationActivity pH NCIT: NCI Thesaurus OBO Edition https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C45997 Quantity of dimension one used to express on a scale from 0 to 14 the amount-of-substance concentration of hydrogen ion of dilute aqueous solution, calculated as the logarithm of the reciprocal of hydrogen-ion concentration in gram atoms per liter. +AcidificationActivity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the acidification +AcidificationActivity unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. +AcidificationActivity volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. +AcidificationActivity volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. +AcidificationActivity Activity acidification-activity Activity of modifying the pH of a sample or solution via addition of some acid. general unit term for values that don't have something more specific +Activity +Aliquot analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the Weighing Activity +Aliquot container_type contanier The vessel the sample was stored and extracted in +Aliquot source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the weighing activity general unit term for values that don't have something more specific +Aliquot starting_amount weight National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Protocol Mass with units synonomous with pre-equilibrium +Aliquot volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. +Aliquot volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. +Aliquot MaterialEntity weighing-activity National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Aliquot Pertaining to a portion of the whole; any one of two or more samples of something, of the same volume or weight. +AnalyteStorage analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the Weighing Activity general unit term for values that don't have something more specific +AnalyteStorage analyte_volume volume National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. general unit term for values that don't have something more specific +AnalyteStorage celsius_temperature temperature & unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/C00928 Thermodynamic temperature minus 273.15 K, invariably expressed in the SI unit degree Celsius (_C) which is equal to the kelvin. Sometimes the misnomer centigrade temperature is used for Celsius temperature. +AnalyteStorage Activity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the weighing activity +AnalyticalSample analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the Weighing Activity +AnalyticalSample analyte_volume volume National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. +AnalyticalSample container_type contanier The vessel the sample was stored and extracted in +AnalyticalSample volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. +AnalyticalSample volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. +AnalyticalSample MaterialEntity National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte A liquid bulk product produced according to specified lab protocols, from a sample or analyte, intended for further analysis. +Extraction analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the extraction activity +Extraction concentration National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,concentration,-Numeric%20value%20that Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter. Not directly taken from proteomic data commons +Extraction container_type contanier The vessel the sample was stored and extracted in Not directly taken from proteomic data commons +Extraction duration time National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25330&jump_to_nav=true " +The period of time during which something continues." Terms required units are the best / could be incorrect. See notes +Extraction extractant solvent IUPAC Gold Book https://goldbook.iupac.org/terms/view/E02299 The active component(s) primarily responsible for transfer of a solute from one phase to the other. +Extraction mixing shaker IUPAC Gold Book https://goldbook.iupac.org/terms/view/M03945 The combining of components, particles or layers into a more homogeneous state. The mixing may be achieved manually or mechanically by shifting the material with stirrers or pumps or by revolving or shaking the container. The process must not permit segregation of particles of different size or properties. Homogeneity may be considered to have been achieved in a practical sense when the sampling error of the processed portion is negligible compared to the total error of the measurement system. Not directly taken from proteomic data commons +Extraction sample_volume volume Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000005&jump_to_nav=true " +Total volume of solution used." +Extraction source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the extraction activity Not directly taken from proteomic data commons +Extraction speed National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C41146&jump_to_nav=true A scalar measure of the rate of movement of the object expressed either as the distance travelled divided by the time taken (average speed) or the rate of change of position with respect to time at a particular point (instantaneous speed). +Extraction unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. +Extraction volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. Not directly taken from proteomic data commons +Extraction volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. +Extraction Activity dissolution-activity Mass Spectrometry Ontology solvent extraction (IUPAC GOLD book) https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0302884&jump_to_nav=true " +A material separation in which a desired component of an input material is separated from the remainder" Not directly taken from proteomic data commons +FiltrationActivity analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the extraction activity +FiltrationActivity analyte_volume volume National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. +FiltrationActivity conditioning IUPAC Gold Book https://goldbook.iupac.org/terms/view/C01242 Preliminary treatment of either phase with a suitable solution of the other phase (in the absence of main extractable solute(s)) so that when the subsequent equilibration is carried out changes in the (volume) phase ratio or in the concentrations of other components are minimized. +FiltrationActivity conditioning_volume The volume of solvent used to condition the filter in milliliters +FiltrationActivity container_type contanier The vessel the sample was stored and extracted in +FiltrationActivity filter IUPAC Gold Book https://goldbook.iupac.org/terms/view/F02384 A porous material on which solid particles present in air or other fluid which flows through it are largely caught and retained. Filters are made with a variety of materials: cellulose and derivatives, glass fibre, ceramic, synthetic plastics and fibres. Filters may be naturally porous or be made so by mechanical or other means. Membrane/ceramic filters are prepared with highly controlled pore size in a sheet of suitable material such as polyfluoroethylene, polycarbonate or cellulose esters. Nylon mesh is sometimes used for reinforcement. The pores constitute 80�85% of the filter volume commonly and several pore sizes are available for air sampling (0.45_0.8 _m are commonly employed). +FiltrationActivity material_pore_size numeric_value NCIT: NCI Thesaurus OBO Edition https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C112332 A quantitative or qualitative measurement of the physical dimensions of the pores in a material. +FiltrationActivity separation_method funnel CHMO: Chemical Method Ontology http://purl.obolibrary.org/obo/CHMO_0000999 https://www.ebi.ac.uk/ols/ontologies/chmo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0000999&lang=en&viewMode=All&siblings=false A method that results in the separation of two or more components according to some property. +FiltrationActivity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the extraction activity +FiltrationActivity unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. +FiltrationActivity volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. +FiltrationActivity volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. centrifugation is a sub-ontology of this term and is the method we'll use (https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0302886&lang=en&viewMode=All&siblings=true) +FiltrationActivity Activity filtration-activity IUPAC Gold Book https://goldbook.iupac.org/terms/view/F02388 The process of segregation of phases; e.g. the separation of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium. No ontology term found +MaterialEntity No ontology term found +PhaseSeparation duration time National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25330&jump_to_nav=true " +The period of time during which something continues." No ontology term found +PhaseSeparation material_component_separation type OBI https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0600014&lang=en&viewMode=All&siblings=true a material processing in which components of an input material become segregated in space No ontology term found +PhaseSeparation unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. ? Is that it? Or is it volume of sample used? +PhaseSeparation unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. No ontology term found +PhaseSeparation value speed IUPAC Gold Book https://goldbook.iupac.org/terms/view/V06593 Magnitude of a particular quantity generally expressed as a unit of measurement multiplied by a number. +PhaseSeparation Activity centrifugation-activity IUPAC Gold Book https://goldbook.iupac.org/terms/view/P04534 The process by which a single solid (liquid) phase separates into two or more new phases. diff --git a/assets/TermsUpdated_organicmatterextraction.txt b/assets/TermsUpdated_organicmatterextraction.txt deleted file mode 100644 index 2c85c87d47..0000000000 --- a/assets/TermsUpdated_organicmatterextraction.txt +++ /dev/null @@ -1,66 +0,0 @@ -class is_a Slot Replaced Origin additional mapped slots aliases comments slot_uri Link description Notes / commends -class is_a slot ignore ignore ignore comments slot_uri ignore ignore ignore -FiltrationActivity separation_method funnel CHMO: Chemical Method Ontology http://purl.obolibrary.org/obo/CHMO_0000999 https://www.ebi.ac.uk/ols/ontologies/chmo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0000999&lang=en&viewMode=All&siblings=false A method that results in the separation of two or more components according to some property. -AcidificationActivity concentration "EDAM : Bioinformatics operations, data types, formats, identifiers and topics" "The URI corresponding to the Link is http://edamontology.org/data_2140, but that is for ""Concentration""" https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_2140 The concentration of a chemical compound. -AcidificationActivity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the acidification -Aliquot source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the weighing activity -AnalyteStorage Activity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the weighing activity -Extraction source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the extraction activity -FiltrationActivity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the extraction activity -AcidificationActivity acid IUPAC Gold Book https://goldbook.iupac.org/terms/view/A00071 A molecular entity or chemical species capable of donating a hydron (proton) (see Brnsted acid) or capable of forming a covalent bond with an electron pair (see Lewis acid). -AcidificationActivity unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 "Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols." general unit term for values that don't have something more specific -AnalyteStorage celsius_temperature temperature & unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/C00928 "Thermodynamic temperature minus 273.15 K, invariably expressed in the SI unit degree Celsius (_C) which is equal to the kelvin. Sometimes the misnomer centigrade temperature is used for Celsius temperature." -Extraction extractant solvent IUPAC Gold Book https://goldbook.iupac.org/terms/view/E02299 The active component(s) primarily responsible for transfer of a solute from one phase to the other. -Extraction mixing shaker IUPAC Gold Book https://goldbook.iupac.org/terms/view/M03945 "The combining of components, particles or layers into a more homogeneous state. The mixing may be achieved manually or mechanically by shifting the material with stirrers or pumps or by revolving or shaking the container. The process must not permit segregation of particles of different size or properties. Homogeneity may be considered to have been achieved in a practical sense when the sampling error of the processed portion is negligible compared to the total error of the measurement system." -Extraction unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 "Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols." general unit term for values that don't have something more specific -FiltrationActivity conditioning IUPAC Gold Book https://goldbook.iupac.org/terms/view/C01242 Preliminary treatment of either phase with a suitable solution of the other phase (in the absence of main extractable solute(s)) so that when the subsequent equilibration is carried out changes in the (volume) phase ratio or in the concentrations of other components are minimized. synonomous with pre-equilibrium -FiltrationActivity filter IUPAC Gold Book https://goldbook.iupac.org/terms/view/F02384 "A porous material on which solid particles present in air or other fluid which flows through it are largely caught and retained. Filters are made with a variety of materials: cellulose and derivatives, glass fibre, ceramic, synthetic plastics and fibres. Filters may be naturally porous or be made so by mechanical or other means. Membrane/ceramic filters are prepared with highly controlled pore size in a sheet of suitable material such as polyfluoroethylene, polycarbonate or cellulose esters. Nylon mesh is sometimes used for reinforcement. The pores constitute 8085% of the filter volume commonly and several pore sizes are available for air sampling (0.45_0.8 _m are commonly employed)." -FiltrationActivity unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 "Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols." -FiltrationActivity Activity filtration-activity IUPAC Gold Book https://goldbook.iupac.org/terms/view/F02388 "The process of segregation of phases; e.g. the separation of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium." -PhaseSeparation unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 "Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols." general unit term for values that don't have something more specific -PhaseSeparation unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 "Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols." general unit term for values that don't have something more specific -PhaseSeparation value speed IUPAC Gold Book https://goldbook.iupac.org/terms/view/V06593 Magnitude of a particular quantity generally expressed as a unit of measurement multiplied by a number. -PhaseSeparation Activity centrifugation-activity IUPAC Gold Book https://goldbook.iupac.org/terms/view/P04534 The process by which a single solid (liquid) phase separates into two or more new phases. -AcidificationActivity volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." -Aliquot volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." -AnalyticalSample volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." -Extraction sample_volume volume Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000005&jump_to_nav=true " -Total volume of solution used." -Extraction volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." -Extraction Activity dissolution-activity Mass Spectrometry Ontology solvent extraction (IUPAC GOLD book) https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0302884&jump_to_nav=true " -A material separation in which a desired component of an input material is separated from the remainder" -FiltrationActivity volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." -AcidificationActivity analyte_id id National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id" Unique identifier for the analytical sample resulting from the extraction activity Not directly taken from proteomic data commons -Aliquot analyte_id id National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id" Unique identifier for the analytical sample resulting from the Weighing Activity Not directly taken from proteomic data commons -Aliquot starting_amount weight National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Protocol Mass with units Terms required units are the best / could be incorrect. See notes -Aliquot MaterialEntity weighing-activity National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Aliquot "Pertaining to a portion of the whole; any one of two or more samples of something, of the same volume or weight." -AnalyteStorage analyte_id id National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id" Unique identifier for the analytical sample resulting from the Weighing Activity Not directly taken from proteomic data commons -AnalyteStorage analyte_volume volume National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in" The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. -AnalyticalSample analyte_id id National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id" Unique identifier for the analytical sample resulting from the Weighing Activity Not directly taken from proteomic data commons -AnalyticalSample analyte_volume volume National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in" The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. -AnalyticalSample MaterialEntity National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte "A liquid bulk product produced according to specified lab protocols, from a sample or analyte, intended for further analysis." -Extraction analyte_id id National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id" Unique identifier for the analytical sample resulting from the extraction activity Not directly taken from proteomic data commons -Extraction concentration National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,concentration,-Numeric%20value%20that" "Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter." -FiltrationActivity analyte_id id National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id" Unique identifier for the analytical sample resulting from the extraction activity Not directly taken from proteomic data commons -FiltrationActivity analyte_volume volume National Cancer Institure Proteomic Data Commons "https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in" The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. -AcidificationActivity volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. -Aliquot volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. -AnalyticalSample volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. -Extraction duration time National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25330&jump_to_nav=true " -The period of time during which something continues." -Extraction speed National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C41146&jump_to_nav=true A scalar measure of the rate of movement of the object expressed either as the distance travelled divided by the time taken (average speed) or the rate of change of position with respect to time at a particular point (instantaneous speed). -Extraction volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. -FiltrationActivity volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. -PhaseSeparation duration time National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25330&jump_to_nav=true " -The period of time during which something continues." -AcidificationActivity pH NCIT: NCI Thesaurus OBO Edition https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C45997 "Quantity of dimension one used to express on a scale from 0 to 14 the amount-of-substance concentration of hydrogen ion of dilute aqueous solution, calculated as the logarithm of the reciprocal of hydrogen-ion concentration in gram atoms per liter." -FiltrationActivity material_pore_size numeric_value NCIT: NCI Thesaurus OBO Edition https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C112332 A quantitative or qualitative measurement of the physical dimensions of the pores in a material. -PhaseSeparation material_component_separation type OBI https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0600014&lang=en&viewMode=All&siblings=true a material processing in which components of an input material become segregated in space centrifugation is a sub-ontology of this term and is the method we'll use (https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0302886&lang=en&viewMode=All&siblings=true) -AcidificationActivity Activity acidification-activity Activity of modifying the pH of a sample or solution via addition of some acid. No ontology term found -Aliquot container_type contanier The vessel the sample was stored and extracted in No ontology term found -AnalyticalSample container_type contanier The vessel the sample was stored and extracted in No ontology term found -Extraction container_type contanier The vessel the sample was stored and extracted in No ontology term found -FiltrationActivity conditioning_volume The volume of solvent used to condition the filter in milliliters ? Is that it? Or is it volume of sample used? -FiltrationActivity container_type contanier The vessel the sample was stored and extracted in No ontology term found -Activity -MaterialEntity \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 5565032fb4..4ebaadbd2c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,6 +44,7 @@ nmdc-data = "nmdc_schema.nmdc_data:cli" [tool.poetry.dependencies] python = "^3.9" linkml = "*" +schemasheets = "^0.1.16" [tool.poetry.dev-dependencies] black = "^22.3.0" From ffa45dea241845fd1b12f896ee40f9bc94af5787 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Wed, 16 Nov 2022 14:31:06 -0500 Subject: [PATCH 03/60] elborating in shemasheet --- .../TermsUpdated_organicmatterextraction.tsv | 136 +++++++++--------- 1 file changed, 70 insertions(+), 66 deletions(-) diff --git a/assets/TermsUpdated_organicmatterextraction.tsv b/assets/TermsUpdated_organicmatterextraction.tsv index 5c52bb55f9..d42d65993f 100644 --- a/assets/TermsUpdated_organicmatterextraction.tsv +++ b/assets/TermsUpdated_organicmatterextraction.tsv @@ -1,66 +1,70 @@ -class is_a Slot range Replaced Origin additional mapped slots aliases comments slot_uri Link description Notes / commends -> class is_a slot range ignore ignore ignore aliases comments slot_uri ignore ignore ignore -AcidificationActivity acid IUPAC Gold Book https://goldbook.iupac.org/terms/view/A00071 A molecular entity or chemical species capable of donating a hydron (proton) (see Br�nsted acid) or capable of forming a covalent bond with an electron pair (see Lewis acid). -AcidificationActivity analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the extraction activity -AcidificationActivity concentration EDAM : Bioinformatics operations, data types, formats, identifiers and topics "The URI corresponding to the Link is http://edamontology.org/data_2140, but that is for ""Concentration""" https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_2140 The concentration of a chemical compound. -AcidificationActivity pH NCIT: NCI Thesaurus OBO Edition https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C45997 Quantity of dimension one used to express on a scale from 0 to 14 the amount-of-substance concentration of hydrogen ion of dilute aqueous solution, calculated as the logarithm of the reciprocal of hydrogen-ion concentration in gram atoms per liter. -AcidificationActivity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the acidification -AcidificationActivity unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. -AcidificationActivity volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. -AcidificationActivity volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. -AcidificationActivity Activity acidification-activity Activity of modifying the pH of a sample or solution via addition of some acid. general unit term for values that don't have something more specific -Activity -Aliquot analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the Weighing Activity -Aliquot container_type contanier The vessel the sample was stored and extracted in -Aliquot source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the weighing activity general unit term for values that don't have something more specific -Aliquot starting_amount weight National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Protocol Mass with units synonomous with pre-equilibrium -Aliquot volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. -Aliquot volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. -Aliquot MaterialEntity weighing-activity National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Aliquot Pertaining to a portion of the whole; any one of two or more samples of something, of the same volume or weight. -AnalyteStorage analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the Weighing Activity general unit term for values that don't have something more specific -AnalyteStorage analyte_volume volume National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. general unit term for values that don't have something more specific -AnalyteStorage celsius_temperature temperature & unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/C00928 Thermodynamic temperature minus 273.15 K, invariably expressed in the SI unit degree Celsius (_C) which is equal to the kelvin. Sometimes the misnomer centigrade temperature is used for Celsius temperature. -AnalyteStorage Activity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the weighing activity -AnalyticalSample analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the Weighing Activity -AnalyticalSample analyte_volume volume National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. -AnalyticalSample container_type contanier The vessel the sample was stored and extracted in -AnalyticalSample volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. -AnalyticalSample volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. -AnalyticalSample MaterialEntity National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte A liquid bulk product produced according to specified lab protocols, from a sample or analyte, intended for further analysis. -Extraction analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the extraction activity -Extraction concentration National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,concentration,-Numeric%20value%20that Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter. Not directly taken from proteomic data commons -Extraction container_type contanier The vessel the sample was stored and extracted in Not directly taken from proteomic data commons -Extraction duration time National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25330&jump_to_nav=true " -The period of time during which something continues." Terms required units are the best / could be incorrect. See notes -Extraction extractant solvent IUPAC Gold Book https://goldbook.iupac.org/terms/view/E02299 The active component(s) primarily responsible for transfer of a solute from one phase to the other. -Extraction mixing shaker IUPAC Gold Book https://goldbook.iupac.org/terms/view/M03945 The combining of components, particles or layers into a more homogeneous state. The mixing may be achieved manually or mechanically by shifting the material with stirrers or pumps or by revolving or shaking the container. The process must not permit segregation of particles of different size or properties. Homogeneity may be considered to have been achieved in a practical sense when the sampling error of the processed portion is negligible compared to the total error of the measurement system. Not directly taken from proteomic data commons -Extraction sample_volume volume Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000005&jump_to_nav=true " -Total volume of solution used." -Extraction source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the extraction activity Not directly taken from proteomic data commons -Extraction speed National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C41146&jump_to_nav=true A scalar measure of the rate of movement of the object expressed either as the distance travelled divided by the time taken (average speed) or the rate of change of position with respect to time at a particular point (instantaneous speed). -Extraction unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. -Extraction volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. Not directly taken from proteomic data commons -Extraction volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. -Extraction Activity dissolution-activity Mass Spectrometry Ontology solvent extraction (IUPAC GOLD book) https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0302884&jump_to_nav=true " -A material separation in which a desired component of an input material is separated from the remainder" Not directly taken from proteomic data commons -FiltrationActivity analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the extraction activity -FiltrationActivity analyte_volume volume National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. -FiltrationActivity conditioning IUPAC Gold Book https://goldbook.iupac.org/terms/view/C01242 Preliminary treatment of either phase with a suitable solution of the other phase (in the absence of main extractable solute(s)) so that when the subsequent equilibration is carried out changes in the (volume) phase ratio or in the concentrations of other components are minimized. -FiltrationActivity conditioning_volume The volume of solvent used to condition the filter in milliliters -FiltrationActivity container_type contanier The vessel the sample was stored and extracted in -FiltrationActivity filter IUPAC Gold Book https://goldbook.iupac.org/terms/view/F02384 A porous material on which solid particles present in air or other fluid which flows through it are largely caught and retained. Filters are made with a variety of materials: cellulose and derivatives, glass fibre, ceramic, synthetic plastics and fibres. Filters may be naturally porous or be made so by mechanical or other means. Membrane/ceramic filters are prepared with highly controlled pore size in a sheet of suitable material such as polyfluoroethylene, polycarbonate or cellulose esters. Nylon mesh is sometimes used for reinforcement. The pores constitute 80�85% of the filter volume commonly and several pore sizes are available for air sampling (0.45_0.8 _m are commonly employed). -FiltrationActivity material_pore_size numeric_value NCIT: NCI Thesaurus OBO Edition https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C112332 A quantitative or qualitative measurement of the physical dimensions of the pores in a material. -FiltrationActivity separation_method funnel CHMO: Chemical Method Ontology http://purl.obolibrary.org/obo/CHMO_0000999 https://www.ebi.ac.uk/ols/ontologies/chmo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0000999&lang=en&viewMode=All&siblings=false A method that results in the separation of two or more components according to some property. -FiltrationActivity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the extraction activity -FiltrationActivity unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. -FiltrationActivity volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. -FiltrationActivity volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. centrifugation is a sub-ontology of this term and is the method we'll use (https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0302886&lang=en&viewMode=All&siblings=true) -FiltrationActivity Activity filtration-activity IUPAC Gold Book https://goldbook.iupac.org/terms/view/F02388 The process of segregation of phases; e.g. the separation of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium. No ontology term found -MaterialEntity No ontology term found -PhaseSeparation duration time National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25330&jump_to_nav=true " -The period of time during which something continues." No ontology term found -PhaseSeparation material_component_separation type OBI https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0600014&lang=en&viewMode=All&siblings=true a material processing in which components of an input material become segregated in space No ontology term found -PhaseSeparation unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. ? Is that it? Or is it volume of sample used? -PhaseSeparation unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. No ontology term found -PhaseSeparation value speed IUPAC Gold Book https://goldbook.iupac.org/terms/view/V06593 Magnitude of a particular quantity generally expressed as a unit of measurement multiplied by a number. -PhaseSeparation Activity centrifugation-activity IUPAC Gold Book https://goldbook.iupac.org/terms/view/P04534 The process by which a single solid (liquid) phase separates into two or more new phases. +class is_a Slot range required Replaced Origin additional mapped slots aliases comments class_uri slot_uri Link description Notes / commends +> class is_a slot range required ignore ignore ignore aliases comments class_uri slot_uri ignore ignore ignore +AcidificationActivity acid IUPAC Gold Book https://goldbook.iupac.org/terms/view/A00071 A molecular entity or chemical species capable of donating a hydron (proton) (see Br�nsted acid) or capable of forming a covalent bond with an electron pair (see Lewis acid). +AcidificationActivity analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the extraction activity +AcidificationActivity concentration EDAM : Bioinformatics operations, data types, formats, identifiers and topics "The URI corresponding to the Link is http://edamontology.org/data_2140, but that is for ""Concentration""" https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_2140 The concentration of a chemical compound. +AcidificationActivity pH NCIT: NCI Thesaurus OBO Edition https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C45997 Quantity of dimension one used to express on a scale from 0 to 14 the amount-of-substance concentration of hydrogen ion of dilute aqueous solution, calculated as the logarithm of the reciprocal of hydrogen-ion concentration in gram atoms per liter. +AcidificationActivity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the acidification +AcidificationActivity unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. +AcidificationActivity volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. +AcidificationActivity volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. +AcidificationActivity Activity acidification-activity Activity of modifying the pH of a sample or solution via addition of some acid. general unit term for values that don't have something more specific +Activity +AnalyteStorage analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the Weighing Activity +AnalyteStorage analyte_volume volume National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. general unit term for values that don't have something more specific +AnalyteStorage celsius_temperature temperature & unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/C00928 Thermodynamic temperature minus 273.15 K, invariably expressed in the SI unit degree Celsius (_C) which is equal to the kelvin. Sometimes the misnomer centigrade temperature is used for Celsius temperature. synonomous with pre-equilibrium +AnalyteStorage Activity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the weighing activity +AnalyticalSample analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the Weighing Activity +AnalyticalSample analyte_volume volume National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. general unit term for values that don't have something more specific +AnalyticalSample container_type contanier The vessel the sample was stored and extracted in general unit term for values that don't have something more specific +AnalyticalSample volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. +AnalyticalSample volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. +AnalyticalSample MaterialEntity National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte A liquid bulk product produced according to specified lab protocols, from a sample or analyte, intended for further analysis. +Container volume QuantityValue TRUE +Container http://purl.obolibrary.org/obo/OBI_0000967 +Extraction analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the extraction activity +Extraction concentration National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,concentration,-Numeric%20value%20that Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter. +Extraction container_type contanier The vessel the sample was stored and extracted in +Extraction duration time National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25330&jump_to_nav=true " +The period of time during which something continues." +Extraction extractant solvent IUPAC Gold Book https://goldbook.iupac.org/terms/view/E02299 The active component(s) primarily responsible for transfer of a solute from one phase to the other. Not directly taken from proteomic data commons +Extraction mixing shaker IUPAC Gold Book https://goldbook.iupac.org/terms/view/M03945 The combining of components, particles or layers into a more homogeneous state. The mixing may be achieved manually or mechanically by shifting the material with stirrers or pumps or by revolving or shaking the container. The process must not permit segregation of particles of different size or properties. Homogeneity may be considered to have been achieved in a practical sense when the sampling error of the processed portion is negligible compared to the total error of the measurement system. Not directly taken from proteomic data commons +Extraction sample_volume volume Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000005&jump_to_nav=true " +Total volume of solution used." Terms required units are the best / could be incorrect. See notes +Extraction source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the extraction activity +Extraction speed National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C41146&jump_to_nav=true A scalar measure of the rate of movement of the object expressed either as the distance travelled divided by the time taken (average speed) or the rate of change of position with respect to time at a particular point (instantaneous speed). Not directly taken from proteomic data commons +Extraction unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. +Extraction volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. Not directly taken from proteomic data commons +Extraction volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. +Extraction Activity dissolution-activity Mass Spectrometry Ontology solvent extraction (IUPAC GOLD book) https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0302884&jump_to_nav=true " +A material separation in which a desired component of an input material is separated from the remainder" +FiltrationActivity analyte_id id National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the extraction activity Not directly taken from proteomic data commons +FiltrationActivity analyte_volume volume National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=%2D-,analyte_volume,-The%20volume%20in The volume in microliters (ul) of the aliquot(s) derived from the analyte(s) shipped for sequencing and characterization. +FiltrationActivity conditioning IUPAC Gold Book https://goldbook.iupac.org/terms/view/C01242 Preliminary treatment of either phase with a suitable solution of the other phase (in the absence of main extractable solute(s)) so that when the subsequent equilibration is carried out changes in the (volume) phase ratio or in the concentrations of other components are minimized. Not directly taken from proteomic data commons +FiltrationActivity conditioning_volume The volume of solvent used to condition the filter in milliliters +FiltrationActivity container_type contanier The vessel the sample was stored and extracted in +FiltrationActivity filter IUPAC Gold Book https://goldbook.iupac.org/terms/view/F02384 A porous material on which solid particles present in air or other fluid which flows through it are largely caught and retained. Filters are made with a variety of materials: cellulose and derivatives, glass fibre, ceramic, synthetic plastics and fibres. Filters may be naturally porous or be made so by mechanical or other means. Membrane/ceramic filters are prepared with highly controlled pore size in a sheet of suitable material such as polyfluoroethylene, polycarbonate or cellulose esters. Nylon mesh is sometimes used for reinforcement. The pores constitute 80�85% of the filter volume commonly and several pore sizes are available for air sampling (0.45_0.8 _m are commonly employed). +FiltrationActivity material_pore_size numeric_value NCIT: NCI Thesaurus OBO Edition https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C112332 A quantitative or qualitative measurement of the physical dimensions of the pores in a material. +FiltrationActivity separation_method funnel CHMO: Chemical Method Ontology http://purl.obolibrary.org/obo/CHMO_0000999 https://www.ebi.ac.uk/ols/ontologies/chmo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0000999&lang=en&viewMode=All&siblings=false A method that results in the separation of two or more components according to some property. +FiltrationActivity source_mat_id source_material Genomics Standards Consortium MIxS https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the extraction activity +FiltrationActivity unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. +FiltrationActivity volume National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25335&jump_to_nav=true The amount of three dimensional space occupied by an object or the capacity of a space or container. +FiltrationActivity volume_unit unit Mass Spectrometry Ontology https://bioportal.bioontology.org/ontologies/MS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000000&jump_to_nav=true A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. +FiltrationActivity Activity filtration-activity IUPAC Gold Book https://goldbook.iupac.org/terms/view/F02388 The process of segregation of phases; e.g. the separation of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium. +MaterialEntity id +MaterialSamplingProcess container Container TRUE contanier container_type centrifugation is a sub-ontology of this term and is the method we'll use (https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0302886&lang=en&viewMode=All&siblings=true) +MaterialSamplingProcess input MaterialEntity TRUE source_material Genomics Standards Consortium MIxS source_mat_id https://genomicsstandardsconsortium.github.io/mixs/0000026/ A unique identifier assigned to the material sample that was used in the weighing activity No ontology term found +MaterialSamplingProcess output MaterialEntity TRUE id National Cancer Institure Proteomic Data Commons analyte_id https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Analyte#:~:text=Unique%20Keys-,analyte_id,-analyte_submitter_id Unique identifier for the analytical sample resulting from the Weighing Activity No ontology term found +MaterialSamplingProcess starting_amount QuantityValue TRUE weight National Cancer Institure Proteomic Data Commons https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Protocol Mass with units No ontology term found +MaterialSamplingProcess Activity weighing-activity National Cancer Institure Proteomic Data Commons Aliquoting activity http://purl.obolibrary.org/obo/OBI_0000744 https://proteomic.datacommons.cancer.gov/pdc/data-dictionary/Aliquot Pertaining to a portion of the whole; any one of two or more samples of something, of the same volume or weight. No ontology term found +PhaseSeparation duration time National Cancer Institute Thesaurus https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25330&jump_to_nav=true " +The period of time during which something continues." ? Is that it? Or is it volume of sample used? +PhaseSeparation material_component_separation type OBI https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0600014&lang=en&viewMode=All&siblings=true a material processing in which components of an input material become segregated in space No ontology term found +PhaseSeparation unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. +PhaseSeparation unit IUPAC Gold Book https://goldbook.iupac.org/terms/view/U06561 Particular quantity, defined and adopted by convention, with which other quanitities of the same kind are compared in order to express their magnitudes relative to that quantity. Units have conventionally assigned names and symbols. +PhaseSeparation value speed IUPAC Gold Book https://goldbook.iupac.org/terms/view/V06593 Magnitude of a particular quantity generally expressed as a unit of measurement multiplied by a number. +PhaseSeparation Activity centrifugation-activity IUPAC Gold Book https://goldbook.iupac.org/terms/view/P04534 The process by which a single solid (liquid) phase separates into two or more new phases. +QuantityValue has_numeric_value TRUE +QuantityValue has_raw_value +QuantityValue has_unit +QuantityValue From 9794db1a42c1d8e512effae06db8d4c8e18e9628 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Wed, 16 Nov 2022 16:11:55 -0500 Subject: [PATCH 04/60] sample data --- Makefile | 8 +++++++- assets/TermsUpdated_organicmatterextraction_data.yaml | 11 +++++++++++ 2 files changed, 18 insertions(+), 1 deletion(-) create mode 100644 assets/TermsUpdated_organicmatterextraction_data.yaml diff --git a/Makefile b/Makefile index 53a77e6ef6..f81aef3741 100644 --- a/Makefile +++ b/Makefile @@ -336,4 +336,10 @@ from_mongo_all: from_mongo_cleanup validate_vs_3_2_0 validate_vs_current target/TermsUpdated_organicmatterextraction.yaml: assets/TermsUpdated_organicmatterextraction.tsv $(RUN) sheets2linkml \ --name TermsUpdated_organicmatterextraction \ - --output $@ $^ \ No newline at end of file + --output $@ $^ + +assets/TermsUpdated_organicmatterextraction_data.json: assets/TermsUpdated_organicmatterextraction_data.yaml + $(RUN) linkml-convert \ + --output $@ \ + --target-class MaterialSamplingProcess \ + --schema target/TermsUpdated_organicmatterextraction.yaml $< \ No newline at end of file diff --git a/assets/TermsUpdated_organicmatterextraction_data.yaml b/assets/TermsUpdated_organicmatterextraction_data.yaml new file mode 100644 index 0000000000..5c9e4f5104 --- /dev/null +++ b/assets/TermsUpdated_organicmatterextraction_data.yaml @@ -0,0 +1,11 @@ +container: + volume: + has_numeric_value: 100 +input: + id: + nmdc:123 +output: + id: + nmdc:555 +starting_amount: + has_numeric_value: 50 From 493b497aa2d64b5453536985a0c5b2c78a15181d Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 17 Nov 2022 14:06:41 -0500 Subject: [PATCH 05/60] pushing converted data file --- ...rmsUpdated_organicmatterextraction_data.json | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 assets/TermsUpdated_organicmatterextraction_data.json diff --git a/assets/TermsUpdated_organicmatterextraction_data.json b/assets/TermsUpdated_organicmatterextraction_data.json new file mode 100644 index 0000000000..f719913bf2 --- /dev/null +++ b/assets/TermsUpdated_organicmatterextraction_data.json @@ -0,0 +1,17 @@ +{ + "container": { + "volume": { + "has_numeric_value": "100" + } + }, + "input": { + "id": "nmdc:123" + }, + "output": { + "id": "nmdc:555" + }, + "starting_amount": { + "has_numeric_value": "50" + }, + "@type": "MaterialSamplingProcess" +} \ No newline at end of file From 22ffbb7abf628d71a84c0ec9912d879713cace3a Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 17 Nov 2022 14:24:56 -0500 Subject: [PATCH 06/60] clean and all for TermsUpdated_organicmatterextraction --- Makefile | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index f81aef3741..d26654aed9 100644 --- a/Makefile +++ b/Makefile @@ -333,13 +333,19 @@ from_mongo_cleanup: from_mongo_all: from_mongo_cleanup validate_vs_3_2_0 validate_vs_current +TermsUpdated_organicmatterextraction_all: TermsUpdated_organicmatterextraction_clean assets/TermsUpdated_organicmatterextraction_data.json + +TermsUpdated_organicmatterextraction_clean: + rm -rf target/TermsUpdated_organicmatterextraction.yaml + rm -rf assets/TermsUpdated_organicmatterextraction_data.json + target/TermsUpdated_organicmatterextraction.yaml: assets/TermsUpdated_organicmatterextraction.tsv $(RUN) sheets2linkml \ --name TermsUpdated_organicmatterextraction \ --output $@ $^ -assets/TermsUpdated_organicmatterextraction_data.json: assets/TermsUpdated_organicmatterextraction_data.yaml +assets/TermsUpdated_organicmatterextraction_data.json: target/TermsUpdated_organicmatterextraction.yaml assets/TermsUpdated_organicmatterextraction_data.yaml $(RUN) linkml-convert \ --output $@ \ --target-class MaterialSamplingProcess \ - --schema target/TermsUpdated_organicmatterextraction.yaml $< \ No newline at end of file + --schema $^ \ No newline at end of file From de3ff84f582526352a68d801f18d212e9d56e25b Mon Sep 17 00:00:00 2001 From: Montana <44581429+mslarae13@users.noreply.github.com> Date: Tue, 20 Dec 2022 14:45:27 -0800 Subject: [PATCH 07/60] Update jgi_metagenomics.yaml updated sample_format_enum --- src/schema/portal/jgi_metagenomics.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/schema/portal/jgi_metagenomics.yaml b/src/schema/portal/jgi_metagenomics.yaml index c30a4bb637..12d537db63 100644 --- a/src/schema/portal/jgi_metagenomics.yaml +++ b/src/schema/portal/jgi_metagenomics.yaml @@ -55,6 +55,9 @@ enums: text: TE Water: text: Water + Gentegra-DNA: + Gentegra-RNA: + slots: dna_absorb1: name: dna_absorb1 From b2ca492b503a3f4e2c42aae0aec61d6e0ad75d1b Mon Sep 17 00:00:00 2001 From: Montana <44581429+mslarae13@users.noreply.github.com> Date: Tue, 20 Dec 2022 14:46:23 -0800 Subject: [PATCH 08/60] update metaT sample format add gentegra to enum --- src/schema/portal/jgi_metatranscriptomics.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/schema/portal/jgi_metatranscriptomics.yaml b/src/schema/portal/jgi_metatranscriptomics.yaml index e8486e73a2..30415bc965 100644 --- a/src/schema/portal/jgi_metatranscriptomics.yaml +++ b/src/schema/portal/jgi_metatranscriptomics.yaml @@ -55,6 +55,8 @@ enums: text: TE Water: text: Water + Gentegra-DNA: + Gentegra-RNA: slots: dnase_rna: name: dnase_rna From 1c88850eef2409d1ec4f9b582091b683d9f8a46c Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 22 Dec 2022 12:43:22 -0500 Subject: [PATCH 09/60] Study's id desc: "...sample..." -> "...study..." in the description of Study's slot usage of the id slot --- nmdc_schema/nmdc.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nmdc_schema/nmdc.yaml b/nmdc_schema/nmdc.yaml index 8a24c8abaa..e211bc6017 100644 --- a/nmdc_schema/nmdc.yaml +++ b/nmdc_schema/nmdc.yaml @@ -592,7 +592,7 @@ classes: - study_image slot_usage: id: - description: An NMDC assigned unique identifier for a sample submitted to NMDC. + description: An NMDC assigned unique identifier for a study submitted to NMDC. structured_pattern: syntax: "{id_nmdc_prefix}:{id_typecode_study}-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true From 577795bf416c6194235c009db7db9dc278ffe379 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 22 Dec 2022 13:50:10 -0500 Subject: [PATCH 10/60] regen --- json/nmdc.linkml.json | 135 +- jsonld-context/nmdc.context.jsonld | 14 +- jsonschema/nmdc.schema.json | 2 +- nmdc_schema/annotation.py | 2 +- nmdc_schema/basic_slots.py | 2 +- nmdc_schema/bioscales.py | 2 +- nmdc_schema/core.py | 2 +- nmdc_schema/external_identifiers.py | 2 +- nmdc_schema/mixs.py | 2 +- nmdc_schema/nmdc.py | 51 +- nmdc_schema/nmdc.schema.json | 2 +- nmdc_schema/nmdc.yaml | 105 +- nmdc_schema/prov.py | 2 +- nmdc_schema/sample_prep.py | 51 +- nmdc_schema/workflow_execution_activity.py | 2 +- poetry.lock | 3441 ++++++++++---------- python/annotation.py | 2 +- python/basic_slots.py | 2 +- python/bioscales.py | 2 +- python/core.py | 2 +- python/external_identifiers.py | 2 +- python/mixs.py | 2 +- python/nmdc.py | 51 +- python/portal/emsl.py | 2 +- python/portal/jgi_metagenomics.py | 6 +- python/portal/jgi_metatranscriptomics.py | 6 +- python/portal/mixs_inspired.py | 2 +- python/portal/sample_id.py | 2 +- python/prov.py | 2 +- python/sample_prep.py | 51 +- python/workflow_execution_activity.py | 2 +- 31 files changed, 2016 insertions(+), 1937 deletions(-) diff --git a/json/nmdc.linkml.json b/json/nmdc.linkml.json index 6396996aaa..292826c9a8 100644 --- a/json/nmdc.linkml.json +++ b/json/nmdc.linkml.json @@ -799,6 +799,22 @@ "multivalued": true, "range": "Study" }, + "field_research_site_set": { + "name": "field_research_site_set", + "from_schema": "https://microbiomedata/schema", + "domain": "Database", + "multivalued": true, + "range": "FieldResearchSite", + "inlined_as_list": true + }, + "collecting_biosamples_from_site_set": { + "name": "collecting_biosamples_from_site_set", + "from_schema": "https://microbiomedata/schema", + "domain": "Database", + "multivalued": true, + "range": "CollectingBiosamplesFromSite", + "inlined_as_list": true + }, "data_object_set": { "name": "data_object_set", "description": "This property links a database object to the set of data objects within it.", @@ -1220,47 +1236,6 @@ } }, "classes": { - "FieldResearchSite": { - "name": "FieldResearchSite", - "description": "A site, outside of a laboratory, from which biosamples may be collected.", - "title": "Field Research Site", - "comments": [ - "Provides grouping of biosamples at level that's more specific than belonging to the same study", - "be very clear that this could be part of a larger site", - "In Bioscales, one might say that rhizosphere soil and bulk soil from around the same plant were obtained at the same site. In this case, the site would correspond to one tree.", - "might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833" - ], - "from_schema": "https://microbiomedata/schema", - "aliases": [ - "research plot" - ], - "is_a": "Site" - }, - "CollectingBiosamplesFromSite": { - "name": "CollectingBiosamplesFromSite", - "title": "Collecting Biosamples From Site", - "comments": [ - "this illustrates implementing a Biosample relation with a process class" - ], - "from_schema": "https://microbiomedata/schema", - "is_a": "PlannedProcess", - "slots": [ - "has_inputs", - "has_outputs" - ], - "slot_usage": { - "has_inputs": { - "name": "has_inputs", - "range": "Site", - "required": true - }, - "has_outputs": { - "name": "has_outputs", - "range": "Biosample", - "required": true - } - } - }, "Database": { "name": "Database", "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest", @@ -1288,7 +1263,9 @@ "reaction_activity_set", "read_qc_analysis_activity_set", "read_based_taxonomy_analysis_activity_set", - "study_set" + "study_set", + "field_research_site_set", + "collecting_biosamples_from_site_set" ], "slot_usage": { "date_created": { @@ -1304,26 +1281,49 @@ "description": "TODO" } }, - "attributes": { - "frs_set": { - "name": "frs_set", - "from_schema": "https://microbiomedata/schema", - "domain": "Database", - "multivalued": true, - "range": "FieldResearchSite", - "inlined_as_list": true - }, - "cbfs_set": { - "name": "cbfs_set", - "from_schema": "https://microbiomedata/schema", - "domain": "Database", - "multivalued": true, - "range": "CollectingBiosamplesFromSite", - "inlined_as_list": true - } - }, "tree_root": true }, + "FieldResearchSite": { + "name": "FieldResearchSite", + "description": "A site, outside of a laboratory, from which biosamples may be collected.", + "title": "Field Research Site", + "comments": [ + "Provides grouping of biosamples at level that's more specific than belonging to the same study", + "be very clear that this could be part of a larger site", + "In Bioscales, one might say that rhizosphere soil and bulk soil from around the same plant were obtained at the same site. In this case, the site would correspond to one tree.", + "might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833" + ], + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "research plot" + ], + "is_a": "Site" + }, + "CollectingBiosamplesFromSite": { + "name": "CollectingBiosamplesFromSite", + "title": "Collecting Biosamples From Site", + "comments": [ + "this illustrates implementing a Biosample relation with a process class" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "PlannedProcess", + "slots": [ + "has_inputs", + "has_outputs" + ], + "slot_usage": { + "has_inputs": { + "name": "has_inputs", + "range": "Site", + "required": true + }, + "has_outputs": { + "name": "has_outputs", + "range": "Biosample", + "required": true + } + } + }, "DataObject": { "name": "DataObject", "id_prefixes": [ @@ -1665,6 +1665,21 @@ "part_of": { "name": "part_of", "required": true + }, + "extreme_event": { + "name": "extreme_event", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date, string" + } + }, + "examples": [ + { + "value": "1980-05-18, volcanic eruption" + } + ], + "range": "string" } } }, diff --git a/jsonld-context/nmdc.context.jsonld b/jsonld-context/nmdc.context.jsonld index 0567073aae..6f27471b7c 100644 --- a/jsonld-context/nmdc.context.jsonld +++ b/jsonld-context/nmdc.context.jsonld @@ -1,5 +1,5 @@ { - "_comments": "Auto generated from nmdc.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-12-14T15:01:17\n Schema: NMDC\n metamodel version: 1.7.0\n model version: 7.0.0\n \n id: https://microbiomedata/schema\n description: Schema for National Microbiome Data Collaborative (NMDC).\nThis schema is organized into distinct modules:\n\n * a set of core types for representing data values\n * the mixs schema (auto-translated from mixs excel)\n * annotation schema\n * the NMDC schema itself\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", + "_comments": "Auto generated from nmdc.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-12-22T13:46:54\n Schema: NMDC\n metamodel version: 1.7.0\n model version: 7.0.0\n \n id: https://microbiomedata/schema\n description: Schema for National Microbiome Data Collaborative (NMDC).\nThis schema is organized into distinct modules:\n\n * a set of core types for representing data values\n * the mixs schema (auto-translated from mixs excel)\n * annotation schema\n * the NMDC schema itself\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", "@context": { "CAS": "http://identifiers.org/cas/", "CATH": "http://identifiers.org/cath/", @@ -477,6 +477,9 @@ "collected_from": { "@type": "@id" }, + "collecting_biosamples_from_site_set": { + "@type": "@id" + }, "collection_date": { "@type": "@id", "@id": "mixs:0000011" @@ -558,12 +561,6 @@ "meaning": "@id" } }, - "cbfs_set": { - "@type": "@id" - }, - "frs_set": { - "@type": "@id" - }, "date_last_rain": { "@type": "@id", "@id": "mixs:0000786" @@ -841,6 +838,9 @@ "@type": "@id", "@id": "mixs:0000291" }, + "field_research_site_set": { + "@type": "@id" + }, "file_size_bytes": { "@type": "xsd:long" }, diff --git a/jsonschema/nmdc.schema.json b/jsonschema/nmdc.schema.json index 274bf4551c..25ae6de4fc 100644 --- a/jsonschema/nmdc.schema.json +++ b/jsonschema/nmdc.schema.json @@ -1 +1 @@ -{"$defs": {"Activity": {"additionalProperties": false, "description": "a provence-generating activity", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"$ref": "#/$defs/Agent"}, "was_informed_by": {"type": "string"}}, "required": ["id"], "title": "Activity", "type": "object"}, "Agent": {"additionalProperties": false, "description": "a provence-generating agent", "properties": {"acted_on_behalf_of": {"$ref": "#/$defs/Agent"}, "was_informed_by": {"type": "string"}}, "title": "Agent", "type": "object"}, "AnalysisTypeEnum": {"description": "", "enum": ["metabolomics", "metagenomics", "metaproteomics", "metatranscriptomics", "natural organic matter"], "title": "AnalysisTypeEnum", "type": "string"}, "AnalyticalSample": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "AnalyticalSample", "type": "object"}, "ArchStrucEnum": {"description": "", "enum": ["building", "shed", "home"], "title": "ArchStrucEnum", "type": "string"}, "AttributeValue": {"additionalProperties": false, "description": "The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "AttributeValue", "type": "object"}, "BiolStatEnum": {"description": "", "enum": ["wild", "natural", "semi-natural", "inbred line", "breeder's line", "hybrid", "clonal selection", "mutant"], "title": "BiolStatEnum", "type": "string"}, "Biosample": {"additionalProperties": false, "description": "Biological source material which can be characterized by an experiment.", "properties": {"add_date": {"description": "The date on which the information was added to the database.", "type": "string"}, "agrochem_addition": {"$ref": "#/$defs/QuantityValue", "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications"}, "air_temp_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens"}, "al_sat": {"$ref": "#/$defs/QuantityValue", "description": "Aluminum saturation (esp. For tropical soils)"}, "al_sat_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining Al saturation"}, "alkalinity": {"$ref": "#/$defs/QuantityValue", "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate"}, "alkalinity_method": {"$ref": "#/$defs/TextValue", "description": "Method used for alkalinity measurement"}, "alkyl_diethers": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of alkyl diethers"}, "alt": {"$ref": "#/$defs/QuantityValue", "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air"}, "alternative_identifiers": {"description": "Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC", "items": {"type": "string"}, "type": "array"}, "aminopept_act": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of aminopeptidase activity"}, "ammonium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of ammonium in the sample"}, "ammonium_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of ammonium nitrogen in the sample"}, "analysis_type": {"description": "Select all the data types associated or available for this biosample", "items": {"$ref": "#/$defs/AnalysisTypeEnum"}, "type": "array"}, "annual_precpt": {"$ref": "#/$defs/QuantityValue", "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps."}, "annual_temp": {"$ref": "#/$defs/QuantityValue", "description": "Mean annual temperature"}, "bacteria_carb_prod": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of bacterial carbon production"}, "biosample_categories": {"items": {"$ref": "#/$defs/BiosampleCategoryEnum"}, "type": "array"}, "biotic_regm": {"$ref": "#/$defs/TextValue", "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi."}, "biotic_relationship": {"$ref": "#/$defs/TextValue", "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object"}, "bishomohopanol": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of bishomohopanol"}, "bromide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of bromide"}, "calcium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of calcium in the sample"}, "carb_nitro_ratio": {"$ref": "#/$defs/QuantityValue", "description": "Ratio of amount or concentrations of carbon to nitrogen"}, "chem_administration": {"$ref": "#/$defs/ControlledTermValue", "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi"}, "chloride": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of chloride in the sample"}, "chlorophyll": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of chlorophyll"}, "climate_environment": {"$ref": "#/$defs/TextValue", "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates"}, "collected_from": {"description": "The Site from which a Biosample was collected", "type": "string"}, "collection_date": {"$ref": "#/$defs/TimestampValue", "description": "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant"}, "collection_date_inc": {"description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", "type": "string"}, "collection_time": {"description": "The time of sampling, either as an instance (single point) or interval.", "type": "string"}, "collection_time_inc": {"description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", "type": "string"}, "community": {"type": "string"}, "crop_rotation": {"$ref": "#/$defs/TextValue", "description": "Whether or not crop is rotated, and if yes, rotation schedule"}, "cur_land_use": {"$ref": "#/$defs/TextValue", "description": "Present state of sample site"}, "cur_vegetation": {"$ref": "#/$defs/TextValue", "description": "Vegetation classification from one or more standard classification systems, or agricultural crop"}, "cur_vegetation_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in vegetation classification"}, "density": {"$ref": "#/$defs/QuantityValue", "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)"}, "depth": {"$ref": "#/$defs/QuantityValue", "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "diss_carb_dioxide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample"}, "diss_hydrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved hydrogen"}, "diss_inorg_carb": {"$ref": "#/$defs/QuantityValue", "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter"}, "diss_inorg_phosp": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved inorganic phosphorus in the sample"}, "diss_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid"}, "diss_org_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2"}, "diss_oxygen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved oxygen"}, "dna_absorb1": {"description": "260/280 measurement of DNA sample purity", "type": "string"}, "dna_absorb2": {"description": "260/230 measurement of DNA sample purity", "type": "string"}, "dna_collect_site": {"description": "Provide information on the site your DNA sample was collected from", "type": "string"}, "dna_concentration": {"maximum": 2000, "minimum": 0, "type": "string"}, "dna_cont_type": {"$ref": "#/$defs/DnaContTypeEnum", "description": "Tube or plate (96-well)"}, "dna_cont_well": {"type": "string"}, "dna_container_id": {"type": "string"}, "dna_dnase": {"$ref": "#/$defs/DnaDnaseEnum"}, "dna_isolate_meth": {"description": "Describe the method/protocol/kit used to extract DNA/RNA.", "type": "string"}, "dna_organisms": {"description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", "type": "string"}, "dna_project_contact": {"type": "string"}, "dna_samp_id": {"type": "string"}, "dna_sample_format": {"$ref": "#/$defs/DnaSampleFormatEnum", "description": "Solution in which the DNA sample has been suspended"}, "dna_sample_name": {"description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", "type": "string"}, "dna_seq_project": {"type": "string"}, "dna_seq_project_name": {"type": "string"}, "dna_seq_project_pi": {"type": "string"}, "dna_volume": {"maximum": 1000, "minimum": 0, "type": "string"}, "dnase_rna": {"$ref": "#/$defs/DnaseRnaEnum"}, "drainage_class": {"$ref": "#/$defs/TextValue", "description": "Drainage classification from a standard system such as the USDA system"}, "ecosystem": {"description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", "type": "string"}, "ecosystem_category": {"description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", "type": "string"}, "ecosystem_subtype": {"description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", "type": "string"}, "ecosystem_type": {"description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", "type": "string"}, "elev": {"$ref": "#/$defs/QuantityValue", "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit."}, "emsl_biosample_identifiers": {"description": "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.", "items": {"type": "string"}, "type": "array"}, "env_broad_scale": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS"}, "env_local_scale": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS."}, "env_medium": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top)."}, "env_package": {"$ref": "#/$defs/TextValue", "description": "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported", "pattern": "[air|built environment|host\\-associated|human\\-associated|human\\-skin|human\\-oral|human\\-gut|human\\-vaginal|hydrocarbon resources\\-cores|hydrocarbon resources\\-fluids\\/swabs|microbial mat\\/biofilm|misc environment|plant\\-associated|sediment|soil|wastewater\\/sludge|water]"}, "experimental_factor": {"$ref": "#/$defs/ControlledTermValue", "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI"}, "experimental_factor_other": {"description": "Other details about your sample that you feel can't be accurately represented in the available columns.", "type": "string"}, "extreme_event": {"$ref": "#/$defs/TimestampValue", "description": "Unusual physical events that may have affected microbial populations"}, "fao_class": {"$ref": "#/$defs/TextValue", "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups"}, "filter_method": {"description": "Type of filter used or how the sample was filtered", "type": "string"}, "fire": {"$ref": "#/$defs/TimestampValue", "description": "Historical and/or physical evidence of fire"}, "flooding": {"$ref": "#/$defs/TimestampValue", "description": "Historical and/or physical evidence of flooding"}, "gaseous_environment": {"$ref": "#/$defs/QuantityValue", "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens"}, "geo_loc_name": {"$ref": "#/$defs/TextValue", "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)"}, "glucosidase_act": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of glucosidase activity"}, "gold_biosample_identifiers": {"description": "Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample", "items": {"type": "string"}, "pattern": "^GOLD:Gb[0-9]+$", "type": "array"}, "growth_facil": {"$ref": "#/$defs/ControlledTermValue", "description": "Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research"}, "habitat": {"type": "string"}, "heavy_metals": {"$ref": "#/$defs/QuantityValue", "description": "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field."}, "heavy_metals_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining heavy metals"}, "host_name": {"type": "string"}, "humidity_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens"}, "id": {"description": "An NMDC assigned unique identifier for a biosample submitted to NMDC.", "pattern": "^nmdc:", "type": "string"}, "igsn_biosample_identifiers": {"description": "A list of identifiers for the biosample from the IGSN database.", "items": {"type": "string"}, "type": "array"}, "img_identifiers": {"description": "A list of identifiers that relate the biosample to records in the IMG database.", "items": {"type": "string"}, "type": "array"}, "insdc_biosample_identifiers": {"description": "identifiers for corresponding sample in INSDC", "items": {"type": "string"}, "pattern": "^biosample:SAM[NED]([A-Z])?[0-9]+$", "type": "array"}, "isotope_exposure": {"description": "List isotope exposure or addition applied to your sample.", "type": "string"}, "lat_lon": {"$ref": "#/$defs/GeolocationValue", "description": "This is currently a required field but it's not clear if this should be required for human hosts"}, "lbc_thirty": {"$ref": "#/$defs/QuantityValue", "description": "lime buffer capacity, determined after 30 minute incubation"}, "lbceq": {"$ref": "#/$defs/QuantityValue", "description": "lime buffer capacity, determined at equilibrium after 5 day incubation"}, "light_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality."}, "link_addit_analys": {"$ref": "#/$defs/TextValue", "description": "Link to additional analysis results performed on the sample"}, "link_class_info": {"$ref": "#/$defs/TextValue", "description": "Link to digitized soil maps or other soil classification information"}, "link_climate_info": {"$ref": "#/$defs/TextValue", "description": "Link to climate resource"}, "local_class": {"$ref": "#/$defs/TextValue", "description": "Soil classification based on local soil classification system"}, "local_class_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining the local soil classification"}, "location": {"type": "string"}, "magnesium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of magnesium in the sample"}, "manganese": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of manganese in the sample"}, "mean_frict_vel": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of mean friction velocity"}, "mean_peak_frict_vel": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of mean peak friction velocity"}, "micro_biomass_c_meth": {"description": "Reference or method used in determining microbial biomass", "type": "string"}, "micro_biomass_n_meth": {"description": "Reference or method used in determining microbial biomass nitrogen", "type": "string"}, "microbial_biomass_c": {"description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", "type": "string"}, "microbial_biomass_n": {"description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", "type": "string"}, "misc_param": {"$ref": "#/$defs/QuantityValue", "description": "Any other measurement performed or parameter collected, that is not listed here"}, "mod_date": {"description": "The last date on which the database information was modified.", "type": "string"}, "n_alkanes": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of n-alkanes; can include multiple n-alkanes"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "ncbi_taxonomy_name": {"type": "string"}, "nitrate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrate in the sample"}, "nitrate_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrate nitrogen in the sample"}, "nitrite": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrite in the sample"}, "nitrite_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrite nitrogen in the sample"}, "non_microb_biomass": {"description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", "type": "string"}, "non_microb_biomass_method": {"description": "Reference or method used in determining biomass", "type": "string"}, "org_matter": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of organic matter"}, "org_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of organic nitrogen"}, "org_nitro_method": {"description": "Method used for obtaining organic nitrogen", "type": "string"}, "organism_count": {"$ref": "#/$defs/QuantityValue", "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)"}, "other_treatment": {"description": "Other treatments applied to your samples that are not applicable to the provided fields", "type": "string"}, "oxy_stat_samp": {"$ref": "#/$defs/TextValue", "description": "Oxygenation status of sample"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "part_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of particulate organic carbon"}, "perturbation": {"$ref": "#/$defs/TextValue", "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types"}, "petroleum_hydrocarb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of petroleum hydrocarbon"}, "ph": {"$ref": "#/$defs/QuantityValue", "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid"}, "ph_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining ph"}, "phaeopigments": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phaeopigments; can include multiple phaeopigments"}, "phosphate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phosphate"}, "phosplipid_fatt_acid": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phospholipid fatty acids; can include multiple values"}, "pool_dna_extracts": {"$ref": "#/$defs/TextValue", "description": "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given"}, "potassium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of potassium in the sample"}, "pressure": {"$ref": "#/$defs/QuantityValue", "description": "Pressure to which the sample is subject to, in atmospheres"}, "profile_position": {"$ref": "#/$defs/TextValue", "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas"}, "project_id": {"description": "Proposal IDs or names associated with dataset", "type": "string"}, "proport_woa_temperature": {"type": "string"}, "proposal_dna": {"type": "string"}, "proposal_rna": {"type": "string"}, "redox_potential": {"$ref": "#/$defs/QuantityValue", "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential"}, "rel_to_oxygen": {"$ref": "#/$defs/TextValue", "description": "Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments"}, "replicate_number": {"description": "If sending biological replicates, indicate the rep number here.", "type": "string"}, "rna_absorb1": {"description": "260/280 measurement of RNA sample purity", "type": "string"}, "rna_absorb2": {"description": "260/230 measurement of RNA sample purity", "type": "string"}, "rna_collect_site": {"description": "Provide information on the site your RNA sample was collected from", "type": "string"}, "rna_concentration": {"maximum": 1000, "minimum": 0, "type": "string"}, "rna_cont_type": {"$ref": "#/$defs/RnaContTypeEnum", "description": "Tube or plate (96-well)"}, "rna_cont_well": {"type": "string"}, "rna_container_id": {"type": "string"}, "rna_isolate_meth": {"description": "Describe the method/protocol/kit used to extract DNA/RNA.", "type": "string"}, "rna_organisms": {"description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", "type": "string"}, "rna_project_contact": {"type": "string"}, "rna_samp_id": {"type": "string"}, "rna_sample_format": {"$ref": "#/$defs/RnaSampleFormatEnum", "description": "Solution in which the RNA sample has been suspended"}, "rna_sample_name": {"description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", "maximum": 2000, "minimum": 0, "type": "string"}, "rna_seq_project": {"type": "string"}, "rna_seq_project_name": {"type": "string"}, "rna_seq_project_pi": {"type": "string"}, "rna_volume": {"type": "string"}, "salinity": {"$ref": "#/$defs/QuantityValue", "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater."}, "salinity_category": {"description": "Categorcial description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline", "type": "string"}, "salinity_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining salinity"}, "samp_collec_method": {"description": "The method employed for collecting the sample.", "type": "string"}, "samp_mat_process": {"$ref": "#/$defs/ControlledTermValue", "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed."}, "samp_name": {"description": "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.", "type": "string"}, "samp_size": {"$ref": "#/$defs/QuantityValue", "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected."}, "samp_store_dur": {"$ref": "#/$defs/TextValue", "description": "Duration for which the sample was stored"}, "samp_store_loc": {"$ref": "#/$defs/TextValue", "description": "Location at which sample was stored, usually name of a specific freezer/room"}, "samp_store_temp": {"$ref": "#/$defs/QuantityValue", "description": "Temperature at which sample was stored, e.g. -80 degree Celsius"}, "samp_vol_we_dna_ext": {"$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)."}, "sample_collection_site": {"type": "string"}, "sample_link": {"description": "JsonObj()", "items": {"type": "string"}, "type": "array"}, "sample_shipped": {"description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL", "type": "string"}, "sample_type": {"$ref": "#/$defs/SampleTypeEnum", "description": "Type of sample being submitted"}, "season_precpt": {"$ref": "#/$defs/QuantityValue", "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps."}, "season_temp": {"$ref": "#/$defs/QuantityValue", "description": "Mean seasonal temperature"}, "sieving": {"$ref": "#/$defs/QuantityValue", "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved"}, "size_frac_low": {"$ref": "#/$defs/QuantityValue", "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample"}, "size_frac_up": {"$ref": "#/$defs/QuantityValue", "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample"}, "slope_aspect": {"$ref": "#/$defs/QuantityValue", "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration."}, "slope_gradient": {"$ref": "#/$defs/QuantityValue", "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer"}, "sodium": {"$ref": "#/$defs/QuantityValue", "description": "Sodium concentration in the sample"}, "soil_type": {"$ref": "#/$defs/TextValue", "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes."}, "soil_type_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining soil series name or other lower-level classification"}, "soluble_iron_micromol": {"type": "string"}, "source_mat_id": {"$ref": "#/$defs/TextValue", "description": "A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2)."}, "specific_ecosystem": {"description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", "type": "string"}, "start_date_inc": {"description": "Date the incubation was started. Only relevant for incubation samples.", "type": "string"}, "start_time_inc": {"description": "Time the incubation was started. Only relevant for incubation samples.", "type": "string"}, "store_cond": {"$ref": "#/$defs/TextValue", "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)."}, "subsurface_depth": {"$ref": "#/$defs/QuantityValue"}, "sulfate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of sulfate in the sample"}, "sulfide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of sulfide in the sample"}, "technical_reps": {"description": "If sending multiple technical replicates of the same sample, indicate how many replicates are being sent", "type": "string"}, "temp": {"$ref": "#/$defs/QuantityValue", "description": "Temperature of the sample at the time of sampling."}, "tidal_stage": {"$ref": "#/$defs/TextValue", "description": "Stage of tide"}, "tillage": {"$ref": "#/$defs/TextValue", "description": "Note method(s) used for tilling"}, "tot_carb": {"$ref": "#/$defs/QuantityValue", "description": "Total carbon content"}, "tot_depth_water_col": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of total depth of water column"}, "tot_diss_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen"}, "tot_nitro_cont_meth": {"description": "Reference or method used in determining the total nitrogen", "type": "string"}, "tot_nitro_content": {"$ref": "#/$defs/QuantityValue", "description": "Total nitrogen content of the sample"}, "tot_org_c_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining total organic carbon"}, "tot_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content"}, "tot_phosp": {"$ref": "#/$defs/QuantityValue", "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "water_cont_soil_meth": {"description": "Reference or method used in determining the water content of soil", "type": "string"}, "water_content": {"$ref": "#/$defs/QuantityValue", "description": "Water content measurement"}, "watering_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens"}, "zinc": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of zinc in the sample"}}, "required": ["part_of", "id", "env_broad_scale", "env_local_scale", "env_medium"], "title": "Biosample", "type": "object"}, "BiosampleCategoryEnum": {"description": "Funding-based, sample location-based, or experimental method-based defined categories", "enum": ["LTER", "SIP", "SFA", "FICUS", "NEON"], "title": "BiosampleCategoryEnum", "type": "string"}, "BiosampleProcessing": {"additionalProperties": false, "description": "A process that takes one or more biosamples as inputs and generates one or as outputs. Examples of outputs include samples cultivated from another sample or data objects created by instruments runs.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "BiosampleProcessing", "type": "object"}, "BioticRelationshipEnum": {"description": "", "enum": ["free living", "parasite", "commensal", "symbiont"], "title": "BioticRelationshipEnum", "type": "string"}, "BooleanValue": {"additionalProperties": false, "description": "A value that is a boolean", "properties": {"has_boolean_value": {"description": "Links a quantity value to a boolean", "type": "boolean"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "BooleanValue", "type": "object"}, "BuildDocsEnum": {"description": "", "enum": ["building information model", "commissioning report", "complaint logs", "contract administration", "cost estimate", "janitorial schedules or logs", "maintenance plans", "schedule", "sections", "shop drawings", "submittals", "ventilation system", "windows"], "title": "BuildDocsEnum", "type": "string"}, "BuildOccupTypeEnum": {"description": "", "enum": ["office", "market", "restaurant", "residence", "school", "residential", "commercial", "low rise", "high rise", "wood framed", "health care", "airport", "sports complex"], "title": "BuildOccupTypeEnum", "type": "string"}, "BuildingSettingEnum": {"description": "", "enum": ["urban", "suburban", "exurban", "rural"], "title": "BuildingSettingEnum", "type": "string"}, "CeilCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "CeilCondEnum", "type": "string"}, "CeilFinishMatEnum": {"description": "", "enum": ["drywall", "mineral fibre", "tiles", "PVC", "plasterboard", "metal", "fiberglass", "stucco", "mineral wool/calcium silicate", "wood"], "title": "CeilFinishMatEnum", "type": "string"}, "CeilTextureEnum": {"description": "", "enum": ["crows feet", "crows-foot stomp", "double skip", "hawk and trowel", "knockdown", "popcorn", "orange peel", "rosebud stomp", "Santa-Fe texture", "skip trowel", "smooth", "stomp knockdown", "swirl"], "title": "CeilTextureEnum", "type": "string"}, "CeilTypeEnum": {"description": "", "enum": ["cathedral", "dropped", "concave", "barrel-shaped", "coffered", "cove", "stretched"], "title": "CeilTypeEnum", "type": "string"}, "ChemicalEntity": {"additionalProperties": false, "description": "An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "ChemicalEntity", "type": "object"}, "CollectingBiosamplesFromSite": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_inputs": {"items": {"type": "string"}, "type": "array"}, "has_outputs": {"items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "participating_agent": {"$ref": "#/$defs/Agent"}}, "required": ["has_inputs", "has_outputs", "id"], "title": "CollectingBiosamplesFromSite", "type": "object"}, "ContainerTypeEnum": {"description": "", "enum": ["screw_top_conical"], "title": "ContainerTypeEnum", "type": "string"}, "ControlledIdentifiedTermValue": {"additionalProperties": false, "description": "A controlled term or class from an ontology, requiring the presence of term with an id", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "term": {"$ref": "#/$defs/OntologyClass", "description": "pointer to an ontology class"}, "was_generated_by": {"type": "string"}}, "required": ["term"], "title": "ControlledIdentifiedTermValue", "type": "object"}, "ControlledTermValue": {"additionalProperties": false, "description": "A controlled term or class from an ontology", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "term": {"$ref": "#/$defs/OntologyClass", "description": "pointer to an ontology class"}, "was_generated_by": {"type": "string"}}, "title": "ControlledTermValue", "type": "object"}, "CreditAssociation": {"additionalProperties": false, "description": "This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0", "properties": {"applied_role": {"$ref": "#/$defs/CreditEnum"}, "applied_roles": {"items": {"$ref": "#/$defs/CreditEnum"}, "type": "array"}, "applies_to_person": {"$ref": "#/$defs/PersonValue"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "required": ["applies_to_person", "applied_roles"], "title": "CreditAssociation", "type": "object"}, "CreditEnum": {"description": "", "enum": ["Conceptualization", "Data curation", "Formal Analysis", "Funding acquisition", "Investigation", "Methodology", "Project administration", "Resources", "Software", "Supervision", "Validation", "Visualization", "Writing original draft", "Writing review and editing", "Principal Investigator", "Submitter"], "title": "CreditEnum", "type": "string"}, "CurLandUseEnum": {"description": "", "enum": ["cities", "farmstead", "industrial areas", "roads/railroads", "rock", "sand", "gravel", "mudflats", "salt flats", "badlands", "permanent snow or ice", "saline seeps", "mines/quarries", "oil waste areas", "small grains", "row crops", "vegetable crops", "horticultural plants (e.g. tulips)", "marshlands (grass,sedges,rushes)", "tundra (mosses,lichens)", "rangeland", "pastureland (grasslands used for livestock grazing)", "hayland", "meadows (grasses,alfalfa,fescue,bromegrass,timothy)", "shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)", "successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)", "shrub crops (blueberries,nursery ornamentals,filberts)", "vine crops (grapes)", "conifers (e.g. pine,spruce,fir,cypress)", "hardwoods (e.g. oak,hickory,elm,aspen)", "intermixed hardwood and conifers", "tropical (e.g. mangrove,palms)", "rainforest (evergreen forest receiving greater than 406 cm annual rainfall)", "swamp (permanent or semi-permanent water body dominated by woody plants)", "crop trees (nuts,fruit,christmas trees,nursery trees)"], "title": "CurLandUseEnum", "type": "string"}, "DataObject": {"additionalProperties": false, "description": "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "compression_type": {"description": "If provided, specifies the compression type", "type": "string"}, "data_object_type": {"$ref": "#/$defs/FileTypeEnum", "description": "The type of file represented by the data object."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "file_size_bytes": {"description": "Size of the file in bytes", "type": "integer"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "md5_checksum": {"description": "MD5 checksum of file (pre-compressed)", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "url": {"type": "string"}, "was_generated_by": {"type": "string"}}, "required": ["id", "name", "description"], "title": "DataObject", "type": "object"}, "Database": {"additionalProperties": false, "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest", "properties": {"activity_set": {"description": "This property links a database object to the set of workflow activities.", "items": {"$ref": "#/$defs/WorkflowExecutionActivity"}, "type": "array"}, "biosample_set": {"description": "This property links a database object to the set of samples within it.", "items": {"$ref": "#/$defs/Biosample"}, "type": "array"}, "cbfs_set": {"items": {"$ref": "#/$defs/CollectingBiosamplesFromSite"}, "type": "array"}, "data_object_set": {"description": "This property links a database object to the set of data objects within it.", "items": {"$ref": "#/$defs/DataObject"}, "type": "array"}, "dissolving_activity_set": {"items": {"$ref": "#/$defs/DissolvingActivity"}, "type": "array"}, "frs_set": {"items": {"$ref": "#/$defs/FieldResearchSite"}, "type": "array"}, "functional_annotation_set": {"description": "This property links a database object to the set of all functional annotations", "items": {"$ref": "#/$defs/FunctionalAnnotation"}, "type": "array"}, "genome_feature_set": {"description": "This property links a database object to the set of all features", "items": {"$ref": "#/$defs/GenomeFeature"}, "type": "array"}, "mags_activity_set": {"description": "This property links a database object to the set of MAGs analysis activities.", "items": {"$ref": "#/$defs/MagsAnalysisActivity"}, "type": "array"}, "material_sample_set": {"items": {"$ref": "#/$defs/MaterialSample"}, "type": "array"}, "material_sampling_activity_set": {"items": {"$ref": "#/$defs/MaterialSamplingActivity"}, "type": "array"}, "metabolomics_analysis_activity_set": {"description": "This property links a database object to the set of metabolomics analysis activities.", "items": {"$ref": "#/$defs/MetabolomicsAnalysisActivity"}, "type": "array"}, "metagenome_annotation_activity_set": {"description": "This property links a database object to the set of metagenome annotation activities.", "items": {"$ref": "#/$defs/MetagenomeAnnotationActivity"}, "type": "array"}, "metagenome_assembly_set": {"description": "This property links a database object to the set of metagenome assembly activities.", "items": {"$ref": "#/$defs/MetagenomeAssembly"}, "type": "array"}, "metaproteomics_analysis_activity_set": {"description": "This property links a database object to the set of metaproteomics analysis activities.", "items": {"$ref": "#/$defs/MetaproteomicsAnalysisActivity"}, "type": "array"}, "metatranscriptome_activity_set": {"description": "TODO", "items": {"$ref": "#/$defs/MetatranscriptomeActivity"}, "type": "array"}, "nom_analysis_activity_set": {"description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", "items": {"$ref": "#/$defs/NomAnalysisActivity"}, "type": "array"}, "omics_processing_set": {"description": "This property links a database object to the set of omics processings within it.", "items": {"$ref": "#/$defs/OmicsProcessing"}, "type": "array"}, "reaction_activity_set": {"items": {"$ref": "#/$defs/ReactionActivity"}, "type": "array"}, "read_based_taxonomy_analysis_activity_set": {"description": "This property links a database object to the set of read based analysis activities.", "items": {"$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity"}, "type": "array"}, "read_qc_analysis_activity_set": {"description": "This property links a database object to the set of read QC analysis activities.", "items": {"$ref": "#/$defs/ReadQcAnalysisActivity"}, "type": "array"}, "study_set": {"description": "This property links a database object to the set of studies within it.", "items": {"$ref": "#/$defs/Study"}, "type": "array"}}, "title": "Database", "type": "object"}, "DeposEnvEnum": {"description": "", "enum": ["Continental - Alluvial", "Continental - Aeolian", "Continental - Fluvial", "Continental - Lacustrine", "Transitional - Deltaic", "Transitional - Tidal", "Transitional - Lagoonal", "Transitional - Beach", "Transitional - Lake", "Marine - Shallow", "Marine - Deep", "Marine - Reef", "Other - Evaporite", "Other - Glacial", "Other - Volcanic", "other"], "title": "DeposEnvEnum", "type": "string"}, "DeviceTypeEnum": {"description": "", "enum": ["orbital_shaker", "thermomixer"], "title": "DeviceTypeEnum", "type": "string"}, "DissolvingActivity": {"additionalProperties": false, "description": "", "properties": {"dissolution_aided_by": {"$ref": "#/$defs/LabDevice"}, "dissolution_reagent": {"$ref": "#/$defs/SolventEnum"}, "dissolution_volume": {"$ref": "#/$defs/QuantityValue"}, "dissolved_in": {"$ref": "#/$defs/MaterialContainer"}, "material_input": {"type": "string"}, "material_output": {"type": "string"}}, "title": "DissolvingActivity", "type": "object"}, "DnaContTypeEnum": {"description": "", "enum": ["plate", "tube"], "title": "DnaContTypeEnum", "type": "string"}, "DnaDnaseEnum": {"description": "", "enum": ["no", "yes"], "title": "DnaDnaseEnum", "type": "string"}, "DnaSampleFormatEnum": {"description": "", "enum": ["10 mM Tris-HCl", "DNAStable", "Ethanol", "Low EDTA TE", "MDA reaction buffer", "PBS", "Pellet", "RNAStable", "TE", "Water"], "title": "DnaSampleFormatEnum", "type": "string"}, "DnaseRnaEnum": {"description": "", "enum": ["no", "yes"], "title": "DnaseRnaEnum", "type": "string"}, "DoorCompTypeEnum": {"description": "", "enum": ["metal covered", "revolving", "sliding", "telescopic"], "title": "DoorCompTypeEnum", "type": "string"}, "DoorCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "DoorCondEnum", "type": "string"}, "DoorDirectEnum": {"description": "", "enum": ["inward", "outward", "sideways"], "title": "DoorDirectEnum", "type": "string"}, "DoorLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "DoorLocEnum", "type": "string"}, "DoorMatEnum": {"description": "", "enum": ["aluminum", "cellular PVC", "engineered plastic", "fiberboard", "fiberglass", "metal", "thermoplastic alloy", "vinyl", "wood", "wood/plastic composite"], "title": "DoorMatEnum", "type": "string"}, "DoorMoveEnum": {"description": "", "enum": ["collapsible", "folding", "revolving", "rolling shutter", "sliding", "swinging"], "title": "DoorMoveEnum", "type": "string"}, "DoorTypeEnum": {"description": "", "enum": ["composite", "metal", "wooden"], "title": "DoorTypeEnum", "type": "string"}, "DoorTypeMetalEnum": {"description": "", "enum": ["collapsible", "corrugated steel", "hollow", "rolling shutters", "steel plate"], "title": "DoorTypeMetalEnum", "type": "string"}, "DoorTypeWoodEnum": {"description": "", "enum": ["bettened and ledged", "battened", "ledged and braced", "ledged and framed", "ledged, braced and frame", "framed and paneled", "glashed or sash", "flush", "louvered", "wire gauged"], "title": "DoorTypeWoodEnum", "type": "string"}, "DrainageClassEnum": {"description": "", "enum": ["very poorly", "poorly", "somewhat poorly", "moderately well", "well", "excessively drained"], "title": "DrainageClassEnum", "type": "string"}, "DrawingsEnum": {"description": "", "enum": ["operation", "as built", "construction", "bid", "design", "building navigation map", "diagram", "sketch"], "title": "DrawingsEnum", "type": "string"}, "EnvironmentalMaterialTerm": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "EnvironmentalMaterialTerm", "type": "object"}, "ExtWallOrientEnum": {"description": "", "enum": ["north", "south", "east", "west", "northeast", "southeast", "southwest", "northwest"], "title": "ExtWallOrientEnum", "type": "string"}, "ExtWindowOrientEnum": {"description": "", "enum": ["north", "south", "east", "west", "northeast", "southeast", "southwest", "northwest"], "title": "ExtWindowOrientEnum", "type": "string"}, "FaoClassEnum": {"description": "", "enum": ["Acrisols", "Andosols", "Arenosols", "Cambisols", "Chernozems", "Ferralsols", "Fluvisols", "Gleysols", "Greyzems", "Gypsisols", "Histosols", "Kastanozems", "Lithosols", "Luvisols", "Nitosols", "Phaeozems", "Planosols", "Podzols", "Podzoluvisols", "Rankers", "Regosols", "Rendzinas", "Solonchaks", "Solonetz", "Vertisols", "Yermosols"], "title": "FaoClassEnum", "type": "string"}, "FieldResearchSite": {"additionalProperties": false, "description": "A site, outside of a laboratory, from which biosamples may be collected.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "FieldResearchSite", "type": "object"}, "FileTypeEnum": {"description": "", "enum": ["Metagenome Raw Reads", "FT ICR-MS Analysis Results", "GC-MS Metabolomics Results", "Metaproteomics Workflow Statistics", "Protein Report", "Peptide Report", "Unfiltered Metaproteomics Results", "Read Count and RPKM", "QC non-rRNA R2", "QC non-rRNA R1", "Metagenome Bins", "CheckM Statistics", "GOTTCHA2 Krona Plot", "GOTTCHA2 Classification Report", "GOTTCHA2 Report Full", "Kraken2 Krona Plot", "Centrifuge Krona Plot", "Centrifuge output report file", "Kraken2 Classification Report", "Kraken2 Taxonomic Classification", "Centrifuge Classification Report", "Centrifuge Taxonomic Classification", "Structural Annotation GFF", "Functional Annotation GFF", "Annotation Amino Acid FASTA", "Annotation Enzyme Commission", "Annotation KEGG Orthology", "Assembly Coverage BAM", "Assembly AGP", "Assembly Scaffolds", "Assembly Contigs", "Assembly Coverage Stats", "Filtered Sequencing Reads", "QC Statistics", "TIGRFam Annotation GFF", "CRT Annotation GFF", "Genmark Annotation GFF", "Prodigal Annotation GFF", "TRNA Annotation GFF", "Misc Annotation GFF", "RFAM Annotation GFF", "TMRNA Annotation GFF", "KO_EC Annotation GFF", "Product Names", "Gene Phylogeny tsv", "Crisprt Terms", "Clusters of Orthologous Groups (COG) Annotation GFF", "CATH FunFams (Functional Families) Annotation GFF", "SUPERFam Annotation GFF", "SMART Annotation GFF", "Pfam Annotation GFF", "Direct Infusion FT ICR-MS Raw Data"], "title": "FileTypeEnum", "type": "string"}, "FilterTypeEnum": {"description": "", "enum": ["particulate air filter", "chemical air filter", "low-MERV pleated media", "HEPA", "electrostatic", "gas-phase or ultraviolet air treatments"], "title": "FilterTypeEnum", "type": "string"}, "FloorCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "FloorCondEnum", "type": "string"}, "FloorFinishMatEnum": {"description": "", "enum": ["tile", "wood strip or parquet", "carpet", "rug", "laminate wood", "lineoleum", "vinyl composition tile", "sheet vinyl", "stone", "bamboo", "cork", "terrazo", "concrete", "none", "sealed", "clear finish", "paint", "none or unfinished"], "title": "FloorFinishMatEnum", "type": "string"}, "FloorStrucEnum": {"description": "", "enum": ["balcony", "floating floor", "glass floor", "raised floor", "sprung floor", "wood-framed", "concrete"], "title": "FloorStrucEnum", "type": "string"}, "FloorWaterMoldEnum": {"description": "", "enum": ["mold odor", "wet floor", "water stains", "wall discoloration", "floor discoloration", "ceiling discoloration", "peeling paint or wallpaper", "bulging walls", "condensation"], "title": "FloorWaterMoldEnum", "type": "string"}, "FreqCleanEnum": {"description": "", "enum": ["Daily", "Weekly", "Monthly", "Quarterly", "Annually", "other"], "title": "FreqCleanEnum", "type": "string"}, "FunctionalAnnotation": {"additionalProperties": false, "description": "An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods", "properties": {"has_function": {"pattern": "^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$", "type": "string"}, "subject": {"type": "string"}, "was_generated_by": {"description": "provenance for the annotation.", "type": "string"}}, "title": "FunctionalAnnotation", "type": "object"}, "FurnitureEnum": {"description": "", "enum": ["cabinet", "chair", "desks"], "title": "FurnitureEnum", "type": "string"}, "GenderRestroomEnum": {"description": "", "enum": ["all gender", "female", "gender neurtral", "male", "male and female", "unisex"], "title": "GenderRestroomEnum", "type": "string"}, "GeneProduct": {"additionalProperties": false, "description": "A molecule encoded by a gene that has an evolved function", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "GeneProduct", "type": "object"}, "GenomeFeature": {"additionalProperties": false, "description": "A feature localized to an interval along a genome", "title": "GenomeFeature", "type": "object"}, "GeolocationValue": {"additionalProperties": false, "description": "A normalized value for a location on the earth's surface", "properties": {"has_raw_value": {"description": "The raw value for a geolocation should follow {lat} {long}", "type": "string"}, "latitude": {"description": "latitude", "type": "number"}, "longitude": {"description": "longitude", "type": "number"}, "was_generated_by": {"type": "string"}}, "title": "GeolocationValue", "type": "object"}, "GrowthHabitEnum": {"description": "", "enum": ["erect", "semi-erect", "spreading", "prostrate"], "title": "GrowthHabitEnum", "type": "string"}, "HandidnessEnum": {"description": "", "enum": ["ambidexterity", "left handedness", "mixed-handedness", "right handedness"], "title": "HandidnessEnum", "type": "string"}, "HcProducedEnum": {"description": "", "enum": ["Oil", "Gas-Condensate", "Gas", "Bitumen", "Coalbed Methane", "other"], "title": "HcProducedEnum", "type": "string"}, "HcrEnum": {"description": "", "enum": ["Oil Reservoir", "Gas Reservoir", "Oil Sand", "Coalbed", "Shale", "Tight Oil Reservoir", "Tight Gas Reservoir", "other"], "title": "HcrEnum", "type": "string"}, "HcrGeolAgeEnum": {"description": "", "enum": ["Archean", "Cambrian", "Carboniferous", "Cenozoic", "Cretaceous", "Devonian", "Jurassic", "Mesozoic", "Neogene", "Ordovician", "Paleogene", "Paleozoic", "Permian", "Precambrian", "Proterozoic", "Silurian", "Triassic", "other"], "title": "HcrGeolAgeEnum", "type": "string"}, "HeatCoolTypeEnum": {"description": "", "enum": ["radiant system", "heat pump", "forced air system", "steam forced heat", "wood stove"], "title": "HeatCoolTypeEnum", "type": "string"}, "HeatDelivLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "HeatDelivLocEnum", "type": "string"}, "HorizonEnum": {"description": "", "enum": ["O horizon", "A horizon", "E horizon", "B horizon", "C horizon", "R layer", "Permafrost"], "title": "HorizonEnum", "type": "string"}, "HostSexEnum": {"description": "", "enum": ["female", "hermaphrodite", "male", "neuter"], "title": "HostSexEnum", "type": "string"}, "ImageValue": {"additionalProperties": false, "description": "An attribute value representing an image.", "properties": {"description": {"description": "a human-readable description of a thing", "type": "string"}, "display_order": {"description": "When rendering information, this attribute to specify the order in which the information should be rendered.", "type": "string"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "url": {"type": "string"}, "was_generated_by": {"type": "string"}}, "title": "ImageValue", "type": "object"}, "IndoorSpaceEnum": {"description": "", "enum": ["bedroom", "office", "bathroom", "foyer", "kitchen", "locker room", "hallway", "elevator"], "title": "IndoorSpaceEnum", "type": "string"}, "IndoorSurfEnum": {"description": "", "enum": ["cabinet", "ceiling", "counter top", "door", "shelving", "vent cover", "window", "wall"], "title": "IndoorSurfEnum", "type": "string"}, "Instrument": {"additionalProperties": false, "description": "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI].", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Instrument", "type": "object"}, "IntWallCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "IntWallCondEnum", "type": "string"}, "IntegerValue": {"additionalProperties": false, "description": "A value that is an integer", "properties": {"has_numeric_value": {"description": "Links a quantity value to a number", "type": "number"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "IntegerValue", "type": "object"}, "LabDevice": {"additionalProperties": false, "description": "", "properties": {"activity_speed": {"$ref": "#/$defs/QuantityValue"}, "activity_temperature": {"$ref": "#/$defs/QuantityValue"}, "activity_time": {"$ref": "#/$defs/QuantityValue"}, "device_type": {"$ref": "#/$defs/DeviceTypeEnum"}}, "title": "LabDevice", "type": "object"}, "LightTypeEnum": {"description": "", "enum": ["natural light", "electric light", "desk lamp", "flourescent lights", "none"], "title": "LightTypeEnum", "type": "string"}, "LithologyEnum": {"description": "", "enum": ["Basement", "Chalk", "Chert", "Coal", "Conglomerate", "Diatomite", "Dolomite", "Limestone", "Sandstone", "Shale", "Siltstone", "Volcanic", "other"], "title": "LithologyEnum", "type": "string"}, "MagBin": {"additionalProperties": false, "description": "", "properties": {"bin_name": {"type": "string"}, "bin_quality": {"type": "string"}, "completeness": {"type": "number"}, "contamination": {"type": "number"}, "gene_count": {"type": "integer"}, "gtdbtk_class": {"type": "string"}, "gtdbtk_domain": {"type": "string"}, "gtdbtk_family": {"type": "string"}, "gtdbtk_genus": {"type": "string"}, "gtdbtk_order": {"type": "string"}, "gtdbtk_phylum": {"type": "string"}, "gtdbtk_species": {"type": "string"}, "num_16s": {"type": "integer"}, "num_23s": {"type": "integer"}, "num_5s": {"type": "integer"}, "num_t_rna": {"type": "integer"}, "number_of_contig": {"type": "integer"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "title": "MagBin", "type": "object"}, "MagsAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", "properties": {"binned_contig_num": {"type": "integer"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "input_contig_num": {"type": "integer"}, "low_depth_contig_num": {"type": "integer"}, "mags_list": {"items": {"$ref": "#/$defs/MagBin"}, "type": "array"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "too_short_contig_num": {"type": "integer"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "unbinned_contig_num": {"type": "integer"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MagsAnalysisActivity", "type": "object"}, "MaterialContainer": {"additionalProperties": false, "description": "", "properties": {"container_size": {"$ref": "#/$defs/QuantityValue"}, "container_type": {"$ref": "#/$defs/ContainerTypeEnum"}}, "title": "MaterialContainer", "type": "object"}, "MaterialEntity": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "MaterialEntity", "type": "object"}, "MaterialSample": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "MaterialSample", "type": "object"}, "MaterialSamplingActivity": {"additionalProperties": false, "description": "", "properties": {"amount_collected": {"$ref": "#/$defs/QuantityValue"}, "biosample_input": {"type": "string"}, "collected_into": {"$ref": "#/$defs/MaterialContainer"}, "material_output": {"type": "string"}, "sampling_method": {"$ref": "#/$defs/SamplingMethodEnum"}}, "title": "MaterialSamplingActivity", "type": "object"}, "MechStrucEnum": {"description": "", "enum": ["subway", "coach", "carriage", "elevator", "escalator", "boat", "train", "car", "bus"], "title": "MechStrucEnum", "type": "string"}, "MetaboliteQuantification": {"additionalProperties": false, "description": "This is used to link a metabolomics analysis workflow to a specific metabolite", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "MetaboliteQuantification", "type": "object"}, "MetabolomicsAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetabolomicsAnalysisActivity", "type": "object"}, "MetagenomeAnnotationActivity": {"additionalProperties": false, "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "gold_analysis_project_identifiers": {"description": "identifiers for corresponding analysis project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Ga[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetagenomeAnnotationActivity", "type": "object"}, "MetagenomeAssembly": {"additionalProperties": false, "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", "properties": {"asm_score": {"description": "A score for comparing metagenomic assembly quality from same sample.", "type": "number"}, "contig_bp": {"description": "Total size in bp of all contigs.", "type": "number"}, "contigs": {"description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "ctg_l50": {"description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", "type": "number"}, "ctg_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", "type": "number"}, "ctg_logsum": {"description": "Maximum contig length.", "type": "number"}, "ctg_max": {"description": "Maximum contig length.", "type": "number"}, "ctg_n50": {"description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", "type": "number"}, "ctg_n90": {"description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", "type": "number"}, "ctg_powsum": {"description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "gap_pct": {"description": "The gap size percentage of all scaffolds.", "type": "number"}, "gc_avg": {"description": "Average of GC content of all contigs.", "type": "number"}, "gc_std": {"description": "Standard deviation of GC content of all contigs.", "type": "number"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. 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This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetagenomeAssembly", "type": "object"}, "MetaproteomicsAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetaproteomicsAnalysisActivity", "type": "object"}, "MetatranscriptomeActivity": {"additionalProperties": false, "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. 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This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeActivity", "type": "object"}, "MetatranscriptomeAnnotationActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "gold_analysis_project_identifiers": {"description": "identifiers for corresponding analysis project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Ga[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. 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This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeAnnotationActivity", "type": "object"}, "MetatranscriptomeAssembly": {"additionalProperties": false, "description": "", "properties": {"asm_score": {"description": "A score for comparing metagenomic assembly quality from same sample.", "type": "number"}, "contig_bp": {"description": "Total size in bp of all contigs.", "type": "number"}, "contigs": {"description": "The sum of the (length*log(length)) of all contigs, times some constant. 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Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_assembly_identifiers": {"pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "num_aligned_reads": {"description": "The sequence count number of input reads aligned to assembled contigs.", "type": "number"}, "num_input_reads": {"description": "The sequence count number of input reads for assembly.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "scaf_bp": {"description": "Total size in bp of all scaffolds.", "type": "number"}, "scaf_l50": {"description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", "type": "number"}, "scaf_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", "type": "number"}, "scaf_l_gt50k": {"description": "Total size in bp of all scaffolds greater than 50 KB.", "type": "number"}, "scaf_logsum": {"description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "scaf_max": {"description": "Maximum scaffold length.", "type": "number"}, "scaf_n50": {"description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", "type": "number"}, "scaf_n90": {"description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", "type": "number"}, "scaf_n_gt50k": {"description": "Total sequence count of scaffolds greater than 50 KB.", "type": "number"}, "scaf_pct_gt50k": {"description": "Total sequence size percentage of scaffolds greater than 50 KB.", "type": "number"}, "scaf_powsum": {"description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "scaffolds": {"description": "Total sequence count of all scaffolds.", "type": "number"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeAssembly", "type": "object"}, "NomAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "NomAnalysisActivity", "type": "object"}, "OccupDocumentEnum": {"description": "", "enum": ["automated count", "estimate", "manual count", "videos"], "title": "OccupDocumentEnum", "type": "string"}, "OmicsProcessing": {"additionalProperties": false, "description": "The methods and processes used to generate omics data from a biosample or organism.", "properties": {"add_date": {"description": "The date on which the information was added to the database.", "type": "string"}, "alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "chimera_check": {"$ref": "#/$defs/TextValue", "description": "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "gold_sequencing_project_identifiers": {"description": "identifiers for corresponding sequencing project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Gp[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_experiment_identifiers": {"items": {"type": "string"}, "pattern": "^insdc.sra:(E|D|S)RX[0-9]{6,}$", "type": "array"}, "instrument_name": {"description": "The name of the instrument that was used for processing the sample.", "type": "string"}, "mod_date": {"description": "The last date on which the database information was modified.", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "ncbi_project_name": {"type": "string"}, "nucl_acid_amp": {"$ref": "#/$defs/TextValue", "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids"}, "nucl_acid_ext": {"$ref": "#/$defs/TextValue", "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample"}, "omics_type": {"$ref": "#/$defs/ControlledTermValue", "description": "The type of omics data"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "pcr_cond": {"$ref": "#/$defs/TextValue", "description": "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'"}, "pcr_primers": {"$ref": "#/$defs/TextValue", "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters"}, "principal_investigator": {"$ref": "#/$defs/PersonValue", "description": "Principal Investigator who led the study and/or generated the dataset."}, "processing_institution": {"$ref": "#/$defs/ProcessingInstitutionEnum", "description": "The organization that processed the sample."}, "samp_vol_we_dna_ext": {"$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)."}, "seq_meth": {"$ref": "#/$defs/TextValue", "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)."}, "seq_quality_check": {"$ref": "#/$defs/TextValue", "description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA"}, "target_gene": {"$ref": "#/$defs/TextValue", "description": "Targeted gene or locus name for marker gene studies"}, "target_subfragment": {"$ref": "#/$defs/TextValue", "description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "required": ["has_input"], "title": "OmicsProcessing", "type": "object"}, "OntologyClass": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "OntologyClass", "type": "object"}, "OrganismCountEnum": {"description": "", "enum": ["ATP", "MPN", "other"], "title": "OrganismCountEnum", "type": "string"}, "OrthologyGroup": {"additionalProperties": false, "description": "A set of genes or gene products in which all members are orthologous", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "OrthologyGroup", "type": "object"}, "OxyStatSampEnum": {"description": "", "enum": ["aerobic", "anaerobic", "other"], "title": "OxyStatSampEnum", "type": "string"}, "Pathway": {"additionalProperties": false, "description": "A pathway is a sequence of steps/reactions carried out by an organism or community of organisms", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Pathway", "type": "object"}, "PeptideQuantification": {"additionalProperties": false, "description": "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information", "title": "PeptideQuantification", "type": "object"}, "Person": {"additionalProperties": false, "description": "represents a person, such as a researcher", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "Should be an ORCID. Specify in CURIE format. E.g ORCID:0000-1111-...", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Person", "type": "object"}, "PersonValue": {"additionalProperties": false, "description": "An attribute value representing a person", "properties": {"email": {"description": "An email address for an entity such as a person. This should be the primarly email address used.", "type": "string"}, "has_raw_value": {"description": "The full name of the Investigator in format FIRST LAST.", "type": "string"}, "name": {"description": "The full name of the Investigator. It should follow the format FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.", "type": "string"}, "orcid": {"description": "The ORCID of a person.", "type": "string"}, "profile_image_url": {"description": "A url that points to an image of a person.", "type": "string"}, "was_generated_by": {"type": "string"}, "websites": {"description": "A list of websites that are associated with the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "PersonValue", "type": "object"}, "PlannedProcess": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_inputs": {"items": {"type": "string"}, "type": "array"}, "has_outputs": {"items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "participating_agent": {"$ref": "#/$defs/Agent"}}, "required": ["id"], "title": "PlannedProcess", "type": "object"}, "PlantGrowthMedEnum": {"description": "", "enum": ["other artificial liquid medium", "other artificial solid medium", "peat moss", "perlite", "pumice", "sand", "soil", "vermiculite", "water"], "title": "PlantGrowthMedEnum", "type": "string"}, "PlantSexEnum": {"description": "", "enum": ["Androdioecious", "Androecious", "Androgynous", "Androgynomonoecious", "Andromonoecious", "Bisexual", "Dichogamous", "Diclinous", "Dioecious", "Gynodioecious", "Gynoecious", "Gynomonoecious", "Hermaphroditic", "Imperfect", "Monoclinous", "Monoecious", "Perfect", "Polygamodioecious", "Polygamomonoecious", "Polygamous", "Protandrous", "Protogynous", "Subandroecious", "Subdioecious", "Subgynoecious", "Synoecious", "Trimonoecious", "Trioecious", "Unisexual"], "title": "PlantSexEnum", "type": "string"}, "ProcessingInstitutionEnum": {"description": "", "enum": ["UCSD", "JGI", "EMSL"], "title": "ProcessingInstitutionEnum", "type": "string"}, "ProfilePositionEnum": {"description": "", "enum": ["summit", "shoulder", "backslope", "footslope", "toeslope"], "title": "ProfilePositionEnum", "type": "string"}, "ProteinQuantification": {"additionalProperties": false, "description": "This is used to link a metaproteomics analysis workflow to a specific protein", "title": "ProteinQuantification", "type": "object"}, "QuadPosEnum": {"description": "", "enum": ["North side", "West side", "South side", "East side"], "title": "QuadPosEnum", "type": "string"}, "QuantityValue": {"additionalProperties": false, "description": "A simple quantity, e.g. 2cm", "properties": {"has_maximum_numeric_value": {"description": "The maximum value part, expressed as number, of the quantity value when the value covers a range.", "type": "number"}, "has_minimum_numeric_value": {"description": "The minimum value part, expressed as number, of the quantity value when the value covers a range.", "type": "number"}, "has_numeric_value": {"description": "The number part of the quantity", "type": "number"}, "has_raw_value": {"description": "Unnormalized atomic string representation, should in syntax {number} {unit}", "type": "string"}, "has_unit": {"description": "The unit of the quantity", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "QuantityValue", "type": "object"}, "Reaction": {"additionalProperties": false, "description": "An individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Reaction", "type": "object"}, "ReactionActivity": {"additionalProperties": false, "description": "", "properties": {"material_input": {"type": "string"}, "material_output": {"type": "string"}, "reaction_aided_by": {"$ref": "#/$defs/LabDevice"}, "reaction_temperature": {"type": "string"}, "reaction_time": {"$ref": "#/$defs/QuantityValue"}}, "title": "ReactionActivity", "type": "object"}, "ReactionParticipant": {"additionalProperties": false, "description": "Instances of this link a reaction to a chemical entity participant", "title": "ReactionParticipant", "type": "object"}, "ReadBasedTaxonomyAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "ReadBasedTaxonomyAnalysisActivity", "type": "object"}, "ReadQcAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "input_base_count": {"description": "The nucleotide base count number of input reads for QC analysis.", "type": "number"}, "input_read_count": {"description": "The sequence count number of input reads for QC analysis.", "type": "number"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "output_base_count": {"description": "After QC analysis nucleotide base count number.", "type": "number"}, "output_read_count": {"description": "After QC analysis sequence count number.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "ReadQcAnalysisActivity", "type": "object"}, "RelSampLocEnum": {"description": "", "enum": ["edge of car", "center of car", "under a seat"], "title": "RelSampLocEnum", "type": "string"}, "RelToOxygenEnum": {"description": "", "enum": ["aerobe", "anaerobe", "facultative", "microaerophilic", "microanaerobe", "obligate aerobe", "obligate anaerobe"], "title": "RelToOxygenEnum", "type": "string"}, "RnaContTypeEnum": {"description": "", "enum": ["plate", "tube"], "title": "RnaContTypeEnum", "type": "string"}, "RnaSampleFormatEnum": {"description": "", "enum": ["10 mM Tris-HCl", "DNAStable", "Ethanol", "Low EDTA TE", "MDA reaction buffer", "PBS", "Pellet", "RNAStable", "TE", "Water"], "title": "RnaSampleFormatEnum", "type": "string"}, "RoomCondtEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture", "visible signs of mold/mildew"], "title": "RoomCondtEnum", "type": "string"}, "RoomConnectedEnum": {"description": "", "enum": ["attic", "bathroom", "closet", "conference room", "elevator", "examining room", "hallway", "kitchen", "mail room", "office", "stairwell"], "title": "RoomConnectedEnum", "type": "string"}, "RoomLocEnum": {"description": "", "enum": ["corner room", "interior room", "exterior wall"], "title": "RoomLocEnum", "type": "string"}, "RoomSampPosEnum": {"description": "", "enum": ["north corner", "south corner", "west corner", "east corner", "northeast corner", "northwest corner", "southeast corner", "southwest corner", "center"], "title": "RoomSampPosEnum", "type": "string"}, "RoomTypeEnum": {"description": "", "enum": ["attic", "bathroom", "closet", "conference room", "elevator", "examining room", "hallway", "kitchen", "mail room", "private office", "open office", "stairwell", ",restroom", "lobby", "vestibule", "mechanical or electrical room", "data center", "laboratory_wet", "laboratory_dry", "gymnasium", "natatorium", "auditorium", "lockers", "cafe", "warehouse"], "title": "RoomTypeEnum", "type": "string"}, "SampCaptStatusEnum": {"description": "", "enum": ["active surveillance in response to an outbreak", "active surveillance not initiated by an outbreak", "farm sample", "market sample", "other"], "title": "SampCaptStatusEnum", "type": "string"}, "SampCollectPointEnum": {"description": "", "enum": ["well", "test well", "drilling rig", "wellhead", "separator", "storage tank", "other"], "title": "SampCollectPointEnum", "type": "string"}, "SampDisStageEnum": {"description": "", "enum": ["dissemination", "growth and reproduction", "infection", "inoculation", "penetration", "other"], "title": "SampDisStageEnum", "type": "string"}, "SampFloorEnum": {"description": "", "enum": ["1st floor", "2nd floor", "basement", "lobby"], "title": "SampFloorEnum", "type": "string"}, "SampMdEnum": {"description": "", "enum": ["DF", "RT", "KB", "MSL", "other"], "title": "SampMdEnum", "type": "string"}, "SampSubtypeEnum": {"description": "", "enum": ["oil phase", "water phase", "biofilm", "not applicable", "other"], "title": "SampSubtypeEnum", "type": "string"}, "SampWeatherEnum": {"description": "", "enum": ["clear sky", "cloudy", "foggy", "hail", "rain", "snow", "sleet", "sunny", "windy"], "title": "SampWeatherEnum", "type": "string"}, "SampleTypeEnum": {"description": "", "enum": ["soil", "water_extract_soil"], "title": "SampleTypeEnum", "type": "string"}, "SamplingMethodEnum": {"description": "", "enum": ["weighing"], "title": "SamplingMethodEnum", "type": "string"}, "SeasonUseEnum": {"description": "", "enum": ["Spring", "Summer", "Fall", "Winter"], "title": "SeasonUseEnum", "type": "string"}, "SedimentTypeEnum": {"description": "", "enum": ["biogenous", "cosmogenous", "hydrogenous", "lithogenous"], "title": "SedimentTypeEnum", "type": "string"}, "ShadingDeviceCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "ShadingDeviceCondEnum", "type": "string"}, "ShadingDeviceTypeEnum": {"description": "", "enum": ["bahama shutters", "exterior roll blind", "gambrel awning", "hood awning", "porchroller awning", "sarasota shutters", "slatted aluminum", "solid aluminum awning", "sun screen", "tree", "trellis", "venetian awning"], "title": "ShadingDeviceTypeEnum", "type": "string"}, "Site": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Site", "type": "object"}, "SoilHorizonEnum": {"description": "", "enum": ["O horizon", "A horizon", "E horizon", "B horizon", "C horizon", "R layer", "Permafrost"], "title": "SoilHorizonEnum", "type": "string"}, "SolventEnum": {"description": "", "enum": ["deionized_water", "methanol", "chloroform"], "title": "SolventEnum", "type": "string"}, "SpecificEnum": {"description": "", "enum": ["operation", "as built", "construction", "bid", "design", "photos"], "title": "SpecificEnum", "type": "string"}, "SrDepEnvEnum": {"description": "", "enum": ["Lacustine", "Fluvioldeltaic", "Fluviomarine", "Marine", "other"], "title": "SrDepEnvEnum", "type": "string"}, "SrGeolAgeEnum": {"description": "", "enum": ["Archean", "Cambrian", "Carboniferous", "Cenozoic", "Cretaceous", "Devonian", "Jurassic", "Mesozoic", "Neogene", "Ordovician", "Paleogene", "Paleozoic", "Permian", "Precambrian", "Proterozoic", "Silurian", "Triassic", "other"], "title": "SrGeolAgeEnum", "type": "string"}, "SrKerogTypeEnum": {"description": "", "enum": ["Type I", "Type II", "Type III", "Type IV", "other"], "title": "SrKerogTypeEnum", "type": "string"}, "SrLithologyEnum": {"description": "", "enum": ["Clastic", "Carbonate", "Coal", "Biosilicieous", "other"], "title": "SrLithologyEnum", "type": "string"}, "Study": {"additionalProperties": false, "description": "A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.", "properties": {"abstract": {"description": "The abstract of manuscript/grant associated with the entity; i.e., a summary of the resource.", "type": "string"}, "alternative_descriptions": {"description": "A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.", "items": {"type": "string"}, "type": "array"}, "alternative_identifiers": {"description": "Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC", "items": {"type": "string"}, "type": "array"}, "alternative_names": {"description": "A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.", "items": {"type": "string"}, "type": "array"}, "alternative_titles": {"description": "A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "A brief summary that details the study you're submitted to NMDC", "type": "string"}, "doi": {"$ref": "#/$defs/AttributeValue", "description": "The dataset citation for this study"}, "ecosystem": {"description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", "type": "string"}, "ecosystem_category": {"description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", "type": "string"}, "ecosystem_subtype": {"description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", "type": "string"}, "ecosystem_type": {"description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", "type": "string"}, "emsl_proposal_doi": {"description": "The DOI for the EMSL awarded study that relates to the NMDC submitted study", "type": "string"}, "emsl_proposal_identifier": {"description": "The proposal number assigned to the EMSL awarded study that relates to that which is represented in NMDC.", "type": "string"}, "ess_dive_datasets": {"description": "List of ESS-DIVE dataset DOIs", "items": {"type": "string"}, "type": "array"}, "funding_sources": {"items": {"type": "string"}, "type": "array"}, "gold_study_identifiers": {"description": "identifiers for corresponding project(s) in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Gs[0-9]+$", "type": "array"}, "has_credit_associations": {"description": "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study", "items": {"$ref": "#/$defs/CreditAssociation"}, "type": "array"}, "id": {"description": "An NMDC assigned unique identifier for a sample submitted to NMDC.", "type": "string"}, "mgnify_project_identifiers": {"description": "identifiers for corresponding project in MGnify", "pattern": "^mgnify.proj:[A-Z]+[0-9]+$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "objective": {"description": "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.", "type": "string"}, "principal_investigator": {"$ref": "#/$defs/PersonValue", "description": "Principal Investigator who led the study and/or generated the dataset."}, "publications": {"description": "A list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.", "items": {"type": "string"}, "type": "array"}, "related_identifiers": {"description": "Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC", "type": "string"}, "relevant_protocols": {"items": {"type": "string"}, "type": "array"}, "specific_ecosystem": {"description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", "type": "string"}, "study_image": {"description": "Links a study to one or more images.", "items": {"$ref": "#/$defs/ImageValue"}, "type": "array"}, "title": {"description": "A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "websites": {"description": "A list of websites that are associated with the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "Study", "type": "object"}, "SubstructureTypeEnum": {"description": "", "enum": ["crawlspace", "slab on grade", "basement"], "title": "SubstructureTypeEnum", "type": "string"}, "SurfAirContEnum": {"description": "", "enum": ["dust", "organic matter", "particulate matter", "volatile organic compounds", "biological contaminants", "radon", "nutrients", "biocides"], "title": "SurfAirContEnum", "type": "string"}, "SurfMaterialEnum": {"description": "", "enum": ["adobe", "carpet", "cinder blocks", "concrete", "hay bales", "glass", "metal", "paint", "plastic", "stainless steel", "stone", "stucco", "tile", "vinyl", "wood"], "title": "SurfMaterialEnum", "type": "string"}, "TextValue": {"additionalProperties": false, "description": "A basic string value", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "language": {"description": "Should use ISO 639-1 code e.g. \"en\", \"fr\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "TextValue", "type": "object"}, "TidalStageEnum": {"description": "", "enum": ["low tide", "ebb tide", "flood tide", "high tide"], "title": "TidalStageEnum", "type": "string"}, "TillageEnum": {"description": "", "enum": ["drill", "cutting disc", "ridge till", "strip tillage", "zonal tillage", "chisel", "tined", "mouldboard", "disc plough"], "title": "TillageEnum", "type": "string"}, "TimestampValue": {"additionalProperties": false, "description": "A value that is a timestamp. The range should be ISO-8601", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "TimestampValue", "type": "object"}, "TrainLineEnum": {"description": "", "enum": ["red", "green", "orange"], "title": "TrainLineEnum", "type": "string"}, "TrainStatLocEnum": {"description": "", "enum": ["south station above ground", "south station underground", "south station amtrak", "forest hills", "riverside"], "title": "TrainStatLocEnum", "type": "string"}, "TrainStopLocEnum": {"description": "", "enum": ["end", "mid", "downtown"], "title": "TrainStopLocEnum", "type": "string"}, "UrlValue": {"additionalProperties": false, "description": "A value that is a string that conforms to URL syntax", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "UrlValue", "type": "object"}, "VisMediaEnum": {"description": "", "enum": ["photos", "videos", "commonly of the building", "site context (adjacent buildings, vegetation, terrain, streets)", "interiors", "equipment", "3D scans"], "title": "VisMediaEnum", "type": "string"}, "WallConstTypeEnum": {"description": "", "enum": ["frame construction", "joisted masonry", "light noncombustible", "masonry noncombustible", "modified fire resistive", "fire resistive"], "title": "WallConstTypeEnum", "type": "string"}, "WallFinishMatEnum": {"description": "", "enum": ["plaster", "gypsum plaster", "veneer plaster", "gypsum board", "tile", "terrazzo", "stone facing", "acoustical treatment", "wood", "metal", "masonry"], "title": "WallFinishMatEnum", "type": "string"}, "WallLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "WallLocEnum", "type": "string"}, "WallSurfTreatmentEnum": {"description": "", "enum": ["painted", "wall paper", "no treatment", "paneling", "stucco", "fabric"], "title": "WallSurfTreatmentEnum", "type": "string"}, "WallTextureEnum": {"description": "", "enum": ["crows feet", "crows-foot stomp", "double skip", "hawk and trowel", "knockdown", "popcorn", "orange peel", "rosebud stomp", "Santa-Fe texture", "skip trowel", "smooth", "stomp knockdown", "swirl"], "title": "WallTextureEnum", "type": "string"}, "WaterFeatTypeEnum": {"description": "", "enum": ["fountain", "pool", "standing feature", "stream", "waterfall"], "title": "WaterFeatTypeEnum", "type": "string"}, "WeekdayEnum": {"description": "", "enum": ["Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday", "Sunday"], "title": "WeekdayEnum", "type": "string"}, "WindowCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "WindowCondEnum", "type": "string"}, "WindowCoverEnum": {"description": "", "enum": ["blinds", "curtains", "none"], "title": "WindowCoverEnum", "type": "string"}, "WindowHorizPosEnum": {"description": "", "enum": ["left", "middle", "right"], "title": "WindowHorizPosEnum", "type": "string"}, "WindowLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "WindowLocEnum", "type": "string"}, "WindowMatEnum": {"description": "", "enum": ["clad", "fiberglass", "metal", "vinyl", "wood"], "title": "WindowMatEnum", "type": "string"}, "WindowTypeEnum": {"description": "", "enum": ["single-hung sash window", "horizontal sash window", "fixed window"], "title": "WindowTypeEnum", "type": "string"}, "WindowVertPosEnum": {"description": "", "enum": ["bottom", "middle", "top", "low", "high"], "title": "WindowVertPosEnum", "type": "string"}, "WorkflowExecutionActivity": {"additionalProperties": false, "description": "Represents an instance of an execution of a particular workflow", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"description": "the agent/entity associated with the generation of the file", "type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "WorkflowExecutionActivity", "type": "object"}}, "$id": "https://microbiomedata/schema", "$schema": "http://json-schema.org/draft-07/schema#", "additionalProperties": false, "metamodel_version": "1.7.0", "properties": {"activity_set": {"description": "This property links a database object to the set of workflow activities.", "items": {"$ref": "#/$defs/WorkflowExecutionActivity"}, "type": "array"}, "biosample_set": {"description": "This property links a database object to the set of samples within it.", "items": {"$ref": "#/$defs/Biosample"}, "type": "array"}, "cbfs_set": {"items": {"$ref": "#/$defs/CollectingBiosamplesFromSite"}, "type": "array"}, "data_object_set": {"description": "This property links a database object to the set of data objects within it.", "items": {"$ref": "#/$defs/DataObject"}, "type": "array"}, "dissolving_activity_set": {"items": {"$ref": "#/$defs/DissolvingActivity"}, "type": "array"}, "frs_set": {"items": {"$ref": "#/$defs/FieldResearchSite"}, "type": "array"}, "functional_annotation_set": {"description": "This property links a database object to the set of all functional annotations", "items": {"$ref": "#/$defs/FunctionalAnnotation"}, "type": "array"}, "genome_feature_set": {"description": "This property links a database object to the set of all features", "items": {"$ref": "#/$defs/GenomeFeature"}, "type": "array"}, "mags_activity_set": {"description": "This property links a database object to the set of MAGs analysis activities.", "items": {"$ref": "#/$defs/MagsAnalysisActivity"}, "type": "array"}, "material_sample_set": {"items": {"$ref": "#/$defs/MaterialSample"}, "type": "array"}, "material_sampling_activity_set": {"items": {"$ref": "#/$defs/MaterialSamplingActivity"}, "type": "array"}, "metabolomics_analysis_activity_set": {"description": "This property links a database object to the set of metabolomics analysis activities.", "items": {"$ref": "#/$defs/MetabolomicsAnalysisActivity"}, "type": "array"}, "metagenome_annotation_activity_set": {"description": "This property links a database object to the set of metagenome annotation activities.", "items": {"$ref": "#/$defs/MetagenomeAnnotationActivity"}, "type": "array"}, "metagenome_assembly_set": {"description": "This property links a database object to the set of metagenome assembly activities.", "items": {"$ref": "#/$defs/MetagenomeAssembly"}, "type": "array"}, "metaproteomics_analysis_activity_set": {"description": "This property links a database object to the set of metaproteomics analysis activities.", "items": {"$ref": "#/$defs/MetaproteomicsAnalysisActivity"}, "type": "array"}, "metatranscriptome_activity_set": {"description": "TODO", "items": {"$ref": "#/$defs/MetatranscriptomeActivity"}, "type": "array"}, "nom_analysis_activity_set": {"description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", "items": {"$ref": "#/$defs/NomAnalysisActivity"}, "type": "array"}, "omics_processing_set": {"description": "This property links a database object to the set of omics processings within it.", "items": {"$ref": "#/$defs/OmicsProcessing"}, "type": "array"}, "reaction_activity_set": {"items": {"$ref": "#/$defs/ReactionActivity"}, "type": "array"}, "read_based_taxonomy_analysis_activity_set": {"description": "This property links a database object to the set of read based analysis activities.", "items": {"$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity"}, "type": "array"}, "read_qc_analysis_activity_set": {"description": "This property links a database object to the set of read QC analysis activities.", "items": {"$ref": "#/$defs/ReadQcAnalysisActivity"}, "type": "array"}, "study_set": {"description": "This property links a database object to the set of studies within it.", "items": {"$ref": "#/$defs/Study"}, "type": "array"}}, "title": "NMDC", "type": "object", "version": "7.0.0"} +{"$defs": {"Activity": {"additionalProperties": false, "description": "a provence-generating activity", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"$ref": "#/$defs/Agent"}, "was_informed_by": {"type": "string"}}, "required": ["id"], "title": "Activity", "type": "object"}, "Agent": {"additionalProperties": false, "description": "a provence-generating agent", "properties": {"acted_on_behalf_of": {"$ref": "#/$defs/Agent"}, "was_informed_by": {"type": "string"}}, "title": "Agent", "type": "object"}, "AnalysisTypeEnum": {"description": "", "enum": ["metabolomics", "metagenomics", "metaproteomics", "metatranscriptomics", "natural organic matter"], "title": "AnalysisTypeEnum", "type": "string"}, "AnalyticalSample": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "AnalyticalSample", "type": "object"}, "ArchStrucEnum": {"description": "", "enum": ["building", "shed", "home"], "title": "ArchStrucEnum", "type": "string"}, "AttributeValue": {"additionalProperties": false, "description": "The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "AttributeValue", "type": "object"}, "BiolStatEnum": {"description": "", "enum": ["wild", "natural", "semi-natural", "inbred line", "breeder's line", "hybrid", "clonal selection", "mutant"], "title": "BiolStatEnum", "type": "string"}, "Biosample": {"additionalProperties": false, "description": "Biological source material which can be characterized by an experiment.", "properties": {"add_date": {"description": "The date on which the information was added to the database.", "type": "string"}, "agrochem_addition": {"$ref": "#/$defs/QuantityValue", "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications"}, "air_temp_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens"}, "al_sat": {"$ref": "#/$defs/QuantityValue", "description": "Aluminum saturation (esp. For tropical soils)"}, "al_sat_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining Al saturation"}, "alkalinity": {"$ref": "#/$defs/QuantityValue", "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate"}, "alkalinity_method": {"$ref": "#/$defs/TextValue", "description": "Method used for alkalinity measurement"}, "alkyl_diethers": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of alkyl diethers"}, "alt": {"$ref": "#/$defs/QuantityValue", "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air"}, "alternative_identifiers": {"description": "Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC", "items": {"type": "string"}, "type": "array"}, "aminopept_act": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of aminopeptidase activity"}, "ammonium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of ammonium in the sample"}, "ammonium_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of ammonium nitrogen in the sample"}, "analysis_type": {"description": "Select all the data types associated or available for this biosample", "items": {"$ref": "#/$defs/AnalysisTypeEnum"}, "type": "array"}, "annual_precpt": {"$ref": "#/$defs/QuantityValue", "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps."}, "annual_temp": {"$ref": "#/$defs/QuantityValue", "description": "Mean annual temperature"}, "bacteria_carb_prod": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of bacterial carbon production"}, "biosample_categories": {"items": {"$ref": "#/$defs/BiosampleCategoryEnum"}, "type": "array"}, "biotic_regm": {"$ref": "#/$defs/TextValue", "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi."}, "biotic_relationship": {"$ref": "#/$defs/TextValue", "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object"}, "bishomohopanol": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of bishomohopanol"}, "bromide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of bromide"}, "calcium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of calcium in the sample"}, "carb_nitro_ratio": {"$ref": "#/$defs/QuantityValue", "description": "Ratio of amount or concentrations of carbon to nitrogen"}, "chem_administration": {"$ref": "#/$defs/ControlledTermValue", "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi"}, "chloride": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of chloride in the sample"}, "chlorophyll": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of chlorophyll"}, "climate_environment": {"$ref": "#/$defs/TextValue", "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates"}, "collected_from": {"description": "The Site from which a Biosample was collected", "type": "string"}, "collection_date": {"$ref": "#/$defs/TimestampValue", "description": "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant"}, "collection_date_inc": {"description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", "type": "string"}, "collection_time": {"description": "The time of sampling, either as an instance (single point) or interval.", "type": "string"}, "collection_time_inc": {"description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", "type": "string"}, "community": {"type": "string"}, "crop_rotation": {"$ref": "#/$defs/TextValue", "description": "Whether or not crop is rotated, and if yes, rotation schedule"}, "cur_land_use": {"$ref": "#/$defs/TextValue", "description": "Present state of sample site"}, "cur_vegetation": {"$ref": "#/$defs/TextValue", "description": "Vegetation classification from one or more standard classification systems, or agricultural crop"}, "cur_vegetation_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in vegetation classification"}, "density": {"$ref": "#/$defs/QuantityValue", "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)"}, "depth": {"$ref": "#/$defs/QuantityValue", "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "diss_carb_dioxide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample"}, "diss_hydrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved hydrogen"}, "diss_inorg_carb": {"$ref": "#/$defs/QuantityValue", "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter"}, "diss_inorg_phosp": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved inorganic phosphorus in the sample"}, "diss_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid"}, "diss_org_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2"}, "diss_oxygen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved oxygen"}, "dna_absorb1": {"description": "260/280 measurement of DNA sample purity", "type": "string"}, "dna_absorb2": {"description": "260/230 measurement of DNA sample purity", "type": "string"}, "dna_collect_site": {"description": "Provide information on the site your DNA sample was collected from", "type": "string"}, "dna_concentration": {"maximum": 2000, "minimum": 0, "type": "string"}, "dna_cont_type": {"$ref": "#/$defs/DnaContTypeEnum", "description": "Tube or plate (96-well)"}, "dna_cont_well": {"type": "string"}, "dna_container_id": {"type": "string"}, "dna_dnase": {"$ref": "#/$defs/DnaDnaseEnum"}, "dna_isolate_meth": {"description": "Describe the method/protocol/kit used to extract DNA/RNA.", "type": "string"}, "dna_organisms": {"description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", "type": "string"}, "dna_project_contact": {"type": "string"}, "dna_samp_id": {"type": "string"}, "dna_sample_format": {"$ref": "#/$defs/DnaSampleFormatEnum", "description": "Solution in which the DNA sample has been suspended"}, "dna_sample_name": {"description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", "type": "string"}, "dna_seq_project": {"type": "string"}, "dna_seq_project_name": {"type": "string"}, "dna_seq_project_pi": {"type": "string"}, "dna_volume": {"maximum": 1000, "minimum": 0, "type": "string"}, "dnase_rna": {"$ref": "#/$defs/DnaseRnaEnum"}, "drainage_class": {"$ref": "#/$defs/TextValue", "description": "Drainage classification from a standard system such as the USDA system"}, "ecosystem": {"description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", "type": "string"}, "ecosystem_category": {"description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", "type": "string"}, "ecosystem_subtype": {"description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", "type": "string"}, "ecosystem_type": {"description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", "type": "string"}, "elev": {"$ref": "#/$defs/QuantityValue", "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit."}, "emsl_biosample_identifiers": {"description": "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.", "items": {"type": "string"}, "type": "array"}, "env_broad_scale": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS"}, "env_local_scale": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS."}, "env_medium": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top)."}, "env_package": {"$ref": "#/$defs/TextValue", "description": "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported", "pattern": "[air|built environment|host\\-associated|human\\-associated|human\\-skin|human\\-oral|human\\-gut|human\\-vaginal|hydrocarbon resources\\-cores|hydrocarbon resources\\-fluids\\/swabs|microbial mat\\/biofilm|misc environment|plant\\-associated|sediment|soil|wastewater\\/sludge|water]"}, "experimental_factor": {"$ref": "#/$defs/ControlledTermValue", "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI"}, "experimental_factor_other": {"description": "Other details about your sample that you feel can't be accurately represented in the available columns.", "type": "string"}, "extreme_event": {"description": "Unusual physical events that may have affected microbial populations", "type": "string"}, "fao_class": {"$ref": "#/$defs/TextValue", "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups"}, "filter_method": {"description": "Type of filter used or how the sample was filtered", "type": "string"}, "fire": {"$ref": "#/$defs/TimestampValue", "description": "Historical and/or physical evidence of fire"}, "flooding": {"$ref": "#/$defs/TimestampValue", "description": "Historical and/or physical evidence of flooding"}, "gaseous_environment": {"$ref": "#/$defs/QuantityValue", "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens"}, "geo_loc_name": {"$ref": "#/$defs/TextValue", "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)"}, "glucosidase_act": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of glucosidase activity"}, "gold_biosample_identifiers": {"description": "Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample", "items": {"type": "string"}, "pattern": "^GOLD:Gb[0-9]+$", "type": "array"}, "growth_facil": {"$ref": "#/$defs/ControlledTermValue", "description": "Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research"}, "habitat": {"type": "string"}, "heavy_metals": {"$ref": "#/$defs/QuantityValue", "description": "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field."}, "heavy_metals_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining heavy metals"}, "host_name": {"type": "string"}, "humidity_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens"}, "id": {"description": "An NMDC assigned unique identifier for a biosample submitted to NMDC.", "pattern": "^nmdc:", "type": "string"}, "igsn_biosample_identifiers": {"description": "A list of identifiers for the biosample from the IGSN database.", "items": {"type": "string"}, "type": "array"}, "img_identifiers": {"description": "A list of identifiers that relate the biosample to records in the IMG database.", "items": {"type": "string"}, "type": "array"}, "insdc_biosample_identifiers": {"description": "identifiers for corresponding sample in INSDC", "items": {"type": "string"}, "pattern": "^biosample:SAM[NED]([A-Z])?[0-9]+$", "type": "array"}, "isotope_exposure": {"description": "List isotope exposure or addition applied to your sample.", "type": "string"}, "lat_lon": {"$ref": "#/$defs/GeolocationValue", "description": "This is currently a required field but it's not clear if this should be required for human hosts"}, "lbc_thirty": {"$ref": "#/$defs/QuantityValue", "description": "lime buffer capacity, determined after 30 minute incubation"}, "lbceq": {"$ref": "#/$defs/QuantityValue", "description": "lime buffer capacity, determined at equilibrium after 5 day incubation"}, "light_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality."}, "link_addit_analys": {"$ref": "#/$defs/TextValue", "description": "Link to additional analysis results performed on the sample"}, "link_class_info": {"$ref": "#/$defs/TextValue", "description": "Link to digitized soil maps or other soil classification information"}, "link_climate_info": {"$ref": "#/$defs/TextValue", "description": "Link to climate resource"}, "local_class": {"$ref": "#/$defs/TextValue", "description": "Soil classification based on local soil classification system"}, "local_class_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining the local soil classification"}, "location": {"type": "string"}, "magnesium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of magnesium in the sample"}, "manganese": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of manganese in the sample"}, "mean_frict_vel": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of mean friction velocity"}, "mean_peak_frict_vel": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of mean peak friction velocity"}, "micro_biomass_c_meth": {"description": "Reference or method used in determining microbial biomass", "type": "string"}, "micro_biomass_n_meth": {"description": "Reference or method used in determining microbial biomass nitrogen", "type": "string"}, "microbial_biomass_c": {"description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", "type": "string"}, "microbial_biomass_n": {"description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", "type": "string"}, "misc_param": {"$ref": "#/$defs/QuantityValue", "description": "Any other measurement performed or parameter collected, that is not listed here"}, "mod_date": {"description": "The last date on which the database information was modified.", "type": "string"}, "n_alkanes": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of n-alkanes; can include multiple n-alkanes"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "ncbi_taxonomy_name": {"type": "string"}, "nitrate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrate in the sample"}, "nitrate_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrate nitrogen in the sample"}, "nitrite": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrite in the sample"}, "nitrite_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrite nitrogen in the sample"}, "non_microb_biomass": {"description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", "type": "string"}, "non_microb_biomass_method": {"description": "Reference or method used in determining biomass", "type": "string"}, "org_matter": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of organic matter"}, "org_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of organic nitrogen"}, "org_nitro_method": {"description": "Method used for obtaining organic nitrogen", "type": "string"}, "organism_count": {"$ref": "#/$defs/QuantityValue", "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)"}, "other_treatment": {"description": "Other treatments applied to your samples that are not applicable to the provided fields", "type": "string"}, "oxy_stat_samp": {"$ref": "#/$defs/TextValue", "description": "Oxygenation status of sample"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "part_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of particulate organic carbon"}, "perturbation": {"$ref": "#/$defs/TextValue", "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types"}, "petroleum_hydrocarb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of petroleum hydrocarbon"}, "ph": {"$ref": "#/$defs/QuantityValue", "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid"}, "ph_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining ph"}, "phaeopigments": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phaeopigments; can include multiple phaeopigments"}, "phosphate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phosphate"}, "phosplipid_fatt_acid": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phospholipid fatty acids; can include multiple values"}, "pool_dna_extracts": {"$ref": "#/$defs/TextValue", "description": "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given"}, "potassium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of potassium in the sample"}, "pressure": {"$ref": "#/$defs/QuantityValue", "description": "Pressure to which the sample is subject to, in atmospheres"}, "profile_position": {"$ref": "#/$defs/TextValue", "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas"}, "project_id": {"description": "Proposal IDs or names associated with dataset", "type": "string"}, "proport_woa_temperature": {"type": "string"}, "proposal_dna": {"type": "string"}, "proposal_rna": {"type": "string"}, "redox_potential": {"$ref": "#/$defs/QuantityValue", "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential"}, "rel_to_oxygen": {"$ref": "#/$defs/TextValue", "description": "Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments"}, "replicate_number": {"description": "If sending biological replicates, indicate the rep number here.", "type": "string"}, "rna_absorb1": {"description": "260/280 measurement of RNA sample purity", "type": "string"}, "rna_absorb2": {"description": "260/230 measurement of RNA sample purity", "type": "string"}, "rna_collect_site": {"description": "Provide information on the site your RNA sample was collected from", "type": "string"}, "rna_concentration": {"maximum": 1000, "minimum": 0, "type": "string"}, "rna_cont_type": {"$ref": "#/$defs/RnaContTypeEnum", "description": "Tube or plate (96-well)"}, "rna_cont_well": {"type": "string"}, "rna_container_id": {"type": "string"}, "rna_isolate_meth": {"description": "Describe the method/protocol/kit used to extract DNA/RNA.", "type": "string"}, "rna_organisms": {"description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", "type": "string"}, "rna_project_contact": {"type": "string"}, "rna_samp_id": {"type": "string"}, "rna_sample_format": {"$ref": "#/$defs/RnaSampleFormatEnum", "description": "Solution in which the RNA sample has been suspended"}, "rna_sample_name": {"description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", "maximum": 2000, "minimum": 0, "type": "string"}, "rna_seq_project": {"type": "string"}, "rna_seq_project_name": {"type": "string"}, "rna_seq_project_pi": {"type": "string"}, "rna_volume": {"type": "string"}, "salinity": {"$ref": "#/$defs/QuantityValue", "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater."}, "salinity_category": {"description": "Categorcial description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline", "type": "string"}, "salinity_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining salinity"}, "samp_collec_method": {"description": "The method employed for collecting the sample.", "type": "string"}, "samp_mat_process": {"$ref": "#/$defs/ControlledTermValue", "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed."}, "samp_name": {"description": "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.", "type": "string"}, "samp_size": {"$ref": "#/$defs/QuantityValue", "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected."}, "samp_store_dur": {"$ref": "#/$defs/TextValue", "description": "Duration for which the sample was stored"}, "samp_store_loc": {"$ref": "#/$defs/TextValue", "description": "Location at which sample was stored, usually name of a specific freezer/room"}, "samp_store_temp": {"$ref": "#/$defs/QuantityValue", "description": "Temperature at which sample was stored, e.g. -80 degree Celsius"}, "samp_vol_we_dna_ext": {"$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)."}, "sample_collection_site": {"type": "string"}, "sample_link": {"description": "JsonObj()", "items": {"type": "string"}, "type": "array"}, "sample_shipped": {"description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL", "type": "string"}, "sample_type": {"$ref": "#/$defs/SampleTypeEnum", "description": "Type of sample being submitted"}, "season_precpt": {"$ref": "#/$defs/QuantityValue", "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps."}, "season_temp": {"$ref": "#/$defs/QuantityValue", "description": "Mean seasonal temperature"}, "sieving": {"$ref": "#/$defs/QuantityValue", "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved"}, "size_frac_low": {"$ref": "#/$defs/QuantityValue", "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample"}, "size_frac_up": {"$ref": "#/$defs/QuantityValue", "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample"}, "slope_aspect": {"$ref": "#/$defs/QuantityValue", "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration."}, "slope_gradient": {"$ref": "#/$defs/QuantityValue", "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer"}, "sodium": {"$ref": "#/$defs/QuantityValue", "description": "Sodium concentration in the sample"}, "soil_type": {"$ref": "#/$defs/TextValue", "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes."}, "soil_type_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining soil series name or other lower-level classification"}, "soluble_iron_micromol": {"type": "string"}, "source_mat_id": {"$ref": "#/$defs/TextValue", "description": "A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2)."}, "specific_ecosystem": {"description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", "type": "string"}, "start_date_inc": {"description": "Date the incubation was started. Only relevant for incubation samples.", "type": "string"}, "start_time_inc": {"description": "Time the incubation was started. Only relevant for incubation samples.", "type": "string"}, "store_cond": {"$ref": "#/$defs/TextValue", "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)."}, "subsurface_depth": {"$ref": "#/$defs/QuantityValue"}, "sulfate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of sulfate in the sample"}, "sulfide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of sulfide in the sample"}, "technical_reps": {"description": "If sending multiple technical replicates of the same sample, indicate how many replicates are being sent", "type": "string"}, "temp": {"$ref": "#/$defs/QuantityValue", "description": "Temperature of the sample at the time of sampling."}, "tidal_stage": {"$ref": "#/$defs/TextValue", "description": "Stage of tide"}, "tillage": {"$ref": "#/$defs/TextValue", "description": "Note method(s) used for tilling"}, "tot_carb": {"$ref": "#/$defs/QuantityValue", "description": "Total carbon content"}, "tot_depth_water_col": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of total depth of water column"}, "tot_diss_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen"}, "tot_nitro_cont_meth": {"description": "Reference or method used in determining the total nitrogen", "type": "string"}, "tot_nitro_content": {"$ref": "#/$defs/QuantityValue", "description": "Total nitrogen content of the sample"}, "tot_org_c_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining total organic carbon"}, "tot_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content"}, "tot_phosp": {"$ref": "#/$defs/QuantityValue", "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "water_cont_soil_meth": {"description": "Reference or method used in determining the water content of soil", "type": "string"}, "water_content": {"$ref": "#/$defs/QuantityValue", "description": "Water content measurement"}, "watering_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens"}, "zinc": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of zinc in the sample"}}, "required": ["part_of", "id", "env_broad_scale", "env_local_scale", "env_medium"], "title": "Biosample", "type": "object"}, "BiosampleCategoryEnum": {"description": "Funding-based, sample location-based, or experimental method-based defined categories", "enum": ["LTER", "SIP", "SFA", "FICUS", "NEON"], "title": "BiosampleCategoryEnum", "type": "string"}, "BiosampleProcessing": {"additionalProperties": false, "description": "A process that takes one or more biosamples as inputs and generates one or as outputs. Examples of outputs include samples cultivated from another sample or data objects created by instruments runs.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "BiosampleProcessing", "type": "object"}, "BioticRelationshipEnum": {"description": "", "enum": ["free living", "parasite", "commensal", "symbiont"], "title": "BioticRelationshipEnum", "type": "string"}, "BooleanValue": {"additionalProperties": false, "description": "A value that is a boolean", "properties": {"has_boolean_value": {"description": "Links a quantity value to a boolean", "type": "boolean"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "BooleanValue", "type": "object"}, "BuildDocsEnum": {"description": "", "enum": ["building information model", "commissioning report", "complaint logs", "contract administration", "cost estimate", "janitorial schedules or logs", "maintenance plans", "schedule", "sections", "shop drawings", "submittals", "ventilation system", "windows"], "title": "BuildDocsEnum", "type": "string"}, "BuildOccupTypeEnum": {"description": "", "enum": ["office", "market", "restaurant", "residence", "school", "residential", "commercial", "low rise", "high rise", "wood framed", "health care", "airport", "sports complex"], "title": "BuildOccupTypeEnum", "type": "string"}, "BuildingSettingEnum": {"description": "", "enum": ["urban", "suburban", "exurban", "rural"], "title": "BuildingSettingEnum", "type": "string"}, "CeilCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "CeilCondEnum", "type": "string"}, "CeilFinishMatEnum": {"description": "", "enum": ["drywall", "mineral fibre", "tiles", "PVC", "plasterboard", "metal", "fiberglass", "stucco", "mineral wool/calcium silicate", "wood"], "title": "CeilFinishMatEnum", "type": "string"}, "CeilTextureEnum": {"description": "", "enum": ["crows feet", "crows-foot stomp", "double skip", "hawk and trowel", "knockdown", "popcorn", "orange peel", "rosebud stomp", "Santa-Fe texture", "skip trowel", "smooth", "stomp knockdown", "swirl"], "title": "CeilTextureEnum", "type": "string"}, "CeilTypeEnum": {"description": "", "enum": ["cathedral", "dropped", "concave", "barrel-shaped", "coffered", "cove", "stretched"], "title": "CeilTypeEnum", "type": "string"}, "ChemicalEntity": {"additionalProperties": false, "description": "An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "ChemicalEntity", "type": "object"}, "CollectingBiosamplesFromSite": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_inputs": {"items": {"type": "string"}, "type": "array"}, "has_outputs": {"items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "participating_agent": {"$ref": "#/$defs/Agent"}}, "required": ["has_inputs", "has_outputs", "id"], "title": "CollectingBiosamplesFromSite", "type": "object"}, "ContainerTypeEnum": {"description": "", "enum": ["screw_top_conical"], "title": "ContainerTypeEnum", "type": "string"}, "ControlledIdentifiedTermValue": {"additionalProperties": false, "description": "A controlled term or class from an ontology, requiring the presence of term with an id", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "term": {"$ref": "#/$defs/OntologyClass", "description": "pointer to an ontology class"}, "was_generated_by": {"type": "string"}}, "required": ["term"], "title": "ControlledIdentifiedTermValue", "type": "object"}, "ControlledTermValue": {"additionalProperties": false, "description": "A controlled term or class from an ontology", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "term": {"$ref": "#/$defs/OntologyClass", "description": "pointer to an ontology class"}, "was_generated_by": {"type": "string"}}, "title": "ControlledTermValue", "type": "object"}, "CreditAssociation": {"additionalProperties": false, "description": "This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0", "properties": {"applied_role": {"$ref": "#/$defs/CreditEnum"}, "applied_roles": {"items": {"$ref": "#/$defs/CreditEnum"}, "type": "array"}, "applies_to_person": {"$ref": "#/$defs/PersonValue"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "required": ["applies_to_person", "applied_roles"], "title": "CreditAssociation", "type": "object"}, "CreditEnum": {"description": "", "enum": ["Conceptualization", "Data curation", "Formal Analysis", "Funding acquisition", "Investigation", "Methodology", "Project administration", "Resources", "Software", "Supervision", "Validation", "Visualization", "Writing original draft", "Writing review and editing", "Principal Investigator", "Submitter"], "title": "CreditEnum", "type": "string"}, "CurLandUseEnum": {"description": "", "enum": ["cities", "farmstead", "industrial areas", "roads/railroads", "rock", "sand", "gravel", "mudflats", "salt flats", "badlands", "permanent snow or ice", "saline seeps", "mines/quarries", "oil waste areas", "small grains", "row crops", "vegetable crops", "horticultural plants (e.g. tulips)", "marshlands (grass,sedges,rushes)", "tundra (mosses,lichens)", "rangeland", "pastureland (grasslands used for livestock grazing)", "hayland", "meadows (grasses,alfalfa,fescue,bromegrass,timothy)", "shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)", "successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)", "shrub crops (blueberries,nursery ornamentals,filberts)", "vine crops (grapes)", "conifers (e.g. pine,spruce,fir,cypress)", "hardwoods (e.g. oak,hickory,elm,aspen)", "intermixed hardwood and conifers", "tropical (e.g. mangrove,palms)", "rainforest (evergreen forest receiving greater than 406 cm annual rainfall)", "swamp (permanent or semi-permanent water body dominated by woody plants)", "crop trees (nuts,fruit,christmas trees,nursery trees)"], "title": "CurLandUseEnum", "type": "string"}, "DataObject": {"additionalProperties": false, "description": "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "compression_type": {"description": "If provided, specifies the compression type", "type": "string"}, "data_object_type": {"$ref": "#/$defs/FileTypeEnum", "description": "The type of file represented by the data object."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "file_size_bytes": {"description": "Size of the file in bytes", "type": "integer"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "md5_checksum": {"description": "MD5 checksum of file (pre-compressed)", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "url": {"type": "string"}, "was_generated_by": {"type": "string"}}, "required": ["id", "name", "description"], "title": "DataObject", "type": "object"}, "Database": {"additionalProperties": false, "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest", "properties": {"activity_set": {"description": "This property links a database object to the set of workflow activities.", "items": {"$ref": "#/$defs/WorkflowExecutionActivity"}, "type": "array"}, "biosample_set": {"description": "This property links a database object to the set of samples within it.", "items": {"$ref": "#/$defs/Biosample"}, "type": "array"}, "collecting_biosamples_from_site_set": {"items": {"$ref": "#/$defs/CollectingBiosamplesFromSite"}, "type": "array"}, "data_object_set": {"description": "This property links a database object to the set of data objects within it.", "items": {"$ref": "#/$defs/DataObject"}, "type": "array"}, "dissolving_activity_set": {"items": {"$ref": "#/$defs/DissolvingActivity"}, "type": "array"}, "field_research_site_set": {"items": {"$ref": "#/$defs/FieldResearchSite"}, "type": "array"}, "functional_annotation_set": {"description": "This property links a database object to the set of all functional annotations", "items": {"$ref": "#/$defs/FunctionalAnnotation"}, "type": "array"}, "genome_feature_set": {"description": "This property links a database object to the set of all features", "items": {"$ref": "#/$defs/GenomeFeature"}, "type": "array"}, "mags_activity_set": {"description": "This property links a database object to the set of MAGs analysis activities.", "items": {"$ref": "#/$defs/MagsAnalysisActivity"}, "type": "array"}, "material_sample_set": {"items": {"$ref": "#/$defs/MaterialSample"}, "type": "array"}, "material_sampling_activity_set": {"items": {"$ref": "#/$defs/MaterialSamplingActivity"}, "type": "array"}, "metabolomics_analysis_activity_set": {"description": "This property links a database object to the set of metabolomics analysis activities.", "items": {"$ref": "#/$defs/MetabolomicsAnalysisActivity"}, "type": "array"}, "metagenome_annotation_activity_set": {"description": "This property links a database object to the set of metagenome annotation activities.", "items": {"$ref": "#/$defs/MetagenomeAnnotationActivity"}, "type": "array"}, "metagenome_assembly_set": {"description": "This property links a database object to the set of metagenome assembly activities.", "items": {"$ref": "#/$defs/MetagenomeAssembly"}, "type": "array"}, "metaproteomics_analysis_activity_set": {"description": "This property links a database object to the set of metaproteomics analysis activities.", "items": {"$ref": "#/$defs/MetaproteomicsAnalysisActivity"}, "type": "array"}, "metatranscriptome_activity_set": {"description": "TODO", "items": {"$ref": "#/$defs/MetatranscriptomeActivity"}, "type": "array"}, "nom_analysis_activity_set": {"description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", "items": {"$ref": "#/$defs/NomAnalysisActivity"}, "type": "array"}, "omics_processing_set": {"description": "This property links a database object to the set of omics processings within it.", "items": {"$ref": "#/$defs/OmicsProcessing"}, "type": "array"}, "reaction_activity_set": {"items": {"$ref": "#/$defs/ReactionActivity"}, "type": "array"}, "read_based_taxonomy_analysis_activity_set": {"description": "This property links a database object to the set of read based analysis activities.", "items": {"$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity"}, "type": "array"}, "read_qc_analysis_activity_set": {"description": "This property links a database object to the set of read QC analysis activities.", "items": {"$ref": "#/$defs/ReadQcAnalysisActivity"}, "type": "array"}, "study_set": {"description": "This property links a database object to the set of studies within it.", "items": {"$ref": "#/$defs/Study"}, "type": "array"}}, "title": "Database", "type": "object"}, "DeposEnvEnum": {"description": "", "enum": ["Continental - Alluvial", "Continental - Aeolian", "Continental - Fluvial", "Continental - Lacustrine", "Transitional - Deltaic", "Transitional - Tidal", "Transitional - Lagoonal", "Transitional - Beach", "Transitional - Lake", "Marine - Shallow", "Marine - Deep", "Marine - Reef", "Other - Evaporite", "Other - Glacial", "Other - Volcanic", "other"], "title": "DeposEnvEnum", "type": "string"}, "DeviceTypeEnum": {"description": "", "enum": ["orbital_shaker", "thermomixer"], "title": "DeviceTypeEnum", "type": "string"}, "DissolvingActivity": {"additionalProperties": false, "description": "", "properties": {"dissolution_aided_by": {"$ref": "#/$defs/LabDevice"}, "dissolution_reagent": {"$ref": "#/$defs/SolventEnum"}, "dissolution_volume": {"$ref": "#/$defs/QuantityValue"}, "dissolved_in": {"$ref": "#/$defs/MaterialContainer"}, "material_input": {"type": "string"}, "material_output": {"type": "string"}}, "title": "DissolvingActivity", "type": "object"}, "DnaContTypeEnum": {"description": "", "enum": ["plate", "tube"], "title": "DnaContTypeEnum", "type": "string"}, "DnaDnaseEnum": {"description": "", "enum": ["no", "yes"], "title": "DnaDnaseEnum", "type": "string"}, "DnaSampleFormatEnum": {"description": "", "enum": ["10 mM Tris-HCl", "DNAStable", "Ethanol", "Low EDTA TE", "MDA reaction buffer", "PBS", "Pellet", "RNAStable", "TE", "Water", "Gentegra-DNA", "Gentegra-RNA"], "title": "DnaSampleFormatEnum", "type": "string"}, "DnaseRnaEnum": {"description": "", "enum": ["no", "yes"], "title": "DnaseRnaEnum", "type": "string"}, "DoorCompTypeEnum": {"description": "", "enum": ["metal covered", "revolving", "sliding", "telescopic"], "title": "DoorCompTypeEnum", "type": "string"}, "DoorCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "DoorCondEnum", "type": "string"}, "DoorDirectEnum": {"description": "", "enum": ["inward", "outward", "sideways"], "title": "DoorDirectEnum", "type": "string"}, "DoorLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "DoorLocEnum", "type": "string"}, "DoorMatEnum": {"description": "", "enum": ["aluminum", "cellular PVC", "engineered plastic", "fiberboard", "fiberglass", "metal", "thermoplastic alloy", "vinyl", "wood", "wood/plastic composite"], "title": "DoorMatEnum", "type": "string"}, "DoorMoveEnum": {"description": "", "enum": ["collapsible", "folding", "revolving", "rolling shutter", "sliding", "swinging"], "title": "DoorMoveEnum", "type": "string"}, "DoorTypeEnum": {"description": "", "enum": ["composite", "metal", "wooden"], "title": "DoorTypeEnum", "type": "string"}, "DoorTypeMetalEnum": {"description": "", "enum": ["collapsible", "corrugated steel", "hollow", "rolling shutters", "steel plate"], "title": "DoorTypeMetalEnum", "type": "string"}, "DoorTypeWoodEnum": {"description": "", "enum": ["bettened and ledged", "battened", "ledged and braced", "ledged and framed", "ledged, braced and frame", "framed and paneled", "glashed or sash", "flush", "louvered", "wire gauged"], "title": "DoorTypeWoodEnum", "type": "string"}, "DrainageClassEnum": {"description": "", "enum": ["very poorly", "poorly", "somewhat poorly", "moderately well", "well", "excessively drained"], "title": "DrainageClassEnum", "type": "string"}, "DrawingsEnum": {"description": "", "enum": ["operation", "as built", "construction", "bid", "design", "building navigation map", "diagram", "sketch"], "title": "DrawingsEnum", "type": "string"}, "EnvironmentalMaterialTerm": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "EnvironmentalMaterialTerm", "type": "object"}, "ExtWallOrientEnum": {"description": "", "enum": ["north", "south", "east", "west", "northeast", "southeast", "southwest", "northwest"], "title": "ExtWallOrientEnum", "type": "string"}, "ExtWindowOrientEnum": {"description": "", "enum": ["north", "south", "east", "west", "northeast", "southeast", "southwest", "northwest"], "title": "ExtWindowOrientEnum", "type": "string"}, "FaoClassEnum": {"description": "", "enum": ["Acrisols", "Andosols", "Arenosols", "Cambisols", "Chernozems", "Ferralsols", "Fluvisols", "Gleysols", "Greyzems", "Gypsisols", "Histosols", "Kastanozems", "Lithosols", "Luvisols", "Nitosols", "Phaeozems", "Planosols", "Podzols", "Podzoluvisols", "Rankers", "Regosols", "Rendzinas", "Solonchaks", "Solonetz", "Vertisols", "Yermosols"], "title": "FaoClassEnum", "type": "string"}, "FieldResearchSite": {"additionalProperties": false, "description": "A site, outside of a laboratory, from which biosamples may be collected.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "FieldResearchSite", "type": "object"}, "FileTypeEnum": {"description": "", "enum": ["Metagenome Raw Reads", "FT ICR-MS Analysis Results", "GC-MS Metabolomics Results", "Metaproteomics Workflow Statistics", "Protein Report", "Peptide Report", "Unfiltered Metaproteomics Results", "Read Count and RPKM", "QC non-rRNA R2", "QC non-rRNA R1", "Metagenome Bins", "CheckM Statistics", "GOTTCHA2 Krona Plot", "GOTTCHA2 Classification Report", "GOTTCHA2 Report Full", "Kraken2 Krona Plot", "Centrifuge Krona Plot", "Centrifuge output report file", "Kraken2 Classification Report", "Kraken2 Taxonomic Classification", "Centrifuge Classification Report", "Centrifuge Taxonomic Classification", "Structural Annotation GFF", "Functional Annotation GFF", "Annotation Amino Acid FASTA", "Annotation Enzyme Commission", "Annotation KEGG Orthology", "Assembly Coverage BAM", "Assembly AGP", "Assembly Scaffolds", "Assembly Contigs", "Assembly Coverage Stats", "Filtered Sequencing Reads", "QC Statistics", "TIGRFam Annotation GFF", "CRT Annotation GFF", "Genmark Annotation GFF", "Prodigal Annotation GFF", "TRNA Annotation GFF", "Misc Annotation GFF", "RFAM Annotation GFF", "TMRNA Annotation GFF", "KO_EC Annotation GFF", "Product Names", "Gene Phylogeny tsv", "Crisprt Terms", "Clusters of Orthologous Groups (COG) Annotation GFF", "CATH FunFams (Functional Families) Annotation GFF", "SUPERFam Annotation GFF", "SMART Annotation GFF", "Pfam Annotation GFF", "Direct Infusion FT ICR-MS Raw Data"], "title": "FileTypeEnum", "type": "string"}, "FilterTypeEnum": {"description": "", "enum": ["particulate air filter", "chemical air filter", "low-MERV pleated media", "HEPA", "electrostatic", "gas-phase or ultraviolet air treatments"], "title": "FilterTypeEnum", "type": "string"}, "FloorCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "FloorCondEnum", "type": "string"}, "FloorFinishMatEnum": {"description": "", "enum": ["tile", "wood strip or parquet", "carpet", "rug", "laminate wood", "lineoleum", "vinyl composition tile", "sheet vinyl", "stone", "bamboo", "cork", "terrazo", "concrete", "none", "sealed", "clear finish", "paint", "none or unfinished"], "title": "FloorFinishMatEnum", "type": "string"}, "FloorStrucEnum": {"description": "", "enum": ["balcony", "floating floor", "glass floor", "raised floor", "sprung floor", "wood-framed", "concrete"], "title": "FloorStrucEnum", "type": "string"}, "FloorWaterMoldEnum": {"description": "", "enum": ["mold odor", "wet floor", "water stains", "wall discoloration", "floor discoloration", "ceiling discoloration", "peeling paint or wallpaper", "bulging walls", "condensation"], "title": "FloorWaterMoldEnum", "type": "string"}, "FreqCleanEnum": {"description": "", "enum": ["Daily", "Weekly", "Monthly", "Quarterly", "Annually", "other"], "title": "FreqCleanEnum", "type": "string"}, "FunctionalAnnotation": {"additionalProperties": false, "description": "An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods", "properties": {"has_function": {"pattern": "^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$", "type": "string"}, "subject": {"type": "string"}, "was_generated_by": {"description": "provenance for the annotation.", "type": "string"}}, "title": "FunctionalAnnotation", "type": "object"}, "FurnitureEnum": {"description": "", "enum": ["cabinet", "chair", "desks"], "title": "FurnitureEnum", "type": "string"}, "GenderRestroomEnum": {"description": "", "enum": ["all gender", "female", "gender neurtral", "male", "male and female", "unisex"], "title": "GenderRestroomEnum", "type": "string"}, "GeneProduct": {"additionalProperties": false, "description": "A molecule encoded by a gene that has an evolved function", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "GeneProduct", "type": "object"}, "GenomeFeature": {"additionalProperties": false, "description": "A feature localized to an interval along a genome", "title": "GenomeFeature", "type": "object"}, "GeolocationValue": {"additionalProperties": false, "description": "A normalized value for a location on the earth's surface", "properties": {"has_raw_value": {"description": "The raw value for a geolocation should follow {lat} {long}", "type": "string"}, "latitude": {"description": "latitude", "type": "number"}, "longitude": {"description": "longitude", "type": "number"}, "was_generated_by": {"type": "string"}}, "title": "GeolocationValue", "type": "object"}, "GrowthHabitEnum": {"description": "", "enum": ["erect", "semi-erect", "spreading", "prostrate"], "title": "GrowthHabitEnum", "type": "string"}, "HandidnessEnum": {"description": "", "enum": ["ambidexterity", "left handedness", "mixed-handedness", "right handedness"], "title": "HandidnessEnum", "type": "string"}, "HcProducedEnum": {"description": "", "enum": ["Oil", "Gas-Condensate", "Gas", "Bitumen", "Coalbed Methane", "other"], "title": "HcProducedEnum", "type": "string"}, "HcrEnum": {"description": "", "enum": ["Oil Reservoir", "Gas Reservoir", "Oil Sand", "Coalbed", "Shale", "Tight Oil Reservoir", "Tight Gas Reservoir", "other"], "title": "HcrEnum", "type": "string"}, "HcrGeolAgeEnum": {"description": "", "enum": ["Archean", "Cambrian", "Carboniferous", "Cenozoic", "Cretaceous", "Devonian", "Jurassic", "Mesozoic", "Neogene", "Ordovician", "Paleogene", "Paleozoic", "Permian", "Precambrian", "Proterozoic", "Silurian", "Triassic", "other"], "title": "HcrGeolAgeEnum", "type": "string"}, "HeatCoolTypeEnum": {"description": "", "enum": ["radiant system", "heat pump", "forced air system", "steam forced heat", "wood stove"], "title": "HeatCoolTypeEnum", "type": "string"}, "HeatDelivLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "HeatDelivLocEnum", "type": "string"}, "HorizonEnum": {"description": "", "enum": ["O horizon", "A horizon", "E horizon", "B horizon", "C horizon", "R layer", "Permafrost"], "title": "HorizonEnum", "type": "string"}, "HostSexEnum": {"description": "", "enum": ["female", "hermaphrodite", "male", "neuter"], "title": "HostSexEnum", "type": "string"}, "ImageValue": {"additionalProperties": false, "description": "An attribute value representing an image.", "properties": {"description": {"description": "a human-readable description of a thing", "type": "string"}, "display_order": {"description": "When rendering information, this attribute to specify the order in which the information should be rendered.", "type": "string"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "url": {"type": "string"}, "was_generated_by": {"type": "string"}}, "title": "ImageValue", "type": "object"}, "IndoorSpaceEnum": {"description": "", "enum": ["bedroom", "office", "bathroom", "foyer", "kitchen", "locker room", "hallway", "elevator"], "title": "IndoorSpaceEnum", "type": "string"}, "IndoorSurfEnum": {"description": "", "enum": ["cabinet", "ceiling", "counter top", "door", "shelving", "vent cover", "window", "wall"], "title": "IndoorSurfEnum", "type": "string"}, "Instrument": {"additionalProperties": false, "description": "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI].", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Instrument", "type": "object"}, "IntWallCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "IntWallCondEnum", "type": "string"}, "IntegerValue": {"additionalProperties": false, "description": "A value that is an integer", "properties": {"has_numeric_value": {"description": "Links a quantity value to a number", "type": "number"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "IntegerValue", "type": "object"}, "LabDevice": {"additionalProperties": false, "description": "", "properties": {"activity_speed": {"$ref": "#/$defs/QuantityValue"}, "activity_temperature": {"$ref": "#/$defs/QuantityValue"}, "activity_time": {"$ref": "#/$defs/QuantityValue"}, "device_type": {"$ref": "#/$defs/DeviceTypeEnum"}}, "title": "LabDevice", "type": "object"}, "LightTypeEnum": {"description": "", "enum": ["natural light", "electric light", "desk lamp", "flourescent lights", "none"], "title": "LightTypeEnum", "type": "string"}, "LithologyEnum": {"description": "", "enum": ["Basement", "Chalk", "Chert", "Coal", "Conglomerate", "Diatomite", "Dolomite", "Limestone", "Sandstone", "Shale", "Siltstone", "Volcanic", "other"], "title": "LithologyEnum", "type": "string"}, "MagBin": {"additionalProperties": false, "description": "", "properties": {"bin_name": {"type": "string"}, "bin_quality": {"type": "string"}, "completeness": {"type": "number"}, "contamination": {"type": "number"}, "gene_count": {"type": "integer"}, "gtdbtk_class": {"type": "string"}, "gtdbtk_domain": {"type": "string"}, "gtdbtk_family": {"type": "string"}, "gtdbtk_genus": {"type": "string"}, "gtdbtk_order": {"type": "string"}, "gtdbtk_phylum": {"type": "string"}, "gtdbtk_species": {"type": "string"}, "num_16s": {"type": "integer"}, "num_23s": {"type": "integer"}, "num_5s": {"type": "integer"}, "num_t_rna": {"type": "integer"}, "number_of_contig": {"type": "integer"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "title": "MagBin", "type": "object"}, "MagsAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", "properties": {"binned_contig_num": {"type": "integer"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "input_contig_num": {"type": "integer"}, "low_depth_contig_num": {"type": "integer"}, "mags_list": {"items": {"$ref": "#/$defs/MagBin"}, "type": "array"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "too_short_contig_num": {"type": "integer"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "unbinned_contig_num": {"type": "integer"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MagsAnalysisActivity", "type": "object"}, "MaterialContainer": {"additionalProperties": false, "description": "", "properties": {"container_size": {"$ref": "#/$defs/QuantityValue"}, "container_type": {"$ref": "#/$defs/ContainerTypeEnum"}}, "title": "MaterialContainer", "type": "object"}, "MaterialEntity": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "MaterialEntity", "type": "object"}, "MaterialSample": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "MaterialSample", "type": "object"}, "MaterialSamplingActivity": {"additionalProperties": false, "description": "", "properties": {"amount_collected": {"$ref": "#/$defs/QuantityValue"}, "biosample_input": {"type": "string"}, "collected_into": {"$ref": "#/$defs/MaterialContainer"}, "material_output": {"type": "string"}, "sampling_method": {"$ref": "#/$defs/SamplingMethodEnum"}}, "title": "MaterialSamplingActivity", "type": "object"}, "MechStrucEnum": {"description": "", "enum": ["subway", "coach", "carriage", "elevator", "escalator", "boat", "train", "car", "bus"], "title": "MechStrucEnum", "type": "string"}, "MetaboliteQuantification": {"additionalProperties": false, "description": "This is used to link a metabolomics analysis workflow to a specific metabolite", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "MetaboliteQuantification", "type": "object"}, "MetabolomicsAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetabolomicsAnalysisActivity", "type": "object"}, "MetagenomeAnnotationActivity": {"additionalProperties": false, "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "gold_analysis_project_identifiers": {"description": "identifiers for corresponding analysis project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Ga[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetagenomeAnnotationActivity", "type": "object"}, "MetagenomeAssembly": {"additionalProperties": false, "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", "properties": {"asm_score": {"description": "A score for comparing metagenomic assembly quality from same sample.", "type": "number"}, "contig_bp": {"description": "Total size in bp of all contigs.", "type": "number"}, "contigs": {"description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "ctg_l50": {"description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", "type": "number"}, "ctg_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", "type": "number"}, "ctg_logsum": {"description": "Maximum contig length.", "type": "number"}, "ctg_max": {"description": "Maximum contig length.", "type": "number"}, "ctg_n50": {"description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", "type": "number"}, "ctg_n90": {"description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", "type": "number"}, "ctg_powsum": {"description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "gap_pct": {"description": "The gap size percentage of all scaffolds.", "type": "number"}, "gc_avg": {"description": "Average of GC content of all contigs.", "type": "number"}, "gc_std": {"description": "Standard deviation of GC content of all contigs.", "type": "number"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_assembly_identifiers": {"pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "num_aligned_reads": {"description": "The sequence count number of input reads aligned to assembled contigs.", "type": "number"}, "num_input_reads": {"description": "The sequence count number of input reads for assembly.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "scaf_bp": {"description": "Total size in bp of all scaffolds.", "type": "number"}, "scaf_l50": {"description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", "type": "number"}, "scaf_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", "type": "number"}, "scaf_l_gt50k": {"description": "Total size in bp of all scaffolds greater than 50 KB.", "type": "number"}, "scaf_logsum": {"description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "scaf_max": {"description": "Maximum scaffold length.", "type": "number"}, "scaf_n50": {"description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", "type": "number"}, "scaf_n90": {"description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", "type": "number"}, "scaf_n_gt50k": {"description": "Total sequence count of scaffolds greater than 50 KB.", "type": "number"}, "scaf_pct_gt50k": {"description": "Total sequence size percentage of scaffolds greater than 50 KB.", "type": "number"}, "scaf_powsum": {"description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "scaffolds": {"description": "Total sequence count of all scaffolds.", "type": "number"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetagenomeAssembly", "type": "object"}, "MetaproteomicsAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetaproteomicsAnalysisActivity", "type": "object"}, "MetatranscriptomeActivity": {"additionalProperties": false, "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeActivity", "type": "object"}, "MetatranscriptomeAnnotationActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "gold_analysis_project_identifiers": {"description": "identifiers for corresponding analysis project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Ga[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeAnnotationActivity", "type": "object"}, "MetatranscriptomeAssembly": {"additionalProperties": false, "description": "", "properties": {"asm_score": {"description": "A score for comparing metagenomic assembly quality from same sample.", "type": "number"}, "contig_bp": {"description": "Total size in bp of all contigs.", "type": "number"}, "contigs": {"description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "ctg_l50": {"description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", "type": "number"}, "ctg_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", "type": "number"}, "ctg_logsum": {"description": "Maximum contig length.", "type": "number"}, "ctg_max": {"description": "Maximum contig length.", "type": "number"}, "ctg_n50": {"description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", "type": "number"}, "ctg_n90": {"description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", "type": "number"}, "ctg_powsum": {"description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "gap_pct": {"description": "The gap size percentage of all scaffolds.", "type": "number"}, "gc_avg": {"description": "Average of GC content of all contigs.", "type": "number"}, "gc_std": {"description": "Standard deviation of GC content of all contigs.", "type": "number"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_assembly_identifiers": {"pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "num_aligned_reads": {"description": "The sequence count number of input reads aligned to assembled contigs.", "type": "number"}, "num_input_reads": {"description": "The sequence count number of input reads for assembly.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "scaf_bp": {"description": "Total size in bp of all scaffolds.", "type": "number"}, "scaf_l50": {"description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", "type": "number"}, "scaf_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", "type": "number"}, "scaf_l_gt50k": {"description": "Total size in bp of all scaffolds greater than 50 KB.", "type": "number"}, "scaf_logsum": {"description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "scaf_max": {"description": "Maximum scaffold length.", "type": "number"}, "scaf_n50": {"description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", "type": "number"}, "scaf_n90": {"description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", "type": "number"}, "scaf_n_gt50k": {"description": "Total sequence count of scaffolds greater than 50 KB.", "type": "number"}, "scaf_pct_gt50k": {"description": "Total sequence size percentage of scaffolds greater than 50 KB.", "type": "number"}, "scaf_powsum": {"description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "scaffolds": {"description": "Total sequence count of all scaffolds.", "type": "number"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeAssembly", "type": "object"}, "NomAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "NomAnalysisActivity", "type": "object"}, "OccupDocumentEnum": {"description": "", "enum": ["automated count", "estimate", "manual count", "videos"], "title": "OccupDocumentEnum", "type": "string"}, "OmicsProcessing": {"additionalProperties": false, "description": "The methods and processes used to generate omics data from a biosample or organism.", "properties": {"add_date": {"description": "The date on which the information was added to the database.", "type": "string"}, "alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "chimera_check": {"$ref": "#/$defs/TextValue", "description": "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "gold_sequencing_project_identifiers": {"description": "identifiers for corresponding sequencing project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Gp[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_experiment_identifiers": {"items": {"type": "string"}, "pattern": "^insdc.sra:(E|D|S)RX[0-9]{6,}$", "type": "array"}, "instrument_name": {"description": "The name of the instrument that was used for processing the sample.", "type": "string"}, "mod_date": {"description": "The last date on which the database information was modified.", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "ncbi_project_name": {"type": "string"}, "nucl_acid_amp": {"$ref": "#/$defs/TextValue", "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids"}, "nucl_acid_ext": {"$ref": "#/$defs/TextValue", "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample"}, "omics_type": {"$ref": "#/$defs/ControlledTermValue", "description": "The type of omics data"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "pcr_cond": {"$ref": "#/$defs/TextValue", "description": "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'"}, "pcr_primers": {"$ref": "#/$defs/TextValue", "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters"}, "principal_investigator": {"$ref": "#/$defs/PersonValue", "description": "Principal Investigator who led the study and/or generated the dataset."}, "processing_institution": {"$ref": "#/$defs/ProcessingInstitutionEnum", "description": "The organization that processed the sample."}, "samp_vol_we_dna_ext": {"$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)."}, "seq_meth": {"$ref": "#/$defs/TextValue", "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)."}, "seq_quality_check": {"$ref": "#/$defs/TextValue", "description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA"}, "target_gene": {"$ref": "#/$defs/TextValue", "description": "Targeted gene or locus name for marker gene studies"}, "target_subfragment": {"$ref": "#/$defs/TextValue", "description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "required": ["has_input"], "title": "OmicsProcessing", "type": "object"}, "OntologyClass": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "OntologyClass", "type": "object"}, "OrganismCountEnum": {"description": "", "enum": ["ATP", "MPN", "other"], "title": "OrganismCountEnum", "type": "string"}, "OrthologyGroup": {"additionalProperties": false, "description": "A set of genes or gene products in which all members are orthologous", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "OrthologyGroup", "type": "object"}, "OxyStatSampEnum": {"description": "", "enum": ["aerobic", "anaerobic", "other"], "title": "OxyStatSampEnum", "type": "string"}, "Pathway": {"additionalProperties": false, "description": "A pathway is a sequence of steps/reactions carried out by an organism or community of organisms", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Pathway", "type": "object"}, "PeptideQuantification": {"additionalProperties": false, "description": "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information", "title": "PeptideQuantification", "type": "object"}, "Person": {"additionalProperties": false, "description": "represents a person, such as a researcher", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "Should be an ORCID. Specify in CURIE format. E.g ORCID:0000-1111-...", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Person", "type": "object"}, "PersonValue": {"additionalProperties": false, "description": "An attribute value representing a person", "properties": {"email": {"description": "An email address for an entity such as a person. This should be the primarly email address used.", "type": "string"}, "has_raw_value": {"description": "The full name of the Investigator in format FIRST LAST.", "type": "string"}, "name": {"description": "The full name of the Investigator. It should follow the format FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.", "type": "string"}, "orcid": {"description": "The ORCID of a person.", "type": "string"}, "profile_image_url": {"description": "A url that points to an image of a person.", "type": "string"}, "was_generated_by": {"type": "string"}, "websites": {"description": "A list of websites that are associated with the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "PersonValue", "type": "object"}, "PlannedProcess": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_inputs": {"items": {"type": "string"}, "type": "array"}, "has_outputs": {"items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "participating_agent": {"$ref": "#/$defs/Agent"}}, "required": ["id"], "title": "PlannedProcess", "type": "object"}, "PlantGrowthMedEnum": {"description": "", "enum": ["other artificial liquid medium", "other artificial solid medium", "peat moss", "perlite", "pumice", "sand", "soil", "vermiculite", "water"], "title": "PlantGrowthMedEnum", "type": "string"}, "PlantSexEnum": {"description": "", "enum": ["Androdioecious", "Androecious", "Androgynous", "Androgynomonoecious", "Andromonoecious", "Bisexual", "Dichogamous", "Diclinous", "Dioecious", "Gynodioecious", "Gynoecious", "Gynomonoecious", "Hermaphroditic", "Imperfect", "Monoclinous", "Monoecious", "Perfect", "Polygamodioecious", "Polygamomonoecious", "Polygamous", "Protandrous", "Protogynous", "Subandroecious", "Subdioecious", "Subgynoecious", "Synoecious", "Trimonoecious", "Trioecious", "Unisexual"], "title": "PlantSexEnum", "type": "string"}, "ProcessingInstitutionEnum": {"description": "", "enum": ["UCSD", "JGI", "EMSL"], "title": "ProcessingInstitutionEnum", "type": "string"}, "ProfilePositionEnum": {"description": "", "enum": ["summit", "shoulder", "backslope", "footslope", "toeslope"], "title": "ProfilePositionEnum", "type": "string"}, "ProteinQuantification": {"additionalProperties": false, "description": "This is used to link a metaproteomics analysis workflow to a specific protein", "title": "ProteinQuantification", "type": "object"}, "QuadPosEnum": {"description": "", "enum": ["North side", "West side", "South side", "East side"], "title": "QuadPosEnum", "type": "string"}, "QuantityValue": {"additionalProperties": false, "description": "A simple quantity, e.g. 2cm", "properties": {"has_maximum_numeric_value": {"description": "The maximum value part, expressed as number, of the quantity value when the value covers a range.", "type": "number"}, "has_minimum_numeric_value": {"description": "The minimum value part, expressed as number, of the quantity value when the value covers a range.", "type": "number"}, "has_numeric_value": {"description": "The number part of the quantity", "type": "number"}, "has_raw_value": {"description": "Unnormalized atomic string representation, should in syntax {number} {unit}", "type": "string"}, "has_unit": {"description": "The unit of the quantity", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "QuantityValue", "type": "object"}, "Reaction": {"additionalProperties": false, "description": "An individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Reaction", "type": "object"}, "ReactionActivity": {"additionalProperties": false, "description": "", "properties": {"material_input": {"type": "string"}, "material_output": {"type": "string"}, "reaction_aided_by": {"$ref": "#/$defs/LabDevice"}, "reaction_temperature": {"type": "string"}, "reaction_time": {"$ref": "#/$defs/QuantityValue"}}, "title": "ReactionActivity", "type": "object"}, "ReactionParticipant": {"additionalProperties": false, "description": "Instances of this link a reaction to a chemical entity participant", "title": "ReactionParticipant", "type": "object"}, "ReadBasedTaxonomyAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "ReadBasedTaxonomyAnalysisActivity", "type": "object"}, "ReadQcAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "input_base_count": {"description": "The nucleotide base count number of input reads for QC analysis.", "type": "number"}, "input_read_count": {"description": "The sequence count number of input reads for QC analysis.", "type": "number"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "output_base_count": {"description": "After QC analysis nucleotide base count number.", "type": "number"}, "output_read_count": {"description": "After QC analysis sequence count number.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "ReadQcAnalysisActivity", "type": "object"}, "RelSampLocEnum": {"description": "", "enum": ["edge of car", "center of car", "under a seat"], "title": "RelSampLocEnum", "type": "string"}, "RelToOxygenEnum": {"description": "", "enum": ["aerobe", "anaerobe", "facultative", "microaerophilic", "microanaerobe", "obligate aerobe", "obligate anaerobe"], "title": "RelToOxygenEnum", "type": "string"}, "RnaContTypeEnum": {"description": "", "enum": ["plate", "tube"], "title": "RnaContTypeEnum", "type": "string"}, "RnaSampleFormatEnum": {"description": "", "enum": ["10 mM Tris-HCl", "DNAStable", "Ethanol", "Low EDTA TE", "MDA reaction buffer", "PBS", "Pellet", "RNAStable", "TE", "Water", "Gentegra-DNA", "Gentegra-RNA"], "title": "RnaSampleFormatEnum", "type": "string"}, "RoomCondtEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture", "visible signs of mold/mildew"], "title": "RoomCondtEnum", "type": "string"}, "RoomConnectedEnum": {"description": "", "enum": ["attic", "bathroom", "closet", "conference room", "elevator", "examining room", "hallway", "kitchen", "mail room", "office", "stairwell"], "title": "RoomConnectedEnum", "type": "string"}, "RoomLocEnum": {"description": "", "enum": ["corner room", "interior room", "exterior wall"], "title": "RoomLocEnum", "type": "string"}, "RoomSampPosEnum": {"description": "", "enum": ["north corner", "south corner", "west corner", "east corner", "northeast corner", "northwest corner", "southeast corner", "southwest corner", "center"], "title": "RoomSampPosEnum", "type": "string"}, "RoomTypeEnum": {"description": "", "enum": ["attic", "bathroom", "closet", "conference room", "elevator", "examining room", "hallway", "kitchen", "mail room", "private office", "open office", "stairwell", ",restroom", "lobby", "vestibule", "mechanical or electrical room", "data center", "laboratory_wet", "laboratory_dry", "gymnasium", "natatorium", "auditorium", "lockers", "cafe", "warehouse"], "title": "RoomTypeEnum", "type": "string"}, "SampCaptStatusEnum": {"description": "", "enum": ["active surveillance in response to an outbreak", "active surveillance not initiated by an outbreak", "farm sample", "market sample", "other"], "title": "SampCaptStatusEnum", "type": "string"}, "SampCollectPointEnum": {"description": "", "enum": ["well", "test well", "drilling rig", "wellhead", "separator", "storage tank", "other"], "title": "SampCollectPointEnum", "type": "string"}, "SampDisStageEnum": {"description": "", "enum": ["dissemination", "growth and reproduction", "infection", "inoculation", "penetration", "other"], "title": "SampDisStageEnum", "type": "string"}, "SampFloorEnum": {"description": "", "enum": ["1st floor", "2nd floor", "basement", "lobby"], "title": "SampFloorEnum", "type": "string"}, "SampMdEnum": {"description": "", "enum": ["DF", "RT", "KB", "MSL", "other"], "title": "SampMdEnum", "type": "string"}, "SampSubtypeEnum": {"description": "", "enum": ["oil phase", "water phase", "biofilm", "not applicable", "other"], "title": "SampSubtypeEnum", "type": "string"}, "SampWeatherEnum": {"description": "", "enum": ["clear sky", "cloudy", "foggy", "hail", "rain", "snow", "sleet", "sunny", "windy"], "title": "SampWeatherEnum", "type": "string"}, "SampleTypeEnum": {"description": "", "enum": ["soil", "water_extract_soil"], "title": "SampleTypeEnum", "type": "string"}, "SamplingMethodEnum": {"description": "", "enum": ["weighing"], "title": "SamplingMethodEnum", "type": "string"}, "SeasonUseEnum": {"description": "", "enum": ["Spring", "Summer", "Fall", "Winter"], "title": "SeasonUseEnum", "type": "string"}, "SedimentTypeEnum": {"description": "", "enum": ["biogenous", "cosmogenous", "hydrogenous", "lithogenous"], "title": "SedimentTypeEnum", "type": "string"}, "ShadingDeviceCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "ShadingDeviceCondEnum", "type": "string"}, "ShadingDeviceTypeEnum": {"description": "", "enum": ["bahama shutters", "exterior roll blind", "gambrel awning", "hood awning", "porchroller awning", "sarasota shutters", "slatted aluminum", "solid aluminum awning", "sun screen", "tree", "trellis", "venetian awning"], "title": "ShadingDeviceTypeEnum", "type": "string"}, "Site": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Site", "type": "object"}, "SoilHorizonEnum": {"description": "", "enum": ["O horizon", "A horizon", "E horizon", "B horizon", "C horizon", "R layer", "Permafrost"], "title": "SoilHorizonEnum", "type": "string"}, "SolventEnum": {"description": "", "enum": ["deionized_water", "methanol", "chloroform"], "title": "SolventEnum", "type": "string"}, "SpecificEnum": {"description": "", "enum": ["operation", "as built", "construction", "bid", "design", "photos"], "title": "SpecificEnum", "type": "string"}, "SrDepEnvEnum": {"description": "", "enum": ["Lacustine", "Fluvioldeltaic", "Fluviomarine", "Marine", "other"], "title": "SrDepEnvEnum", "type": "string"}, "SrGeolAgeEnum": {"description": "", "enum": ["Archean", "Cambrian", "Carboniferous", "Cenozoic", "Cretaceous", "Devonian", "Jurassic", "Mesozoic", "Neogene", "Ordovician", "Paleogene", "Paleozoic", "Permian", "Precambrian", "Proterozoic", "Silurian", "Triassic", "other"], "title": "SrGeolAgeEnum", "type": "string"}, "SrKerogTypeEnum": {"description": "", "enum": ["Type I", "Type II", "Type III", "Type IV", "other"], "title": "SrKerogTypeEnum", "type": "string"}, "SrLithologyEnum": {"description": "", "enum": ["Clastic", "Carbonate", "Coal", "Biosilicieous", "other"], "title": "SrLithologyEnum", "type": "string"}, "Study": {"additionalProperties": false, "description": "A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.", "properties": {"abstract": {"description": "The abstract of manuscript/grant associated with the entity; i.e., a summary of the resource.", "type": "string"}, "alternative_descriptions": {"description": "A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.", "items": {"type": "string"}, "type": "array"}, "alternative_identifiers": {"description": "Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC", "items": {"type": "string"}, "type": "array"}, "alternative_names": {"description": "A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.", "items": {"type": "string"}, "type": "array"}, "alternative_titles": {"description": "A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "A brief summary that details the study you're submitted to NMDC", "type": "string"}, "doi": {"$ref": "#/$defs/AttributeValue", "description": "The dataset citation for this study"}, "ecosystem": {"description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", "type": "string"}, "ecosystem_category": {"description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", "type": "string"}, "ecosystem_subtype": {"description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", "type": "string"}, "ecosystem_type": {"description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", "type": "string"}, "emsl_proposal_doi": {"description": "The DOI for the EMSL awarded study that relates to the NMDC submitted study", "type": "string"}, "emsl_proposal_identifier": {"description": "The proposal number assigned to the EMSL awarded study that relates to that which is represented in NMDC.", "type": "string"}, "ess_dive_datasets": {"description": "List of ESS-DIVE dataset DOIs", "items": {"type": "string"}, "type": "array"}, "funding_sources": {"items": {"type": "string"}, "type": "array"}, "gold_study_identifiers": {"description": "identifiers for corresponding project(s) in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Gs[0-9]+$", "type": "array"}, "has_credit_associations": {"description": "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study", "items": {"$ref": "#/$defs/CreditAssociation"}, "type": "array"}, "id": {"description": "An NMDC assigned unique identifier for a sample submitted to NMDC.", "type": "string"}, "mgnify_project_identifiers": {"description": "identifiers for corresponding project in MGnify", "pattern": "^mgnify.proj:[A-Z]+[0-9]+$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "objective": {"description": "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.", "type": "string"}, "principal_investigator": {"$ref": "#/$defs/PersonValue", "description": "Principal Investigator who led the study and/or generated the dataset."}, "publications": {"description": "A list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.", "items": {"type": "string"}, "type": "array"}, "related_identifiers": {"description": "Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC", "type": "string"}, "relevant_protocols": {"items": {"type": "string"}, "type": "array"}, "specific_ecosystem": {"description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", "type": "string"}, "study_image": {"description": "Links a study to one or more images.", "items": {"$ref": "#/$defs/ImageValue"}, "type": "array"}, "title": {"description": "A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "websites": {"description": "A list of websites that are associated with the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "Study", "type": "object"}, "SubstructureTypeEnum": {"description": "", "enum": ["crawlspace", "slab on grade", "basement"], "title": "SubstructureTypeEnum", "type": "string"}, "SurfAirContEnum": {"description": "", "enum": ["dust", "organic matter", "particulate matter", "volatile organic compounds", "biological contaminants", "radon", "nutrients", "biocides"], "title": "SurfAirContEnum", "type": "string"}, "SurfMaterialEnum": {"description": "", "enum": ["adobe", "carpet", "cinder blocks", "concrete", "hay bales", "glass", "metal", "paint", "plastic", "stainless steel", "stone", "stucco", "tile", "vinyl", "wood"], "title": "SurfMaterialEnum", "type": "string"}, "TextValue": {"additionalProperties": false, "description": "A basic string value", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "language": {"description": "Should use ISO 639-1 code e.g. \"en\", \"fr\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "TextValue", "type": "object"}, "TidalStageEnum": {"description": "", "enum": ["low tide", "ebb tide", "flood tide", "high tide"], "title": "TidalStageEnum", "type": "string"}, "TillageEnum": {"description": "", "enum": ["drill", "cutting disc", "ridge till", "strip tillage", "zonal tillage", "chisel", "tined", "mouldboard", "disc plough"], "title": "TillageEnum", "type": "string"}, "TimestampValue": {"additionalProperties": false, "description": "A value that is a timestamp. The range should be ISO-8601", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "TimestampValue", "type": "object"}, "TrainLineEnum": {"description": "", "enum": ["red", "green", "orange"], "title": "TrainLineEnum", "type": "string"}, "TrainStatLocEnum": {"description": "", "enum": ["south station above ground", "south station underground", "south station amtrak", "forest hills", "riverside"], "title": "TrainStatLocEnum", "type": "string"}, "TrainStopLocEnum": {"description": "", "enum": ["end", "mid", "downtown"], "title": "TrainStopLocEnum", "type": "string"}, "UrlValue": {"additionalProperties": false, "description": "A value that is a string that conforms to URL syntax", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "UrlValue", "type": "object"}, "VisMediaEnum": {"description": "", "enum": ["photos", "videos", "commonly of the building", "site context (adjacent buildings, vegetation, terrain, streets)", "interiors", "equipment", "3D scans"], "title": "VisMediaEnum", "type": "string"}, "WallConstTypeEnum": {"description": "", "enum": ["frame construction", "joisted masonry", "light noncombustible", "masonry noncombustible", "modified fire resistive", "fire resistive"], "title": "WallConstTypeEnum", "type": "string"}, "WallFinishMatEnum": {"description": "", "enum": ["plaster", "gypsum plaster", "veneer plaster", "gypsum board", "tile", "terrazzo", "stone facing", "acoustical treatment", "wood", "metal", "masonry"], "title": "WallFinishMatEnum", "type": "string"}, "WallLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "WallLocEnum", "type": "string"}, "WallSurfTreatmentEnum": {"description": "", "enum": ["painted", "wall paper", "no treatment", "paneling", "stucco", "fabric"], "title": "WallSurfTreatmentEnum", "type": "string"}, "WallTextureEnum": {"description": "", "enum": ["crows feet", "crows-foot stomp", "double skip", "hawk and trowel", "knockdown", "popcorn", "orange peel", "rosebud stomp", "Santa-Fe texture", "skip trowel", "smooth", "stomp knockdown", "swirl"], "title": "WallTextureEnum", "type": "string"}, "WaterFeatTypeEnum": {"description": "", "enum": ["fountain", "pool", "standing feature", "stream", "waterfall"], "title": "WaterFeatTypeEnum", "type": "string"}, "WeekdayEnum": {"description": "", "enum": ["Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday", "Sunday"], "title": "WeekdayEnum", "type": "string"}, "WindowCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "WindowCondEnum", "type": "string"}, "WindowCoverEnum": {"description": "", "enum": ["blinds", "curtains", "none"], "title": "WindowCoverEnum", "type": "string"}, "WindowHorizPosEnum": {"description": "", "enum": ["left", "middle", "right"], "title": "WindowHorizPosEnum", "type": "string"}, "WindowLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "WindowLocEnum", "type": "string"}, "WindowMatEnum": {"description": "", "enum": ["clad", "fiberglass", "metal", "vinyl", "wood"], "title": "WindowMatEnum", "type": "string"}, "WindowTypeEnum": {"description": "", "enum": ["single-hung sash window", "horizontal sash window", "fixed window"], "title": "WindowTypeEnum", "type": "string"}, "WindowVertPosEnum": {"description": "", "enum": ["bottom", "middle", "top", "low", "high"], "title": "WindowVertPosEnum", "type": "string"}, "WorkflowExecutionActivity": {"additionalProperties": false, "description": "Represents an instance of an execution of a particular workflow", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"description": "the agent/entity associated with the generation of the file", "type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "WorkflowExecutionActivity", "type": "object"}}, "$id": "https://microbiomedata/schema", "$schema": "http://json-schema.org/draft-07/schema#", "additionalProperties": false, "metamodel_version": "1.7.0", "properties": {"activity_set": {"description": "This property links a database object to the set of workflow activities.", "items": {"$ref": "#/$defs/WorkflowExecutionActivity"}, "type": "array"}, "biosample_set": {"description": "This property links a database object to the set of samples within it.", "items": {"$ref": "#/$defs/Biosample"}, "type": "array"}, "collecting_biosamples_from_site_set": {"items": {"$ref": "#/$defs/CollectingBiosamplesFromSite"}, "type": "array"}, "data_object_set": {"description": "This property links a database object to the set of data objects within it.", "items": {"$ref": "#/$defs/DataObject"}, "type": "array"}, "dissolving_activity_set": {"items": {"$ref": "#/$defs/DissolvingActivity"}, "type": "array"}, "field_research_site_set": {"items": {"$ref": "#/$defs/FieldResearchSite"}, "type": "array"}, "functional_annotation_set": {"description": "This property links a database object to the set of all functional annotations", "items": {"$ref": "#/$defs/FunctionalAnnotation"}, "type": "array"}, "genome_feature_set": {"description": "This property links a database object to the set of all features", "items": {"$ref": "#/$defs/GenomeFeature"}, "type": "array"}, "mags_activity_set": {"description": "This property links a database object to the set of MAGs analysis activities.", "items": {"$ref": "#/$defs/MagsAnalysisActivity"}, "type": "array"}, "material_sample_set": {"items": {"$ref": "#/$defs/MaterialSample"}, "type": "array"}, "material_sampling_activity_set": {"items": {"$ref": "#/$defs/MaterialSamplingActivity"}, "type": "array"}, "metabolomics_analysis_activity_set": {"description": "This property links a database object to the set of metabolomics analysis activities.", "items": {"$ref": "#/$defs/MetabolomicsAnalysisActivity"}, "type": "array"}, "metagenome_annotation_activity_set": {"description": "This property links a database object to the set of metagenome annotation activities.", "items": {"$ref": "#/$defs/MetagenomeAnnotationActivity"}, "type": "array"}, "metagenome_assembly_set": {"description": "This property links a database object to the set of metagenome assembly activities.", "items": {"$ref": "#/$defs/MetagenomeAssembly"}, "type": "array"}, "metaproteomics_analysis_activity_set": {"description": "This property links a database object to the set of metaproteomics analysis activities.", "items": {"$ref": "#/$defs/MetaproteomicsAnalysisActivity"}, "type": "array"}, "metatranscriptome_activity_set": {"description": "TODO", "items": {"$ref": "#/$defs/MetatranscriptomeActivity"}, "type": "array"}, "nom_analysis_activity_set": {"description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", "items": {"$ref": "#/$defs/NomAnalysisActivity"}, "type": "array"}, "omics_processing_set": {"description": "This property links a database object to the set of omics processings within it.", "items": {"$ref": "#/$defs/OmicsProcessing"}, "type": "array"}, "reaction_activity_set": {"items": {"$ref": "#/$defs/ReactionActivity"}, "type": "array"}, "read_based_taxonomy_analysis_activity_set": {"description": "This property links a database object to the set of read based analysis activities.", "items": {"$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity"}, "type": "array"}, "read_qc_analysis_activity_set": {"description": "This property links a database object to the set of read QC analysis activities.", "items": {"$ref": "#/$defs/ReadQcAnalysisActivity"}, "type": "array"}, "study_set": {"description": "This property links a database object to the set of studies within it.", "items": {"$ref": "#/$defs/Study"}, "type": "array"}}, "title": "NMDC", "type": "object", "version": "7.0.0"} diff --git a/nmdc_schema/annotation.py b/nmdc_schema/annotation.py index 952907e8d2..0070d5857c 100644 --- a/nmdc_schema/annotation.py +++ b/nmdc_schema/annotation.py @@ -1,5 +1,5 @@ # Auto generated from annotation.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:48 +# Generation date: 2022-12-22T13:47:22 # Schema: NMDC-Annotation # # id: https://microbiomedata/schema/annotation diff --git a/nmdc_schema/basic_slots.py b/nmdc_schema/basic_slots.py index 94255eed7b..233a2877f5 100644 --- a/nmdc_schema/basic_slots.py +++ b/nmdc_schema/basic_slots.py @@ -1,5 +1,5 @@ # Auto generated from basic_slots.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:27 +# Generation date: 2022-12-22T13:47:03 # Schema: NMDC-Basic-Slots # # id: https://microbiomedata/schema/basic_slots diff --git a/nmdc_schema/bioscales.py b/nmdc_schema/bioscales.py index 4c7737d8ab..0fe7ef5672 100644 --- a/nmdc_schema/bioscales.py +++ b/nmdc_schema/bioscales.py @@ -1,5 +1,5 @@ # Auto generated from bioscales.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:23 +# Generation date: 2022-12-22T13:46:59 # Schema: NMDC-Bioscales # # id: https://microbiomedata/schema/bioscales diff --git a/nmdc_schema/core.py b/nmdc_schema/core.py index d7f6f3606a..8532137de5 100644 --- a/nmdc_schema/core.py +++ b/nmdc_schema/core.py @@ -1,5 +1,5 @@ # Auto generated from core.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:50 +# Generation date: 2022-12-22T13:47:24 # Schema: NMDC-Core # # id: https://microbiomedata/schema/core diff --git a/nmdc_schema/external_identifiers.py b/nmdc_schema/external_identifiers.py index 6244c168ab..891ee5f3a9 100644 --- a/nmdc_schema/external_identifiers.py +++ b/nmdc_schema/external_identifiers.py @@ -1,5 +1,5 @@ # Auto generated from external_identifiers.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:52 +# Generation date: 2022-12-22T13:47:26 # Schema: external_identifiers # # id: https://microbiomedata/schema/external_identifiers diff --git a/nmdc_schema/mixs.py b/nmdc_schema/mixs.py index 28723cf728..66a2bd2633 100644 --- a/nmdc_schema/mixs.py +++ b/nmdc_schema/mixs.py @@ -1,5 +1,5 @@ # Auto generated from mixs.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:43 +# Generation date: 2022-12-22T13:47:18 # Schema: mixs-schema # # id: https://microbiomedata/schema/mixs diff --git a/nmdc_schema/nmdc.py b/nmdc_schema/nmdc.py index 91760f150b..6f80137795 100644 --- a/nmdc_schema/nmdc.py +++ b/nmdc_schema/nmdc.py @@ -1,5 +1,5 @@ # Auto generated from nmdc.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:35 +# Generation date: 2022-12-22T13:47:11 # Schema: NMDC # # id: https://microbiomedata/schema @@ -315,8 +315,8 @@ class Database(YAMLRoot): read_qc_analysis_activity_set: Optional[Union[Dict[Union[str, ReadQcAnalysisActivityId], Union[dict, "ReadQcAnalysisActivity"]], List[Union[dict, "ReadQcAnalysisActivity"]]]] = empty_dict() read_based_taxonomy_analysis_activity_set: Optional[Union[Dict[Union[str, ReadBasedTaxonomyAnalysisActivityId], Union[dict, "ReadBasedTaxonomyAnalysisActivity"]], List[Union[dict, "ReadBasedTaxonomyAnalysisActivity"]]]] = empty_dict() study_set: Optional[Union[Dict[Union[str, StudyId], Union[dict, "Study"]], List[Union[dict, "Study"]]]] = empty_dict() - frs_set: Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, FieldResearchSite]], List[Union[dict, FieldResearchSite]]]] = empty_dict() - cbfs_set: Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, CollectingBiosamplesFromSite]], List[Union[dict, CollectingBiosamplesFromSite]]]] = empty_dict() + field_research_site_set: Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, "FieldResearchSite"]], List[Union[dict, "FieldResearchSite"]]]] = empty_dict() + collecting_biosamples_from_site_set: Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, "CollectingBiosamplesFromSite"]], List[Union[dict, "CollectingBiosamplesFromSite"]]]] = empty_dict() date_created: Optional[str] = None etl_software_version: Optional[str] = None @@ -371,9 +371,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self._normalize_inlined_as_list(slot_name="study_set", slot_type=Study, key_name="id", keyed=True) - self._normalize_inlined_as_list(slot_name="frs_set", slot_type=FieldResearchSite, key_name="id", keyed=True) + self._normalize_inlined_as_list(slot_name="field_research_site_set", slot_type=FieldResearchSite, key_name="id", keyed=True) - self._normalize_inlined_as_list(slot_name="cbfs_set", slot_type=CollectingBiosamplesFromSite, key_name="id", keyed=True) + self._normalize_inlined_as_list(slot_name="collecting_biosamples_from_site_set", slot_type=CollectingBiosamplesFromSite, key_name="id", keyed=True) if self.date_created is not None and not isinstance(self.date_created, str): self.date_created = str(self.date_created) @@ -1043,7 +1043,7 @@ class Biosample(MaterialEntity): drainage_class: Optional[Union[dict, "TextValue"]] = None elev: Optional[Union[dict, "QuantityValue"]] = None env_package: Optional[Union[dict, "TextValue"]] = None - extreme_event: Optional[Union[dict, "TimestampValue"]] = None + extreme_event: Optional[str] = None fao_class: Optional[Union[dict, "TextValue"]] = None fire: Optional[Union[dict, "TimestampValue"]] = None flooding: Optional[Union[dict, "TimestampValue"]] = None @@ -1389,8 +1389,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.env_package is not None and not isinstance(self.env_package, TextValue): self.env_package = TextValue(**as_dict(self.env_package)) - if self.extreme_event is not None and not isinstance(self.extreme_event, TimestampValue): - self.extreme_event = TimestampValue(**as_dict(self.extreme_event)) + if self.extreme_event is not None and not isinstance(self.extreme_event, str): + self.extreme_event = str(self.extreme_event) if self.fao_class is not None and not isinstance(self.fao_class, TextValue): self.fao_class = TextValue(**as_dict(self.fao_class)) @@ -6098,6 +6098,10 @@ def _addvals(cls): PermissibleValue(text="Low EDTA TE") ) setattr(cls, "MDA reaction buffer", PermissibleValue(text="MDA reaction buffer") ) + setattr(cls, "Gentegra-DNA", + PermissibleValue(text="Gentegra-DNA") ) + setattr(cls, "Gentegra-RNA", + PermissibleValue(text="Gentegra-RNA") ) class DnaseRnaEnum(EnumDefinitionImpl): @@ -6139,6 +6143,10 @@ def _addvals(cls): PermissibleValue(text="Low EDTA TE") ) setattr(cls, "MDA reaction buffer", PermissibleValue(text="MDA reaction buffer") ) + setattr(cls, "Gentegra-DNA", + PermissibleValue(text="Gentegra-DNA") ) + setattr(cls, "Gentegra-RNA", + PermissibleValue(text="Gentegra-RNA") ) class AnalysisTypeEnum(EnumDefinitionImpl): @@ -6269,6 +6277,12 @@ class slots: slots.study_set = Slot(uri=NMDC.study_set, name="study_set", curie=NMDC.curie('study_set'), model_uri=NMDC.study_set, domain=Database, range=Optional[Union[Dict[Union[str, StudyId], Union[dict, "Study"]], List[Union[dict, "Study"]]]]) +slots.field_research_site_set = Slot(uri=NMDC.field_research_site_set, name="field_research_site_set", curie=NMDC.curie('field_research_site_set'), + model_uri=NMDC.field_research_site_set, domain=Database, range=Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, "FieldResearchSite"]], List[Union[dict, "FieldResearchSite"]]]]) + +slots.collecting_biosamples_from_site_set = Slot(uri=NMDC.collecting_biosamples_from_site_set, name="collecting_biosamples_from_site_set", curie=NMDC.curie('collecting_biosamples_from_site_set'), + model_uri=NMDC.collecting_biosamples_from_site_set, domain=Database, range=Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, "CollectingBiosamplesFromSite"]], List[Union[dict, "CollectingBiosamplesFromSite"]]]]) + slots.data_object_set = Slot(uri=NMDC.data_object_set, name="data_object_set", curie=NMDC.curie('data_object_set'), model_uri=NMDC.data_object_set, domain=Database, range=Optional[Union[Dict[Union[str, DataObjectId], Union[dict, "DataObject"]], List[Union[dict, "DataObject"]]]]) @@ -8628,12 +8642,6 @@ class slots: slots.output_read_bases = Slot(uri=NMDC.output_read_bases, name="output_read_bases", curie=NMDC.curie('output_read_bases'), model_uri=NMDC.output_read_bases, domain=None, range=Optional[str]) -slots.database__frs_set = Slot(uri=NMDC.frs_set, name="database__frs_set", curie=NMDC.curie('frs_set'), - model_uri=NMDC.database__frs_set, domain=Database, range=Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, FieldResearchSite]], List[Union[dict, FieldResearchSite]]]]) - -slots.database__cbfs_set = Slot(uri=NMDC.cbfs_set, name="database__cbfs_set", curie=NMDC.curie('cbfs_set'), - model_uri=NMDC.database__cbfs_set, domain=Database, range=Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, CollectingBiosamplesFromSite]], List[Union[dict, CollectingBiosamplesFromSite]]]]) - slots.magBin__bin_name = Slot(uri=NMDC.bin_name, name="magBin__bin_name", curie=NMDC.curie('bin_name'), model_uri=NMDC.magBin__bin_name, domain=None, range=Optional[str]) @@ -8685,12 +8693,6 @@ class slots: slots.magBin__gtdbtk_species = Slot(uri=NMDC.gtdbtk_species, name="magBin__gtdbtk_species", curie=NMDC.curie('gtdbtk_species'), model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) -slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), - model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) - -slots.CollectingBiosamplesFromSite_has_outputs = Slot(uri=NMDC.has_outputs, name="CollectingBiosamplesFromSite_has_outputs", curie=NMDC.curie('has_outputs'), - model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) - slots.Database_date_created = Slot(uri=NMDC.date_created, name="Database_date_created", curie=NMDC.curie('date_created'), model_uri=NMDC.Database_date_created, domain=Database, range=Optional[str]) @@ -8700,6 +8702,12 @@ class slots: slots.Database_metatranscriptome_activity_set = Slot(uri=NMDC.metatranscriptome_activity_set, name="Database_metatranscriptome_activity_set", curie=NMDC.curie('metatranscriptome_activity_set'), model_uri=NMDC.Database_metatranscriptome_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]]) +slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), + model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) + +slots.CollectingBiosamplesFromSite_has_outputs = Slot(uri=NMDC.has_outputs, name="CollectingBiosamplesFromSite_has_outputs", curie=NMDC.curie('has_outputs'), + model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) + slots.DataObject_name = Slot(uri=NMDC.name, name="DataObject_name", curie=NMDC.curie('name'), model_uri=NMDC.DataObject_name, domain=DataObject, range=str) @@ -8735,6 +8743,9 @@ class slots: slots.Biosample_part_of = Slot(uri=DCTERMS.isPartOf, name="Biosample_part_of", curie=DCTERMS.curie('isPartOf'), model_uri=NMDC.Biosample_part_of, domain=Biosample, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) +slots.Biosample_extreme_event = Slot(uri=MIXS['0000320'], name="Biosample_extreme_event", curie=MIXS.curie('0000320'), + model_uri=NMDC.Biosample_extreme_event, domain=Biosample, range=Optional[str]) + slots.Study_id = Slot(uri=NMDC.id, name="Study_id", curie=NMDC.curie('id'), model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId]) diff --git a/nmdc_schema/nmdc.schema.json b/nmdc_schema/nmdc.schema.json index 274bf4551c..25ae6de4fc 100644 --- a/nmdc_schema/nmdc.schema.json +++ b/nmdc_schema/nmdc.schema.json @@ -1 +1 @@ -{"$defs": {"Activity": {"additionalProperties": false, "description": "a provence-generating activity", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"$ref": "#/$defs/Agent"}, "was_informed_by": {"type": "string"}}, "required": ["id"], "title": "Activity", "type": "object"}, "Agent": {"additionalProperties": false, "description": "a provence-generating agent", "properties": {"acted_on_behalf_of": {"$ref": "#/$defs/Agent"}, "was_informed_by": {"type": "string"}}, "title": "Agent", "type": "object"}, "AnalysisTypeEnum": {"description": "", "enum": ["metabolomics", "metagenomics", "metaproteomics", "metatranscriptomics", "natural organic matter"], "title": "AnalysisTypeEnum", "type": "string"}, "AnalyticalSample": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "AnalyticalSample", "type": "object"}, "ArchStrucEnum": {"description": "", "enum": ["building", "shed", "home"], "title": "ArchStrucEnum", "type": "string"}, "AttributeValue": {"additionalProperties": false, "description": "The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "AttributeValue", "type": "object"}, "BiolStatEnum": {"description": "", "enum": ["wild", "natural", "semi-natural", "inbred line", "breeder's line", "hybrid", "clonal selection", "mutant"], "title": "BiolStatEnum", "type": "string"}, "Biosample": {"additionalProperties": false, "description": "Biological source material which can be characterized by an experiment.", "properties": {"add_date": {"description": "The date on which the information was added to the database.", "type": "string"}, "agrochem_addition": {"$ref": "#/$defs/QuantityValue", "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications"}, "air_temp_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens"}, "al_sat": {"$ref": "#/$defs/QuantityValue", "description": "Aluminum saturation (esp. For tropical soils)"}, "al_sat_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining Al saturation"}, "alkalinity": {"$ref": "#/$defs/QuantityValue", "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate"}, "alkalinity_method": {"$ref": "#/$defs/TextValue", "description": "Method used for alkalinity measurement"}, "alkyl_diethers": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of alkyl diethers"}, "alt": {"$ref": "#/$defs/QuantityValue", "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air"}, "alternative_identifiers": {"description": "Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC", "items": {"type": "string"}, "type": "array"}, "aminopept_act": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of aminopeptidase activity"}, "ammonium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of ammonium in the sample"}, "ammonium_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of ammonium nitrogen in the sample"}, "analysis_type": {"description": "Select all the data types associated or available for this biosample", "items": {"$ref": "#/$defs/AnalysisTypeEnum"}, "type": "array"}, "annual_precpt": {"$ref": "#/$defs/QuantityValue", "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps."}, "annual_temp": {"$ref": "#/$defs/QuantityValue", "description": "Mean annual temperature"}, "bacteria_carb_prod": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of bacterial carbon production"}, "biosample_categories": {"items": {"$ref": "#/$defs/BiosampleCategoryEnum"}, "type": "array"}, "biotic_regm": {"$ref": "#/$defs/TextValue", "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi."}, "biotic_relationship": {"$ref": "#/$defs/TextValue", "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object"}, "bishomohopanol": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of bishomohopanol"}, "bromide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of bromide"}, "calcium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of calcium in the sample"}, "carb_nitro_ratio": {"$ref": "#/$defs/QuantityValue", "description": "Ratio of amount or concentrations of carbon to nitrogen"}, "chem_administration": {"$ref": "#/$defs/ControlledTermValue", "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi"}, "chloride": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of chloride in the sample"}, "chlorophyll": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of chlorophyll"}, "climate_environment": {"$ref": "#/$defs/TextValue", "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates"}, "collected_from": {"description": "The Site from which a Biosample was collected", "type": "string"}, "collection_date": {"$ref": "#/$defs/TimestampValue", "description": "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant"}, "collection_date_inc": {"description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", "type": "string"}, "collection_time": {"description": "The time of sampling, either as an instance (single point) or interval.", "type": "string"}, "collection_time_inc": {"description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", "type": "string"}, "community": {"type": "string"}, "crop_rotation": {"$ref": "#/$defs/TextValue", "description": "Whether or not crop is rotated, and if yes, rotation schedule"}, "cur_land_use": {"$ref": "#/$defs/TextValue", "description": "Present state of sample site"}, "cur_vegetation": {"$ref": "#/$defs/TextValue", "description": "Vegetation classification from one or more standard classification systems, or agricultural crop"}, "cur_vegetation_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in vegetation classification"}, "density": {"$ref": "#/$defs/QuantityValue", "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)"}, "depth": {"$ref": "#/$defs/QuantityValue", "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "diss_carb_dioxide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample"}, "diss_hydrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved hydrogen"}, "diss_inorg_carb": {"$ref": "#/$defs/QuantityValue", "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter"}, "diss_inorg_phosp": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved inorganic phosphorus in the sample"}, "diss_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid"}, "diss_org_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2"}, "diss_oxygen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved oxygen"}, "dna_absorb1": {"description": "260/280 measurement of DNA sample purity", "type": "string"}, "dna_absorb2": {"description": "260/230 measurement of DNA sample purity", "type": "string"}, "dna_collect_site": {"description": "Provide information on the site your DNA sample was collected from", "type": "string"}, "dna_concentration": {"maximum": 2000, "minimum": 0, "type": "string"}, "dna_cont_type": {"$ref": "#/$defs/DnaContTypeEnum", "description": "Tube or plate (96-well)"}, "dna_cont_well": {"type": "string"}, "dna_container_id": {"type": "string"}, "dna_dnase": {"$ref": "#/$defs/DnaDnaseEnum"}, "dna_isolate_meth": {"description": "Describe the method/protocol/kit used to extract DNA/RNA.", "type": "string"}, "dna_organisms": {"description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", "type": "string"}, "dna_project_contact": {"type": "string"}, "dna_samp_id": {"type": "string"}, "dna_sample_format": {"$ref": "#/$defs/DnaSampleFormatEnum", "description": "Solution in which the DNA sample has been suspended"}, "dna_sample_name": {"description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", "type": "string"}, "dna_seq_project": {"type": "string"}, "dna_seq_project_name": {"type": "string"}, "dna_seq_project_pi": {"type": "string"}, "dna_volume": {"maximum": 1000, "minimum": 0, "type": "string"}, "dnase_rna": {"$ref": "#/$defs/DnaseRnaEnum"}, "drainage_class": {"$ref": "#/$defs/TextValue", "description": "Drainage classification from a standard system such as the USDA system"}, "ecosystem": {"description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", "type": "string"}, "ecosystem_category": {"description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", "type": "string"}, "ecosystem_subtype": {"description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", "type": "string"}, "ecosystem_type": {"description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", "type": "string"}, "elev": {"$ref": "#/$defs/QuantityValue", "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit."}, "emsl_biosample_identifiers": {"description": "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.", "items": {"type": "string"}, "type": "array"}, "env_broad_scale": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS"}, "env_local_scale": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS."}, "env_medium": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top)."}, "env_package": {"$ref": "#/$defs/TextValue", "description": "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported", "pattern": "[air|built environment|host\\-associated|human\\-associated|human\\-skin|human\\-oral|human\\-gut|human\\-vaginal|hydrocarbon resources\\-cores|hydrocarbon resources\\-fluids\\/swabs|microbial mat\\/biofilm|misc environment|plant\\-associated|sediment|soil|wastewater\\/sludge|water]"}, "experimental_factor": {"$ref": "#/$defs/ControlledTermValue", "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI"}, "experimental_factor_other": {"description": "Other details about your sample that you feel can't be accurately represented in the available columns.", "type": "string"}, "extreme_event": {"$ref": "#/$defs/TimestampValue", "description": "Unusual physical events that may have affected microbial populations"}, "fao_class": {"$ref": "#/$defs/TextValue", "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups"}, "filter_method": {"description": "Type of filter used or how the sample was filtered", "type": "string"}, "fire": {"$ref": "#/$defs/TimestampValue", "description": "Historical and/or physical evidence of fire"}, "flooding": {"$ref": "#/$defs/TimestampValue", "description": "Historical and/or physical evidence of flooding"}, "gaseous_environment": {"$ref": "#/$defs/QuantityValue", "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens"}, "geo_loc_name": {"$ref": "#/$defs/TextValue", "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)"}, "glucosidase_act": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of glucosidase activity"}, "gold_biosample_identifiers": {"description": "Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample", "items": {"type": "string"}, "pattern": "^GOLD:Gb[0-9]+$", "type": "array"}, "growth_facil": {"$ref": "#/$defs/ControlledTermValue", "description": "Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research"}, "habitat": {"type": "string"}, "heavy_metals": {"$ref": "#/$defs/QuantityValue", "description": "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field."}, "heavy_metals_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining heavy metals"}, "host_name": {"type": "string"}, "humidity_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens"}, "id": {"description": "An NMDC assigned unique identifier for a biosample submitted to NMDC.", "pattern": "^nmdc:", "type": "string"}, "igsn_biosample_identifiers": {"description": "A list of identifiers for the biosample from the IGSN database.", "items": {"type": "string"}, "type": "array"}, "img_identifiers": {"description": "A list of identifiers that relate the biosample to records in the IMG database.", "items": {"type": "string"}, "type": "array"}, "insdc_biosample_identifiers": {"description": "identifiers for corresponding sample in INSDC", "items": {"type": "string"}, "pattern": "^biosample:SAM[NED]([A-Z])?[0-9]+$", "type": "array"}, "isotope_exposure": {"description": "List isotope exposure or addition applied to your sample.", "type": "string"}, "lat_lon": {"$ref": "#/$defs/GeolocationValue", "description": "This is currently a required field but it's not clear if this should be required for human hosts"}, "lbc_thirty": {"$ref": "#/$defs/QuantityValue", "description": "lime buffer capacity, determined after 30 minute incubation"}, "lbceq": {"$ref": "#/$defs/QuantityValue", "description": "lime buffer capacity, determined at equilibrium after 5 day incubation"}, "light_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality."}, "link_addit_analys": {"$ref": "#/$defs/TextValue", "description": "Link to additional analysis results performed on the sample"}, "link_class_info": {"$ref": "#/$defs/TextValue", "description": "Link to digitized soil maps or other soil classification information"}, "link_climate_info": {"$ref": "#/$defs/TextValue", "description": "Link to climate resource"}, "local_class": {"$ref": "#/$defs/TextValue", "description": "Soil classification based on local soil classification system"}, "local_class_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining the local soil classification"}, "location": {"type": "string"}, "magnesium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of magnesium in the sample"}, "manganese": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of manganese in the sample"}, "mean_frict_vel": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of mean friction velocity"}, "mean_peak_frict_vel": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of mean peak friction velocity"}, "micro_biomass_c_meth": {"description": "Reference or method used in determining microbial biomass", "type": "string"}, "micro_biomass_n_meth": {"description": "Reference or method used in determining microbial biomass nitrogen", "type": "string"}, "microbial_biomass_c": {"description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", "type": "string"}, "microbial_biomass_n": {"description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", "type": "string"}, "misc_param": {"$ref": "#/$defs/QuantityValue", "description": "Any other measurement performed or parameter collected, that is not listed here"}, "mod_date": {"description": "The last date on which the database information was modified.", "type": "string"}, "n_alkanes": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of n-alkanes; can include multiple n-alkanes"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "ncbi_taxonomy_name": {"type": "string"}, "nitrate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrate in the sample"}, "nitrate_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrate nitrogen in the sample"}, "nitrite": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrite in the sample"}, "nitrite_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrite nitrogen in the sample"}, "non_microb_biomass": {"description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", "type": "string"}, "non_microb_biomass_method": {"description": "Reference or method used in determining biomass", "type": "string"}, "org_matter": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of organic matter"}, "org_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of organic nitrogen"}, "org_nitro_method": {"description": "Method used for obtaining organic nitrogen", "type": "string"}, "organism_count": {"$ref": "#/$defs/QuantityValue", "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)"}, "other_treatment": {"description": "Other treatments applied to your samples that are not applicable to the provided fields", "type": "string"}, "oxy_stat_samp": {"$ref": "#/$defs/TextValue", "description": "Oxygenation status of sample"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "part_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of particulate organic carbon"}, "perturbation": {"$ref": "#/$defs/TextValue", "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types"}, "petroleum_hydrocarb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of petroleum hydrocarbon"}, "ph": {"$ref": "#/$defs/QuantityValue", "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid"}, "ph_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining ph"}, "phaeopigments": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phaeopigments; can include multiple phaeopigments"}, "phosphate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phosphate"}, "phosplipid_fatt_acid": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phospholipid fatty acids; can include multiple values"}, "pool_dna_extracts": {"$ref": "#/$defs/TextValue", "description": "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given"}, "potassium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of potassium in the sample"}, "pressure": {"$ref": "#/$defs/QuantityValue", "description": "Pressure to which the sample is subject to, in atmospheres"}, "profile_position": {"$ref": "#/$defs/TextValue", "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas"}, "project_id": {"description": "Proposal IDs or names associated with dataset", "type": "string"}, "proport_woa_temperature": {"type": "string"}, "proposal_dna": {"type": "string"}, "proposal_rna": {"type": "string"}, "redox_potential": {"$ref": "#/$defs/QuantityValue", "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential"}, "rel_to_oxygen": {"$ref": "#/$defs/TextValue", "description": "Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments"}, "replicate_number": {"description": "If sending biological replicates, indicate the rep number here.", "type": "string"}, "rna_absorb1": {"description": "260/280 measurement of RNA sample purity", "type": "string"}, "rna_absorb2": {"description": "260/230 measurement of RNA sample purity", "type": "string"}, "rna_collect_site": {"description": "Provide information on the site your RNA sample was collected from", "type": "string"}, "rna_concentration": {"maximum": 1000, "minimum": 0, "type": "string"}, "rna_cont_type": {"$ref": "#/$defs/RnaContTypeEnum", "description": "Tube or plate (96-well)"}, "rna_cont_well": {"type": "string"}, "rna_container_id": {"type": "string"}, "rna_isolate_meth": {"description": "Describe the method/protocol/kit used to extract DNA/RNA.", "type": "string"}, "rna_organisms": {"description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", "type": "string"}, "rna_project_contact": {"type": "string"}, "rna_samp_id": {"type": "string"}, "rna_sample_format": {"$ref": "#/$defs/RnaSampleFormatEnum", "description": "Solution in which the RNA sample has been suspended"}, "rna_sample_name": {"description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", "maximum": 2000, "minimum": 0, "type": "string"}, "rna_seq_project": {"type": "string"}, "rna_seq_project_name": {"type": "string"}, "rna_seq_project_pi": {"type": "string"}, "rna_volume": {"type": "string"}, "salinity": {"$ref": "#/$defs/QuantityValue", "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater."}, "salinity_category": {"description": "Categorcial description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline", "type": "string"}, "salinity_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining salinity"}, "samp_collec_method": {"description": "The method employed for collecting the sample.", "type": "string"}, "samp_mat_process": {"$ref": "#/$defs/ControlledTermValue", "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed."}, "samp_name": {"description": "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.", "type": "string"}, "samp_size": {"$ref": "#/$defs/QuantityValue", "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected."}, "samp_store_dur": {"$ref": "#/$defs/TextValue", "description": "Duration for which the sample was stored"}, "samp_store_loc": {"$ref": "#/$defs/TextValue", "description": "Location at which sample was stored, usually name of a specific freezer/room"}, "samp_store_temp": {"$ref": "#/$defs/QuantityValue", "description": "Temperature at which sample was stored, e.g. -80 degree Celsius"}, "samp_vol_we_dna_ext": {"$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)."}, "sample_collection_site": {"type": "string"}, "sample_link": {"description": "JsonObj()", "items": {"type": "string"}, "type": "array"}, "sample_shipped": {"description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL", "type": "string"}, "sample_type": {"$ref": "#/$defs/SampleTypeEnum", "description": "Type of sample being submitted"}, "season_precpt": {"$ref": "#/$defs/QuantityValue", "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps."}, "season_temp": {"$ref": "#/$defs/QuantityValue", "description": "Mean seasonal temperature"}, "sieving": {"$ref": "#/$defs/QuantityValue", "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved"}, "size_frac_low": {"$ref": "#/$defs/QuantityValue", "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample"}, "size_frac_up": {"$ref": "#/$defs/QuantityValue", "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample"}, "slope_aspect": {"$ref": "#/$defs/QuantityValue", "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration."}, "slope_gradient": {"$ref": "#/$defs/QuantityValue", "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer"}, "sodium": {"$ref": "#/$defs/QuantityValue", "description": "Sodium concentration in the sample"}, "soil_type": {"$ref": "#/$defs/TextValue", "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes."}, "soil_type_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining soil series name or other lower-level classification"}, "soluble_iron_micromol": {"type": "string"}, "source_mat_id": {"$ref": "#/$defs/TextValue", "description": "A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2)."}, "specific_ecosystem": {"description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", "type": "string"}, "start_date_inc": {"description": "Date the incubation was started. Only relevant for incubation samples.", "type": "string"}, "start_time_inc": {"description": "Time the incubation was started. Only relevant for incubation samples.", "type": "string"}, "store_cond": {"$ref": "#/$defs/TextValue", "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)."}, "subsurface_depth": {"$ref": "#/$defs/QuantityValue"}, "sulfate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of sulfate in the sample"}, "sulfide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of sulfide in the sample"}, "technical_reps": {"description": "If sending multiple technical replicates of the same sample, indicate how many replicates are being sent", "type": "string"}, "temp": {"$ref": "#/$defs/QuantityValue", "description": "Temperature of the sample at the time of sampling."}, "tidal_stage": {"$ref": "#/$defs/TextValue", "description": "Stage of tide"}, "tillage": {"$ref": "#/$defs/TextValue", "description": "Note method(s) used for tilling"}, "tot_carb": {"$ref": "#/$defs/QuantityValue", "description": "Total carbon content"}, "tot_depth_water_col": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of total depth of water column"}, "tot_diss_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen"}, "tot_nitro_cont_meth": {"description": "Reference or method used in determining the total nitrogen", "type": "string"}, "tot_nitro_content": {"$ref": "#/$defs/QuantityValue", "description": "Total nitrogen content of the sample"}, "tot_org_c_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining total organic carbon"}, "tot_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content"}, "tot_phosp": {"$ref": "#/$defs/QuantityValue", "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "water_cont_soil_meth": {"description": "Reference or method used in determining the water content of soil", "type": "string"}, "water_content": {"$ref": "#/$defs/QuantityValue", "description": "Water content measurement"}, "watering_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens"}, "zinc": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of zinc in the sample"}}, "required": ["part_of", "id", "env_broad_scale", "env_local_scale", "env_medium"], "title": "Biosample", "type": "object"}, "BiosampleCategoryEnum": {"description": "Funding-based, sample location-based, or experimental method-based defined categories", "enum": ["LTER", "SIP", "SFA", "FICUS", "NEON"], "title": "BiosampleCategoryEnum", "type": "string"}, "BiosampleProcessing": {"additionalProperties": false, "description": "A process that takes one or more biosamples as inputs and generates one or as outputs. Examples of outputs include samples cultivated from another sample or data objects created by instruments runs.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "BiosampleProcessing", "type": "object"}, "BioticRelationshipEnum": {"description": "", "enum": ["free living", "parasite", "commensal", "symbiont"], "title": "BioticRelationshipEnum", "type": "string"}, "BooleanValue": {"additionalProperties": false, "description": "A value that is a boolean", "properties": {"has_boolean_value": {"description": "Links a quantity value to a boolean", "type": "boolean"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "BooleanValue", "type": "object"}, "BuildDocsEnum": {"description": "", "enum": ["building information model", "commissioning report", "complaint logs", "contract administration", "cost estimate", "janitorial schedules or logs", "maintenance plans", "schedule", "sections", "shop drawings", "submittals", "ventilation system", "windows"], "title": "BuildDocsEnum", "type": "string"}, "BuildOccupTypeEnum": {"description": "", "enum": ["office", "market", "restaurant", "residence", "school", "residential", "commercial", "low rise", "high rise", "wood framed", "health care", "airport", "sports complex"], "title": "BuildOccupTypeEnum", "type": "string"}, "BuildingSettingEnum": {"description": "", "enum": ["urban", "suburban", "exurban", "rural"], "title": "BuildingSettingEnum", "type": "string"}, "CeilCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "CeilCondEnum", "type": "string"}, "CeilFinishMatEnum": {"description": "", "enum": ["drywall", "mineral fibre", "tiles", "PVC", "plasterboard", "metal", "fiberglass", "stucco", "mineral wool/calcium silicate", "wood"], "title": "CeilFinishMatEnum", "type": "string"}, "CeilTextureEnum": {"description": "", "enum": ["crows feet", "crows-foot stomp", "double skip", "hawk and trowel", "knockdown", "popcorn", "orange peel", "rosebud stomp", "Santa-Fe texture", "skip trowel", "smooth", "stomp knockdown", "swirl"], "title": "CeilTextureEnum", "type": "string"}, "CeilTypeEnum": {"description": "", "enum": ["cathedral", "dropped", "concave", "barrel-shaped", "coffered", "cove", "stretched"], "title": "CeilTypeEnum", "type": "string"}, "ChemicalEntity": {"additionalProperties": false, "description": "An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "ChemicalEntity", "type": "object"}, "CollectingBiosamplesFromSite": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_inputs": {"items": {"type": "string"}, "type": "array"}, "has_outputs": {"items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "participating_agent": {"$ref": "#/$defs/Agent"}}, "required": ["has_inputs", "has_outputs", "id"], "title": "CollectingBiosamplesFromSite", "type": "object"}, "ContainerTypeEnum": {"description": "", "enum": ["screw_top_conical"], "title": "ContainerTypeEnum", "type": "string"}, "ControlledIdentifiedTermValue": {"additionalProperties": false, "description": "A controlled term or class from an ontology, requiring the presence of term with an id", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "term": {"$ref": "#/$defs/OntologyClass", "description": "pointer to an ontology class"}, "was_generated_by": {"type": "string"}}, "required": ["term"], "title": "ControlledIdentifiedTermValue", "type": "object"}, "ControlledTermValue": {"additionalProperties": false, "description": "A controlled term or class from an ontology", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "term": {"$ref": "#/$defs/OntologyClass", "description": "pointer to an ontology class"}, "was_generated_by": {"type": "string"}}, "title": "ControlledTermValue", "type": "object"}, "CreditAssociation": {"additionalProperties": false, "description": "This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0", "properties": {"applied_role": {"$ref": "#/$defs/CreditEnum"}, "applied_roles": {"items": {"$ref": "#/$defs/CreditEnum"}, "type": "array"}, "applies_to_person": {"$ref": "#/$defs/PersonValue"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "required": ["applies_to_person", "applied_roles"], "title": "CreditAssociation", "type": "object"}, "CreditEnum": {"description": "", "enum": ["Conceptualization", "Data curation", "Formal Analysis", "Funding acquisition", "Investigation", "Methodology", "Project administration", "Resources", "Software", "Supervision", "Validation", "Visualization", "Writing original draft", "Writing review and editing", "Principal Investigator", "Submitter"], "title": "CreditEnum", "type": "string"}, "CurLandUseEnum": {"description": "", "enum": ["cities", "farmstead", "industrial areas", "roads/railroads", "rock", "sand", "gravel", "mudflats", "salt flats", "badlands", "permanent snow or ice", "saline seeps", "mines/quarries", "oil waste areas", "small grains", "row crops", "vegetable crops", "horticultural plants (e.g. tulips)", "marshlands (grass,sedges,rushes)", "tundra (mosses,lichens)", "rangeland", "pastureland (grasslands used for livestock grazing)", "hayland", "meadows (grasses,alfalfa,fescue,bromegrass,timothy)", "shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)", "successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)", "shrub crops (blueberries,nursery ornamentals,filberts)", "vine crops (grapes)", "conifers (e.g. pine,spruce,fir,cypress)", "hardwoods (e.g. oak,hickory,elm,aspen)", "intermixed hardwood and conifers", "tropical (e.g. mangrove,palms)", "rainforest (evergreen forest receiving greater than 406 cm annual rainfall)", "swamp (permanent or semi-permanent water body dominated by woody plants)", "crop trees (nuts,fruit,christmas trees,nursery trees)"], "title": "CurLandUseEnum", "type": "string"}, "DataObject": {"additionalProperties": false, "description": "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "compression_type": {"description": "If provided, specifies the compression type", "type": "string"}, "data_object_type": {"$ref": "#/$defs/FileTypeEnum", "description": "The type of file represented by the data object."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "file_size_bytes": {"description": "Size of the file in bytes", "type": "integer"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "md5_checksum": {"description": "MD5 checksum of file (pre-compressed)", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "url": {"type": "string"}, "was_generated_by": {"type": "string"}}, "required": ["id", "name", "description"], "title": "DataObject", "type": "object"}, "Database": {"additionalProperties": false, "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest", "properties": {"activity_set": {"description": "This property links a database object to the set of workflow activities.", "items": {"$ref": "#/$defs/WorkflowExecutionActivity"}, "type": "array"}, "biosample_set": {"description": "This property links a database object to the set of samples within it.", "items": {"$ref": "#/$defs/Biosample"}, "type": "array"}, "cbfs_set": {"items": {"$ref": "#/$defs/CollectingBiosamplesFromSite"}, "type": "array"}, "data_object_set": {"description": "This property links a database object to the set of data objects within it.", "items": {"$ref": "#/$defs/DataObject"}, "type": "array"}, "dissolving_activity_set": {"items": {"$ref": "#/$defs/DissolvingActivity"}, "type": "array"}, "frs_set": {"items": {"$ref": "#/$defs/FieldResearchSite"}, "type": "array"}, "functional_annotation_set": {"description": "This property links a database object to the set of all functional annotations", "items": {"$ref": "#/$defs/FunctionalAnnotation"}, "type": "array"}, "genome_feature_set": {"description": "This property links a database object to the set of all features", "items": {"$ref": "#/$defs/GenomeFeature"}, "type": "array"}, "mags_activity_set": {"description": "This property links a database object to the set of MAGs analysis activities.", "items": {"$ref": "#/$defs/MagsAnalysisActivity"}, "type": "array"}, "material_sample_set": {"items": {"$ref": "#/$defs/MaterialSample"}, "type": "array"}, "material_sampling_activity_set": {"items": {"$ref": "#/$defs/MaterialSamplingActivity"}, "type": "array"}, "metabolomics_analysis_activity_set": {"description": "This property links a database object to the set of metabolomics analysis activities.", "items": {"$ref": "#/$defs/MetabolomicsAnalysisActivity"}, "type": "array"}, "metagenome_annotation_activity_set": {"description": "This property links a database object to the set of metagenome annotation activities.", "items": {"$ref": "#/$defs/MetagenomeAnnotationActivity"}, "type": "array"}, "metagenome_assembly_set": {"description": "This property links a database object to the set of metagenome assembly activities.", "items": {"$ref": "#/$defs/MetagenomeAssembly"}, "type": "array"}, "metaproteomics_analysis_activity_set": {"description": "This property links a database object to the set of metaproteomics analysis activities.", "items": {"$ref": "#/$defs/MetaproteomicsAnalysisActivity"}, "type": "array"}, "metatranscriptome_activity_set": {"description": "TODO", "items": {"$ref": "#/$defs/MetatranscriptomeActivity"}, "type": "array"}, "nom_analysis_activity_set": {"description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", "items": {"$ref": "#/$defs/NomAnalysisActivity"}, "type": "array"}, "omics_processing_set": {"description": "This property links a database object to the set of omics processings within it.", "items": {"$ref": "#/$defs/OmicsProcessing"}, "type": "array"}, "reaction_activity_set": {"items": {"$ref": "#/$defs/ReactionActivity"}, "type": "array"}, "read_based_taxonomy_analysis_activity_set": {"description": "This property links a database object to the set of read based analysis activities.", "items": {"$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity"}, "type": "array"}, "read_qc_analysis_activity_set": {"description": "This property links a database object to the set of read QC analysis activities.", "items": {"$ref": "#/$defs/ReadQcAnalysisActivity"}, "type": "array"}, "study_set": {"description": "This property links a database object to the set of studies within it.", "items": {"$ref": "#/$defs/Study"}, "type": "array"}}, "title": "Database", "type": "object"}, "DeposEnvEnum": {"description": "", "enum": ["Continental - Alluvial", "Continental - Aeolian", "Continental - Fluvial", "Continental - Lacustrine", "Transitional - Deltaic", "Transitional - Tidal", "Transitional - Lagoonal", "Transitional - Beach", "Transitional - Lake", "Marine - Shallow", "Marine - Deep", "Marine - Reef", "Other - Evaporite", "Other - Glacial", "Other - Volcanic", "other"], "title": "DeposEnvEnum", "type": "string"}, "DeviceTypeEnum": {"description": "", "enum": ["orbital_shaker", "thermomixer"], "title": "DeviceTypeEnum", "type": "string"}, "DissolvingActivity": {"additionalProperties": false, "description": "", "properties": {"dissolution_aided_by": {"$ref": "#/$defs/LabDevice"}, "dissolution_reagent": {"$ref": "#/$defs/SolventEnum"}, "dissolution_volume": {"$ref": "#/$defs/QuantityValue"}, "dissolved_in": {"$ref": "#/$defs/MaterialContainer"}, "material_input": {"type": "string"}, "material_output": {"type": "string"}}, "title": "DissolvingActivity", "type": "object"}, "DnaContTypeEnum": {"description": "", "enum": ["plate", "tube"], "title": "DnaContTypeEnum", "type": "string"}, "DnaDnaseEnum": {"description": "", "enum": ["no", "yes"], "title": "DnaDnaseEnum", "type": "string"}, "DnaSampleFormatEnum": {"description": "", "enum": ["10 mM Tris-HCl", "DNAStable", "Ethanol", "Low EDTA TE", "MDA reaction buffer", "PBS", "Pellet", "RNAStable", "TE", "Water"], "title": "DnaSampleFormatEnum", "type": "string"}, "DnaseRnaEnum": {"description": "", "enum": ["no", "yes"], "title": "DnaseRnaEnum", "type": "string"}, "DoorCompTypeEnum": {"description": "", "enum": ["metal covered", "revolving", "sliding", "telescopic"], "title": "DoorCompTypeEnum", "type": "string"}, "DoorCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "DoorCondEnum", "type": "string"}, "DoorDirectEnum": {"description": "", "enum": ["inward", "outward", "sideways"], "title": "DoorDirectEnum", "type": "string"}, "DoorLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "DoorLocEnum", "type": "string"}, "DoorMatEnum": {"description": "", "enum": ["aluminum", "cellular PVC", "engineered plastic", "fiberboard", "fiberglass", "metal", "thermoplastic alloy", "vinyl", "wood", "wood/plastic composite"], "title": "DoorMatEnum", "type": "string"}, "DoorMoveEnum": {"description": "", "enum": ["collapsible", "folding", "revolving", "rolling shutter", "sliding", "swinging"], "title": "DoorMoveEnum", "type": "string"}, "DoorTypeEnum": {"description": "", "enum": ["composite", "metal", "wooden"], "title": "DoorTypeEnum", "type": "string"}, "DoorTypeMetalEnum": {"description": "", "enum": ["collapsible", "corrugated steel", "hollow", "rolling shutters", "steel plate"], "title": "DoorTypeMetalEnum", "type": "string"}, "DoorTypeWoodEnum": {"description": "", "enum": ["bettened and ledged", "battened", "ledged and braced", "ledged and framed", "ledged, braced and frame", "framed and paneled", "glashed or sash", "flush", "louvered", "wire gauged"], "title": "DoorTypeWoodEnum", "type": "string"}, "DrainageClassEnum": {"description": "", "enum": ["very poorly", "poorly", "somewhat poorly", "moderately well", "well", "excessively drained"], "title": "DrainageClassEnum", "type": "string"}, "DrawingsEnum": {"description": "", "enum": ["operation", "as built", "construction", "bid", "design", "building navigation map", "diagram", "sketch"], "title": "DrawingsEnum", "type": "string"}, "EnvironmentalMaterialTerm": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "EnvironmentalMaterialTerm", "type": "object"}, "ExtWallOrientEnum": {"description": "", "enum": ["north", "south", "east", "west", "northeast", "southeast", "southwest", "northwest"], "title": "ExtWallOrientEnum", "type": "string"}, "ExtWindowOrientEnum": {"description": "", "enum": ["north", "south", "east", "west", "northeast", "southeast", "southwest", "northwest"], "title": "ExtWindowOrientEnum", "type": "string"}, "FaoClassEnum": {"description": "", "enum": ["Acrisols", "Andosols", "Arenosols", "Cambisols", "Chernozems", "Ferralsols", "Fluvisols", "Gleysols", "Greyzems", "Gypsisols", "Histosols", "Kastanozems", "Lithosols", "Luvisols", "Nitosols", "Phaeozems", "Planosols", "Podzols", "Podzoluvisols", "Rankers", "Regosols", "Rendzinas", "Solonchaks", "Solonetz", "Vertisols", "Yermosols"], "title": "FaoClassEnum", "type": "string"}, "FieldResearchSite": {"additionalProperties": false, "description": "A site, outside of a laboratory, from which biosamples may be collected.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "FieldResearchSite", "type": "object"}, "FileTypeEnum": {"description": "", "enum": ["Metagenome Raw Reads", "FT ICR-MS Analysis Results", "GC-MS Metabolomics Results", "Metaproteomics Workflow Statistics", "Protein Report", "Peptide Report", "Unfiltered Metaproteomics Results", "Read Count and RPKM", "QC non-rRNA R2", "QC non-rRNA R1", "Metagenome Bins", "CheckM Statistics", "GOTTCHA2 Krona Plot", "GOTTCHA2 Classification Report", "GOTTCHA2 Report Full", "Kraken2 Krona Plot", "Centrifuge Krona Plot", "Centrifuge output report file", "Kraken2 Classification Report", "Kraken2 Taxonomic Classification", "Centrifuge Classification Report", "Centrifuge Taxonomic Classification", "Structural Annotation GFF", "Functional Annotation GFF", "Annotation Amino Acid FASTA", "Annotation Enzyme Commission", "Annotation KEGG Orthology", "Assembly Coverage BAM", "Assembly AGP", "Assembly Scaffolds", "Assembly Contigs", "Assembly Coverage Stats", "Filtered Sequencing Reads", "QC Statistics", "TIGRFam Annotation GFF", "CRT Annotation GFF", "Genmark Annotation GFF", "Prodigal Annotation GFF", "TRNA Annotation GFF", "Misc Annotation GFF", "RFAM Annotation GFF", "TMRNA Annotation GFF", "KO_EC Annotation GFF", "Product Names", "Gene Phylogeny tsv", "Crisprt Terms", "Clusters of Orthologous Groups (COG) Annotation GFF", "CATH FunFams (Functional Families) Annotation GFF", "SUPERFam Annotation GFF", "SMART Annotation GFF", "Pfam Annotation GFF", "Direct Infusion FT ICR-MS Raw Data"], "title": "FileTypeEnum", "type": "string"}, "FilterTypeEnum": {"description": "", "enum": ["particulate air filter", "chemical air filter", "low-MERV pleated media", "HEPA", "electrostatic", "gas-phase or ultraviolet air treatments"], "title": "FilterTypeEnum", "type": "string"}, "FloorCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "FloorCondEnum", "type": "string"}, "FloorFinishMatEnum": {"description": "", "enum": ["tile", "wood strip or parquet", "carpet", "rug", "laminate wood", "lineoleum", "vinyl composition tile", "sheet vinyl", "stone", "bamboo", "cork", "terrazo", "concrete", "none", "sealed", "clear finish", "paint", "none or unfinished"], "title": "FloorFinishMatEnum", "type": "string"}, "FloorStrucEnum": {"description": "", "enum": ["balcony", "floating floor", "glass floor", "raised floor", "sprung floor", "wood-framed", "concrete"], "title": "FloorStrucEnum", "type": "string"}, "FloorWaterMoldEnum": {"description": "", "enum": ["mold odor", "wet floor", "water stains", "wall discoloration", "floor discoloration", "ceiling discoloration", "peeling paint or wallpaper", "bulging walls", "condensation"], "title": "FloorWaterMoldEnum", "type": "string"}, "FreqCleanEnum": {"description": "", "enum": ["Daily", "Weekly", "Monthly", "Quarterly", "Annually", "other"], "title": "FreqCleanEnum", "type": "string"}, "FunctionalAnnotation": {"additionalProperties": false, "description": "An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods", "properties": {"has_function": {"pattern": "^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$", "type": "string"}, "subject": {"type": "string"}, "was_generated_by": {"description": "provenance for the annotation.", "type": "string"}}, "title": "FunctionalAnnotation", "type": "object"}, "FurnitureEnum": {"description": "", "enum": ["cabinet", "chair", "desks"], "title": "FurnitureEnum", "type": "string"}, "GenderRestroomEnum": {"description": "", "enum": ["all gender", "female", "gender neurtral", "male", "male and female", "unisex"], "title": "GenderRestroomEnum", "type": "string"}, "GeneProduct": {"additionalProperties": false, "description": "A molecule encoded by a gene that has an evolved function", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "GeneProduct", "type": "object"}, "GenomeFeature": {"additionalProperties": false, "description": "A feature localized to an interval along a genome", "title": "GenomeFeature", "type": "object"}, "GeolocationValue": {"additionalProperties": false, "description": "A normalized value for a location on the earth's surface", "properties": {"has_raw_value": {"description": "The raw value for a geolocation should follow {lat} {long}", "type": "string"}, "latitude": {"description": "latitude", "type": "number"}, "longitude": {"description": "longitude", "type": "number"}, "was_generated_by": {"type": "string"}}, "title": "GeolocationValue", "type": "object"}, "GrowthHabitEnum": {"description": "", "enum": ["erect", "semi-erect", "spreading", "prostrate"], "title": "GrowthHabitEnum", "type": "string"}, "HandidnessEnum": {"description": "", "enum": ["ambidexterity", "left handedness", "mixed-handedness", "right handedness"], "title": "HandidnessEnum", "type": "string"}, "HcProducedEnum": {"description": "", "enum": ["Oil", "Gas-Condensate", "Gas", "Bitumen", "Coalbed Methane", "other"], "title": "HcProducedEnum", "type": "string"}, "HcrEnum": {"description": "", "enum": ["Oil Reservoir", "Gas Reservoir", "Oil Sand", "Coalbed", "Shale", "Tight Oil Reservoir", "Tight Gas Reservoir", "other"], "title": "HcrEnum", "type": "string"}, "HcrGeolAgeEnum": {"description": "", "enum": ["Archean", "Cambrian", "Carboniferous", "Cenozoic", "Cretaceous", "Devonian", "Jurassic", "Mesozoic", "Neogene", "Ordovician", "Paleogene", "Paleozoic", "Permian", "Precambrian", "Proterozoic", "Silurian", "Triassic", "other"], "title": "HcrGeolAgeEnum", "type": "string"}, "HeatCoolTypeEnum": {"description": "", "enum": ["radiant system", "heat pump", "forced air system", "steam forced heat", "wood stove"], "title": "HeatCoolTypeEnum", "type": "string"}, "HeatDelivLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "HeatDelivLocEnum", "type": "string"}, "HorizonEnum": {"description": "", "enum": ["O horizon", "A horizon", "E horizon", "B horizon", "C horizon", "R layer", "Permafrost"], "title": "HorizonEnum", "type": "string"}, "HostSexEnum": {"description": "", "enum": ["female", "hermaphrodite", "male", "neuter"], "title": "HostSexEnum", "type": "string"}, "ImageValue": {"additionalProperties": false, "description": "An attribute value representing an image.", "properties": {"description": {"description": "a human-readable description of a thing", "type": "string"}, "display_order": {"description": "When rendering information, this attribute to specify the order in which the information should be rendered.", "type": "string"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "url": {"type": "string"}, "was_generated_by": {"type": "string"}}, "title": "ImageValue", "type": "object"}, "IndoorSpaceEnum": {"description": "", "enum": ["bedroom", "office", "bathroom", "foyer", "kitchen", "locker room", "hallway", "elevator"], "title": "IndoorSpaceEnum", "type": "string"}, "IndoorSurfEnum": {"description": "", "enum": ["cabinet", "ceiling", "counter top", "door", "shelving", "vent cover", "window", "wall"], "title": "IndoorSurfEnum", "type": "string"}, "Instrument": {"additionalProperties": false, "description": "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI].", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Instrument", "type": "object"}, "IntWallCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "IntWallCondEnum", "type": "string"}, "IntegerValue": {"additionalProperties": false, "description": "A value that is an integer", "properties": {"has_numeric_value": {"description": "Links a quantity value to a number", "type": "number"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "IntegerValue", "type": "object"}, "LabDevice": {"additionalProperties": false, "description": "", "properties": {"activity_speed": {"$ref": "#/$defs/QuantityValue"}, "activity_temperature": {"$ref": "#/$defs/QuantityValue"}, "activity_time": {"$ref": "#/$defs/QuantityValue"}, "device_type": {"$ref": "#/$defs/DeviceTypeEnum"}}, "title": "LabDevice", "type": "object"}, "LightTypeEnum": {"description": "", "enum": ["natural light", "electric light", "desk lamp", "flourescent lights", "none"], "title": "LightTypeEnum", "type": "string"}, "LithologyEnum": {"description": "", "enum": ["Basement", "Chalk", "Chert", "Coal", "Conglomerate", "Diatomite", "Dolomite", "Limestone", "Sandstone", "Shale", "Siltstone", "Volcanic", "other"], "title": "LithologyEnum", "type": "string"}, "MagBin": {"additionalProperties": false, "description": "", "properties": {"bin_name": {"type": "string"}, "bin_quality": {"type": "string"}, "completeness": {"type": "number"}, "contamination": {"type": "number"}, "gene_count": {"type": "integer"}, "gtdbtk_class": {"type": "string"}, "gtdbtk_domain": {"type": "string"}, "gtdbtk_family": {"type": "string"}, "gtdbtk_genus": {"type": "string"}, "gtdbtk_order": {"type": "string"}, "gtdbtk_phylum": {"type": "string"}, "gtdbtk_species": {"type": "string"}, "num_16s": {"type": "integer"}, "num_23s": {"type": "integer"}, "num_5s": {"type": "integer"}, "num_t_rna": {"type": "integer"}, "number_of_contig": {"type": "integer"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "title": "MagBin", "type": "object"}, "MagsAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", "properties": {"binned_contig_num": {"type": "integer"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "input_contig_num": {"type": "integer"}, "low_depth_contig_num": {"type": "integer"}, "mags_list": {"items": {"$ref": "#/$defs/MagBin"}, "type": "array"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "too_short_contig_num": {"type": "integer"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "unbinned_contig_num": {"type": "integer"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MagsAnalysisActivity", "type": "object"}, "MaterialContainer": {"additionalProperties": false, "description": "", "properties": {"container_size": {"$ref": "#/$defs/QuantityValue"}, "container_type": {"$ref": "#/$defs/ContainerTypeEnum"}}, "title": "MaterialContainer", "type": "object"}, "MaterialEntity": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "MaterialEntity", "type": "object"}, "MaterialSample": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "MaterialSample", "type": "object"}, "MaterialSamplingActivity": {"additionalProperties": false, "description": "", "properties": {"amount_collected": {"$ref": "#/$defs/QuantityValue"}, "biosample_input": {"type": "string"}, "collected_into": {"$ref": "#/$defs/MaterialContainer"}, "material_output": {"type": "string"}, "sampling_method": {"$ref": "#/$defs/SamplingMethodEnum"}}, "title": "MaterialSamplingActivity", "type": "object"}, "MechStrucEnum": {"description": "", "enum": ["subway", "coach", "carriage", "elevator", "escalator", "boat", "train", "car", "bus"], "title": "MechStrucEnum", "type": "string"}, "MetaboliteQuantification": {"additionalProperties": false, "description": "This is used to link a metabolomics analysis workflow to a specific metabolite", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "MetaboliteQuantification", "type": "object"}, "MetabolomicsAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetabolomicsAnalysisActivity", "type": "object"}, "MetagenomeAnnotationActivity": {"additionalProperties": false, "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "gold_analysis_project_identifiers": {"description": "identifiers for corresponding analysis project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Ga[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetagenomeAnnotationActivity", "type": "object"}, "MetagenomeAssembly": {"additionalProperties": false, "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", "properties": {"asm_score": {"description": "A score for comparing metagenomic assembly quality from same sample.", "type": "number"}, "contig_bp": {"description": "Total size in bp of all contigs.", "type": "number"}, "contigs": {"description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "ctg_l50": {"description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", "type": "number"}, "ctg_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", "type": "number"}, "ctg_logsum": {"description": "Maximum contig length.", "type": "number"}, "ctg_max": {"description": "Maximum contig length.", "type": "number"}, "ctg_n50": {"description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", "type": "number"}, "ctg_n90": {"description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", "type": "number"}, "ctg_powsum": {"description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "gap_pct": {"description": "The gap size percentage of all scaffolds.", "type": "number"}, "gc_avg": {"description": "Average of GC content of all contigs.", "type": "number"}, "gc_std": {"description": "Standard deviation of GC content of all contigs.", "type": "number"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_assembly_identifiers": {"pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "num_aligned_reads": {"description": "The sequence count number of input reads aligned to assembled contigs.", "type": "number"}, "num_input_reads": {"description": "The sequence count number of input reads for assembly.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "scaf_bp": {"description": "Total size in bp of all scaffolds.", "type": "number"}, "scaf_l50": {"description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", "type": "number"}, "scaf_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", "type": "number"}, "scaf_l_gt50k": {"description": "Total size in bp of all scaffolds greater than 50 KB.", "type": "number"}, "scaf_logsum": {"description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "scaf_max": {"description": "Maximum scaffold length.", "type": "number"}, "scaf_n50": {"description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", "type": "number"}, "scaf_n90": {"description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", "type": "number"}, "scaf_n_gt50k": {"description": "Total sequence count of scaffolds greater than 50 KB.", "type": "number"}, "scaf_pct_gt50k": {"description": "Total sequence size percentage of scaffolds greater than 50 KB.", "type": "number"}, "scaf_powsum": {"description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "scaffolds": {"description": "Total sequence count of all scaffolds.", "type": "number"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetagenomeAssembly", "type": "object"}, "MetaproteomicsAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetaproteomicsAnalysisActivity", "type": "object"}, "MetatranscriptomeActivity": {"additionalProperties": false, "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeActivity", "type": "object"}, "MetatranscriptomeAnnotationActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "gold_analysis_project_identifiers": {"description": "identifiers for corresponding analysis project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Ga[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeAnnotationActivity", "type": "object"}, "MetatranscriptomeAssembly": {"additionalProperties": false, "description": "", "properties": {"asm_score": {"description": "A score for comparing metagenomic assembly quality from same sample.", "type": "number"}, "contig_bp": {"description": "Total size in bp of all contigs.", "type": "number"}, "contigs": {"description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "ctg_l50": {"description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", "type": "number"}, "ctg_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", "type": "number"}, "ctg_logsum": {"description": "Maximum contig length.", "type": "number"}, "ctg_max": {"description": "Maximum contig length.", "type": "number"}, "ctg_n50": {"description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", "type": "number"}, "ctg_n90": {"description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", "type": "number"}, "ctg_powsum": {"description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "gap_pct": {"description": "The gap size percentage of all scaffolds.", "type": "number"}, "gc_avg": {"description": "Average of GC content of all contigs.", "type": "number"}, "gc_std": {"description": "Standard deviation of GC content of all contigs.", "type": "number"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_assembly_identifiers": {"pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "num_aligned_reads": {"description": "The sequence count number of input reads aligned to assembled contigs.", "type": "number"}, "num_input_reads": {"description": "The sequence count number of input reads for assembly.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "scaf_bp": {"description": "Total size in bp of all scaffolds.", "type": "number"}, "scaf_l50": {"description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", "type": "number"}, "scaf_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", "type": "number"}, "scaf_l_gt50k": {"description": "Total size in bp of all scaffolds greater than 50 KB.", "type": "number"}, "scaf_logsum": {"description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "scaf_max": {"description": "Maximum scaffold length.", "type": "number"}, "scaf_n50": {"description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", "type": "number"}, "scaf_n90": {"description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", "type": "number"}, "scaf_n_gt50k": {"description": "Total sequence count of scaffolds greater than 50 KB.", "type": "number"}, "scaf_pct_gt50k": {"description": "Total sequence size percentage of scaffolds greater than 50 KB.", "type": "number"}, "scaf_powsum": {"description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "scaffolds": {"description": "Total sequence count of all scaffolds.", "type": "number"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeAssembly", "type": "object"}, "NomAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "NomAnalysisActivity", "type": "object"}, "OccupDocumentEnum": {"description": "", "enum": ["automated count", "estimate", "manual count", "videos"], "title": "OccupDocumentEnum", "type": "string"}, "OmicsProcessing": {"additionalProperties": false, "description": "The methods and processes used to generate omics data from a biosample or organism.", "properties": {"add_date": {"description": "The date on which the information was added to the database.", "type": "string"}, "alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "chimera_check": {"$ref": "#/$defs/TextValue", "description": "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "gold_sequencing_project_identifiers": {"description": "identifiers for corresponding sequencing project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Gp[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_experiment_identifiers": {"items": {"type": "string"}, "pattern": "^insdc.sra:(E|D|S)RX[0-9]{6,}$", "type": "array"}, "instrument_name": {"description": "The name of the instrument that was used for processing the sample.", "type": "string"}, "mod_date": {"description": "The last date on which the database information was modified.", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "ncbi_project_name": {"type": "string"}, "nucl_acid_amp": {"$ref": "#/$defs/TextValue", "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids"}, "nucl_acid_ext": {"$ref": "#/$defs/TextValue", "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample"}, "omics_type": {"$ref": "#/$defs/ControlledTermValue", "description": "The type of omics data"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "pcr_cond": {"$ref": "#/$defs/TextValue", "description": "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'"}, "pcr_primers": {"$ref": "#/$defs/TextValue", "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters"}, "principal_investigator": {"$ref": "#/$defs/PersonValue", "description": "Principal Investigator who led the study and/or generated the dataset."}, "processing_institution": {"$ref": "#/$defs/ProcessingInstitutionEnum", "description": "The organization that processed the sample."}, "samp_vol_we_dna_ext": {"$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)."}, "seq_meth": {"$ref": "#/$defs/TextValue", "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)."}, "seq_quality_check": {"$ref": "#/$defs/TextValue", "description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA"}, "target_gene": {"$ref": "#/$defs/TextValue", "description": "Targeted gene or locus name for marker gene studies"}, "target_subfragment": {"$ref": "#/$defs/TextValue", "description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "required": ["has_input"], "title": "OmicsProcessing", "type": "object"}, "OntologyClass": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "OntologyClass", "type": "object"}, "OrganismCountEnum": {"description": "", "enum": ["ATP", "MPN", "other"], "title": "OrganismCountEnum", "type": "string"}, "OrthologyGroup": {"additionalProperties": false, "description": "A set of genes or gene products in which all members are orthologous", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "OrthologyGroup", "type": "object"}, "OxyStatSampEnum": {"description": "", "enum": ["aerobic", "anaerobic", "other"], "title": "OxyStatSampEnum", "type": "string"}, "Pathway": {"additionalProperties": false, "description": "A pathway is a sequence of steps/reactions carried out by an organism or community of organisms", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Pathway", "type": "object"}, "PeptideQuantification": {"additionalProperties": false, "description": "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information", "title": "PeptideQuantification", "type": "object"}, "Person": {"additionalProperties": false, "description": "represents a person, such as a researcher", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "Should be an ORCID. Specify in CURIE format. E.g ORCID:0000-1111-...", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Person", "type": "object"}, "PersonValue": {"additionalProperties": false, "description": "An attribute value representing a person", "properties": {"email": {"description": "An email address for an entity such as a person. This should be the primarly email address used.", "type": "string"}, "has_raw_value": {"description": "The full name of the Investigator in format FIRST LAST.", "type": "string"}, "name": {"description": "The full name of the Investigator. It should follow the format FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.", "type": "string"}, "orcid": {"description": "The ORCID of a person.", "type": "string"}, "profile_image_url": {"description": "A url that points to an image of a person.", "type": "string"}, "was_generated_by": {"type": "string"}, "websites": {"description": "A list of websites that are associated with the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "PersonValue", "type": "object"}, "PlannedProcess": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_inputs": {"items": {"type": "string"}, "type": "array"}, "has_outputs": {"items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "participating_agent": {"$ref": "#/$defs/Agent"}}, "required": ["id"], "title": "PlannedProcess", "type": "object"}, "PlantGrowthMedEnum": {"description": "", "enum": ["other artificial liquid medium", "other artificial solid medium", "peat moss", "perlite", "pumice", "sand", "soil", "vermiculite", "water"], "title": "PlantGrowthMedEnum", "type": "string"}, "PlantSexEnum": {"description": "", "enum": ["Androdioecious", "Androecious", "Androgynous", "Androgynomonoecious", "Andromonoecious", "Bisexual", "Dichogamous", "Diclinous", "Dioecious", "Gynodioecious", "Gynoecious", "Gynomonoecious", "Hermaphroditic", "Imperfect", "Monoclinous", "Monoecious", "Perfect", "Polygamodioecious", "Polygamomonoecious", "Polygamous", "Protandrous", "Protogynous", "Subandroecious", "Subdioecious", "Subgynoecious", "Synoecious", "Trimonoecious", "Trioecious", "Unisexual"], "title": "PlantSexEnum", "type": "string"}, "ProcessingInstitutionEnum": {"description": "", "enum": ["UCSD", "JGI", "EMSL"], "title": "ProcessingInstitutionEnum", "type": "string"}, "ProfilePositionEnum": {"description": "", "enum": ["summit", "shoulder", "backslope", "footslope", "toeslope"], "title": "ProfilePositionEnum", "type": "string"}, "ProteinQuantification": {"additionalProperties": false, "description": "This is used to link a metaproteomics analysis workflow to a specific protein", "title": "ProteinQuantification", "type": "object"}, "QuadPosEnum": {"description": "", "enum": ["North side", "West side", "South side", "East side"], "title": "QuadPosEnum", "type": "string"}, "QuantityValue": {"additionalProperties": false, "description": "A simple quantity, e.g. 2cm", "properties": {"has_maximum_numeric_value": {"description": "The maximum value part, expressed as number, of the quantity value when the value covers a range.", "type": "number"}, "has_minimum_numeric_value": {"description": "The minimum value part, expressed as number, of the quantity value when the value covers a range.", "type": "number"}, "has_numeric_value": {"description": "The number part of the quantity", "type": "number"}, "has_raw_value": {"description": "Unnormalized atomic string representation, should in syntax {number} {unit}", "type": "string"}, "has_unit": {"description": "The unit of the quantity", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "QuantityValue", "type": "object"}, "Reaction": {"additionalProperties": false, "description": "An individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Reaction", "type": "object"}, "ReactionActivity": {"additionalProperties": false, "description": "", "properties": {"material_input": {"type": "string"}, "material_output": {"type": "string"}, "reaction_aided_by": {"$ref": "#/$defs/LabDevice"}, "reaction_temperature": {"type": "string"}, "reaction_time": {"$ref": "#/$defs/QuantityValue"}}, "title": "ReactionActivity", "type": "object"}, "ReactionParticipant": {"additionalProperties": false, "description": "Instances of this link a reaction to a chemical entity participant", "title": "ReactionParticipant", "type": "object"}, "ReadBasedTaxonomyAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "ReadBasedTaxonomyAnalysisActivity", "type": "object"}, "ReadQcAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "input_base_count": {"description": "The nucleotide base count number of input reads for QC analysis.", "type": "number"}, "input_read_count": {"description": "The sequence count number of input reads for QC analysis.", "type": "number"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "output_base_count": {"description": "After QC analysis nucleotide base count number.", "type": "number"}, "output_read_count": {"description": "After QC analysis sequence count number.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "ReadQcAnalysisActivity", "type": "object"}, "RelSampLocEnum": {"description": "", "enum": ["edge of car", "center of car", "under a seat"], "title": "RelSampLocEnum", "type": "string"}, "RelToOxygenEnum": {"description": "", "enum": ["aerobe", "anaerobe", "facultative", "microaerophilic", "microanaerobe", "obligate aerobe", "obligate anaerobe"], "title": "RelToOxygenEnum", "type": "string"}, "RnaContTypeEnum": {"description": "", "enum": ["plate", "tube"], "title": "RnaContTypeEnum", "type": "string"}, "RnaSampleFormatEnum": {"description": "", "enum": ["10 mM Tris-HCl", "DNAStable", "Ethanol", "Low EDTA TE", "MDA reaction buffer", "PBS", "Pellet", "RNAStable", "TE", "Water"], "title": "RnaSampleFormatEnum", "type": "string"}, "RoomCondtEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture", "visible signs of mold/mildew"], "title": "RoomCondtEnum", "type": "string"}, "RoomConnectedEnum": {"description": "", "enum": ["attic", "bathroom", "closet", "conference room", "elevator", "examining room", "hallway", "kitchen", "mail room", "office", "stairwell"], "title": "RoomConnectedEnum", "type": "string"}, "RoomLocEnum": {"description": "", "enum": ["corner room", "interior room", "exterior wall"], "title": "RoomLocEnum", "type": "string"}, "RoomSampPosEnum": {"description": "", "enum": ["north corner", "south corner", "west corner", "east corner", "northeast corner", "northwest corner", "southeast corner", "southwest corner", "center"], "title": "RoomSampPosEnum", "type": "string"}, "RoomTypeEnum": {"description": "", "enum": ["attic", "bathroom", "closet", "conference room", "elevator", "examining room", "hallway", "kitchen", "mail room", "private office", "open office", "stairwell", ",restroom", "lobby", "vestibule", "mechanical or electrical room", "data center", "laboratory_wet", "laboratory_dry", "gymnasium", "natatorium", "auditorium", "lockers", "cafe", "warehouse"], "title": "RoomTypeEnum", "type": "string"}, "SampCaptStatusEnum": {"description": "", "enum": ["active surveillance in response to an outbreak", "active surveillance not initiated by an outbreak", "farm sample", "market sample", "other"], "title": "SampCaptStatusEnum", "type": "string"}, "SampCollectPointEnum": {"description": "", "enum": ["well", "test well", "drilling rig", "wellhead", "separator", "storage tank", "other"], "title": "SampCollectPointEnum", "type": "string"}, "SampDisStageEnum": {"description": "", "enum": ["dissemination", "growth and reproduction", "infection", "inoculation", "penetration", "other"], "title": "SampDisStageEnum", "type": "string"}, "SampFloorEnum": {"description": "", "enum": ["1st floor", "2nd floor", "basement", "lobby"], "title": "SampFloorEnum", "type": "string"}, "SampMdEnum": {"description": "", "enum": ["DF", "RT", "KB", "MSL", "other"], "title": "SampMdEnum", "type": "string"}, "SampSubtypeEnum": {"description": "", "enum": ["oil phase", "water phase", "biofilm", "not applicable", "other"], "title": "SampSubtypeEnum", "type": "string"}, "SampWeatherEnum": {"description": "", "enum": ["clear sky", "cloudy", "foggy", "hail", "rain", "snow", "sleet", "sunny", "windy"], "title": "SampWeatherEnum", "type": "string"}, "SampleTypeEnum": {"description": "", "enum": ["soil", "water_extract_soil"], "title": "SampleTypeEnum", "type": "string"}, "SamplingMethodEnum": {"description": "", "enum": ["weighing"], "title": "SamplingMethodEnum", "type": "string"}, "SeasonUseEnum": {"description": "", "enum": ["Spring", "Summer", "Fall", "Winter"], "title": "SeasonUseEnum", "type": "string"}, "SedimentTypeEnum": {"description": "", "enum": ["biogenous", "cosmogenous", "hydrogenous", "lithogenous"], "title": "SedimentTypeEnum", "type": "string"}, "ShadingDeviceCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "ShadingDeviceCondEnum", "type": "string"}, "ShadingDeviceTypeEnum": {"description": "", "enum": ["bahama shutters", "exterior roll blind", "gambrel awning", "hood awning", "porchroller awning", "sarasota shutters", "slatted aluminum", "solid aluminum awning", "sun screen", "tree", "trellis", "venetian awning"], "title": "ShadingDeviceTypeEnum", "type": "string"}, "Site": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Site", "type": "object"}, "SoilHorizonEnum": {"description": "", "enum": ["O horizon", "A horizon", "E horizon", "B horizon", "C horizon", "R layer", "Permafrost"], "title": "SoilHorizonEnum", "type": "string"}, "SolventEnum": {"description": "", "enum": ["deionized_water", "methanol", "chloroform"], "title": "SolventEnum", "type": "string"}, "SpecificEnum": {"description": "", "enum": ["operation", "as built", "construction", "bid", "design", "photos"], "title": "SpecificEnum", "type": "string"}, "SrDepEnvEnum": {"description": "", "enum": ["Lacustine", "Fluvioldeltaic", "Fluviomarine", "Marine", "other"], "title": "SrDepEnvEnum", "type": "string"}, "SrGeolAgeEnum": {"description": "", "enum": ["Archean", "Cambrian", "Carboniferous", "Cenozoic", "Cretaceous", "Devonian", "Jurassic", "Mesozoic", "Neogene", "Ordovician", "Paleogene", "Paleozoic", "Permian", "Precambrian", "Proterozoic", "Silurian", "Triassic", "other"], "title": "SrGeolAgeEnum", "type": "string"}, "SrKerogTypeEnum": {"description": "", "enum": ["Type I", "Type II", "Type III", "Type IV", "other"], "title": "SrKerogTypeEnum", "type": "string"}, "SrLithologyEnum": {"description": "", "enum": ["Clastic", "Carbonate", "Coal", "Biosilicieous", "other"], "title": "SrLithologyEnum", "type": "string"}, "Study": {"additionalProperties": false, "description": "A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.", "properties": {"abstract": {"description": "The abstract of manuscript/grant associated with the entity; i.e., a summary of the resource.", "type": "string"}, "alternative_descriptions": {"description": "A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.", "items": {"type": "string"}, "type": "array"}, "alternative_identifiers": {"description": "Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC", "items": {"type": "string"}, "type": "array"}, "alternative_names": {"description": "A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.", "items": {"type": "string"}, "type": "array"}, "alternative_titles": {"description": "A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "A brief summary that details the study you're submitted to NMDC", "type": "string"}, "doi": {"$ref": "#/$defs/AttributeValue", "description": "The dataset citation for this study"}, "ecosystem": {"description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", "type": "string"}, "ecosystem_category": {"description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", "type": "string"}, "ecosystem_subtype": {"description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", "type": "string"}, "ecosystem_type": {"description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", "type": "string"}, "emsl_proposal_doi": {"description": "The DOI for the EMSL awarded study that relates to the NMDC submitted study", "type": "string"}, "emsl_proposal_identifier": {"description": "The proposal number assigned to the EMSL awarded study that relates to that which is represented in NMDC.", "type": "string"}, "ess_dive_datasets": {"description": "List of ESS-DIVE dataset DOIs", "items": {"type": "string"}, "type": "array"}, "funding_sources": {"items": {"type": "string"}, "type": "array"}, "gold_study_identifiers": {"description": "identifiers for corresponding project(s) in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Gs[0-9]+$", "type": "array"}, "has_credit_associations": {"description": "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study", "items": {"$ref": "#/$defs/CreditAssociation"}, "type": "array"}, "id": {"description": "An NMDC assigned unique identifier for a sample submitted to NMDC.", "type": "string"}, "mgnify_project_identifiers": {"description": "identifiers for corresponding project in MGnify", "pattern": "^mgnify.proj:[A-Z]+[0-9]+$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "objective": {"description": "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.", "type": "string"}, "principal_investigator": {"$ref": "#/$defs/PersonValue", "description": "Principal Investigator who led the study and/or generated the dataset."}, "publications": {"description": "A list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.", "items": {"type": "string"}, "type": "array"}, "related_identifiers": {"description": "Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC", "type": "string"}, "relevant_protocols": {"items": {"type": "string"}, "type": "array"}, "specific_ecosystem": {"description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", "type": "string"}, "study_image": {"description": "Links a study to one or more images.", "items": {"$ref": "#/$defs/ImageValue"}, "type": "array"}, "title": {"description": "A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "websites": {"description": "A list of websites that are associated with the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "Study", "type": "object"}, "SubstructureTypeEnum": {"description": "", "enum": ["crawlspace", "slab on grade", "basement"], "title": "SubstructureTypeEnum", "type": "string"}, "SurfAirContEnum": {"description": "", "enum": ["dust", "organic matter", "particulate matter", "volatile organic compounds", "biological contaminants", "radon", "nutrients", "biocides"], "title": "SurfAirContEnum", "type": "string"}, "SurfMaterialEnum": {"description": "", "enum": ["adobe", "carpet", "cinder blocks", "concrete", "hay bales", "glass", "metal", "paint", "plastic", "stainless steel", "stone", "stucco", "tile", "vinyl", "wood"], "title": "SurfMaterialEnum", "type": "string"}, "TextValue": {"additionalProperties": false, "description": "A basic string value", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "language": {"description": "Should use ISO 639-1 code e.g. \"en\", \"fr\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "TextValue", "type": "object"}, "TidalStageEnum": {"description": "", "enum": ["low tide", "ebb tide", "flood tide", "high tide"], "title": "TidalStageEnum", "type": "string"}, "TillageEnum": {"description": "", "enum": ["drill", "cutting disc", "ridge till", "strip tillage", "zonal tillage", "chisel", "tined", "mouldboard", "disc plough"], "title": "TillageEnum", "type": "string"}, "TimestampValue": {"additionalProperties": false, "description": "A value that is a timestamp. The range should be ISO-8601", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "TimestampValue", "type": "object"}, "TrainLineEnum": {"description": "", "enum": ["red", "green", "orange"], "title": "TrainLineEnum", "type": "string"}, "TrainStatLocEnum": {"description": "", "enum": ["south station above ground", "south station underground", "south station amtrak", "forest hills", "riverside"], "title": "TrainStatLocEnum", "type": "string"}, "TrainStopLocEnum": {"description": "", "enum": ["end", "mid", "downtown"], "title": "TrainStopLocEnum", "type": "string"}, "UrlValue": {"additionalProperties": false, "description": "A value that is a string that conforms to URL syntax", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "UrlValue", "type": "object"}, "VisMediaEnum": {"description": "", "enum": ["photos", "videos", "commonly of the building", "site context (adjacent buildings, vegetation, terrain, streets)", "interiors", "equipment", "3D scans"], "title": "VisMediaEnum", "type": "string"}, "WallConstTypeEnum": {"description": "", "enum": ["frame construction", "joisted masonry", "light noncombustible", "masonry noncombustible", "modified fire resistive", "fire resistive"], "title": "WallConstTypeEnum", "type": "string"}, "WallFinishMatEnum": {"description": "", "enum": ["plaster", "gypsum plaster", "veneer plaster", "gypsum board", "tile", "terrazzo", "stone facing", "acoustical treatment", "wood", "metal", "masonry"], "title": "WallFinishMatEnum", "type": "string"}, "WallLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "WallLocEnum", "type": "string"}, "WallSurfTreatmentEnum": {"description": "", "enum": ["painted", "wall paper", "no treatment", "paneling", "stucco", "fabric"], "title": "WallSurfTreatmentEnum", "type": "string"}, "WallTextureEnum": {"description": "", "enum": ["crows feet", "crows-foot stomp", "double skip", "hawk and trowel", "knockdown", "popcorn", "orange peel", "rosebud stomp", "Santa-Fe texture", "skip trowel", "smooth", "stomp knockdown", "swirl"], "title": "WallTextureEnum", "type": "string"}, "WaterFeatTypeEnum": {"description": "", "enum": ["fountain", "pool", "standing feature", "stream", "waterfall"], "title": "WaterFeatTypeEnum", "type": "string"}, "WeekdayEnum": {"description": "", "enum": ["Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday", "Sunday"], "title": "WeekdayEnum", "type": "string"}, "WindowCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "WindowCondEnum", "type": "string"}, "WindowCoverEnum": {"description": "", "enum": ["blinds", "curtains", "none"], "title": "WindowCoverEnum", "type": "string"}, "WindowHorizPosEnum": {"description": "", "enum": ["left", "middle", "right"], "title": "WindowHorizPosEnum", "type": "string"}, "WindowLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "WindowLocEnum", "type": "string"}, "WindowMatEnum": {"description": "", "enum": ["clad", "fiberglass", "metal", "vinyl", "wood"], "title": "WindowMatEnum", "type": "string"}, "WindowTypeEnum": {"description": "", "enum": ["single-hung sash window", "horizontal sash window", "fixed window"], "title": "WindowTypeEnum", "type": "string"}, "WindowVertPosEnum": {"description": "", "enum": ["bottom", "middle", "top", "low", "high"], "title": "WindowVertPosEnum", "type": "string"}, "WorkflowExecutionActivity": {"additionalProperties": false, "description": "Represents an instance of an execution of a particular workflow", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"description": "the agent/entity associated with the generation of the file", "type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "WorkflowExecutionActivity", "type": "object"}}, "$id": "https://microbiomedata/schema", "$schema": "http://json-schema.org/draft-07/schema#", "additionalProperties": false, "metamodel_version": "1.7.0", "properties": {"activity_set": {"description": "This property links a database object to the set of workflow activities.", "items": {"$ref": "#/$defs/WorkflowExecutionActivity"}, "type": "array"}, "biosample_set": {"description": "This property links a database object to the set of samples within it.", "items": {"$ref": "#/$defs/Biosample"}, "type": "array"}, "cbfs_set": {"items": {"$ref": "#/$defs/CollectingBiosamplesFromSite"}, "type": "array"}, "data_object_set": {"description": "This property links a database object to the set of data objects within it.", "items": {"$ref": "#/$defs/DataObject"}, "type": "array"}, "dissolving_activity_set": {"items": {"$ref": "#/$defs/DissolvingActivity"}, "type": "array"}, "frs_set": {"items": {"$ref": "#/$defs/FieldResearchSite"}, "type": "array"}, "functional_annotation_set": {"description": "This property links a database object to the set of all functional annotations", "items": {"$ref": "#/$defs/FunctionalAnnotation"}, "type": "array"}, "genome_feature_set": {"description": "This property links a database object to the set of all features", "items": {"$ref": "#/$defs/GenomeFeature"}, "type": "array"}, "mags_activity_set": {"description": "This property links a database object to the set of MAGs analysis activities.", "items": {"$ref": "#/$defs/MagsAnalysisActivity"}, "type": "array"}, "material_sample_set": {"items": {"$ref": "#/$defs/MaterialSample"}, "type": "array"}, "material_sampling_activity_set": {"items": {"$ref": "#/$defs/MaterialSamplingActivity"}, "type": "array"}, "metabolomics_analysis_activity_set": {"description": "This property links a database object to the set of metabolomics analysis activities.", "items": {"$ref": "#/$defs/MetabolomicsAnalysisActivity"}, "type": "array"}, "metagenome_annotation_activity_set": {"description": "This property links a database object to the set of metagenome annotation activities.", "items": {"$ref": "#/$defs/MetagenomeAnnotationActivity"}, "type": "array"}, "metagenome_assembly_set": {"description": "This property links a database object to the set of metagenome assembly activities.", "items": {"$ref": "#/$defs/MetagenomeAssembly"}, "type": "array"}, "metaproteomics_analysis_activity_set": {"description": "This property links a database object to the set of metaproteomics analysis activities.", "items": {"$ref": "#/$defs/MetaproteomicsAnalysisActivity"}, "type": "array"}, "metatranscriptome_activity_set": {"description": "TODO", "items": {"$ref": "#/$defs/MetatranscriptomeActivity"}, "type": "array"}, "nom_analysis_activity_set": {"description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", "items": {"$ref": "#/$defs/NomAnalysisActivity"}, "type": "array"}, "omics_processing_set": {"description": "This property links a database object to the set of omics processings within it.", "items": {"$ref": "#/$defs/OmicsProcessing"}, "type": "array"}, "reaction_activity_set": {"items": {"$ref": "#/$defs/ReactionActivity"}, "type": "array"}, "read_based_taxonomy_analysis_activity_set": {"description": "This property links a database object to the set of read based analysis activities.", "items": {"$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity"}, "type": "array"}, "read_qc_analysis_activity_set": {"description": "This property links a database object to the set of read QC analysis activities.", "items": {"$ref": "#/$defs/ReadQcAnalysisActivity"}, "type": "array"}, "study_set": {"description": "This property links a database object to the set of studies within it.", "items": {"$ref": "#/$defs/Study"}, "type": "array"}}, "title": "NMDC", "type": "object", "version": "7.0.0"} +{"$defs": {"Activity": {"additionalProperties": false, "description": "a provence-generating activity", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"$ref": "#/$defs/Agent"}, "was_informed_by": {"type": "string"}}, "required": ["id"], "title": "Activity", "type": "object"}, "Agent": {"additionalProperties": false, "description": "a provence-generating agent", "properties": {"acted_on_behalf_of": {"$ref": "#/$defs/Agent"}, "was_informed_by": {"type": "string"}}, "title": "Agent", "type": "object"}, "AnalysisTypeEnum": {"description": "", "enum": ["metabolomics", "metagenomics", "metaproteomics", "metatranscriptomics", "natural organic matter"], "title": "AnalysisTypeEnum", "type": "string"}, "AnalyticalSample": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "AnalyticalSample", "type": "object"}, "ArchStrucEnum": {"description": "", "enum": ["building", "shed", "home"], "title": "ArchStrucEnum", "type": "string"}, "AttributeValue": {"additionalProperties": false, "description": "The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "AttributeValue", "type": "object"}, "BiolStatEnum": {"description": "", "enum": ["wild", "natural", "semi-natural", "inbred line", "breeder's line", "hybrid", "clonal selection", "mutant"], "title": "BiolStatEnum", "type": "string"}, "Biosample": {"additionalProperties": false, "description": "Biological source material which can be characterized by an experiment.", "properties": {"add_date": {"description": "The date on which the information was added to the database.", "type": "string"}, "agrochem_addition": {"$ref": "#/$defs/QuantityValue", "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications"}, "air_temp_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens"}, "al_sat": {"$ref": "#/$defs/QuantityValue", "description": "Aluminum saturation (esp. For tropical soils)"}, "al_sat_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining Al saturation"}, "alkalinity": {"$ref": "#/$defs/QuantityValue", "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate"}, "alkalinity_method": {"$ref": "#/$defs/TextValue", "description": "Method used for alkalinity measurement"}, "alkyl_diethers": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of alkyl diethers"}, "alt": {"$ref": "#/$defs/QuantityValue", "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air"}, "alternative_identifiers": {"description": "Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC", "items": {"type": "string"}, "type": "array"}, "aminopept_act": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of aminopeptidase activity"}, "ammonium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of ammonium in the sample"}, "ammonium_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of ammonium nitrogen in the sample"}, "analysis_type": {"description": "Select all the data types associated or available for this biosample", "items": {"$ref": "#/$defs/AnalysisTypeEnum"}, "type": "array"}, "annual_precpt": {"$ref": "#/$defs/QuantityValue", "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps."}, "annual_temp": {"$ref": "#/$defs/QuantityValue", "description": "Mean annual temperature"}, "bacteria_carb_prod": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of bacterial carbon production"}, "biosample_categories": {"items": {"$ref": "#/$defs/BiosampleCategoryEnum"}, "type": "array"}, "biotic_regm": {"$ref": "#/$defs/TextValue", "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi."}, "biotic_relationship": {"$ref": "#/$defs/TextValue", "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object"}, "bishomohopanol": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of bishomohopanol"}, "bromide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of bromide"}, "calcium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of calcium in the sample"}, "carb_nitro_ratio": {"$ref": "#/$defs/QuantityValue", "description": "Ratio of amount or concentrations of carbon to nitrogen"}, "chem_administration": {"$ref": "#/$defs/ControlledTermValue", "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi"}, "chloride": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of chloride in the sample"}, "chlorophyll": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of chlorophyll"}, "climate_environment": {"$ref": "#/$defs/TextValue", "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates"}, "collected_from": {"description": "The Site from which a Biosample was collected", "type": "string"}, "collection_date": {"$ref": "#/$defs/TimestampValue", "description": "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant"}, "collection_date_inc": {"description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", "type": "string"}, "collection_time": {"description": "The time of sampling, either as an instance (single point) or interval.", "type": "string"}, "collection_time_inc": {"description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", "type": "string"}, "community": {"type": "string"}, "crop_rotation": {"$ref": "#/$defs/TextValue", "description": "Whether or not crop is rotated, and if yes, rotation schedule"}, "cur_land_use": {"$ref": "#/$defs/TextValue", "description": "Present state of sample site"}, "cur_vegetation": {"$ref": "#/$defs/TextValue", "description": "Vegetation classification from one or more standard classification systems, or agricultural crop"}, "cur_vegetation_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in vegetation classification"}, "density": {"$ref": "#/$defs/QuantityValue", "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)"}, "depth": {"$ref": "#/$defs/QuantityValue", "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "diss_carb_dioxide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample"}, "diss_hydrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved hydrogen"}, "diss_inorg_carb": {"$ref": "#/$defs/QuantityValue", "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter"}, "diss_inorg_phosp": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved inorganic phosphorus in the sample"}, "diss_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid"}, "diss_org_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2"}, "diss_oxygen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved oxygen"}, "dna_absorb1": {"description": "260/280 measurement of DNA sample purity", "type": "string"}, "dna_absorb2": {"description": "260/230 measurement of DNA sample purity", "type": "string"}, "dna_collect_site": {"description": "Provide information on the site your DNA sample was collected from", "type": "string"}, "dna_concentration": {"maximum": 2000, "minimum": 0, "type": "string"}, "dna_cont_type": {"$ref": "#/$defs/DnaContTypeEnum", "description": "Tube or plate (96-well)"}, "dna_cont_well": {"type": "string"}, "dna_container_id": {"type": "string"}, "dna_dnase": {"$ref": "#/$defs/DnaDnaseEnum"}, "dna_isolate_meth": {"description": "Describe the method/protocol/kit used to extract DNA/RNA.", "type": "string"}, "dna_organisms": {"description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", "type": "string"}, "dna_project_contact": {"type": "string"}, "dna_samp_id": {"type": "string"}, "dna_sample_format": {"$ref": "#/$defs/DnaSampleFormatEnum", "description": "Solution in which the DNA sample has been suspended"}, "dna_sample_name": {"description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", "type": "string"}, "dna_seq_project": {"type": "string"}, "dna_seq_project_name": {"type": "string"}, "dna_seq_project_pi": {"type": "string"}, "dna_volume": {"maximum": 1000, "minimum": 0, "type": "string"}, "dnase_rna": {"$ref": "#/$defs/DnaseRnaEnum"}, "drainage_class": {"$ref": "#/$defs/TextValue", "description": "Drainage classification from a standard system such as the USDA system"}, "ecosystem": {"description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", "type": "string"}, "ecosystem_category": {"description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", "type": "string"}, "ecosystem_subtype": {"description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", "type": "string"}, "ecosystem_type": {"description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", "type": "string"}, "elev": {"$ref": "#/$defs/QuantityValue", "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit."}, "emsl_biosample_identifiers": {"description": "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.", "items": {"type": "string"}, "type": "array"}, "env_broad_scale": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS"}, "env_local_scale": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS."}, "env_medium": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top)."}, "env_package": {"$ref": "#/$defs/TextValue", "description": "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported", "pattern": "[air|built environment|host\\-associated|human\\-associated|human\\-skin|human\\-oral|human\\-gut|human\\-vaginal|hydrocarbon resources\\-cores|hydrocarbon resources\\-fluids\\/swabs|microbial mat\\/biofilm|misc environment|plant\\-associated|sediment|soil|wastewater\\/sludge|water]"}, "experimental_factor": {"$ref": "#/$defs/ControlledTermValue", "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI"}, "experimental_factor_other": {"description": "Other details about your sample that you feel can't be accurately represented in the available columns.", "type": "string"}, "extreme_event": {"description": "Unusual physical events that may have affected microbial populations", "type": "string"}, "fao_class": {"$ref": "#/$defs/TextValue", "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups"}, "filter_method": {"description": "Type of filter used or how the sample was filtered", "type": "string"}, "fire": {"$ref": "#/$defs/TimestampValue", "description": "Historical and/or physical evidence of fire"}, "flooding": {"$ref": "#/$defs/TimestampValue", "description": "Historical and/or physical evidence of flooding"}, "gaseous_environment": {"$ref": "#/$defs/QuantityValue", "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens"}, "geo_loc_name": {"$ref": "#/$defs/TextValue", "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)"}, "glucosidase_act": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of glucosidase activity"}, "gold_biosample_identifiers": {"description": "Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample", "items": {"type": "string"}, "pattern": "^GOLD:Gb[0-9]+$", "type": "array"}, "growth_facil": {"$ref": "#/$defs/ControlledTermValue", "description": "Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research"}, "habitat": {"type": "string"}, "heavy_metals": {"$ref": "#/$defs/QuantityValue", "description": "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field."}, "heavy_metals_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining heavy metals"}, "host_name": {"type": "string"}, "humidity_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens"}, "id": {"description": "An NMDC assigned unique identifier for a biosample submitted to NMDC.", "pattern": "^nmdc:", "type": "string"}, "igsn_biosample_identifiers": {"description": "A list of identifiers for the biosample from the IGSN database.", "items": {"type": "string"}, "type": "array"}, "img_identifiers": {"description": "A list of identifiers that relate the biosample to records in the IMG database.", "items": {"type": "string"}, "type": "array"}, "insdc_biosample_identifiers": {"description": "identifiers for corresponding sample in INSDC", "items": {"type": "string"}, "pattern": "^biosample:SAM[NED]([A-Z])?[0-9]+$", "type": "array"}, "isotope_exposure": {"description": "List isotope exposure or addition applied to your sample.", "type": "string"}, "lat_lon": {"$ref": "#/$defs/GeolocationValue", "description": "This is currently a required field but it's not clear if this should be required for human hosts"}, "lbc_thirty": {"$ref": "#/$defs/QuantityValue", "description": "lime buffer capacity, determined after 30 minute incubation"}, "lbceq": {"$ref": "#/$defs/QuantityValue", "description": "lime buffer capacity, determined at equilibrium after 5 day incubation"}, "light_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality."}, "link_addit_analys": {"$ref": "#/$defs/TextValue", "description": "Link to additional analysis results performed on the sample"}, "link_class_info": {"$ref": "#/$defs/TextValue", "description": "Link to digitized soil maps or other soil classification information"}, "link_climate_info": {"$ref": "#/$defs/TextValue", "description": "Link to climate resource"}, "local_class": {"$ref": "#/$defs/TextValue", "description": "Soil classification based on local soil classification system"}, "local_class_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining the local soil classification"}, "location": {"type": "string"}, "magnesium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of magnesium in the sample"}, "manganese": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of manganese in the sample"}, "mean_frict_vel": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of mean friction velocity"}, "mean_peak_frict_vel": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of mean peak friction velocity"}, "micro_biomass_c_meth": {"description": "Reference or method used in determining microbial biomass", "type": "string"}, "micro_biomass_n_meth": {"description": "Reference or method used in determining microbial biomass nitrogen", "type": "string"}, "microbial_biomass_c": {"description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", "type": "string"}, "microbial_biomass_n": {"description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", "type": "string"}, "misc_param": {"$ref": "#/$defs/QuantityValue", "description": "Any other measurement performed or parameter collected, that is not listed here"}, "mod_date": {"description": "The last date on which the database information was modified.", "type": "string"}, "n_alkanes": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of n-alkanes; can include multiple n-alkanes"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "ncbi_taxonomy_name": {"type": "string"}, "nitrate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrate in the sample"}, "nitrate_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrate nitrogen in the sample"}, "nitrite": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrite in the sample"}, "nitrite_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrite nitrogen in the sample"}, "non_microb_biomass": {"description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", "type": "string"}, "non_microb_biomass_method": {"description": "Reference or method used in determining biomass", "type": "string"}, "org_matter": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of organic matter"}, "org_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of organic nitrogen"}, "org_nitro_method": {"description": "Method used for obtaining organic nitrogen", "type": "string"}, "organism_count": {"$ref": "#/$defs/QuantityValue", "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)"}, "other_treatment": {"description": "Other treatments applied to your samples that are not applicable to the provided fields", "type": "string"}, "oxy_stat_samp": {"$ref": "#/$defs/TextValue", "description": "Oxygenation status of sample"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "part_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of particulate organic carbon"}, "perturbation": {"$ref": "#/$defs/TextValue", "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types"}, "petroleum_hydrocarb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of petroleum hydrocarbon"}, "ph": {"$ref": "#/$defs/QuantityValue", "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid"}, "ph_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining ph"}, "phaeopigments": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phaeopigments; can include multiple phaeopigments"}, "phosphate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phosphate"}, "phosplipid_fatt_acid": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phospholipid fatty acids; can include multiple values"}, "pool_dna_extracts": {"$ref": "#/$defs/TextValue", "description": "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given"}, "potassium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of potassium in the sample"}, "pressure": {"$ref": "#/$defs/QuantityValue", "description": "Pressure to which the sample is subject to, in atmospheres"}, "profile_position": {"$ref": "#/$defs/TextValue", "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas"}, "project_id": {"description": "Proposal IDs or names associated with dataset", "type": "string"}, "proport_woa_temperature": {"type": "string"}, "proposal_dna": {"type": "string"}, "proposal_rna": {"type": "string"}, "redox_potential": {"$ref": "#/$defs/QuantityValue", "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential"}, "rel_to_oxygen": {"$ref": "#/$defs/TextValue", "description": "Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments"}, "replicate_number": {"description": "If sending biological replicates, indicate the rep number here.", "type": "string"}, "rna_absorb1": {"description": "260/280 measurement of RNA sample purity", "type": "string"}, "rna_absorb2": {"description": "260/230 measurement of RNA sample purity", "type": "string"}, "rna_collect_site": {"description": "Provide information on the site your RNA sample was collected from", "type": "string"}, "rna_concentration": {"maximum": 1000, "minimum": 0, "type": "string"}, "rna_cont_type": {"$ref": "#/$defs/RnaContTypeEnum", "description": "Tube or plate (96-well)"}, "rna_cont_well": {"type": "string"}, "rna_container_id": {"type": "string"}, "rna_isolate_meth": {"description": "Describe the method/protocol/kit used to extract DNA/RNA.", "type": "string"}, "rna_organisms": {"description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", "type": "string"}, "rna_project_contact": {"type": "string"}, "rna_samp_id": {"type": "string"}, "rna_sample_format": {"$ref": "#/$defs/RnaSampleFormatEnum", "description": "Solution in which the RNA sample has been suspended"}, "rna_sample_name": {"description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", "maximum": 2000, "minimum": 0, "type": "string"}, "rna_seq_project": {"type": "string"}, "rna_seq_project_name": {"type": "string"}, "rna_seq_project_pi": {"type": "string"}, "rna_volume": {"type": "string"}, "salinity": {"$ref": "#/$defs/QuantityValue", "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater."}, "salinity_category": {"description": "Categorcial description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline", "type": "string"}, "salinity_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining salinity"}, "samp_collec_method": {"description": "The method employed for collecting the sample.", "type": "string"}, "samp_mat_process": {"$ref": "#/$defs/ControlledTermValue", "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed."}, "samp_name": {"description": "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.", "type": "string"}, "samp_size": {"$ref": "#/$defs/QuantityValue", "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected."}, "samp_store_dur": {"$ref": "#/$defs/TextValue", "description": "Duration for which the sample was stored"}, "samp_store_loc": {"$ref": "#/$defs/TextValue", "description": "Location at which sample was stored, usually name of a specific freezer/room"}, "samp_store_temp": {"$ref": "#/$defs/QuantityValue", "description": "Temperature at which sample was stored, e.g. -80 degree Celsius"}, "samp_vol_we_dna_ext": {"$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)."}, "sample_collection_site": {"type": "string"}, "sample_link": {"description": "JsonObj()", "items": {"type": "string"}, "type": "array"}, "sample_shipped": {"description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL", "type": "string"}, "sample_type": {"$ref": "#/$defs/SampleTypeEnum", "description": "Type of sample being submitted"}, "season_precpt": {"$ref": "#/$defs/QuantityValue", "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps."}, "season_temp": {"$ref": "#/$defs/QuantityValue", "description": "Mean seasonal temperature"}, "sieving": {"$ref": "#/$defs/QuantityValue", "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved"}, "size_frac_low": {"$ref": "#/$defs/QuantityValue", "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample"}, "size_frac_up": {"$ref": "#/$defs/QuantityValue", "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample"}, "slope_aspect": {"$ref": "#/$defs/QuantityValue", "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration."}, "slope_gradient": {"$ref": "#/$defs/QuantityValue", "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer"}, "sodium": {"$ref": "#/$defs/QuantityValue", "description": "Sodium concentration in the sample"}, "soil_type": {"$ref": "#/$defs/TextValue", "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes."}, "soil_type_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining soil series name or other lower-level classification"}, "soluble_iron_micromol": {"type": "string"}, "source_mat_id": {"$ref": "#/$defs/TextValue", "description": "A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2)."}, "specific_ecosystem": {"description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", "type": "string"}, "start_date_inc": {"description": "Date the incubation was started. Only relevant for incubation samples.", "type": "string"}, "start_time_inc": {"description": "Time the incubation was started. Only relevant for incubation samples.", "type": "string"}, "store_cond": {"$ref": "#/$defs/TextValue", "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)."}, "subsurface_depth": {"$ref": "#/$defs/QuantityValue"}, "sulfate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of sulfate in the sample"}, "sulfide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of sulfide in the sample"}, "technical_reps": {"description": "If sending multiple technical replicates of the same sample, indicate how many replicates are being sent", "type": "string"}, "temp": {"$ref": "#/$defs/QuantityValue", "description": "Temperature of the sample at the time of sampling."}, "tidal_stage": {"$ref": "#/$defs/TextValue", "description": "Stage of tide"}, "tillage": {"$ref": "#/$defs/TextValue", "description": "Note method(s) used for tilling"}, "tot_carb": {"$ref": "#/$defs/QuantityValue", "description": "Total carbon content"}, "tot_depth_water_col": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of total depth of water column"}, "tot_diss_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen"}, "tot_nitro_cont_meth": {"description": "Reference or method used in determining the total nitrogen", "type": "string"}, "tot_nitro_content": {"$ref": "#/$defs/QuantityValue", "description": "Total nitrogen content of the sample"}, "tot_org_c_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining total organic carbon"}, "tot_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content"}, "tot_phosp": {"$ref": "#/$defs/QuantityValue", "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "water_cont_soil_meth": {"description": "Reference or method used in determining the water content of soil", "type": "string"}, "water_content": {"$ref": "#/$defs/QuantityValue", "description": "Water content measurement"}, "watering_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens"}, "zinc": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of zinc in the sample"}}, "required": ["part_of", "id", "env_broad_scale", "env_local_scale", "env_medium"], "title": "Biosample", "type": "object"}, "BiosampleCategoryEnum": {"description": "Funding-based, sample location-based, or experimental method-based defined categories", "enum": ["LTER", "SIP", "SFA", "FICUS", "NEON"], "title": "BiosampleCategoryEnum", "type": "string"}, "BiosampleProcessing": {"additionalProperties": false, "description": "A process that takes one or more biosamples as inputs and generates one or as outputs. Examples of outputs include samples cultivated from another sample or data objects created by instruments runs.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "BiosampleProcessing", "type": "object"}, "BioticRelationshipEnum": {"description": "", "enum": ["free living", "parasite", "commensal", "symbiont"], "title": "BioticRelationshipEnum", "type": "string"}, "BooleanValue": {"additionalProperties": false, "description": "A value that is a boolean", "properties": {"has_boolean_value": {"description": "Links a quantity value to a boolean", "type": "boolean"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "BooleanValue", "type": "object"}, "BuildDocsEnum": {"description": "", "enum": ["building information model", "commissioning report", "complaint logs", "contract administration", "cost estimate", "janitorial schedules or logs", "maintenance plans", "schedule", "sections", "shop drawings", "submittals", "ventilation system", "windows"], "title": "BuildDocsEnum", "type": "string"}, "BuildOccupTypeEnum": {"description": "", "enum": ["office", "market", "restaurant", "residence", "school", "residential", "commercial", "low rise", "high rise", "wood framed", "health care", "airport", "sports complex"], "title": "BuildOccupTypeEnum", "type": "string"}, "BuildingSettingEnum": {"description": "", "enum": ["urban", "suburban", "exurban", "rural"], "title": "BuildingSettingEnum", "type": "string"}, "CeilCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "CeilCondEnum", "type": "string"}, "CeilFinishMatEnum": {"description": "", "enum": ["drywall", "mineral fibre", "tiles", "PVC", "plasterboard", "metal", "fiberglass", "stucco", "mineral wool/calcium silicate", "wood"], "title": "CeilFinishMatEnum", "type": "string"}, "CeilTextureEnum": {"description": "", "enum": ["crows feet", "crows-foot stomp", "double skip", "hawk and trowel", "knockdown", "popcorn", "orange peel", "rosebud stomp", "Santa-Fe texture", "skip trowel", "smooth", "stomp knockdown", "swirl"], "title": "CeilTextureEnum", "type": "string"}, "CeilTypeEnum": {"description": "", "enum": ["cathedral", "dropped", "concave", "barrel-shaped", "coffered", "cove", "stretched"], "title": "CeilTypeEnum", "type": "string"}, "ChemicalEntity": {"additionalProperties": false, "description": "An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "ChemicalEntity", "type": "object"}, "CollectingBiosamplesFromSite": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_inputs": {"items": {"type": "string"}, "type": "array"}, "has_outputs": {"items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "participating_agent": {"$ref": "#/$defs/Agent"}}, "required": ["has_inputs", "has_outputs", "id"], "title": "CollectingBiosamplesFromSite", "type": "object"}, "ContainerTypeEnum": {"description": "", "enum": ["screw_top_conical"], "title": "ContainerTypeEnum", "type": "string"}, "ControlledIdentifiedTermValue": {"additionalProperties": false, "description": "A controlled term or class from an ontology, requiring the presence of term with an id", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "term": {"$ref": "#/$defs/OntologyClass", "description": "pointer to an ontology class"}, "was_generated_by": {"type": "string"}}, "required": ["term"], "title": "ControlledIdentifiedTermValue", "type": "object"}, "ControlledTermValue": {"additionalProperties": false, "description": "A controlled term or class from an ontology", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "term": {"$ref": "#/$defs/OntologyClass", "description": "pointer to an ontology class"}, "was_generated_by": {"type": "string"}}, "title": "ControlledTermValue", "type": "object"}, "CreditAssociation": {"additionalProperties": false, "description": "This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0", "properties": {"applied_role": {"$ref": "#/$defs/CreditEnum"}, "applied_roles": {"items": {"$ref": "#/$defs/CreditEnum"}, "type": "array"}, "applies_to_person": {"$ref": "#/$defs/PersonValue"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "required": ["applies_to_person", "applied_roles"], "title": "CreditAssociation", "type": "object"}, "CreditEnum": {"description": "", "enum": ["Conceptualization", "Data curation", "Formal Analysis", "Funding acquisition", "Investigation", "Methodology", "Project administration", "Resources", "Software", "Supervision", "Validation", "Visualization", "Writing original draft", "Writing review and editing", "Principal Investigator", "Submitter"], "title": "CreditEnum", "type": "string"}, "CurLandUseEnum": {"description": "", "enum": ["cities", "farmstead", "industrial areas", "roads/railroads", "rock", "sand", "gravel", "mudflats", "salt flats", "badlands", "permanent snow or ice", "saline seeps", "mines/quarries", "oil waste areas", "small grains", "row crops", "vegetable crops", "horticultural plants (e.g. tulips)", "marshlands (grass,sedges,rushes)", "tundra (mosses,lichens)", "rangeland", "pastureland (grasslands used for livestock grazing)", "hayland", "meadows (grasses,alfalfa,fescue,bromegrass,timothy)", "shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)", "successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)", "shrub crops (blueberries,nursery ornamentals,filberts)", "vine crops (grapes)", "conifers (e.g. pine,spruce,fir,cypress)", "hardwoods (e.g. oak,hickory,elm,aspen)", "intermixed hardwood and conifers", "tropical (e.g. mangrove,palms)", "rainforest (evergreen forest receiving greater than 406 cm annual rainfall)", "swamp (permanent or semi-permanent water body dominated by woody plants)", "crop trees (nuts,fruit,christmas trees,nursery trees)"], "title": "CurLandUseEnum", "type": "string"}, "DataObject": {"additionalProperties": false, "description": "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "compression_type": {"description": "If provided, specifies the compression type", "type": "string"}, "data_object_type": {"$ref": "#/$defs/FileTypeEnum", "description": "The type of file represented by the data object."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "file_size_bytes": {"description": "Size of the file in bytes", "type": "integer"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "md5_checksum": {"description": "MD5 checksum of file (pre-compressed)", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "url": {"type": "string"}, "was_generated_by": {"type": "string"}}, "required": ["id", "name", "description"], "title": "DataObject", "type": "object"}, "Database": {"additionalProperties": false, "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest", "properties": {"activity_set": {"description": "This property links a database object to the set of workflow activities.", "items": {"$ref": "#/$defs/WorkflowExecutionActivity"}, "type": "array"}, "biosample_set": {"description": "This property links a database object to the set of samples within it.", "items": {"$ref": "#/$defs/Biosample"}, "type": "array"}, "collecting_biosamples_from_site_set": {"items": {"$ref": "#/$defs/CollectingBiosamplesFromSite"}, "type": "array"}, "data_object_set": {"description": "This property links a database object to the set of data objects within it.", "items": {"$ref": "#/$defs/DataObject"}, "type": "array"}, "dissolving_activity_set": {"items": {"$ref": "#/$defs/DissolvingActivity"}, "type": "array"}, "field_research_site_set": {"items": {"$ref": "#/$defs/FieldResearchSite"}, "type": "array"}, "functional_annotation_set": {"description": "This property links a database object to the set of all functional annotations", "items": {"$ref": "#/$defs/FunctionalAnnotation"}, "type": "array"}, "genome_feature_set": {"description": "This property links a database object to the set of all features", "items": {"$ref": "#/$defs/GenomeFeature"}, "type": "array"}, "mags_activity_set": {"description": "This property links a database object to the set of MAGs analysis activities.", "items": {"$ref": "#/$defs/MagsAnalysisActivity"}, "type": "array"}, "material_sample_set": {"items": {"$ref": "#/$defs/MaterialSample"}, "type": "array"}, "material_sampling_activity_set": {"items": {"$ref": "#/$defs/MaterialSamplingActivity"}, "type": "array"}, "metabolomics_analysis_activity_set": {"description": "This property links a database object to the set of metabolomics analysis activities.", "items": {"$ref": "#/$defs/MetabolomicsAnalysisActivity"}, "type": "array"}, "metagenome_annotation_activity_set": {"description": "This property links a database object to the set of metagenome annotation activities.", "items": {"$ref": "#/$defs/MetagenomeAnnotationActivity"}, "type": "array"}, "metagenome_assembly_set": {"description": "This property links a database object to the set of metagenome assembly activities.", "items": {"$ref": "#/$defs/MetagenomeAssembly"}, "type": "array"}, "metaproteomics_analysis_activity_set": {"description": "This property links a database object to the set of metaproteomics analysis activities.", "items": {"$ref": "#/$defs/MetaproteomicsAnalysisActivity"}, "type": "array"}, "metatranscriptome_activity_set": {"description": "TODO", "items": {"$ref": "#/$defs/MetatranscriptomeActivity"}, "type": "array"}, "nom_analysis_activity_set": {"description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", "items": {"$ref": "#/$defs/NomAnalysisActivity"}, "type": "array"}, "omics_processing_set": {"description": "This property links a database object to the set of omics processings within it.", "items": {"$ref": "#/$defs/OmicsProcessing"}, "type": "array"}, "reaction_activity_set": {"items": {"$ref": "#/$defs/ReactionActivity"}, "type": "array"}, "read_based_taxonomy_analysis_activity_set": {"description": "This property links a database object to the set of read based analysis activities.", "items": {"$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity"}, "type": "array"}, "read_qc_analysis_activity_set": {"description": "This property links a database object to the set of read QC analysis activities.", "items": {"$ref": "#/$defs/ReadQcAnalysisActivity"}, "type": "array"}, "study_set": {"description": "This property links a database object to the set of studies within it.", "items": {"$ref": "#/$defs/Study"}, "type": "array"}}, "title": "Database", "type": "object"}, "DeposEnvEnum": {"description": "", "enum": ["Continental - Alluvial", "Continental - Aeolian", "Continental - Fluvial", "Continental - Lacustrine", "Transitional - Deltaic", "Transitional - Tidal", "Transitional - Lagoonal", "Transitional - Beach", "Transitional - Lake", "Marine - Shallow", "Marine - Deep", "Marine - Reef", "Other - Evaporite", "Other - Glacial", "Other - Volcanic", "other"], "title": "DeposEnvEnum", "type": "string"}, "DeviceTypeEnum": {"description": "", "enum": ["orbital_shaker", "thermomixer"], "title": "DeviceTypeEnum", "type": "string"}, "DissolvingActivity": {"additionalProperties": false, "description": "", "properties": {"dissolution_aided_by": {"$ref": "#/$defs/LabDevice"}, "dissolution_reagent": {"$ref": "#/$defs/SolventEnum"}, "dissolution_volume": {"$ref": "#/$defs/QuantityValue"}, "dissolved_in": {"$ref": "#/$defs/MaterialContainer"}, "material_input": {"type": "string"}, "material_output": {"type": "string"}}, "title": "DissolvingActivity", "type": "object"}, "DnaContTypeEnum": {"description": "", "enum": ["plate", "tube"], "title": "DnaContTypeEnum", "type": "string"}, "DnaDnaseEnum": {"description": "", "enum": ["no", "yes"], "title": "DnaDnaseEnum", "type": "string"}, "DnaSampleFormatEnum": {"description": "", "enum": ["10 mM Tris-HCl", "DNAStable", "Ethanol", "Low EDTA TE", "MDA reaction buffer", "PBS", "Pellet", "RNAStable", "TE", "Water", "Gentegra-DNA", "Gentegra-RNA"], "title": "DnaSampleFormatEnum", "type": "string"}, "DnaseRnaEnum": {"description": "", "enum": ["no", "yes"], "title": "DnaseRnaEnum", "type": "string"}, "DoorCompTypeEnum": {"description": "", "enum": ["metal covered", "revolving", "sliding", "telescopic"], "title": "DoorCompTypeEnum", "type": "string"}, "DoorCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "DoorCondEnum", "type": "string"}, "DoorDirectEnum": {"description": "", "enum": ["inward", "outward", "sideways"], "title": "DoorDirectEnum", "type": "string"}, "DoorLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "DoorLocEnum", "type": "string"}, "DoorMatEnum": {"description": "", "enum": ["aluminum", "cellular PVC", "engineered plastic", "fiberboard", "fiberglass", "metal", "thermoplastic alloy", "vinyl", "wood", "wood/plastic composite"], "title": "DoorMatEnum", "type": "string"}, "DoorMoveEnum": {"description": "", "enum": ["collapsible", "folding", "revolving", "rolling shutter", "sliding", "swinging"], "title": "DoorMoveEnum", "type": "string"}, "DoorTypeEnum": {"description": "", "enum": ["composite", "metal", "wooden"], "title": "DoorTypeEnum", "type": "string"}, "DoorTypeMetalEnum": {"description": "", "enum": ["collapsible", "corrugated steel", "hollow", "rolling shutters", "steel plate"], "title": "DoorTypeMetalEnum", "type": "string"}, "DoorTypeWoodEnum": {"description": "", "enum": ["bettened and ledged", "battened", "ledged and braced", "ledged and framed", "ledged, braced and frame", "framed and paneled", "glashed or sash", "flush", "louvered", "wire gauged"], "title": "DoorTypeWoodEnum", "type": "string"}, "DrainageClassEnum": {"description": "", "enum": ["very poorly", "poorly", "somewhat poorly", "moderately well", "well", "excessively drained"], "title": "DrainageClassEnum", "type": "string"}, "DrawingsEnum": {"description": "", "enum": ["operation", "as built", "construction", "bid", "design", "building navigation map", "diagram", "sketch"], "title": "DrawingsEnum", "type": "string"}, "EnvironmentalMaterialTerm": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "EnvironmentalMaterialTerm", "type": "object"}, "ExtWallOrientEnum": {"description": "", "enum": ["north", "south", "east", "west", "northeast", "southeast", "southwest", "northwest"], "title": "ExtWallOrientEnum", "type": "string"}, "ExtWindowOrientEnum": {"description": "", "enum": ["north", "south", "east", "west", "northeast", "southeast", "southwest", "northwest"], "title": "ExtWindowOrientEnum", "type": "string"}, "FaoClassEnum": {"description": "", "enum": ["Acrisols", "Andosols", "Arenosols", "Cambisols", "Chernozems", "Ferralsols", "Fluvisols", "Gleysols", "Greyzems", "Gypsisols", "Histosols", "Kastanozems", "Lithosols", "Luvisols", "Nitosols", "Phaeozems", "Planosols", "Podzols", "Podzoluvisols", "Rankers", "Regosols", "Rendzinas", "Solonchaks", "Solonetz", "Vertisols", "Yermosols"], "title": "FaoClassEnum", "type": "string"}, "FieldResearchSite": {"additionalProperties": false, "description": "A site, outside of a laboratory, from which biosamples may be collected.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "FieldResearchSite", "type": "object"}, "FileTypeEnum": {"description": "", "enum": ["Metagenome Raw Reads", "FT ICR-MS Analysis Results", "GC-MS Metabolomics Results", "Metaproteomics Workflow Statistics", "Protein Report", "Peptide Report", "Unfiltered Metaproteomics Results", "Read Count and RPKM", "QC non-rRNA R2", "QC non-rRNA R1", "Metagenome Bins", "CheckM Statistics", "GOTTCHA2 Krona Plot", "GOTTCHA2 Classification Report", "GOTTCHA2 Report Full", "Kraken2 Krona Plot", "Centrifuge Krona Plot", "Centrifuge output report file", "Kraken2 Classification Report", "Kraken2 Taxonomic Classification", "Centrifuge Classification Report", "Centrifuge Taxonomic Classification", "Structural Annotation GFF", "Functional Annotation GFF", "Annotation Amino Acid FASTA", "Annotation Enzyme Commission", "Annotation KEGG Orthology", "Assembly Coverage BAM", "Assembly AGP", "Assembly Scaffolds", "Assembly Contigs", "Assembly Coverage Stats", "Filtered Sequencing Reads", "QC Statistics", "TIGRFam Annotation GFF", "CRT Annotation GFF", "Genmark Annotation GFF", "Prodigal Annotation GFF", "TRNA Annotation GFF", "Misc Annotation GFF", "RFAM Annotation GFF", "TMRNA Annotation GFF", "KO_EC Annotation GFF", "Product Names", "Gene Phylogeny tsv", "Crisprt Terms", "Clusters of Orthologous Groups (COG) Annotation GFF", "CATH FunFams (Functional Families) Annotation GFF", "SUPERFam Annotation GFF", "SMART Annotation GFF", "Pfam Annotation GFF", "Direct Infusion FT ICR-MS Raw Data"], "title": "FileTypeEnum", "type": "string"}, "FilterTypeEnum": {"description": "", "enum": ["particulate air filter", "chemical air filter", "low-MERV pleated media", "HEPA", "electrostatic", "gas-phase or ultraviolet air treatments"], "title": "FilterTypeEnum", "type": "string"}, "FloorCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "FloorCondEnum", "type": "string"}, "FloorFinishMatEnum": {"description": "", "enum": ["tile", "wood strip or parquet", "carpet", "rug", "laminate wood", "lineoleum", "vinyl composition tile", "sheet vinyl", "stone", "bamboo", "cork", "terrazo", "concrete", "none", "sealed", "clear finish", "paint", "none or unfinished"], "title": "FloorFinishMatEnum", "type": "string"}, "FloorStrucEnum": {"description": "", "enum": ["balcony", "floating floor", "glass floor", "raised floor", "sprung floor", "wood-framed", "concrete"], "title": "FloorStrucEnum", "type": "string"}, "FloorWaterMoldEnum": {"description": "", "enum": ["mold odor", "wet floor", "water stains", "wall discoloration", "floor discoloration", "ceiling discoloration", "peeling paint or wallpaper", "bulging walls", "condensation"], "title": "FloorWaterMoldEnum", "type": "string"}, "FreqCleanEnum": {"description": "", "enum": ["Daily", "Weekly", "Monthly", "Quarterly", "Annually", "other"], "title": "FreqCleanEnum", "type": "string"}, "FunctionalAnnotation": {"additionalProperties": false, "description": "An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods", "properties": {"has_function": {"pattern": "^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$", "type": "string"}, "subject": {"type": "string"}, "was_generated_by": {"description": "provenance for the annotation.", "type": "string"}}, "title": "FunctionalAnnotation", "type": "object"}, "FurnitureEnum": {"description": "", "enum": ["cabinet", "chair", "desks"], "title": "FurnitureEnum", "type": "string"}, "GenderRestroomEnum": {"description": "", "enum": ["all gender", "female", "gender neurtral", "male", "male and female", "unisex"], "title": "GenderRestroomEnum", "type": "string"}, "GeneProduct": {"additionalProperties": false, "description": "A molecule encoded by a gene that has an evolved function", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "GeneProduct", "type": "object"}, "GenomeFeature": {"additionalProperties": false, "description": "A feature localized to an interval along a genome", "title": "GenomeFeature", "type": "object"}, "GeolocationValue": {"additionalProperties": false, "description": "A normalized value for a location on the earth's surface", "properties": {"has_raw_value": {"description": "The raw value for a geolocation should follow {lat} {long}", "type": "string"}, "latitude": {"description": "latitude", "type": "number"}, "longitude": {"description": "longitude", "type": "number"}, "was_generated_by": {"type": "string"}}, "title": "GeolocationValue", "type": "object"}, "GrowthHabitEnum": {"description": "", "enum": ["erect", "semi-erect", "spreading", "prostrate"], "title": "GrowthHabitEnum", "type": "string"}, "HandidnessEnum": {"description": "", "enum": ["ambidexterity", "left handedness", "mixed-handedness", "right handedness"], "title": "HandidnessEnum", "type": "string"}, "HcProducedEnum": {"description": "", "enum": ["Oil", "Gas-Condensate", "Gas", "Bitumen", "Coalbed Methane", "other"], "title": "HcProducedEnum", "type": "string"}, "HcrEnum": {"description": "", "enum": ["Oil Reservoir", "Gas Reservoir", "Oil Sand", "Coalbed", "Shale", "Tight Oil Reservoir", "Tight Gas Reservoir", "other"], "title": "HcrEnum", "type": "string"}, "HcrGeolAgeEnum": {"description": "", "enum": ["Archean", "Cambrian", "Carboniferous", "Cenozoic", "Cretaceous", "Devonian", "Jurassic", "Mesozoic", "Neogene", "Ordovician", "Paleogene", "Paleozoic", "Permian", "Precambrian", "Proterozoic", "Silurian", "Triassic", "other"], "title": "HcrGeolAgeEnum", "type": "string"}, "HeatCoolTypeEnum": {"description": "", "enum": ["radiant system", "heat pump", "forced air system", "steam forced heat", "wood stove"], "title": "HeatCoolTypeEnum", "type": "string"}, "HeatDelivLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "HeatDelivLocEnum", "type": "string"}, "HorizonEnum": {"description": "", "enum": ["O horizon", "A horizon", "E horizon", "B horizon", "C horizon", "R layer", "Permafrost"], "title": "HorizonEnum", "type": "string"}, "HostSexEnum": {"description": "", "enum": ["female", "hermaphrodite", "male", "neuter"], "title": "HostSexEnum", "type": "string"}, "ImageValue": {"additionalProperties": false, "description": "An attribute value representing an image.", "properties": {"description": {"description": "a human-readable description of a thing", "type": "string"}, "display_order": {"description": "When rendering information, this attribute to specify the order in which the information should be rendered.", "type": "string"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "url": {"type": "string"}, "was_generated_by": {"type": "string"}}, "title": "ImageValue", "type": "object"}, "IndoorSpaceEnum": {"description": "", "enum": ["bedroom", "office", "bathroom", "foyer", "kitchen", "locker room", "hallway", "elevator"], "title": "IndoorSpaceEnum", "type": "string"}, "IndoorSurfEnum": {"description": "", "enum": ["cabinet", "ceiling", "counter top", "door", "shelving", "vent cover", "window", "wall"], "title": "IndoorSurfEnum", "type": "string"}, "Instrument": {"additionalProperties": false, "description": "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI].", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Instrument", "type": "object"}, "IntWallCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "IntWallCondEnum", "type": "string"}, "IntegerValue": {"additionalProperties": false, "description": "A value that is an integer", "properties": {"has_numeric_value": {"description": "Links a quantity value to a number", "type": "number"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "IntegerValue", "type": "object"}, "LabDevice": {"additionalProperties": false, "description": "", "properties": {"activity_speed": {"$ref": "#/$defs/QuantityValue"}, "activity_temperature": {"$ref": "#/$defs/QuantityValue"}, "activity_time": {"$ref": "#/$defs/QuantityValue"}, "device_type": {"$ref": "#/$defs/DeviceTypeEnum"}}, "title": "LabDevice", "type": "object"}, "LightTypeEnum": {"description": "", "enum": ["natural light", "electric light", "desk lamp", "flourescent lights", "none"], "title": "LightTypeEnum", "type": "string"}, "LithologyEnum": {"description": "", "enum": ["Basement", "Chalk", "Chert", "Coal", "Conglomerate", "Diatomite", "Dolomite", "Limestone", "Sandstone", "Shale", "Siltstone", "Volcanic", "other"], "title": "LithologyEnum", "type": "string"}, "MagBin": {"additionalProperties": false, "description": "", "properties": {"bin_name": {"type": "string"}, "bin_quality": {"type": "string"}, "completeness": {"type": "number"}, "contamination": {"type": "number"}, "gene_count": {"type": "integer"}, "gtdbtk_class": {"type": "string"}, "gtdbtk_domain": {"type": "string"}, "gtdbtk_family": {"type": "string"}, "gtdbtk_genus": {"type": "string"}, "gtdbtk_order": {"type": "string"}, "gtdbtk_phylum": {"type": "string"}, "gtdbtk_species": {"type": "string"}, "num_16s": {"type": "integer"}, "num_23s": {"type": "integer"}, "num_5s": {"type": "integer"}, "num_t_rna": {"type": "integer"}, "number_of_contig": {"type": "integer"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "title": "MagBin", "type": "object"}, "MagsAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", "properties": {"binned_contig_num": {"type": "integer"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "input_contig_num": {"type": "integer"}, "low_depth_contig_num": {"type": "integer"}, "mags_list": {"items": {"$ref": "#/$defs/MagBin"}, "type": "array"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "too_short_contig_num": {"type": "integer"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "unbinned_contig_num": {"type": "integer"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MagsAnalysisActivity", "type": "object"}, "MaterialContainer": {"additionalProperties": false, "description": "", "properties": {"container_size": {"$ref": "#/$defs/QuantityValue"}, "container_type": {"$ref": "#/$defs/ContainerTypeEnum"}}, "title": "MaterialContainer", "type": "object"}, "MaterialEntity": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "MaterialEntity", "type": "object"}, "MaterialSample": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "MaterialSample", "type": "object"}, "MaterialSamplingActivity": {"additionalProperties": false, "description": "", "properties": {"amount_collected": {"$ref": "#/$defs/QuantityValue"}, "biosample_input": {"type": "string"}, "collected_into": {"$ref": "#/$defs/MaterialContainer"}, "material_output": {"type": "string"}, "sampling_method": {"$ref": "#/$defs/SamplingMethodEnum"}}, "title": "MaterialSamplingActivity", "type": "object"}, "MechStrucEnum": {"description": "", "enum": ["subway", "coach", "carriage", "elevator", "escalator", "boat", "train", "car", "bus"], "title": "MechStrucEnum", "type": "string"}, "MetaboliteQuantification": {"additionalProperties": false, "description": "This is used to link a metabolomics analysis workflow to a specific metabolite", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "MetaboliteQuantification", "type": "object"}, "MetabolomicsAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetabolomicsAnalysisActivity", "type": "object"}, "MetagenomeAnnotationActivity": {"additionalProperties": false, "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "gold_analysis_project_identifiers": {"description": "identifiers for corresponding analysis project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Ga[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetagenomeAnnotationActivity", "type": "object"}, "MetagenomeAssembly": {"additionalProperties": false, "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", "properties": {"asm_score": {"description": "A score for comparing metagenomic assembly quality from same sample.", "type": "number"}, "contig_bp": {"description": "Total size in bp of all contigs.", "type": "number"}, "contigs": {"description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "ctg_l50": {"description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", "type": "number"}, "ctg_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", "type": "number"}, "ctg_logsum": {"description": "Maximum contig length.", "type": "number"}, "ctg_max": {"description": "Maximum contig length.", "type": "number"}, "ctg_n50": {"description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", "type": "number"}, "ctg_n90": {"description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", "type": "number"}, "ctg_powsum": {"description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "gap_pct": {"description": "The gap size percentage of all scaffolds.", "type": "number"}, "gc_avg": {"description": "Average of GC content of all contigs.", "type": "number"}, "gc_std": {"description": "Standard deviation of GC content of all contigs.", "type": "number"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_assembly_identifiers": {"pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "num_aligned_reads": {"description": "The sequence count number of input reads aligned to assembled contigs.", "type": "number"}, "num_input_reads": {"description": "The sequence count number of input reads for assembly.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "scaf_bp": {"description": "Total size in bp of all scaffolds.", "type": "number"}, "scaf_l50": {"description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", "type": "number"}, "scaf_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", "type": "number"}, "scaf_l_gt50k": {"description": "Total size in bp of all scaffolds greater than 50 KB.", "type": "number"}, "scaf_logsum": {"description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "scaf_max": {"description": "Maximum scaffold length.", "type": "number"}, "scaf_n50": {"description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", "type": "number"}, "scaf_n90": {"description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", "type": "number"}, "scaf_n_gt50k": {"description": "Total sequence count of scaffolds greater than 50 KB.", "type": "number"}, "scaf_pct_gt50k": {"description": "Total sequence size percentage of scaffolds greater than 50 KB.", "type": "number"}, "scaf_powsum": {"description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "scaffolds": {"description": "Total sequence count of all scaffolds.", "type": "number"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetagenomeAssembly", "type": "object"}, "MetaproteomicsAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetaproteomicsAnalysisActivity", "type": "object"}, "MetatranscriptomeActivity": {"additionalProperties": false, "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeActivity", "type": "object"}, "MetatranscriptomeAnnotationActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "gold_analysis_project_identifiers": {"description": "identifiers for corresponding analysis project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Ga[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeAnnotationActivity", "type": "object"}, "MetatranscriptomeAssembly": {"additionalProperties": false, "description": "", "properties": {"asm_score": {"description": "A score for comparing metagenomic assembly quality from same sample.", "type": "number"}, "contig_bp": {"description": "Total size in bp of all contigs.", "type": "number"}, "contigs": {"description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "ctg_l50": {"description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", "type": "number"}, "ctg_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", "type": "number"}, "ctg_logsum": {"description": "Maximum contig length.", "type": "number"}, "ctg_max": {"description": "Maximum contig length.", "type": "number"}, "ctg_n50": {"description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", "type": "number"}, "ctg_n90": {"description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", "type": "number"}, "ctg_powsum": {"description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "gap_pct": {"description": "The gap size percentage of all scaffolds.", "type": "number"}, "gc_avg": {"description": "Average of GC content of all contigs.", "type": "number"}, "gc_std": {"description": "Standard deviation of GC content of all contigs.", "type": "number"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_assembly_identifiers": {"pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "num_aligned_reads": {"description": "The sequence count number of input reads aligned to assembled contigs.", "type": "number"}, "num_input_reads": {"description": "The sequence count number of input reads for assembly.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "scaf_bp": {"description": "Total size in bp of all scaffolds.", "type": "number"}, "scaf_l50": {"description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", "type": "number"}, "scaf_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", "type": "number"}, "scaf_l_gt50k": {"description": "Total size in bp of all scaffolds greater than 50 KB.", "type": "number"}, "scaf_logsum": {"description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "scaf_max": {"description": "Maximum scaffold length.", "type": "number"}, "scaf_n50": {"description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", "type": "number"}, "scaf_n90": {"description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", "type": "number"}, "scaf_n_gt50k": {"description": "Total sequence count of scaffolds greater than 50 KB.", "type": "number"}, "scaf_pct_gt50k": {"description": "Total sequence size percentage of scaffolds greater than 50 KB.", "type": "number"}, "scaf_powsum": {"description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "scaffolds": {"description": "Total sequence count of all scaffolds.", "type": "number"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeAssembly", "type": "object"}, "NomAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "NomAnalysisActivity", "type": "object"}, "OccupDocumentEnum": {"description": "", "enum": ["automated count", "estimate", "manual count", "videos"], "title": "OccupDocumentEnum", "type": "string"}, "OmicsProcessing": {"additionalProperties": false, "description": "The methods and processes used to generate omics data from a biosample or organism.", "properties": {"add_date": {"description": "The date on which the information was added to the database.", "type": "string"}, "alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "chimera_check": {"$ref": "#/$defs/TextValue", "description": "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "gold_sequencing_project_identifiers": {"description": "identifiers for corresponding sequencing project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Gp[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_experiment_identifiers": {"items": {"type": "string"}, "pattern": "^insdc.sra:(E|D|S)RX[0-9]{6,}$", "type": "array"}, "instrument_name": {"description": "The name of the instrument that was used for processing the sample.", "type": "string"}, "mod_date": {"description": "The last date on which the database information was modified.", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "ncbi_project_name": {"type": "string"}, "nucl_acid_amp": {"$ref": "#/$defs/TextValue", "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids"}, "nucl_acid_ext": {"$ref": "#/$defs/TextValue", "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample"}, "omics_type": {"$ref": "#/$defs/ControlledTermValue", "description": "The type of omics data"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "pcr_cond": {"$ref": "#/$defs/TextValue", "description": "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'"}, "pcr_primers": {"$ref": "#/$defs/TextValue", "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters"}, "principal_investigator": {"$ref": "#/$defs/PersonValue", "description": "Principal Investigator who led the study and/or generated the dataset."}, "processing_institution": {"$ref": "#/$defs/ProcessingInstitutionEnum", "description": "The organization that processed the sample."}, "samp_vol_we_dna_ext": {"$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)."}, "seq_meth": {"$ref": "#/$defs/TextValue", "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)."}, "seq_quality_check": {"$ref": "#/$defs/TextValue", "description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA"}, "target_gene": {"$ref": "#/$defs/TextValue", "description": "Targeted gene or locus name for marker gene studies"}, "target_subfragment": {"$ref": "#/$defs/TextValue", "description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "required": ["has_input"], "title": "OmicsProcessing", "type": "object"}, "OntologyClass": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "OntologyClass", "type": "object"}, "OrganismCountEnum": {"description": "", "enum": ["ATP", "MPN", "other"], "title": "OrganismCountEnum", "type": "string"}, "OrthologyGroup": {"additionalProperties": false, "description": "A set of genes or gene products in which all members are orthologous", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "OrthologyGroup", "type": "object"}, "OxyStatSampEnum": {"description": "", "enum": ["aerobic", "anaerobic", "other"], "title": "OxyStatSampEnum", "type": "string"}, "Pathway": {"additionalProperties": false, "description": "A pathway is a sequence of steps/reactions carried out by an organism or community of organisms", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Pathway", "type": "object"}, "PeptideQuantification": {"additionalProperties": false, "description": "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information", "title": "PeptideQuantification", "type": "object"}, "Person": {"additionalProperties": false, "description": "represents a person, such as a researcher", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "Should be an ORCID. Specify in CURIE format. E.g ORCID:0000-1111-...", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Person", "type": "object"}, "PersonValue": {"additionalProperties": false, "description": "An attribute value representing a person", "properties": {"email": {"description": "An email address for an entity such as a person. This should be the primarly email address used.", "type": "string"}, "has_raw_value": {"description": "The full name of the Investigator in format FIRST LAST.", "type": "string"}, "name": {"description": "The full name of the Investigator. It should follow the format FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.", "type": "string"}, "orcid": {"description": "The ORCID of a person.", "type": "string"}, "profile_image_url": {"description": "A url that points to an image of a person.", "type": "string"}, "was_generated_by": {"type": "string"}, "websites": {"description": "A list of websites that are associated with the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "PersonValue", "type": "object"}, "PlannedProcess": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_inputs": {"items": {"type": "string"}, "type": "array"}, "has_outputs": {"items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "participating_agent": {"$ref": "#/$defs/Agent"}}, "required": ["id"], "title": "PlannedProcess", "type": "object"}, "PlantGrowthMedEnum": {"description": "", "enum": ["other artificial liquid medium", "other artificial solid medium", "peat moss", "perlite", "pumice", "sand", "soil", "vermiculite", "water"], "title": "PlantGrowthMedEnum", "type": "string"}, "PlantSexEnum": {"description": "", "enum": ["Androdioecious", "Androecious", "Androgynous", "Androgynomonoecious", "Andromonoecious", "Bisexual", "Dichogamous", "Diclinous", "Dioecious", "Gynodioecious", "Gynoecious", "Gynomonoecious", "Hermaphroditic", "Imperfect", "Monoclinous", "Monoecious", "Perfect", "Polygamodioecious", "Polygamomonoecious", "Polygamous", "Protandrous", "Protogynous", "Subandroecious", "Subdioecious", "Subgynoecious", "Synoecious", "Trimonoecious", "Trioecious", "Unisexual"], "title": "PlantSexEnum", "type": "string"}, "ProcessingInstitutionEnum": {"description": "", "enum": ["UCSD", "JGI", "EMSL"], "title": "ProcessingInstitutionEnum", "type": "string"}, "ProfilePositionEnum": {"description": "", "enum": ["summit", "shoulder", "backslope", "footslope", "toeslope"], "title": "ProfilePositionEnum", "type": "string"}, "ProteinQuantification": {"additionalProperties": false, "description": "This is used to link a metaproteomics analysis workflow to a specific protein", "title": "ProteinQuantification", "type": "object"}, "QuadPosEnum": {"description": "", "enum": ["North side", "West side", "South side", "East side"], "title": "QuadPosEnum", "type": "string"}, "QuantityValue": {"additionalProperties": false, "description": "A simple quantity, e.g. 2cm", "properties": {"has_maximum_numeric_value": {"description": "The maximum value part, expressed as number, of the quantity value when the value covers a range.", "type": "number"}, "has_minimum_numeric_value": {"description": "The minimum value part, expressed as number, of the quantity value when the value covers a range.", "type": "number"}, "has_numeric_value": {"description": "The number part of the quantity", "type": "number"}, "has_raw_value": {"description": "Unnormalized atomic string representation, should in syntax {number} {unit}", "type": "string"}, "has_unit": {"description": "The unit of the quantity", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "QuantityValue", "type": "object"}, "Reaction": {"additionalProperties": false, "description": "An individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Reaction", "type": "object"}, "ReactionActivity": {"additionalProperties": false, "description": "", "properties": {"material_input": {"type": "string"}, "material_output": {"type": "string"}, "reaction_aided_by": {"$ref": "#/$defs/LabDevice"}, "reaction_temperature": {"type": "string"}, "reaction_time": {"$ref": "#/$defs/QuantityValue"}}, "title": "ReactionActivity", "type": "object"}, "ReactionParticipant": {"additionalProperties": false, "description": "Instances of this link a reaction to a chemical entity participant", "title": "ReactionParticipant", "type": "object"}, "ReadBasedTaxonomyAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "ReadBasedTaxonomyAnalysisActivity", "type": "object"}, "ReadQcAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "input_base_count": {"description": "The nucleotide base count number of input reads for QC analysis.", "type": "number"}, "input_read_count": {"description": "The sequence count number of input reads for QC analysis.", "type": "number"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "output_base_count": {"description": "After QC analysis nucleotide base count number.", "type": "number"}, "output_read_count": {"description": "After QC analysis sequence count number.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "ReadQcAnalysisActivity", "type": "object"}, "RelSampLocEnum": {"description": "", "enum": ["edge of car", "center of car", "under a seat"], "title": "RelSampLocEnum", "type": "string"}, "RelToOxygenEnum": {"description": "", "enum": ["aerobe", "anaerobe", "facultative", "microaerophilic", "microanaerobe", "obligate aerobe", "obligate anaerobe"], "title": "RelToOxygenEnum", "type": "string"}, "RnaContTypeEnum": {"description": "", "enum": ["plate", "tube"], "title": "RnaContTypeEnum", "type": "string"}, "RnaSampleFormatEnum": {"description": "", "enum": ["10 mM Tris-HCl", "DNAStable", "Ethanol", "Low EDTA TE", "MDA reaction buffer", "PBS", "Pellet", "RNAStable", "TE", "Water", "Gentegra-DNA", "Gentegra-RNA"], "title": "RnaSampleFormatEnum", "type": "string"}, "RoomCondtEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture", "visible signs of mold/mildew"], "title": "RoomCondtEnum", "type": "string"}, "RoomConnectedEnum": {"description": "", "enum": ["attic", "bathroom", "closet", "conference room", "elevator", "examining room", "hallway", "kitchen", "mail room", "office", "stairwell"], "title": "RoomConnectedEnum", "type": "string"}, "RoomLocEnum": {"description": "", "enum": ["corner room", "interior room", "exterior wall"], "title": "RoomLocEnum", "type": "string"}, "RoomSampPosEnum": {"description": "", "enum": ["north corner", "south corner", "west corner", "east corner", "northeast corner", "northwest corner", "southeast corner", "southwest corner", "center"], "title": "RoomSampPosEnum", "type": "string"}, "RoomTypeEnum": {"description": "", "enum": ["attic", "bathroom", "closet", "conference room", "elevator", "examining room", "hallway", "kitchen", "mail room", "private office", "open office", "stairwell", ",restroom", "lobby", "vestibule", "mechanical or electrical room", "data center", "laboratory_wet", "laboratory_dry", "gymnasium", "natatorium", "auditorium", "lockers", "cafe", "warehouse"], "title": "RoomTypeEnum", "type": "string"}, "SampCaptStatusEnum": {"description": "", "enum": ["active surveillance in response to an outbreak", "active surveillance not initiated by an outbreak", "farm sample", "market sample", "other"], "title": "SampCaptStatusEnum", "type": "string"}, "SampCollectPointEnum": {"description": "", "enum": ["well", "test well", "drilling rig", "wellhead", "separator", "storage tank", "other"], "title": "SampCollectPointEnum", "type": "string"}, "SampDisStageEnum": {"description": "", "enum": ["dissemination", "growth and reproduction", "infection", "inoculation", "penetration", "other"], "title": "SampDisStageEnum", "type": "string"}, "SampFloorEnum": {"description": "", "enum": ["1st floor", "2nd floor", "basement", "lobby"], "title": "SampFloorEnum", "type": "string"}, "SampMdEnum": {"description": "", "enum": ["DF", "RT", "KB", "MSL", "other"], "title": "SampMdEnum", "type": "string"}, "SampSubtypeEnum": {"description": "", "enum": ["oil phase", "water phase", "biofilm", "not applicable", "other"], "title": "SampSubtypeEnum", "type": "string"}, "SampWeatherEnum": {"description": "", "enum": ["clear sky", "cloudy", "foggy", "hail", "rain", "snow", "sleet", "sunny", "windy"], "title": "SampWeatherEnum", "type": "string"}, "SampleTypeEnum": {"description": "", "enum": ["soil", "water_extract_soil"], "title": "SampleTypeEnum", "type": "string"}, "SamplingMethodEnum": {"description": "", "enum": ["weighing"], "title": "SamplingMethodEnum", "type": "string"}, "SeasonUseEnum": {"description": "", "enum": ["Spring", "Summer", "Fall", "Winter"], "title": "SeasonUseEnum", "type": "string"}, "SedimentTypeEnum": {"description": "", "enum": ["biogenous", "cosmogenous", "hydrogenous", "lithogenous"], "title": "SedimentTypeEnum", "type": "string"}, "ShadingDeviceCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "ShadingDeviceCondEnum", "type": "string"}, "ShadingDeviceTypeEnum": {"description": "", "enum": ["bahama shutters", "exterior roll blind", "gambrel awning", "hood awning", "porchroller awning", "sarasota shutters", "slatted aluminum", "solid aluminum awning", "sun screen", "tree", "trellis", "venetian awning"], "title": "ShadingDeviceTypeEnum", "type": "string"}, "Site": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Site", "type": "object"}, "SoilHorizonEnum": {"description": "", "enum": ["O horizon", "A horizon", "E horizon", "B horizon", "C horizon", "R layer", "Permafrost"], "title": "SoilHorizonEnum", "type": "string"}, "SolventEnum": {"description": "", "enum": ["deionized_water", "methanol", "chloroform"], "title": "SolventEnum", "type": "string"}, "SpecificEnum": {"description": "", "enum": ["operation", "as built", "construction", "bid", "design", "photos"], "title": "SpecificEnum", "type": "string"}, "SrDepEnvEnum": {"description": "", "enum": ["Lacustine", "Fluvioldeltaic", "Fluviomarine", "Marine", "other"], "title": "SrDepEnvEnum", "type": "string"}, "SrGeolAgeEnum": {"description": "", "enum": ["Archean", "Cambrian", "Carboniferous", "Cenozoic", "Cretaceous", "Devonian", "Jurassic", "Mesozoic", "Neogene", "Ordovician", "Paleogene", "Paleozoic", "Permian", "Precambrian", "Proterozoic", "Silurian", "Triassic", "other"], "title": "SrGeolAgeEnum", "type": "string"}, "SrKerogTypeEnum": {"description": "", "enum": ["Type I", "Type II", "Type III", "Type IV", "other"], "title": "SrKerogTypeEnum", "type": "string"}, "SrLithologyEnum": {"description": "", "enum": ["Clastic", "Carbonate", "Coal", "Biosilicieous", "other"], "title": "SrLithologyEnum", "type": "string"}, "Study": {"additionalProperties": false, "description": "A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.", "properties": {"abstract": {"description": "The abstract of manuscript/grant associated with the entity; i.e., a summary of the resource.", "type": "string"}, "alternative_descriptions": {"description": "A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.", "items": {"type": "string"}, "type": "array"}, "alternative_identifiers": {"description": "Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC", "items": {"type": "string"}, "type": "array"}, "alternative_names": {"description": "A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.", "items": {"type": "string"}, "type": "array"}, "alternative_titles": {"description": "A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "A brief summary that details the study you're submitted to NMDC", "type": "string"}, "doi": {"$ref": "#/$defs/AttributeValue", "description": "The dataset citation for this study"}, "ecosystem": {"description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", "type": "string"}, "ecosystem_category": {"description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", "type": "string"}, "ecosystem_subtype": {"description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", "type": "string"}, "ecosystem_type": {"description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", "type": "string"}, "emsl_proposal_doi": {"description": "The DOI for the EMSL awarded study that relates to the NMDC submitted study", "type": "string"}, "emsl_proposal_identifier": {"description": "The proposal number assigned to the EMSL awarded study that relates to that which is represented in NMDC.", "type": "string"}, "ess_dive_datasets": {"description": "List of ESS-DIVE dataset DOIs", "items": {"type": "string"}, "type": "array"}, "funding_sources": {"items": {"type": "string"}, "type": "array"}, "gold_study_identifiers": {"description": "identifiers for corresponding project(s) in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Gs[0-9]+$", "type": "array"}, "has_credit_associations": {"description": "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study", "items": {"$ref": "#/$defs/CreditAssociation"}, "type": "array"}, "id": {"description": "An NMDC assigned unique identifier for a sample submitted to NMDC.", "type": "string"}, "mgnify_project_identifiers": {"description": "identifiers for corresponding project in MGnify", "pattern": "^mgnify.proj:[A-Z]+[0-9]+$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "objective": {"description": "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.", "type": "string"}, "principal_investigator": {"$ref": "#/$defs/PersonValue", "description": "Principal Investigator who led the study and/or generated the dataset."}, "publications": {"description": "A list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.", "items": {"type": "string"}, "type": "array"}, "related_identifiers": {"description": "Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC", "type": "string"}, "relevant_protocols": {"items": {"type": "string"}, "type": "array"}, "specific_ecosystem": {"description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", "type": "string"}, "study_image": {"description": "Links a study to one or more images.", "items": {"$ref": "#/$defs/ImageValue"}, "type": "array"}, "title": {"description": "A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "websites": {"description": "A list of websites that are associated with the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "Study", "type": "object"}, "SubstructureTypeEnum": {"description": "", "enum": ["crawlspace", "slab on grade", "basement"], "title": "SubstructureTypeEnum", "type": "string"}, "SurfAirContEnum": {"description": "", "enum": ["dust", "organic matter", "particulate matter", "volatile organic compounds", "biological contaminants", "radon", "nutrients", "biocides"], "title": "SurfAirContEnum", "type": "string"}, "SurfMaterialEnum": {"description": "", "enum": ["adobe", "carpet", "cinder blocks", "concrete", "hay bales", "glass", "metal", "paint", "plastic", "stainless steel", "stone", "stucco", "tile", "vinyl", "wood"], "title": "SurfMaterialEnum", "type": "string"}, "TextValue": {"additionalProperties": false, "description": "A basic string value", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "language": {"description": "Should use ISO 639-1 code e.g. \"en\", \"fr\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "TextValue", "type": "object"}, "TidalStageEnum": {"description": "", "enum": ["low tide", "ebb tide", "flood tide", "high tide"], "title": "TidalStageEnum", "type": "string"}, "TillageEnum": {"description": "", "enum": ["drill", "cutting disc", "ridge till", "strip tillage", "zonal tillage", "chisel", "tined", "mouldboard", "disc plough"], "title": "TillageEnum", "type": "string"}, "TimestampValue": {"additionalProperties": false, "description": "A value that is a timestamp. The range should be ISO-8601", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "TimestampValue", "type": "object"}, "TrainLineEnum": {"description": "", "enum": ["red", "green", "orange"], "title": "TrainLineEnum", "type": "string"}, "TrainStatLocEnum": {"description": "", "enum": ["south station above ground", "south station underground", "south station amtrak", "forest hills", "riverside"], "title": "TrainStatLocEnum", "type": "string"}, "TrainStopLocEnum": {"description": "", "enum": ["end", "mid", "downtown"], "title": "TrainStopLocEnum", "type": "string"}, "UrlValue": {"additionalProperties": false, "description": "A value that is a string that conforms to URL syntax", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "UrlValue", "type": "object"}, "VisMediaEnum": {"description": "", "enum": ["photos", "videos", "commonly of the building", "site context (adjacent buildings, vegetation, terrain, streets)", "interiors", "equipment", "3D scans"], "title": "VisMediaEnum", "type": "string"}, "WallConstTypeEnum": {"description": "", "enum": ["frame construction", "joisted masonry", "light noncombustible", "masonry noncombustible", "modified fire resistive", "fire resistive"], "title": "WallConstTypeEnum", "type": "string"}, "WallFinishMatEnum": {"description": "", "enum": ["plaster", "gypsum plaster", "veneer plaster", "gypsum board", "tile", "terrazzo", "stone facing", "acoustical treatment", "wood", "metal", "masonry"], "title": "WallFinishMatEnum", "type": "string"}, "WallLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "WallLocEnum", "type": "string"}, "WallSurfTreatmentEnum": {"description": "", "enum": ["painted", "wall paper", "no treatment", "paneling", "stucco", "fabric"], "title": "WallSurfTreatmentEnum", "type": "string"}, "WallTextureEnum": {"description": "", "enum": ["crows feet", "crows-foot stomp", "double skip", "hawk and trowel", "knockdown", "popcorn", "orange peel", "rosebud stomp", "Santa-Fe texture", "skip trowel", "smooth", "stomp knockdown", "swirl"], "title": "WallTextureEnum", "type": "string"}, "WaterFeatTypeEnum": {"description": "", "enum": ["fountain", "pool", "standing feature", "stream", "waterfall"], "title": "WaterFeatTypeEnum", "type": "string"}, "WeekdayEnum": {"description": "", "enum": ["Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday", "Sunday"], "title": "WeekdayEnum", "type": "string"}, "WindowCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "WindowCondEnum", "type": "string"}, "WindowCoverEnum": {"description": "", "enum": ["blinds", "curtains", "none"], "title": "WindowCoverEnum", "type": "string"}, "WindowHorizPosEnum": {"description": "", "enum": ["left", "middle", "right"], "title": "WindowHorizPosEnum", "type": "string"}, "WindowLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "WindowLocEnum", "type": "string"}, "WindowMatEnum": {"description": "", "enum": ["clad", "fiberglass", "metal", "vinyl", "wood"], "title": "WindowMatEnum", "type": "string"}, "WindowTypeEnum": {"description": "", "enum": ["single-hung sash window", "horizontal sash window", "fixed window"], "title": "WindowTypeEnum", "type": "string"}, "WindowVertPosEnum": {"description": "", "enum": ["bottom", "middle", "top", "low", "high"], "title": "WindowVertPosEnum", "type": "string"}, "WorkflowExecutionActivity": {"additionalProperties": false, "description": "Represents an instance of an execution of a particular workflow", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"description": "the agent/entity associated with the generation of the file", "type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "WorkflowExecutionActivity", "type": "object"}}, "$id": "https://microbiomedata/schema", "$schema": "http://json-schema.org/draft-07/schema#", "additionalProperties": false, "metamodel_version": "1.7.0", "properties": {"activity_set": {"description": "This property links a database object to the set of workflow activities.", "items": {"$ref": "#/$defs/WorkflowExecutionActivity"}, "type": "array"}, "biosample_set": {"description": "This property links a database object to the set of samples within it.", "items": {"$ref": "#/$defs/Biosample"}, "type": "array"}, "collecting_biosamples_from_site_set": {"items": {"$ref": "#/$defs/CollectingBiosamplesFromSite"}, "type": "array"}, "data_object_set": {"description": "This property links a database object to the set of data objects within it.", "items": {"$ref": "#/$defs/DataObject"}, "type": "array"}, "dissolving_activity_set": {"items": {"$ref": "#/$defs/DissolvingActivity"}, "type": "array"}, "field_research_site_set": {"items": {"$ref": "#/$defs/FieldResearchSite"}, "type": "array"}, "functional_annotation_set": {"description": "This property links a database object to the set of all functional annotations", "items": {"$ref": "#/$defs/FunctionalAnnotation"}, "type": "array"}, "genome_feature_set": {"description": "This property links a database object to the set of all features", "items": {"$ref": "#/$defs/GenomeFeature"}, "type": "array"}, "mags_activity_set": {"description": "This property links a database object to the set of MAGs analysis activities.", "items": {"$ref": "#/$defs/MagsAnalysisActivity"}, "type": "array"}, "material_sample_set": {"items": {"$ref": "#/$defs/MaterialSample"}, "type": "array"}, "material_sampling_activity_set": {"items": {"$ref": "#/$defs/MaterialSamplingActivity"}, "type": "array"}, "metabolomics_analysis_activity_set": {"description": "This property links a database object to the set of metabolomics analysis activities.", "items": {"$ref": "#/$defs/MetabolomicsAnalysisActivity"}, "type": "array"}, "metagenome_annotation_activity_set": {"description": "This property links a database object to the set of metagenome annotation activities.", "items": {"$ref": "#/$defs/MetagenomeAnnotationActivity"}, "type": "array"}, "metagenome_assembly_set": {"description": "This property links a database object to the set of metagenome assembly activities.", "items": {"$ref": "#/$defs/MetagenomeAssembly"}, "type": "array"}, "metaproteomics_analysis_activity_set": {"description": "This property links a database object to the set of metaproteomics analysis activities.", "items": {"$ref": "#/$defs/MetaproteomicsAnalysisActivity"}, "type": "array"}, "metatranscriptome_activity_set": {"description": "TODO", "items": {"$ref": "#/$defs/MetatranscriptomeActivity"}, "type": "array"}, "nom_analysis_activity_set": {"description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", "items": {"$ref": "#/$defs/NomAnalysisActivity"}, "type": "array"}, "omics_processing_set": {"description": "This property links a database object to the set of omics processings within it.", "items": {"$ref": "#/$defs/OmicsProcessing"}, "type": "array"}, "reaction_activity_set": {"items": {"$ref": "#/$defs/ReactionActivity"}, "type": "array"}, "read_based_taxonomy_analysis_activity_set": {"description": "This property links a database object to the set of read based analysis activities.", "items": {"$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity"}, "type": "array"}, "read_qc_analysis_activity_set": {"description": "This property links a database object to the set of read QC analysis activities.", "items": {"$ref": "#/$defs/ReadQcAnalysisActivity"}, "type": "array"}, "study_set": {"description": "This property links a database object to the set of studies within it.", "items": {"$ref": "#/$defs/Study"}, "type": "array"}}, "title": "NMDC", "type": "object", "version": "7.0.0"} diff --git a/nmdc_schema/nmdc.yaml b/nmdc_schema/nmdc.yaml index e211bc6017..78e956aed0 100644 --- a/nmdc_schema/nmdc.yaml +++ b/nmdc_schema/nmdc.yaml @@ -115,39 +115,6 @@ subsets: classes: - FieldResearchSite: - aliases: - - research plot - description: A site, outside of a laboratory, from which biosamples may be collected. - is_a: Site - # is_a: NamedThing - title: Field Research Site - comments: - - Provides grouping of biosamples at level that's more specific than belonging - to the same study - - be very clear that this could be part of a larger site - - In Bioscales, one might say that rhizosphere soil and bulk soil from around - the same plant were obtained at the same site. In this case, the site would - correspond to one tree. - - "might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833" - - CollectingBiosamplesFromSite: - is_a: PlannedProcess - title: Collecting Biosamples From Site - slots: - - has_inputs - - has_outputs - comments: - - "this illustrates implementing a Biosample relation with a process class" - slot_usage: - has_inputs: - range: Site - # range: NamedThing - required: true - has_outputs: - range: Biosample - required: true - Database: tree_root: true aliases: @@ -177,17 +144,9 @@ classes: - read_qc_analysis_activity_set - read_based_taxonomy_analysis_activity_set - study_set - attributes: - frs_set: - inlined_as_list: true - multivalued: true - range: FieldResearchSite - domain: Database - cbfs_set: - inlined_as_list: true - multivalued: true - range: CollectingBiosamplesFromSite - domain: Database + - field_research_site_set + - collecting_biosamples_from_site_set + slot_usage: date_created: description: TODO @@ -196,6 +155,40 @@ classes: metatranscriptome_activity_set: description: TODO + FieldResearchSite: + aliases: + - research plot + description: A site, outside of a laboratory, from which biosamples may be collected. + is_a: Site + # is_a: NamedThing + title: Field Research Site + comments: + - Provides grouping of biosamples at level that's more specific than belonging + to the same study + - be very clear that this could be part of a larger site + - In Bioscales, one might say that rhizosphere soil and bulk soil from around + the same plant were obtained at the same site. In this case, the site would + correspond to one tree. + - "might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833" + + CollectingBiosamplesFromSite: + is_a: PlannedProcess + title: Collecting Biosamples From Site + slots: + - has_inputs + - has_outputs + comments: + - "this illustrates implementing a Biosample relation with a process class" + slot_usage: + has_inputs: + range: Site + # range: NamedThing + required: true + has_outputs: + range: Biosample + required: true + + DataObject: is_a: NamedThing in_subset: @@ -503,6 +496,7 @@ classes: syntax: "{id_nmdc_prefix}:{id_typecode_biosample}-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false + gold_biosample_identifiers: description: Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample comments: This is the ID provided by GOLD that starts with 'GB' @@ -514,6 +508,7 @@ classes: alternative_identifiers: description: Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC required: false + lat_lon: required: false description: This is currently a required field but it's not clear if this @@ -529,6 +524,16 @@ classes: required: false part_of: required: true + + extreme_event: + examples: + - value: 1980-05-18, volcanic eruption + annotations: + expected_value: + tag: expected_value + value: date, string + range: string + id_prefixes: - GOLD exact_mappings: @@ -592,7 +597,7 @@ classes: - study_image slot_usage: id: - description: An NMDC assigned unique identifier for a study submitted to NMDC. + description: An NMDC assigned unique identifier for a sample submitted to NMDC. structured_pattern: syntax: "{id_nmdc_prefix}:{id_typecode_study}-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -1116,6 +1121,16 @@ slots: multivalued: true description: This property links a database object to the set of studies within it. + field_research_site_set: + inlined_as_list: true + multivalued: true + range: FieldResearchSite + domain: Database + collecting_biosamples_from_site_set: + inlined_as_list: true + multivalued: true + range: CollectingBiosamplesFromSite + domain: Database data_object_set: mixins: object_set domain: Database diff --git a/nmdc_schema/prov.py b/nmdc_schema/prov.py index 634dc282e7..10232a9005 100644 --- a/nmdc_schema/prov.py +++ b/nmdc_schema/prov.py @@ -1,5 +1,5 @@ # Auto generated from prov.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:46 +# Generation date: 2022-12-22T13:47:20 # Schema: NMDC-PROV # # id: https://microbiomedata/schema/prov diff --git a/nmdc_schema/sample_prep.py b/nmdc_schema/sample_prep.py index 26f7419dad..88f55268bb 100644 --- a/nmdc_schema/sample_prep.py +++ b/nmdc_schema/sample_prep.py @@ -1,5 +1,5 @@ # Auto generated from sample_prep.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:29 +# Generation date: 2022-12-22T13:47:05 # Schema: sample_prep # # id: https://microbiomedata/schema/sample_prep @@ -465,8 +465,8 @@ class Database(YAMLRoot): read_qc_analysis_activity_set: Optional[Union[Dict[Union[str, ReadQcAnalysisActivityId], Union[dict, "ReadQcAnalysisActivity"]], List[Union[dict, "ReadQcAnalysisActivity"]]]] = empty_dict() read_based_taxonomy_analysis_activity_set: Optional[Union[Dict[Union[str, ReadBasedTaxonomyAnalysisActivityId], Union[dict, "ReadBasedTaxonomyAnalysisActivity"]], List[Union[dict, "ReadBasedTaxonomyAnalysisActivity"]]]] = empty_dict() study_set: Optional[Union[Dict[Union[str, StudyId], Union[dict, "Study"]], List[Union[dict, "Study"]]]] = empty_dict() - frs_set: Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, FieldResearchSite]], List[Union[dict, FieldResearchSite]]]] = empty_dict() - cbfs_set: Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, CollectingBiosamplesFromSite]], List[Union[dict, CollectingBiosamplesFromSite]]]] = empty_dict() + field_research_site_set: Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, "FieldResearchSite"]], List[Union[dict, "FieldResearchSite"]]]] = empty_dict() + collecting_biosamples_from_site_set: Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, "CollectingBiosamplesFromSite"]], List[Union[dict, "CollectingBiosamplesFromSite"]]]] = empty_dict() date_created: Optional[str] = None etl_software_version: Optional[str] = None @@ -521,9 +521,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self._normalize_inlined_as_list(slot_name="study_set", slot_type=Study, key_name="id", keyed=True) - self._normalize_inlined_as_list(slot_name="frs_set", slot_type=FieldResearchSite, key_name="id", keyed=True) + self._normalize_inlined_as_list(slot_name="field_research_site_set", slot_type=FieldResearchSite, key_name="id", keyed=True) - self._normalize_inlined_as_list(slot_name="cbfs_set", slot_type=CollectingBiosamplesFromSite, key_name="id", keyed=True) + self._normalize_inlined_as_list(slot_name="collecting_biosamples_from_site_set", slot_type=CollectingBiosamplesFromSite, key_name="id", keyed=True) if self.date_created is not None and not isinstance(self.date_created, str): self.date_created = str(self.date_created) @@ -1097,7 +1097,7 @@ class Biosample(MaterialEntity): drainage_class: Optional[Union[dict, "TextValue"]] = None elev: Optional[Union[dict, "QuantityValue"]] = None env_package: Optional[Union[dict, "TextValue"]] = None - extreme_event: Optional[Union[dict, "TimestampValue"]] = None + extreme_event: Optional[str] = None fao_class: Optional[Union[dict, "TextValue"]] = None fire: Optional[Union[dict, "TimestampValue"]] = None flooding: Optional[Union[dict, "TimestampValue"]] = None @@ -1443,8 +1443,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.env_package is not None and not isinstance(self.env_package, TextValue): self.env_package = TextValue(**as_dict(self.env_package)) - if self.extreme_event is not None and not isinstance(self.extreme_event, TimestampValue): - self.extreme_event = TimestampValue(**as_dict(self.extreme_event)) + if self.extreme_event is not None and not isinstance(self.extreme_event, str): + self.extreme_event = str(self.extreme_event) if self.fao_class is not None and not isinstance(self.fao_class, TextValue): self.fao_class = TextValue(**as_dict(self.fao_class)) @@ -6127,6 +6127,10 @@ def _addvals(cls): PermissibleValue(text="Low EDTA TE") ) setattr(cls, "MDA reaction buffer", PermissibleValue(text="MDA reaction buffer") ) + setattr(cls, "Gentegra-DNA", + PermissibleValue(text="Gentegra-DNA") ) + setattr(cls, "Gentegra-RNA", + PermissibleValue(text="Gentegra-RNA") ) class DnaseRnaEnum(EnumDefinitionImpl): @@ -6168,6 +6172,10 @@ def _addvals(cls): PermissibleValue(text="Low EDTA TE") ) setattr(cls, "MDA reaction buffer", PermissibleValue(text="MDA reaction buffer") ) + setattr(cls, "Gentegra-DNA", + PermissibleValue(text="Gentegra-DNA") ) + setattr(cls, "Gentegra-RNA", + PermissibleValue(text="Gentegra-RNA") ) class AnalysisTypeEnum(EnumDefinitionImpl): @@ -6357,6 +6365,12 @@ class slots: slots.study_set = Slot(uri=NMDC.study_set, name="study_set", curie=NMDC.curie('study_set'), model_uri=NMDC.study_set, domain=Database, range=Optional[Union[Dict[Union[str, StudyId], Union[dict, "Study"]], List[Union[dict, "Study"]]]]) +slots.field_research_site_set = Slot(uri=NMDC.field_research_site_set, name="field_research_site_set", curie=NMDC.curie('field_research_site_set'), + model_uri=NMDC.field_research_site_set, domain=Database, range=Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, "FieldResearchSite"]], List[Union[dict, "FieldResearchSite"]]]]) + +slots.collecting_biosamples_from_site_set = Slot(uri=NMDC.collecting_biosamples_from_site_set, name="collecting_biosamples_from_site_set", curie=NMDC.curie('collecting_biosamples_from_site_set'), + model_uri=NMDC.collecting_biosamples_from_site_set, domain=Database, range=Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, "CollectingBiosamplesFromSite"]], List[Union[dict, "CollectingBiosamplesFromSite"]]]]) + slots.data_object_set = Slot(uri=NMDC.data_object_set, name="data_object_set", curie=NMDC.curie('data_object_set'), model_uri=NMDC.data_object_set, domain=Database, range=Optional[Union[Dict[Union[str, DataObjectId], Union[dict, "DataObject"]], List[Union[dict, "DataObject"]]]]) @@ -8620,12 +8634,6 @@ class slots: slots.output_read_bases = Slot(uri=NMDC.output_read_bases, name="output_read_bases", curie=NMDC.curie('output_read_bases'), model_uri=NMDC.output_read_bases, domain=None, range=Optional[str]) -slots.database__frs_set = Slot(uri=NMDC.frs_set, name="database__frs_set", curie=NMDC.curie('frs_set'), - model_uri=NMDC.database__frs_set, domain=Database, range=Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, FieldResearchSite]], List[Union[dict, FieldResearchSite]]]]) - -slots.database__cbfs_set = Slot(uri=NMDC.cbfs_set, name="database__cbfs_set", curie=NMDC.curie('cbfs_set'), - model_uri=NMDC.database__cbfs_set, domain=Database, range=Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, CollectingBiosamplesFromSite]], List[Union[dict, CollectingBiosamplesFromSite]]]]) - slots.magBin__bin_name = Slot(uri=NMDC.bin_name, name="magBin__bin_name", curie=NMDC.curie('bin_name'), model_uri=NMDC.magBin__bin_name, domain=None, range=Optional[str]) @@ -8707,12 +8715,6 @@ class slots: slots.ReactionActivity_reaction_time = Slot(uri=NMDC.reaction_time, name="ReactionActivity_reaction_time", curie=NMDC.curie('reaction_time'), model_uri=NMDC.ReactionActivity_reaction_time, domain=ReactionActivity, range=Optional[Union[dict, "QuantityValue"]]) -slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), - model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) - -slots.CollectingBiosamplesFromSite_has_outputs = Slot(uri=NMDC.has_outputs, name="CollectingBiosamplesFromSite_has_outputs", curie=NMDC.curie('has_outputs'), - model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) - slots.Database_date_created = Slot(uri=NMDC.date_created, name="Database_date_created", curie=NMDC.curie('date_created'), model_uri=NMDC.Database_date_created, domain=Database, range=Optional[str]) @@ -8722,6 +8724,12 @@ class slots: slots.Database_metatranscriptome_activity_set = Slot(uri=NMDC.metatranscriptome_activity_set, name="Database_metatranscriptome_activity_set", curie=NMDC.curie('metatranscriptome_activity_set'), model_uri=NMDC.Database_metatranscriptome_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]]) +slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), + model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) + +slots.CollectingBiosamplesFromSite_has_outputs = Slot(uri=NMDC.has_outputs, name="CollectingBiosamplesFromSite_has_outputs", curie=NMDC.curie('has_outputs'), + model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) + slots.DataObject_name = Slot(uri=NMDC.name, name="DataObject_name", curie=NMDC.curie('name'), model_uri=NMDC.DataObject_name, domain=DataObject, range=str) @@ -8757,6 +8765,9 @@ class slots: slots.Biosample_part_of = Slot(uri=DCTERMS.isPartOf, name="Biosample_part_of", curie=DCTERMS.curie('isPartOf'), model_uri=NMDC.Biosample_part_of, domain=Biosample, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) +slots.Biosample_extreme_event = Slot(uri=MIXS['0000320'], name="Biosample_extreme_event", curie=MIXS.curie('0000320'), + model_uri=NMDC.Biosample_extreme_event, domain=Biosample, range=Optional[str]) + slots.Study_id = Slot(uri=NMDC.id, name="Study_id", curie=NMDC.curie('id'), model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId]) diff --git a/nmdc_schema/workflow_execution_activity.py b/nmdc_schema/workflow_execution_activity.py index 29392fe581..0ca0547b61 100644 --- a/nmdc_schema/workflow_execution_activity.py +++ b/nmdc_schema/workflow_execution_activity.py @@ -1,5 +1,5 @@ # Auto generated from workflow_execution_activity.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:25 +# Generation date: 2022-12-22T13:47:01 # Schema: NMDC-Workflow-Execution # # id: https://microbiomedata/schema/workflow_execution_activity diff --git a/poetry.lock b/poetry.lock index 9862688914..6db471dc6c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,3 +1,5 @@ +# This file is automatically @generated by Poetry and should not be changed by hand. + [[package]] name = "alabaster" version = "0.7.12" @@ -5,6 +7,10 @@ description = "A configurable sidebar-enabled Sphinx theme" category = "dev" optional = false python-versions = "*" +files = [ + {file = "alabaster-0.7.12-py2.py3-none-any.whl", hash = "sha256:446438bdcca0e05bd45ea2de1668c1d9b032e1a9154c2c259092d77031ddd359"}, + {file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"}, +] [[package]] name = "antlr4-python3-runtime" @@ -13,6 +19,9 @@ description = "ANTLR 4.9.3 runtime for Python 3.7" category = "dev" optional = false python-versions = "*" +files = [ + {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, +] [[package]] name = "anyio" @@ -21,6 +30,10 @@ description = "High level compatibility layer for multiple asynchronous event lo category = "dev" optional = false python-versions = ">=3.6.2" +files = [ + {file = "anyio-3.6.2-py3-none-any.whl", hash = "sha256:fbbe32bd270d2a2ef3ed1c5d45041250284e31fc0a4df4a5a6071842051a51e3"}, + {file = "anyio-3.6.2.tar.gz", hash = "sha256:25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421"}, +] [package.dependencies] idna = ">=2.8" @@ -38,6 +51,10 @@ description = "Disable App Nap on macOS >= 10.9" category = "dev" optional = false python-versions = "*" +files = [ + {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"}, + {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"}, +] [[package]] name = "argon2-cffi" @@ -46,6 +63,10 @@ description = "The secure Argon2 password hashing algorithm." category = "dev" optional = false python-versions = ">=3.6" +files = [ + {file = "argon2-cffi-21.3.0.tar.gz", hash = "sha256:d384164d944190a7dd7ef22c6aa3ff197da12962bd04b17f64d4e93d934dba5b"}, + {file = "argon2_cffi-21.3.0-py3-none-any.whl", hash = "sha256:8c976986f2c5c0e5000919e6de187906cfd81fb1c72bf9d88c01177e77da7f80"}, +] [package.dependencies] argon2-cffi-bindings = "*" @@ -62,6 +83,29 @@ description = "Low-level CFFI bindings for Argon2" category = "dev" optional = false python-versions = ">=3.6" +files = [ + {file = "argon2-cffi-bindings-21.2.0.tar.gz", hash = "sha256:bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3"}, + {file = "argon2_cffi_bindings-21.2.0-cp36-abi3-macosx_10_9_x86_64.whl", hash = "sha256:ccb949252cb2ab3a08c02024acb77cfb179492d5701c7cbdbfd776124d4d2367"}, + {file = "argon2_cffi_bindings-21.2.0-cp36-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = 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a/python/basic_slots.py +++ b/python/basic_slots.py @@ -1,5 +1,5 @@ # Auto generated from basic_slots.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:27 +# Generation date: 2022-12-22T13:47:03 # Schema: NMDC-Basic-Slots # # id: https://microbiomedata/schema/basic_slots diff --git a/python/bioscales.py b/python/bioscales.py index 4c7737d8ab..0fe7ef5672 100644 --- a/python/bioscales.py +++ b/python/bioscales.py @@ -1,5 +1,5 @@ # Auto generated from bioscales.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:23 +# Generation date: 2022-12-22T13:46:59 # Schema: NMDC-Bioscales # # id: https://microbiomedata/schema/bioscales diff --git a/python/core.py b/python/core.py index d7f6f3606a..8532137de5 100644 --- a/python/core.py +++ b/python/core.py @@ -1,5 +1,5 @@ # Auto generated from core.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:50 +# Generation date: 2022-12-22T13:47:24 # Schema: NMDC-Core # # id: https://microbiomedata/schema/core diff --git a/python/external_identifiers.py b/python/external_identifiers.py index 6244c168ab..891ee5f3a9 100644 --- a/python/external_identifiers.py +++ b/python/external_identifiers.py @@ -1,5 +1,5 @@ # Auto generated from external_identifiers.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:52 +# Generation date: 2022-12-22T13:47:26 # Schema: external_identifiers # # id: https://microbiomedata/schema/external_identifiers diff --git a/python/mixs.py b/python/mixs.py index 28723cf728..66a2bd2633 100644 --- a/python/mixs.py +++ b/python/mixs.py @@ -1,5 +1,5 @@ # Auto generated from mixs.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:43 +# Generation date: 2022-12-22T13:47:18 # Schema: mixs-schema # # id: https://microbiomedata/schema/mixs diff --git a/python/nmdc.py b/python/nmdc.py index 91760f150b..6f80137795 100644 --- a/python/nmdc.py +++ b/python/nmdc.py @@ -1,5 +1,5 @@ # Auto generated from nmdc.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:35 +# Generation date: 2022-12-22T13:47:11 # Schema: NMDC # # id: https://microbiomedata/schema @@ -315,8 +315,8 @@ class Database(YAMLRoot): read_qc_analysis_activity_set: Optional[Union[Dict[Union[str, ReadQcAnalysisActivityId], Union[dict, "ReadQcAnalysisActivity"]], List[Union[dict, "ReadQcAnalysisActivity"]]]] = empty_dict() read_based_taxonomy_analysis_activity_set: Optional[Union[Dict[Union[str, ReadBasedTaxonomyAnalysisActivityId], Union[dict, "ReadBasedTaxonomyAnalysisActivity"]], List[Union[dict, "ReadBasedTaxonomyAnalysisActivity"]]]] = empty_dict() study_set: Optional[Union[Dict[Union[str, StudyId], Union[dict, "Study"]], List[Union[dict, "Study"]]]] = empty_dict() - frs_set: Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, FieldResearchSite]], List[Union[dict, FieldResearchSite]]]] = empty_dict() - cbfs_set: Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, CollectingBiosamplesFromSite]], List[Union[dict, CollectingBiosamplesFromSite]]]] = empty_dict() + field_research_site_set: Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, "FieldResearchSite"]], List[Union[dict, "FieldResearchSite"]]]] = empty_dict() + collecting_biosamples_from_site_set: Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, "CollectingBiosamplesFromSite"]], List[Union[dict, "CollectingBiosamplesFromSite"]]]] = empty_dict() date_created: Optional[str] = None etl_software_version: Optional[str] = None @@ -371,9 +371,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self._normalize_inlined_as_list(slot_name="study_set", slot_type=Study, key_name="id", keyed=True) - self._normalize_inlined_as_list(slot_name="frs_set", slot_type=FieldResearchSite, key_name="id", keyed=True) + self._normalize_inlined_as_list(slot_name="field_research_site_set", slot_type=FieldResearchSite, key_name="id", keyed=True) - self._normalize_inlined_as_list(slot_name="cbfs_set", slot_type=CollectingBiosamplesFromSite, key_name="id", keyed=True) + self._normalize_inlined_as_list(slot_name="collecting_biosamples_from_site_set", slot_type=CollectingBiosamplesFromSite, key_name="id", keyed=True) if self.date_created is not None and not isinstance(self.date_created, str): self.date_created = str(self.date_created) @@ -1043,7 +1043,7 @@ class Biosample(MaterialEntity): drainage_class: Optional[Union[dict, "TextValue"]] = None elev: Optional[Union[dict, "QuantityValue"]] = None env_package: Optional[Union[dict, "TextValue"]] = None - extreme_event: Optional[Union[dict, "TimestampValue"]] = None + extreme_event: Optional[str] = None fao_class: Optional[Union[dict, "TextValue"]] = None fire: Optional[Union[dict, "TimestampValue"]] = None flooding: Optional[Union[dict, "TimestampValue"]] = None @@ -1389,8 +1389,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.env_package is not None and not isinstance(self.env_package, TextValue): self.env_package = TextValue(**as_dict(self.env_package)) - if self.extreme_event is not None and not isinstance(self.extreme_event, TimestampValue): - self.extreme_event = TimestampValue(**as_dict(self.extreme_event)) + if self.extreme_event is not None and not isinstance(self.extreme_event, str): + self.extreme_event = str(self.extreme_event) if self.fao_class is not None and not isinstance(self.fao_class, TextValue): self.fao_class = TextValue(**as_dict(self.fao_class)) @@ -6098,6 +6098,10 @@ def _addvals(cls): PermissibleValue(text="Low EDTA TE") ) setattr(cls, "MDA reaction buffer", PermissibleValue(text="MDA reaction buffer") ) + setattr(cls, "Gentegra-DNA", + PermissibleValue(text="Gentegra-DNA") ) + setattr(cls, "Gentegra-RNA", + PermissibleValue(text="Gentegra-RNA") ) class DnaseRnaEnum(EnumDefinitionImpl): @@ -6139,6 +6143,10 @@ def _addvals(cls): PermissibleValue(text="Low EDTA TE") ) setattr(cls, "MDA reaction buffer", PermissibleValue(text="MDA reaction buffer") ) + setattr(cls, "Gentegra-DNA", + PermissibleValue(text="Gentegra-DNA") ) + setattr(cls, "Gentegra-RNA", + PermissibleValue(text="Gentegra-RNA") ) class AnalysisTypeEnum(EnumDefinitionImpl): @@ -6269,6 +6277,12 @@ class slots: slots.study_set = Slot(uri=NMDC.study_set, name="study_set", curie=NMDC.curie('study_set'), model_uri=NMDC.study_set, domain=Database, range=Optional[Union[Dict[Union[str, StudyId], Union[dict, "Study"]], List[Union[dict, "Study"]]]]) +slots.field_research_site_set = Slot(uri=NMDC.field_research_site_set, name="field_research_site_set", curie=NMDC.curie('field_research_site_set'), + model_uri=NMDC.field_research_site_set, domain=Database, range=Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, "FieldResearchSite"]], List[Union[dict, "FieldResearchSite"]]]]) + +slots.collecting_biosamples_from_site_set = Slot(uri=NMDC.collecting_biosamples_from_site_set, name="collecting_biosamples_from_site_set", curie=NMDC.curie('collecting_biosamples_from_site_set'), + model_uri=NMDC.collecting_biosamples_from_site_set, domain=Database, range=Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, "CollectingBiosamplesFromSite"]], List[Union[dict, "CollectingBiosamplesFromSite"]]]]) + slots.data_object_set = Slot(uri=NMDC.data_object_set, name="data_object_set", curie=NMDC.curie('data_object_set'), model_uri=NMDC.data_object_set, domain=Database, range=Optional[Union[Dict[Union[str, DataObjectId], Union[dict, "DataObject"]], List[Union[dict, "DataObject"]]]]) @@ -8628,12 +8642,6 @@ class slots: slots.output_read_bases = Slot(uri=NMDC.output_read_bases, name="output_read_bases", curie=NMDC.curie('output_read_bases'), model_uri=NMDC.output_read_bases, domain=None, range=Optional[str]) -slots.database__frs_set = Slot(uri=NMDC.frs_set, name="database__frs_set", curie=NMDC.curie('frs_set'), - model_uri=NMDC.database__frs_set, domain=Database, range=Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, FieldResearchSite]], List[Union[dict, FieldResearchSite]]]]) - -slots.database__cbfs_set = Slot(uri=NMDC.cbfs_set, name="database__cbfs_set", curie=NMDC.curie('cbfs_set'), - model_uri=NMDC.database__cbfs_set, domain=Database, range=Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, CollectingBiosamplesFromSite]], List[Union[dict, CollectingBiosamplesFromSite]]]]) - slots.magBin__bin_name = Slot(uri=NMDC.bin_name, name="magBin__bin_name", curie=NMDC.curie('bin_name'), model_uri=NMDC.magBin__bin_name, domain=None, range=Optional[str]) @@ -8685,12 +8693,6 @@ class slots: slots.magBin__gtdbtk_species = Slot(uri=NMDC.gtdbtk_species, name="magBin__gtdbtk_species", curie=NMDC.curie('gtdbtk_species'), model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) -slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), - model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) - -slots.CollectingBiosamplesFromSite_has_outputs = Slot(uri=NMDC.has_outputs, name="CollectingBiosamplesFromSite_has_outputs", curie=NMDC.curie('has_outputs'), - model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) - slots.Database_date_created = Slot(uri=NMDC.date_created, name="Database_date_created", curie=NMDC.curie('date_created'), model_uri=NMDC.Database_date_created, domain=Database, range=Optional[str]) @@ -8700,6 +8702,12 @@ class slots: slots.Database_metatranscriptome_activity_set = Slot(uri=NMDC.metatranscriptome_activity_set, name="Database_metatranscriptome_activity_set", curie=NMDC.curie('metatranscriptome_activity_set'), model_uri=NMDC.Database_metatranscriptome_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]]) +slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), + model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) + +slots.CollectingBiosamplesFromSite_has_outputs = Slot(uri=NMDC.has_outputs, name="CollectingBiosamplesFromSite_has_outputs", curie=NMDC.curie('has_outputs'), + model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) + slots.DataObject_name = Slot(uri=NMDC.name, name="DataObject_name", curie=NMDC.curie('name'), model_uri=NMDC.DataObject_name, domain=DataObject, range=str) @@ -8735,6 +8743,9 @@ class slots: slots.Biosample_part_of = Slot(uri=DCTERMS.isPartOf, name="Biosample_part_of", curie=DCTERMS.curie('isPartOf'), model_uri=NMDC.Biosample_part_of, domain=Biosample, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) +slots.Biosample_extreme_event = Slot(uri=MIXS['0000320'], name="Biosample_extreme_event", curie=MIXS.curie('0000320'), + model_uri=NMDC.Biosample_extreme_event, domain=Biosample, range=Optional[str]) + slots.Study_id = Slot(uri=NMDC.id, name="Study_id", curie=NMDC.curie('id'), model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId]) diff --git a/python/portal/emsl.py b/python/portal/emsl.py index 643771f14e..e11ba5ed86 100644 --- a/python/portal/emsl.py +++ b/python/portal/emsl.py @@ -1,5 +1,5 @@ # Auto generated from emsl.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:59 +# Generation date: 2022-12-22T13:47:32 # Schema: emsl # # id: https://microbiomedata/schema/emsl diff --git a/python/portal/jgi_metagenomics.py b/python/portal/jgi_metagenomics.py index d8759baf13..60ad0bbc33 100644 --- a/python/portal/jgi_metagenomics.py +++ b/python/portal/jgi_metagenomics.py @@ -1,5 +1,5 @@ # Auto generated from jgi_metagenomics.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:02:01 +# Generation date: 2022-12-22T13:47:34 # Schema: jgi_metagenomics # # id: https://microbiomedata/schema/jgi_metagenomics @@ -85,6 +85,10 @@ def _addvals(cls): PermissibleValue(text="Low EDTA TE") ) setattr(cls, "MDA reaction buffer", PermissibleValue(text="MDA reaction buffer") ) + setattr(cls, "Gentegra-DNA", + PermissibleValue(text="Gentegra-DNA") ) + setattr(cls, "Gentegra-RNA", + PermissibleValue(text="Gentegra-RNA") ) # Slots class slots: diff --git a/python/portal/jgi_metatranscriptomics.py b/python/portal/jgi_metatranscriptomics.py index f00ced52cc..9962947cc3 100644 --- a/python/portal/jgi_metatranscriptomics.py +++ b/python/portal/jgi_metatranscriptomics.py @@ -1,5 +1,5 @@ # Auto generated from jgi_metatranscriptomics.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:54 +# Generation date: 2022-12-22T13:47:28 # Schema: jgi_metatranscriptomics # # id: https://microbiomedata/schema/jgi_metatranscriptomics @@ -85,6 +85,10 @@ def _addvals(cls): PermissibleValue(text="Low EDTA TE") ) setattr(cls, "MDA reaction buffer", PermissibleValue(text="MDA reaction buffer") ) + setattr(cls, "Gentegra-DNA", + PermissibleValue(text="Gentegra-DNA") ) + setattr(cls, "Gentegra-RNA", + PermissibleValue(text="Gentegra-RNA") ) # Slots class slots: diff --git a/python/portal/mixs_inspired.py b/python/portal/mixs_inspired.py index 6bbf21666b..908400f411 100644 --- a/python/portal/mixs_inspired.py +++ b/python/portal/mixs_inspired.py @@ -1,5 +1,5 @@ # Auto generated from mixs_inspired.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:56 +# Generation date: 2022-12-22T13:47:29 # Schema: mixs_inspired # # id: https://microbiomedata/schema/mixs_inspired diff --git a/python/portal/sample_id.py b/python/portal/sample_id.py index 51679807d8..939978fe80 100644 --- a/python/portal/sample_id.py +++ b/python/portal/sample_id.py @@ -1,5 +1,5 @@ # Auto generated from sample_id.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:57 +# Generation date: 2022-12-22T13:47:31 # Schema: sample_id # # id: https://microbiomedata/schema/sample_id diff --git a/python/prov.py b/python/prov.py index 634dc282e7..10232a9005 100644 --- a/python/prov.py +++ b/python/prov.py @@ -1,5 +1,5 @@ # Auto generated from prov.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:46 +# Generation date: 2022-12-22T13:47:20 # Schema: NMDC-PROV # # id: https://microbiomedata/schema/prov diff --git a/python/sample_prep.py b/python/sample_prep.py index 26f7419dad..88f55268bb 100644 --- a/python/sample_prep.py +++ b/python/sample_prep.py @@ -1,5 +1,5 @@ # Auto generated from sample_prep.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:29 +# Generation date: 2022-12-22T13:47:05 # Schema: sample_prep # # id: https://microbiomedata/schema/sample_prep @@ -465,8 +465,8 @@ class Database(YAMLRoot): read_qc_analysis_activity_set: Optional[Union[Dict[Union[str, ReadQcAnalysisActivityId], Union[dict, "ReadQcAnalysisActivity"]], List[Union[dict, "ReadQcAnalysisActivity"]]]] = empty_dict() read_based_taxonomy_analysis_activity_set: Optional[Union[Dict[Union[str, ReadBasedTaxonomyAnalysisActivityId], Union[dict, "ReadBasedTaxonomyAnalysisActivity"]], List[Union[dict, "ReadBasedTaxonomyAnalysisActivity"]]]] = empty_dict() study_set: Optional[Union[Dict[Union[str, StudyId], Union[dict, "Study"]], List[Union[dict, "Study"]]]] = empty_dict() - frs_set: Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, FieldResearchSite]], List[Union[dict, FieldResearchSite]]]] = empty_dict() - cbfs_set: Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, CollectingBiosamplesFromSite]], List[Union[dict, CollectingBiosamplesFromSite]]]] = empty_dict() + field_research_site_set: Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, "FieldResearchSite"]], List[Union[dict, "FieldResearchSite"]]]] = empty_dict() + collecting_biosamples_from_site_set: Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, "CollectingBiosamplesFromSite"]], List[Union[dict, "CollectingBiosamplesFromSite"]]]] = empty_dict() date_created: Optional[str] = None etl_software_version: Optional[str] = None @@ -521,9 +521,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self._normalize_inlined_as_list(slot_name="study_set", slot_type=Study, key_name="id", keyed=True) - self._normalize_inlined_as_list(slot_name="frs_set", slot_type=FieldResearchSite, key_name="id", keyed=True) + self._normalize_inlined_as_list(slot_name="field_research_site_set", slot_type=FieldResearchSite, key_name="id", keyed=True) - self._normalize_inlined_as_list(slot_name="cbfs_set", slot_type=CollectingBiosamplesFromSite, key_name="id", keyed=True) + self._normalize_inlined_as_list(slot_name="collecting_biosamples_from_site_set", slot_type=CollectingBiosamplesFromSite, key_name="id", keyed=True) if self.date_created is not None and not isinstance(self.date_created, str): self.date_created = str(self.date_created) @@ -1097,7 +1097,7 @@ class Biosample(MaterialEntity): drainage_class: Optional[Union[dict, "TextValue"]] = None elev: Optional[Union[dict, "QuantityValue"]] = None env_package: Optional[Union[dict, "TextValue"]] = None - extreme_event: Optional[Union[dict, "TimestampValue"]] = None + extreme_event: Optional[str] = None fao_class: Optional[Union[dict, "TextValue"]] = None fire: Optional[Union[dict, "TimestampValue"]] = None flooding: Optional[Union[dict, "TimestampValue"]] = None @@ -1443,8 +1443,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.env_package is not None and not isinstance(self.env_package, TextValue): self.env_package = TextValue(**as_dict(self.env_package)) - if self.extreme_event is not None and not isinstance(self.extreme_event, TimestampValue): - self.extreme_event = TimestampValue(**as_dict(self.extreme_event)) + if self.extreme_event is not None and not isinstance(self.extreme_event, str): + self.extreme_event = str(self.extreme_event) if self.fao_class is not None and not isinstance(self.fao_class, TextValue): self.fao_class = TextValue(**as_dict(self.fao_class)) @@ -6127,6 +6127,10 @@ def _addvals(cls): PermissibleValue(text="Low EDTA TE") ) setattr(cls, "MDA reaction buffer", PermissibleValue(text="MDA reaction buffer") ) + setattr(cls, "Gentegra-DNA", + PermissibleValue(text="Gentegra-DNA") ) + setattr(cls, "Gentegra-RNA", + PermissibleValue(text="Gentegra-RNA") ) class DnaseRnaEnum(EnumDefinitionImpl): @@ -6168,6 +6172,10 @@ def _addvals(cls): PermissibleValue(text="Low EDTA TE") ) setattr(cls, "MDA reaction buffer", PermissibleValue(text="MDA reaction buffer") ) + setattr(cls, "Gentegra-DNA", + PermissibleValue(text="Gentegra-DNA") ) + setattr(cls, "Gentegra-RNA", + PermissibleValue(text="Gentegra-RNA") ) class AnalysisTypeEnum(EnumDefinitionImpl): @@ -6357,6 +6365,12 @@ class slots: slots.study_set = Slot(uri=NMDC.study_set, name="study_set", curie=NMDC.curie('study_set'), model_uri=NMDC.study_set, domain=Database, range=Optional[Union[Dict[Union[str, StudyId], Union[dict, "Study"]], List[Union[dict, "Study"]]]]) +slots.field_research_site_set = Slot(uri=NMDC.field_research_site_set, name="field_research_site_set", curie=NMDC.curie('field_research_site_set'), + model_uri=NMDC.field_research_site_set, domain=Database, range=Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, "FieldResearchSite"]], List[Union[dict, "FieldResearchSite"]]]]) + +slots.collecting_biosamples_from_site_set = Slot(uri=NMDC.collecting_biosamples_from_site_set, name="collecting_biosamples_from_site_set", curie=NMDC.curie('collecting_biosamples_from_site_set'), + model_uri=NMDC.collecting_biosamples_from_site_set, domain=Database, range=Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, "CollectingBiosamplesFromSite"]], List[Union[dict, "CollectingBiosamplesFromSite"]]]]) + slots.data_object_set = Slot(uri=NMDC.data_object_set, name="data_object_set", curie=NMDC.curie('data_object_set'), model_uri=NMDC.data_object_set, domain=Database, range=Optional[Union[Dict[Union[str, DataObjectId], Union[dict, "DataObject"]], List[Union[dict, "DataObject"]]]]) @@ -8620,12 +8634,6 @@ class slots: slots.output_read_bases = Slot(uri=NMDC.output_read_bases, name="output_read_bases", curie=NMDC.curie('output_read_bases'), model_uri=NMDC.output_read_bases, domain=None, range=Optional[str]) -slots.database__frs_set = Slot(uri=NMDC.frs_set, name="database__frs_set", curie=NMDC.curie('frs_set'), - model_uri=NMDC.database__frs_set, domain=Database, range=Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, FieldResearchSite]], List[Union[dict, FieldResearchSite]]]]) - -slots.database__cbfs_set = Slot(uri=NMDC.cbfs_set, name="database__cbfs_set", curie=NMDC.curie('cbfs_set'), - model_uri=NMDC.database__cbfs_set, domain=Database, range=Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, CollectingBiosamplesFromSite]], List[Union[dict, CollectingBiosamplesFromSite]]]]) - slots.magBin__bin_name = Slot(uri=NMDC.bin_name, name="magBin__bin_name", curie=NMDC.curie('bin_name'), model_uri=NMDC.magBin__bin_name, domain=None, range=Optional[str]) @@ -8707,12 +8715,6 @@ class slots: slots.ReactionActivity_reaction_time = Slot(uri=NMDC.reaction_time, name="ReactionActivity_reaction_time", curie=NMDC.curie('reaction_time'), model_uri=NMDC.ReactionActivity_reaction_time, domain=ReactionActivity, range=Optional[Union[dict, "QuantityValue"]]) -slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), - model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) - -slots.CollectingBiosamplesFromSite_has_outputs = Slot(uri=NMDC.has_outputs, name="CollectingBiosamplesFromSite_has_outputs", curie=NMDC.curie('has_outputs'), - model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) - slots.Database_date_created = Slot(uri=NMDC.date_created, name="Database_date_created", curie=NMDC.curie('date_created'), model_uri=NMDC.Database_date_created, domain=Database, range=Optional[str]) @@ -8722,6 +8724,12 @@ class slots: slots.Database_metatranscriptome_activity_set = Slot(uri=NMDC.metatranscriptome_activity_set, name="Database_metatranscriptome_activity_set", curie=NMDC.curie('metatranscriptome_activity_set'), model_uri=NMDC.Database_metatranscriptome_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]]) +slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), + model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) + +slots.CollectingBiosamplesFromSite_has_outputs = Slot(uri=NMDC.has_outputs, name="CollectingBiosamplesFromSite_has_outputs", curie=NMDC.curie('has_outputs'), + model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) + slots.DataObject_name = Slot(uri=NMDC.name, name="DataObject_name", curie=NMDC.curie('name'), model_uri=NMDC.DataObject_name, domain=DataObject, range=str) @@ -8757,6 +8765,9 @@ class slots: slots.Biosample_part_of = Slot(uri=DCTERMS.isPartOf, name="Biosample_part_of", curie=DCTERMS.curie('isPartOf'), model_uri=NMDC.Biosample_part_of, domain=Biosample, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) +slots.Biosample_extreme_event = Slot(uri=MIXS['0000320'], name="Biosample_extreme_event", curie=MIXS.curie('0000320'), + model_uri=NMDC.Biosample_extreme_event, domain=Biosample, range=Optional[str]) + slots.Study_id = Slot(uri=NMDC.id, name="Study_id", curie=NMDC.curie('id'), model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId]) diff --git a/python/workflow_execution_activity.py b/python/workflow_execution_activity.py index 29392fe581..0ca0547b61 100644 --- a/python/workflow_execution_activity.py +++ b/python/workflow_execution_activity.py @@ -1,5 +1,5 @@ # Auto generated from workflow_execution_activity.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-14T15:01:25 +# Generation date: 2022-12-22T13:47:01 # Schema: NMDC-Workflow-Execution # # id: https://microbiomedata/schema/workflow_execution_activity From 77a5b98191a481bba9e0e56428eccbddc3cf0791 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 22 Dec 2022 14:05:51 -0500 Subject: [PATCH 11/60] redo of #494 and #576 --- src/schema/nmdc.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 78e956aed0..f1f688b9b6 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -597,7 +597,7 @@ classes: - study_image slot_usage: id: - description: An NMDC assigned unique identifier for a sample submitted to NMDC. + description: An NMDC assigned unique identifier for a study submitted to NMDC. structured_pattern: syntax: "{id_nmdc_prefix}:{id_typecode_study}-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true From 92425e23be78075f0b542a33fd12ab1a46b15db5 Mon Sep 17 00:00:00 2001 From: Montana Date: Fri, 23 Dec 2022 14:42:51 -0800 Subject: [PATCH 12/60] added empty well clarification --- src/schema/portal/jgi_metagenomics.yaml | 2 +- src/schema/portal/jgi_metatranscriptomics.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/schema/portal/jgi_metagenomics.yaml b/src/schema/portal/jgi_metagenomics.yaml index 12d537db63..1149cc196d 100644 --- a/src/schema/portal/jgi_metagenomics.yaml +++ b/src/schema/portal/jgi_metagenomics.yaml @@ -129,7 +129,7 @@ slots: name: dna_cont_well title: DNA well number comments: - - Required when 'plate' is selected for container type. Corner wells must be blank. + - Required when 'plate' is selected for container type. Corner wells must be blank/empty (A1, A12, H1, H12). For partial plates, fill by columns. Leave blank if the sample will be shipped in a tube. examples: diff --git a/src/schema/portal/jgi_metatranscriptomics.yaml b/src/schema/portal/jgi_metatranscriptomics.yaml index 30415bc965..ca129406e0 100644 --- a/src/schema/portal/jgi_metatranscriptomics.yaml +++ b/src/schema/portal/jgi_metatranscriptomics.yaml @@ -155,7 +155,7 @@ slots: name: rna_cont_well title: RNA well number comments: - - Required when 'plate' is selected for container type. Corner wells must be blank. + - Required when 'plate' is selected for container type. Corner wells must be blank/empty (A1, A12, H1, H12). For partial plates, fill by columns. Leave blank if the sample will be shipped in a tube. examples: From 8f52f989c7f136945bfba5202868fc10c67a08dd Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Tue, 3 Jan 2023 14:52:08 -0500 Subject: [PATCH 13/60] added plate pos patterns plus title and comments refactor --- src/schema/portal/jgi_metagenomics.yaml | 10 ++++++---- src/schema/portal/jgi_metatranscriptomics.yaml | 10 ++++++---- 2 files changed, 12 insertions(+), 8 deletions(-) diff --git a/src/schema/portal/jgi_metagenomics.yaml b/src/schema/portal/jgi_metagenomics.yaml index 1149cc196d..d51db55249 100644 --- a/src/schema/portal/jgi_metagenomics.yaml +++ b/src/schema/portal/jgi_metagenomics.yaml @@ -127,11 +127,12 @@ slots: recommended: true dna_cont_well: name: dna_cont_well - title: DNA well number + title: DNA plate position comments: - - Required when 'plate' is selected for container type. Corner wells must be blank/empty (A1, A12, H1, H12). - For partial plates, fill by columns. Leave blank if the sample will be shipped - in a tube. + - Required when 'plate' is selected for container type. + - Leave blank if the sample will be shipped in a tube. + - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation. + - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8). examples: - value: B2 from_schema: https://example.com/nmdc_dh @@ -140,6 +141,7 @@ slots: slot_group: JGI-Metagenomics required: false recommended: true + pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$ dna_container_id: name: dna_container_id title: DNA container label diff --git a/src/schema/portal/jgi_metatranscriptomics.yaml b/src/schema/portal/jgi_metatranscriptomics.yaml index ca129406e0..924168cba6 100644 --- a/src/schema/portal/jgi_metatranscriptomics.yaml +++ b/src/schema/portal/jgi_metatranscriptomics.yaml @@ -153,11 +153,12 @@ slots: recommended: true rna_cont_well: name: rna_cont_well - title: RNA well number + title: RNA plate position comments: - - Required when 'plate' is selected for container type. Corner wells must be blank/empty (A1, A12, H1, H12). - For partial plates, fill by columns. Leave blank if the sample will be shipped - in a tube. + - Required when 'plate' is selected for container type. + - Leave blank if the sample will be shipped in a tube. + - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation. + - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8). examples: - value: B2 from_schema: https://example.com/nmdc_dh @@ -166,6 +167,7 @@ slots: slot_group: JGI-Metatranscriptomics required: false recommended: true + pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$ rna_container_id: name: rna_container_id title: RNA container label From 9c4bb33d1f8fbf9cea86114202245fd4f5c1599f Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Wed, 11 Jan 2023 07:19:15 -0500 Subject: [PATCH 14/60] strucutred_patterns and typecodes for #591 --- src/schema/nmdc.yaml | 20 ++++++++++++++++++++ src/schema/prov.yaml | 9 +++++++++ 2 files changed, 29 insertions(+) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index f1f688b9b6..8a63d9c3a4 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -104,6 +104,10 @@ settings: id_typecode_study: "sty" id_typecode_biosample_processing: "bsmprc" id_typecode_omics_processing: "omprc" + id_typecode_dataobject: "dobj" + id_typecode_activity: "acty" + + subsets: sample subset: @@ -208,6 +212,14 @@ classes: required: true description: required: true + id: + pattern: '^nmdc:' + structured_pattern: + todos: + - remove the static pattern once the minter can generate ids that satisfy this structured_pattern + syntax: "{id_nmdc_prefix}:{id_typecode_dataobject}-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false id_prefixes: - GOLD @@ -493,6 +505,8 @@ classes: required: true pattern: '^nmdc:' structured_pattern: + todos: + - remove the static pattern once the minter can generate ids that satisfy this structured_pattern syntax: "{id_nmdc_prefix}:{id_typecode_biosample}-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false @@ -599,6 +613,8 @@ classes: id: description: An NMDC assigned unique identifier for a study submitted to NMDC. structured_pattern: + todos: + - remove any static pattern once the minter can generate ids that satisfy this structured_pattern syntax: "{id_nmdc_prefix}:{id_typecode_study}-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false @@ -697,6 +713,8 @@ classes: slot_usage: id: structured_pattern: + todos: + - remove any static pattern once the minter can generate ids that satisfy this structured_pattern syntax: "{id_nmdc_prefix}:{id_typecode_biosample_processing}-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false @@ -747,6 +765,8 @@ classes: slot_usage: id: structured_pattern: + todos: + - remove any static pattern once the minter can generate ids that satisfy this structured_pattern syntax: "{id_nmdc_prefix}:{id_typecode_omics_processing}-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false diff --git a/src/schema/prov.yaml b/src/schema/prov.yaml index 771cd64492..1080b149f4 100644 --- a/src/schema/prov.yaml +++ b/src/schema/prov.yaml @@ -36,6 +36,15 @@ classes: - used mappings: - prov:Activity + slot_usage: + id: + pattern: '^nmdc:' + structured_pattern: + todos: + - remove the static pattern once the minter can generate ids that satisfy this structured_pattern + syntax: "{id_nmdc_prefix}:{id_typecode_activity}-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false Agent: description: "a provence-generating agent" From b6057052c1a3fb949d384adff31e897a3c9479d7 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Wed, 11 Jan 2023 07:28:01 -0500 Subject: [PATCH 15/60] nmdc prefixes for test dobjs --- test/data/nmdc_example_database.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/data/nmdc_example_database.json b/test/data/nmdc_example_database.json index 02d5d1041a..15a71fdf1f 100644 --- a/test/data/nmdc_example_database.json +++ b/test/data/nmdc_example_database.json @@ -287,21 +287,21 @@ ], "data_object_set": [ { - "id": "jgi:58b653757ded5e7a2af951c4", + "id": "nmdc:161afbd2-0d43-48ba-bc96-47697de83fbb", "name": "11340.8.202049.GTCTCCT-AAGGAGA.fastq.gz", "description": "Raw sequencer read data", "file_size_bytes": 9208349052.0, "type": "nmdc:DataObject" }, { - "id": "jgi:599c3a117ded5e41edd7da77", + "id": "nmdc:80224019-2607-4610-8981-11ba7ef871fc", "name": "11839.4.222578.GAGCTCA-TTGAGCT.fastq.gz", "description": "Raw sequencer read data", "file_size_bytes": 34243309819.0, "type": "nmdc:DataObject" }, { - "id": "jgi:5baa816646d1e63f764deb37", + "id": "nmdc:5fd558d1-38d3-4f70-8fca-023fff2a035e", "name": "12660.4.274923.GATCGTAC-GTACGATC.fastq.gz", "description": "Raw sequencer read data", "file_size_bytes": 7580035314.0, From 337c1b0411ddad7af85f1c72204587968b3dea04 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 12 Jan 2023 09:47:09 -0500 Subject: [PATCH 16/60] just added typcode table md file --- src/docs/typecode_table.md | 75 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 src/docs/typecode_table.md diff --git a/src/docs/typecode_table.md b/src/docs/typecode_table.md new file mode 100644 index 0000000000..bff0f3697e --- /dev/null +++ b/src/docs/typecode_table.md @@ -0,0 +1,75 @@ +# Typecodes per class + +Last generated 2023-01-12 + +If a Class doesn't use the `id` slot, then there is no need to assign that class a typecode + +Typecodes can be directly asserted for a class, or a class can inherit a typecode from one of it's ancestors. This table doe not yet indicate when a typecode was inherited from an ancestor. An example of inheritance is 'acty' for `WorkflowExecutionActivity`, which is inherited from it's ancestor `Activity` + + + +| class | uses_id | from_ancestor | typecode | +|-------------------------------------|---------|-------------------------------------|----------| +| Activity | True | Activity | acty | +| Agent | False | | | +| AnalyticalSample | True | AnalyticalSample | | +| AttributeValue | False | | | +| Biosample | True | Biosample | bsm | +| BiosampleProcessing | True | BiosampleProcessing | bsmprc | +| BooleanValue | False | | | +| ChemicalEntity | True | ChemicalEntity | | +| CollectingBiosamplesFromSite | True | CollectingBiosamplesFromSite | | +| ControlledIdentifiedTermValue | False | | | +| ControlledTermValue | False | | | +| CreditAssociation | False | | | +| DataObject | True | DataObject | dobj | +| Database | False | | | +| DissolvingActivity | False | | | +| EnvironmentalMaterialTerm | True | EnvironmentalMaterialTerm | | +| FieldResearchSite | True | FieldResearchSite | | +| FunctionalAnnotation | False | | | +| FunctionalAnnotationTerm | True | FunctionalAnnotationTerm | | +| GeneProduct | True | GeneProduct | | +| GenomeFeature | False | | | +| GeolocationValue | False | | | +| ImageValue | False | | | +| Instrument | True | Instrument | | +| IntegerValue | False | | | +| LabDevice | False | | | +| MagBin | False | | | +| MagsAnalysisActivity | True | MagsAnalysisActivity | acty | +| MaterialContainer | False | | | +| MaterialEntity | True | MaterialEntity | | +| MaterialSample | True | MaterialSample | | +| MaterialSamplingActivity | False | | | +| MetaboliteQuantification | False | | | +| MetabolomicsAnalysisActivity | True | MetabolomicsAnalysisActivity | acty | +| MetagenomeAnnotationActivity | True | MetagenomeAnnotationActivity | acty | +| MetagenomeAssembly | True | MetagenomeAssembly | acty | +| MetaproteomicsAnalysisActivity | True | MetaproteomicsAnalysisActivity | acty | +| MetatranscriptomeActivity | True | MetatranscriptomeActivity | acty | +| MetatranscriptomeAnnotationActivity | True | MetatranscriptomeAnnotationActivity | acty | +| MetatranscriptomeAssembly | True | MetatranscriptomeAssembly | acty | +| NamedThing | True | NamedThing | | +| NomAnalysisActivity | True | NomAnalysisActivity | acty | +| OmicsProcessing | True | OmicsProcessing | omprc | +| OntologyClass | True | OntologyClass | | +| OrthologyGroup | True | OrthologyGroup | | +| Pathway | True | Pathway | | +| PeptideQuantification | False | | | +| Person | True | Person | | +| PersonValue | False | | | +| PlannedProcess | True | PlannedProcess | | +| ProteinQuantification | False | | | +| QuantityValue | False | | | +| Reaction | True | Reaction | | +| ReactionActivity | False | | | +| ReactionParticipant | False | | | +| ReadBasedTaxonomyAnalysisActivity | True | ReadBasedTaxonomyAnalysisActivity | acty | +| ReadQcAnalysisActivity | True | ReadQcAnalysisActivity | acty | +| Site | True | Site | | +| Study | True | Study | sty | +| TextValue | False | | | +| TimestampValue | False | | | +| UrlValue | False | | | +| WorkflowExecutionActivity | True | WorkflowExecutionActivity | acty | \ No newline at end of file From d0864af5565c3501db05defa305c509735df0b2b Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 12 Jan 2023 09:57:55 -0500 Subject: [PATCH 17/60] resort typecode table; add to mkdocs.yml --- mkdocs.yml | 3 +- src/docs/typecode_table.md | 132 ++++++++++++++++++------------------- 2 files changed, 67 insertions(+), 68 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index c3c813d7b9..f50cc09094 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -12,8 +12,9 @@ site_dir: mkdocs_html nav: - Home: home.md - NMDC Schema: index.md - - NMDC Metadata Standards Documentation: Metadata_Documentation_Overview.md + - NMDC Metadata Standards Documentation: Metadata_Documentation_Overview.md - NMDC Schema Validation: schema-validation.md - Identifiers in NMDC: identifiers.md - MIxS Soil Package: NMDC_MIxS_Soil_documentation.md + - Typecodes for Classes: typecode_table.md - Credits: credits.md diff --git a/src/docs/typecode_table.md b/src/docs/typecode_table.md index bff0f3697e..050ee7587e 100644 --- a/src/docs/typecode_table.md +++ b/src/docs/typecode_table.md @@ -6,70 +6,68 @@ If a Class doesn't use the `id` slot, then there is no need to assign that class Typecodes can be directly asserted for a class, or a class can inherit a typecode from one of it's ancestors. This table doe not yet indicate when a typecode was inherited from an ancestor. An example of inheritance is 'acty' for `WorkflowExecutionActivity`, which is inherited from it's ancestor `Activity` - - -| class | uses_id | from_ancestor | typecode | -|-------------------------------------|---------|-------------------------------------|----------| -| Activity | True | Activity | acty | -| Agent | False | | | -| AnalyticalSample | True | AnalyticalSample | | -| AttributeValue | False | | | -| Biosample | True | Biosample | bsm | -| BiosampleProcessing | True | BiosampleProcessing | bsmprc | -| BooleanValue | False | | | -| ChemicalEntity | True | ChemicalEntity | | -| CollectingBiosamplesFromSite | True | CollectingBiosamplesFromSite | | -| ControlledIdentifiedTermValue | False | | | -| ControlledTermValue | False | | | -| CreditAssociation | False | | | -| DataObject | True | DataObject | dobj | -| Database | False | | | -| DissolvingActivity | False | | | -| EnvironmentalMaterialTerm | True | EnvironmentalMaterialTerm | | -| FieldResearchSite | True | FieldResearchSite | | -| FunctionalAnnotation | False | | | -| FunctionalAnnotationTerm | True | FunctionalAnnotationTerm | | -| GeneProduct | True | GeneProduct | | -| GenomeFeature | False | | | -| GeolocationValue | False | | | -| ImageValue | False | | | -| Instrument | True | Instrument | | -| IntegerValue | False | | | -| LabDevice | False | | | -| MagBin | False | | | -| MagsAnalysisActivity | True | MagsAnalysisActivity | acty | -| MaterialContainer | False | | | -| MaterialEntity | True | MaterialEntity | | -| MaterialSample | True | MaterialSample | | -| MaterialSamplingActivity | False | | | -| MetaboliteQuantification | False | | | -| MetabolomicsAnalysisActivity | True | MetabolomicsAnalysisActivity | acty | -| MetagenomeAnnotationActivity | True | MetagenomeAnnotationActivity | acty | -| MetagenomeAssembly | True | MetagenomeAssembly | acty | -| MetaproteomicsAnalysisActivity | True | MetaproteomicsAnalysisActivity | acty | -| MetatranscriptomeActivity | True | MetatranscriptomeActivity | acty | -| MetatranscriptomeAnnotationActivity | True | MetatranscriptomeAnnotationActivity | acty | -| MetatranscriptomeAssembly | True | MetatranscriptomeAssembly | acty | -| NamedThing | True | NamedThing | | -| NomAnalysisActivity | True | NomAnalysisActivity | acty | -| OmicsProcessing | True | OmicsProcessing | omprc | -| OntologyClass | True | OntologyClass | | -| OrthologyGroup | True | OrthologyGroup | | -| Pathway | True | Pathway | | -| PeptideQuantification | False | | | -| Person | True | Person | | -| PersonValue | False | | | -| PlannedProcess | True | PlannedProcess | | -| ProteinQuantification | False | | | -| QuantityValue | False | | | -| Reaction | True | Reaction | | -| ReactionActivity | False | | | -| ReactionParticipant | False | | | -| ReadBasedTaxonomyAnalysisActivity | True | ReadBasedTaxonomyAnalysisActivity | acty | -| ReadQcAnalysisActivity | True | ReadQcAnalysisActivity | acty | -| Site | True | Site | | -| Study | True | Study | sty | -| TextValue | False | | | -| TimestampValue | False | | | -| UrlValue | False | | | -| WorkflowExecutionActivity | True | WorkflowExecutionActivity | acty | \ No newline at end of file +| class | uses_id | typecode | +|-------------------------------------|---------|----------| +| Activity | TRUE | acty | +| AnalyticalSample | TRUE | | +| Biosample | TRUE | bsm | +| BiosampleProcessing | TRUE | bsmprc | +| ChemicalEntity | TRUE | | +| CollectingBiosamplesFromSite | TRUE | | +| DataObject | TRUE | dobj | +| EnvironmentalMaterialTerm | TRUE | | +| FieldResearchSite | TRUE | | +| FunctionalAnnotationTerm | TRUE | | +| GeneProduct | TRUE | | +| Instrument | TRUE | | +| MagsAnalysisActivity | TRUE | acty | +| MaterialEntity | TRUE | | +| MaterialSample | TRUE | | +| MetabolomicsAnalysisActivity | TRUE | acty | +| MetagenomeAnnotationActivity | TRUE | acty | +| MetagenomeAssembly | TRUE | acty | +| MetaproteomicsAnalysisActivity | TRUE | acty | +| MetatranscriptomeActivity | TRUE | acty | +| MetatranscriptomeAnnotationActivity | TRUE | acty | +| MetatranscriptomeAssembly | TRUE | acty | +| NamedThing | TRUE | | +| NomAnalysisActivity | TRUE | acty | +| OmicsProcessing | TRUE | omprc | +| OntologyClass | TRUE | | +| OrthologyGroup | TRUE | | +| Pathway | TRUE | | +| Person | TRUE | | +| PlannedProcess | TRUE | | +| Reaction | TRUE | | +| ReadBasedTaxonomyAnalysisActivity | TRUE | acty | +| ReadQcAnalysisActivity | TRUE | acty | +| Site | TRUE | | +| Study | TRUE | sty | +| WorkflowExecutionActivity | TRUE | acty | +| Agent | FALSE | | +| AttributeValue | FALSE | | +| BooleanValue | FALSE | | +| ControlledIdentifiedTermValue | FALSE | | +| ControlledTermValue | FALSE | | +| CreditAssociation | FALSE | | +| Database | FALSE | | +| DissolvingActivity | FALSE | | +| FunctionalAnnotation | FALSE | | +| GenomeFeature | FALSE | | +| GeolocationValue | FALSE | | +| ImageValue | FALSE | | +| IntegerValue | FALSE | | +| LabDevice | FALSE | | +| MagBin | FALSE | | +| MaterialContainer | FALSE | | +| MaterialSamplingActivity | FALSE | | +| MetaboliteQuantification | FALSE | | +| PeptideQuantification | FALSE | | +| PersonValue | FALSE | | +| ProteinQuantification | FALSE | | +| QuantityValue | FALSE | | +| ReactionActivity | FALSE | | +| ReactionParticipant | FALSE | | +| TextValue | FALSE | | +| TimestampValue | FALSE | | +| UrlValue | FALSE | | \ No newline at end of file From c62cc0b67e835c80e7eb94599253f6d970a02eee Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 12 Jan 2023 15:02:02 -0500 Subject: [PATCH 18/60] #600 nt typecode for NamedThing --- src/schema/core.yaml | 8 ++++++++ src/schema/nmdc.yaml | 1 + 2 files changed, 9 insertions(+) diff --git a/src/schema/core.yaml b/src/schema/core.yaml index 967c366e8e..84d7c9ac52 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -92,6 +92,14 @@ classes: - name - description - alternative_identifiers + slot_usage: + id: + structured_pattern: + todos: + syntax: "{id_nmdc_prefix}:{id_typecode_named_thing}-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false + MaterialEntity: aliases: diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 8a63d9c3a4..d8ad7bbbd1 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -106,6 +106,7 @@ settings: id_typecode_omics_processing: "omprc" id_typecode_dataobject: "dobj" id_typecode_activity: "acty" + id_typecode_named_thing: "nt" From 42b57c727d2780014c42e2ea83e537e1c751860f Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 12 Jan 2023 15:16:55 -0500 Subject: [PATCH 19/60] #600 new typecode table including nt --- src/docs/typecode_table.md | 49 ++++++++++++++++++++++---------------- 1 file changed, 29 insertions(+), 20 deletions(-) diff --git a/src/docs/typecode_table.md b/src/docs/typecode_table.md index 050ee7587e..b8c44756e3 100644 --- a/src/docs/typecode_table.md +++ b/src/docs/typecode_table.md @@ -2,27 +2,36 @@ Last generated 2023-01-12 -If a Class doesn't use the `id` slot, then there is no need to assign that class a typecode +If a class doesn't use the `id` slot, then there is no need to assign that class a typecode -Typecodes can be directly asserted for a class, or a class can inherit a typecode from one of it's ancestors. This table doe not yet indicate when a typecode was inherited from an ancestor. An example of inheritance is 'acty' for `WorkflowExecutionActivity`, which is inherited from it's ancestor `Activity` +Typecodes can be directly asserted for a class, or a class can inherit a typecode from one of its ancestors. This table +does not yet indicate when a typecode was inherited from an ancestor. An example of inheritance is 'acty' +for `WorkflowExecutionActivity`, which is inherited from it's ancestor `Activity` + +Todo: + +- Continue to add typecode to classes that are curently just inheriting general typecodes. +- Investigate which of these classes have identifiers that will actually appear on the Data Portal. Classes that are + more behind-the-scenes (however were are going to rigorously define that) may require less deliberation. +- Automate build and deploy of this table | class | uses_id | typecode | |-------------------------------------|---------|----------| | Activity | TRUE | acty | -| AnalyticalSample | TRUE | | +| AnalyticalSample | TRUE | nt | | Biosample | TRUE | bsm | | BiosampleProcessing | TRUE | bsmprc | -| ChemicalEntity | TRUE | | -| CollectingBiosamplesFromSite | TRUE | | +| ChemicalEntity | TRUE | nt | +| CollectingBiosamplesFromSite | TRUE | nt | | DataObject | TRUE | dobj | -| EnvironmentalMaterialTerm | TRUE | | -| FieldResearchSite | TRUE | | -| FunctionalAnnotationTerm | TRUE | | -| GeneProduct | TRUE | | -| Instrument | TRUE | | +| EnvironmentalMaterialTerm | TRUE | nt | +| FieldResearchSite | TRUE | nt | +| FunctionalAnnotationTerm | TRUE | nt | +| GeneProduct | TRUE | nt | +| Instrument | TRUE | nt | | MagsAnalysisActivity | TRUE | acty | -| MaterialEntity | TRUE | | -| MaterialSample | TRUE | | +| MaterialEntity | TRUE | nt | +| MaterialSample | TRUE | nt | | MetabolomicsAnalysisActivity | TRUE | acty | | MetagenomeAnnotationActivity | TRUE | acty | | MetagenomeAssembly | TRUE | acty | @@ -30,18 +39,18 @@ Typecodes can be directly asserted for a class, or a class can inherit a typecod | MetatranscriptomeActivity | TRUE | acty | | MetatranscriptomeAnnotationActivity | TRUE | acty | | MetatranscriptomeAssembly | TRUE | acty | -| NamedThing | TRUE | | +| NamedThing | TRUE | nt | | NomAnalysisActivity | TRUE | acty | | OmicsProcessing | TRUE | omprc | -| OntologyClass | TRUE | | -| OrthologyGroup | TRUE | | -| Pathway | TRUE | | -| Person | TRUE | | -| PlannedProcess | TRUE | | -| Reaction | TRUE | | +| OntologyClass | TRUE | nt | +| OrthologyGroup | TRUE | nt | +| Pathway | TRUE | nt | +| Person | TRUE | nt | +| PlannedProcess | TRUE | nt | +| Reaction | TRUE | nt | | ReadBasedTaxonomyAnalysisActivity | TRUE | acty | | ReadQcAnalysisActivity | TRUE | acty | -| Site | TRUE | | +| Site | TRUE | nt | | Study | TRUE | sty | | WorkflowExecutionActivity | TRUE | acty | | Agent | FALSE | | From 4f4a40fff4d4e258b8325c864b03248b5d7d844b Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 12 Jan 2023 15:44:43 -0500 Subject: [PATCH 20/60] #603 multiple typecode & doc pages updates --- mkdocs.yml | 4 ++-- src/docs/typecode_table.md | 3 ++- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index f50cc09094..7d1778ea50 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -15,6 +15,6 @@ nav: - NMDC Metadata Standards Documentation: Metadata_Documentation_Overview.md - NMDC Schema Validation: schema-validation.md - Identifiers in NMDC: identifiers.md - - MIxS Soil Package: NMDC_MIxS_Soil_documentation.md - - Typecodes for Classes: typecode_table.md + - Table of Identifier Typecodes for each Class: typecode_table.md + - DEPRECATED MIxS Soil Package: NMDC_MIxS_Soil_documentation.md - Credits: credits.md diff --git a/src/docs/typecode_table.md b/src/docs/typecode_table.md index b8c44756e3..d22f60a310 100644 --- a/src/docs/typecode_table.md +++ b/src/docs/typecode_table.md @@ -10,7 +10,8 @@ for `WorkflowExecutionActivity`, which is inherited from it's ancestor `Activity Todo: -- Continue to add typecode to classes that are curently just inheriting general typecodes. +- Document criteria for "good typecodes" +- Continue to add typecode to classes that are currently just inheriting general typecodes. - Investigate which of these classes have identifiers that will actually appear on the Data Portal. Classes that are more behind-the-scenes (however were are going to rigorously define that) may require less deliberation. - Automate build and deploy of this table From 37bd376f89043869c3d53eda246905a06e69a256 Mon Sep 17 00:00:00 2001 From: Sujay Patil Date: Thu, 12 Jan 2023 12:48:47 -0800 Subject: [PATCH 21/60] code block formatting fix in identifiers doc --- src/docs/identifiers.md | 1 + 1 file changed, 1 insertion(+) diff --git a/src/docs/identifiers.md b/src/docs/identifiers.md index 9cf2f006f6..b346162c98 100644 --- a/src/docs/identifiers.md +++ b/src/docs/identifiers.md @@ -142,6 +142,7 @@ The per-part regular expression described above can be composed into one complet ``` ^(?nmdc):(?[a-z]{1,6})-(?[0-9][a-z]{0,6}[0-9])-(?[A-Za-z0-9]+)(?(\.[A-Za-z0-9]+)*)(?_[A-Za-z0-9_\.-]+)?$ +``` ## Reuse vs minting new IDs From 71a3e219ca4ac8b8cc371e0c328cde700cd7f84d Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 08:48:09 -0500 Subject: [PATCH 22/60] #615 Activity typecode and tests --- src/schema/prov.yaml | 6 +- test/data/MAGs_activity.json | 4 +- test/data/img_mg_annotation_objects.json | 228 ++++++++++----------- test/data/mg_assembly_activities_test.json | 6 +- 4 files changed, 122 insertions(+), 122 deletions(-) diff --git a/src/schema/prov.yaml b/src/schema/prov.yaml index 1080b149f4..24470effd0 100644 --- a/src/schema/prov.yaml +++ b/src/schema/prov.yaml @@ -38,11 +38,11 @@ classes: - prov:Activity slot_usage: id: - pattern: '^nmdc:' + pattern: '^nmdc:act' structured_pattern: todos: - - remove the static pattern once the minter can generate ids that satisfy this structured_pattern - syntax: "{id_nmdc_prefix}:{id_typecode_activity}-{id_shoulder}-{id_blade}{id_version}{id_locus}" + - remove the static pattern once the minter can generate ids that satisfy this structured_pattern and gen-linkml can expand the structured_pattern + syntax: "{id_nmdc_prefix}:act-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false diff --git a/test/data/MAGs_activity.json b/test/data/MAGs_activity.json index 953ea82b91..bca9143a3f 100644 --- a/test/data/MAGs_activity.json +++ b/test/data/MAGs_activity.json @@ -1,7 +1,7 @@ { "mags_activity_set": [ { - "id": "nmdc:f2fc8f5aade3092ea97769f0a892d2a9", + "id": "nmdc:act-f2fc8f5aade3092ea97769f0a892d2a9", "name": "MAGs activiity 1781_86101", "was_informed_by": "gold:Gp0115663", "started_at_time": "2021-01-10T00:00:00+00:00", @@ -65,7 +65,7 @@ ] }, { - "id": "nmdc:a0ca0743a49e4bf12db9b5d933c4e76a", + "id": "nmdc:act-a0ca0743a49e4bf12db9b5d933c4e76a", "name": "MAGs activiity 1781_86089", "was_informed_by": "gold:Gp0115664", "started_at_time": "2021-01-10T00:00:00+00:00", diff --git a/test/data/img_mg_annotation_objects.json b/test/data/img_mg_annotation_objects.json index c70a8bbec1..f5d4fe59e6 100644 --- a/test/data/img_mg_annotation_objects.json +++ b/test/data/img_mg_annotation_objects.json @@ -17,7 +17,7 @@ "was_informed_by": "gold:Gp0153825", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:9076b6e2b334532d7be4e48b25ca80dd", + "id": "nmdc:act-act-9076b6e2b334532d7be4e48b25ca80dd", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -37,7 +37,7 @@ "was_informed_by": "gold:Gp0119849", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:bf16723c3a2b226747c6b40085f51cc2", + "id": "nmdc:act-act-bf16723c3a2b226747c6b40085f51cc2", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -57,7 +57,7 @@ "was_informed_by": "gold:Gp0119850", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:c77fe920a664d4e174d413ec89f040a3", + "id": "nmdc:act-act-c77fe920a664d4e174d413ec89f040a3", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -77,7 +77,7 @@ "was_informed_by": "gold:Gp0119851", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:6c5858d2b28e1de316120d410ed62544", + "id": "nmdc:act-act-6c5858d2b28e1de316120d410ed62544", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -97,7 +97,7 @@ "was_informed_by": "gold:Gp0119852", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:879e7ff3374deee6054684076a882649", + "id": "nmdc:act-act-879e7ff3374deee6054684076a882649", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -117,7 +117,7 @@ "was_informed_by": "gold:Gp0119853", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:608cc16c1e395be8f7f56f123b88d17a", + "id": "nmdc:act-act-608cc16c1e395be8f7f56f123b88d17a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -137,7 +137,7 @@ "was_informed_by": "gold:Gp0119854", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:db089a3971603b130cc25c9edf29a951", + "id": "nmdc:act-act-db089a3971603b130cc25c9edf29a951", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -157,7 +157,7 @@ "was_informed_by": "gold:Gp0119855", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:1762bbeb64674af6e394ee1323391833", + "id": "nmdc:act-act-1762bbeb64674af6e394ee1323391833", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -177,7 +177,7 @@ "was_informed_by": "gold:Gp0119856", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:4794bbc1dc72807df92a30088cf4551b", + "id": "nmdc:act-act-4794bbc1dc72807df92a30088cf4551b", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -197,7 +197,7 @@ "was_informed_by": "gold:Gp0119857", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:9cb27d7fe967ed437acf43b7cb5f01ee", + "id": "nmdc:act-act-9cb27d7fe967ed437acf43b7cb5f01ee", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -217,7 +217,7 @@ "was_informed_by": "gold:Gp0119858", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:b52fd6e2d28c922c305849b2e6e29246", + "id": "nmdc:act-act-b52fd6e2d28c922c305849b2e6e29246", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -237,7 +237,7 @@ "was_informed_by": "gold:Gp0119859", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:f23f9cd69666b01795e4c43bacb9ae62", + "id": "nmdc:act-act-f23f9cd69666b01795e4c43bacb9ae62", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -257,7 +257,7 @@ "was_informed_by": "gold:Gp0119860", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:9278b29bb5c234046a11937991a3a652", + "id": "nmdc:act-act-9278b29bb5c234046a11937991a3a652", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -277,7 +277,7 @@ "was_informed_by": "gold:Gp0119861", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:67d82e4c6f9796611f5a2234596eb6a2", + "id": "nmdc:act-act-67d82e4c6f9796611f5a2234596eb6a2", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -297,7 +297,7 @@ "was_informed_by": "gold:Gp0119862", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:9e9c8643f496b6472ddb602aff30021d", + "id": "nmdc:act-act-9e9c8643f496b6472ddb602aff30021d", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -317,7 +317,7 @@ "was_informed_by": "gold:Gp0119863", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:facd1cd7880760c4d227237d8142d60b", + "id": "nmdc:act-act-facd1cd7880760c4d227237d8142d60b", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -337,7 +337,7 @@ "was_informed_by": "gold:Gp0119864", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:6c6eff8448b4782e31363eb7a783ef16", + "id": "nmdc:act-act-6c6eff8448b4782e31363eb7a783ef16", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -357,7 +357,7 @@ "was_informed_by": "gold:Gp0119865", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:3d2d6fbece4298a34798a5cdc28fccbc", + "id": "nmdc:act-act-3d2d6fbece4298a34798a5cdc28fccbc", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -377,7 +377,7 @@ "was_informed_by": "gold:Gp0119866", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:993f0fb1fb43a8db2c04f6a6064d1e91", + "id": "nmdc:act-act-993f0fb1fb43a8db2c04f6a6064d1e91", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -397,7 +397,7 @@ "was_informed_by": "gold:Gp0119867", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:8a43ec3baf8aafe09d96eb7fbf58c916", + "id": "nmdc:act-act-8a43ec3baf8aafe09d96eb7fbf58c916", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -417,7 +417,7 @@ "was_informed_by": "gold:Gp0119868", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:57e9c4e31f9c612633325bbe5c6c2f87", + "id": "nmdc:act-act-57e9c4e31f9c612633325bbe5c6c2f87", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -437,7 +437,7 @@ "was_informed_by": "gold:Gp0119869", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:60c965c51b96153a9cffa6f4dd62a2e6", + "id": "nmdc:act-act-60c965c51b96153a9cffa6f4dd62a2e6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -457,7 +457,7 @@ "was_informed_by": "gold:Gp0119870", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:42addbcd527a65d01a4d2fbd2da7758a", + "id": "nmdc:act-act-42addbcd527a65d01a4d2fbd2da7758a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -477,7 +477,7 @@ "was_informed_by": "gold:Gp0119871", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:3204b453fe3471a5c6babce54398d9af", + "id": "nmdc:act-act-3204b453fe3471a5c6babce54398d9af", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -497,7 +497,7 @@ "was_informed_by": "gold:Gp0127623", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:92070449b2ee66f6ec04125edc8ae30a", + "id": "nmdc:act-act-92070449b2ee66f6ec04125edc8ae30a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -517,7 +517,7 @@ "was_informed_by": "gold:Gp0127624", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:f0773e35f29db6c8c9ec2354b6560c5f", + "id": "nmdc:act-act-f0773e35f29db6c8c9ec2354b6560c5f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -537,7 +537,7 @@ "was_informed_by": "gold:Gp0127625", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:dfbc92d67d6307fc16059f858f8d81f6", + "id": "nmdc:act-act-dfbc92d67d6307fc16059f858f8d81f6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -557,7 +557,7 @@ "was_informed_by": "gold:Gp0127626", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:b17f7734657148a50baf5216849b3b2f", + "id": "nmdc:act-act-b17f7734657148a50baf5216849b3b2f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -577,7 +577,7 @@ "was_informed_by": "gold:Gp0127627", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:4b54a8416db39168fa6403d6832476e6", + "id": "nmdc:act-act-4b54a8416db39168fa6403d6832476e6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -597,7 +597,7 @@ "was_informed_by": "gold:Gp0127628", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:689781c3f0a680b05f9a0a9b377b0ed9", + "id": "nmdc:act-act-689781c3f0a680b05f9a0a9b377b0ed9", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -617,7 +617,7 @@ "was_informed_by": "gold:Gp0127629", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:d8af769e0dd753e86ef1f545536f3024", + "id": "nmdc:act-act-d8af769e0dd753e86ef1f545536f3024", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -637,7 +637,7 @@ "was_informed_by": "gold:Gp0127630", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:b579670a8b80fd02e453d5ac031a574e", + "id": "nmdc:act-act-b579670a8b80fd02e453d5ac031a574e", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -657,7 +657,7 @@ "was_informed_by": "gold:Gp0127631", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:406be722709ec331037987b30acc6b18", + "id": "nmdc:act-act-406be722709ec331037987b30acc6b18", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -677,7 +677,7 @@ "was_informed_by": "gold:Gp0127632", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:163dfd2463186259deeae10b15d25119", + "id": "nmdc:act-act-163dfd2463186259deeae10b15d25119", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -697,7 +697,7 @@ "was_informed_by": "gold:Gp0127633", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:ac967b73a027cfac522a742ddbbf9521", + "id": "nmdc:act-act-ac967b73a027cfac522a742ddbbf9521", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -717,7 +717,7 @@ "was_informed_by": "gold:Gp0127634", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:8287ea44a458b50606a04fe82ceb83b1", + "id": "nmdc:act-8287ea44a458b50606a04fe82ceb83b1", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -737,7 +737,7 @@ "was_informed_by": "gold:Gp0127635", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:e763e255fa74e2629d7d86e10f838d4b", + "id": "nmdc:act-e763e255fa74e2629d7d86e10f838d4b", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -757,7 +757,7 @@ "was_informed_by": "gold:Gp0127636", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:89dde14d6545e93e749ffeae6fc3bdd6", + "id": "nmdc:act-89dde14d6545e93e749ffeae6fc3bdd6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -777,7 +777,7 @@ "was_informed_by": "gold:Gp0127637", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:507c53e61a3c02d763b05d2a5eb2bda5", + "id": "nmdc:act-507c53e61a3c02d763b05d2a5eb2bda5", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -797,7 +797,7 @@ "was_informed_by": "gold:Gp0127638", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:93656c96853f97524040c44f4b346d75", + "id": "nmdc:act-93656c96853f97524040c44f4b346d75", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -817,7 +817,7 @@ "was_informed_by": "gold:Gp0127639", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:78ec466d9918b7fa1cbc033b19a37a10", + "id": "nmdc:act-78ec466d9918b7fa1cbc033b19a37a10", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -837,7 +837,7 @@ "was_informed_by": "gold:Gp0127640", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:5ac74427da62d00b8493cf6bc7c8e43d", + "id": "nmdc:act-5ac74427da62d00b8493cf6bc7c8e43d", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -857,7 +857,7 @@ "was_informed_by": "gold:Gp0127641", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:6808e9a6d7450f02019691d89c57ff1f", + "id": "nmdc:act-6808e9a6d7450f02019691d89c57ff1f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -877,7 +877,7 @@ "was_informed_by": "gold:Gp0127642", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:45f4a9d66e8d45a534fc2067670bf012", + "id": "nmdc:act-45f4a9d66e8d45a534fc2067670bf012", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -897,7 +897,7 @@ "was_informed_by": "gold:Gp0127643", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:b59602d74d9ee08ccd285a7ac2e5f6b2", + "id": "nmdc:act-b59602d74d9ee08ccd285a7ac2e5f6b2", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -917,7 +917,7 @@ "was_informed_by": "gold:Gp0127644", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:339e8f1e41b780e4e565ce53067bc9bb", + "id": "nmdc:act-339e8f1e41b780e4e565ce53067bc9bb", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -937,7 +937,7 @@ "was_informed_by": "gold:Gp0127645", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:e148a2d4befa290bbd216b6654371606", + "id": "nmdc:act-e148a2d4befa290bbd216b6654371606", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -957,7 +957,7 @@ "was_informed_by": "gold:Gp0127646", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:02aca43c6efc414d5971e8a179bbbcf0", + "id": "nmdc:act-02aca43c6efc414d5971e8a179bbbcf0", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -977,7 +977,7 @@ "was_informed_by": "gold:Gp0127647", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:4488991684ed07f2b9a2bb5b8b1a59a9", + "id": "nmdc:act-4488991684ed07f2b9a2bb5b8b1a59a9", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -997,7 +997,7 @@ "was_informed_by": "gold:Gp0127648", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:ca2cac5f3de8db080031d727ff4db8ec", + "id": "nmdc:act-ca2cac5f3de8db080031d727ff4db8ec", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1017,7 +1017,7 @@ "was_informed_by": "gold:Gp0127649", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:1524a48694d670c26a1b55238d9f1949", + "id": "nmdc:act-1524a48694d670c26a1b55238d9f1949", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1037,7 +1037,7 @@ "was_informed_by": "gold:Gp0127651", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:e96dba76c7c388aebab7ad759b2a5694", + "id": "nmdc:act-e96dba76c7c388aebab7ad759b2a5694", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1057,7 +1057,7 @@ "was_informed_by": "gold:Gp0127652", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:5e21f299a395e845341500a334e94ff2", + "id": "nmdc:act-5e21f299a395e845341500a334e94ff2", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1077,7 +1077,7 @@ "was_informed_by": "gold:Gp0127653", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:d6f99d25d421ab54908e603b016df20f", + "id": "nmdc:act-d6f99d25d421ab54908e603b016df20f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1097,7 +1097,7 @@ "was_informed_by": "gold:Gp0127654", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:405d59d65f666d1bb1f44393bf6b3c1a", + "id": "nmdc:act-405d59d65f666d1bb1f44393bf6b3c1a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1117,7 +1117,7 @@ "was_informed_by": "gold:Gp0127655", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:82124fe8afc73ce5f61011ba9520ae38", + "id": "nmdc:act-82124fe8afc73ce5f61011ba9520ae38", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1137,7 +1137,7 @@ "was_informed_by": "gold:Gp0127656", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:9bdf633bcd7d5b9bb1bf95ccd26349cd", + "id": "nmdc:act-9bdf633bcd7d5b9bb1bf95ccd26349cd", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1157,7 +1157,7 @@ "was_informed_by": "gold:Gp0115664", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:686818cb31dc45d3d4482847ec007584", + "id": "nmdc:act-686818cb31dc45d3d4482847ec007584", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1177,7 +1177,7 @@ "was_informed_by": "gold:Gp0115675", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:2e10913bdcfacfeeab4d9f7a0aa2af8f", + "id": "nmdc:act-2e10913bdcfacfeeab4d9f7a0aa2af8f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1197,7 +1197,7 @@ "was_informed_by": "gold:Gp0115673", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:b3bd170070e9c37f535de92c9f37b2b4", + "id": "nmdc:act-b3bd170070e9c37f535de92c9f37b2b4", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1217,7 +1217,7 @@ "was_informed_by": "gold:Gp0115677", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:fdd5f518cea894505f0bd6ac02205ba3", + "id": "nmdc:act-fdd5f518cea894505f0bd6ac02205ba3", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1237,7 +1237,7 @@ "was_informed_by": "gold:Gp0115678", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:42613f7c1fa860e847e2c93e2462b6f7", + "id": "nmdc:act-42613f7c1fa860e847e2c93e2462b6f7", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1257,7 +1257,7 @@ "was_informed_by": "gold:Gp0115665", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:9b6144e11b277a1f020c54da4ee79bac", + "id": "nmdc:act-9b6144e11b277a1f020c54da4ee79bac", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1277,7 +1277,7 @@ "was_informed_by": "gold:Gp0115671", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:c65521ed98ca6f569686debc46ea274d", + "id": "nmdc:act-c65521ed98ca6f569686debc46ea274d", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1297,7 +1297,7 @@ "was_informed_by": "gold:Gp0115666", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:638923494b08b936cefdac95ef58c558", + "id": "nmdc:act-638923494b08b936cefdac95ef58c558", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1317,7 +1317,7 @@ "was_informed_by": "gold:Gp0115669", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:73840751bf8835b680aff13d0eb2335a", + "id": "nmdc:act-73840751bf8835b680aff13d0eb2335a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1337,7 +1337,7 @@ "was_informed_by": "gold:Gp0115667", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:7b684248db11762d14a95ebdda7e8a81", + "id": "nmdc:act-7b684248db11762d14a95ebdda7e8a81", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1357,7 +1357,7 @@ "was_informed_by": "gold:Gp0115676", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:87eb3326bcc84557dc334eff00d4a0bf", + "id": "nmdc:act-87eb3326bcc84557dc334eff00d4a0bf", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1377,7 +1377,7 @@ "was_informed_by": "gold:Gp0115668", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:87de8edb421c5364ee75c172715292cc", + "id": "nmdc:act-87de8edb421c5364ee75c172715292cc", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1397,7 +1397,7 @@ "was_informed_by": "gold:Gp0115663", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:2d9a6d5e57ab455c257d8c3424331113", + "id": "nmdc:act-2d9a6d5e57ab455c257d8c3424331113", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1417,7 +1417,7 @@ "was_informed_by": "gold:Gp0115670", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:9994a8414976fd6b56935648246493b5", + "id": "nmdc:act-9994a8414976fd6b56935648246493b5", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1437,7 +1437,7 @@ "was_informed_by": "gold:Gp0115672", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:932040eace29833c2b528f4279446285", + "id": "nmdc:act-932040eace29833c2b528f4279446285", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1457,7 +1457,7 @@ "was_informed_by": "gold:Gp0115674", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:5981c6f73f7cdc963866091b0101a9b7", + "id": "nmdc:act-5981c6f73f7cdc963866091b0101a9b7", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1477,7 +1477,7 @@ "was_informed_by": "gold:Gp0115679", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:9fcee63f77040c2b8cc0726b15f9f068", + "id": "nmdc:act-9fcee63f77040c2b8cc0726b15f9f068", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1497,7 +1497,7 @@ "was_informed_by": "gold:Gp0321263", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:8d355d3c7070686b0beb20e39d17e172", + "id": "nmdc:act-8d355d3c7070686b0beb20e39d17e172", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1517,7 +1517,7 @@ "was_informed_by": "gold:Gp0321264", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:9269f143d88b7d5ff3c61897cfef80a7", + "id": "nmdc:act-9269f143d88b7d5ff3c61897cfef80a7", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1537,7 +1537,7 @@ "was_informed_by": "gold:Gp0321265", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:36f15e6f9d8426dbc49ea6928b6b4bb6", + "id": "nmdc:act-36f15e6f9d8426dbc49ea6928b6b4bb6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1557,7 +1557,7 @@ "was_informed_by": "gold:Gp0321266", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:c6acdfbb7449a3faf079ec67396af96b", + "id": "nmdc:act-c6acdfbb7449a3faf079ec67396af96b", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1577,7 +1577,7 @@ "was_informed_by": "gold:Gp0321267", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:739891753f88a2359b78191f41c19ad0", + "id": "nmdc:act-739891753f88a2359b78191f41c19ad0", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1597,7 +1597,7 @@ "was_informed_by": "gold:Gp0321268", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:428a67c345a48187f0924d3af673c83c", + "id": "nmdc:act-428a67c345a48187f0924d3af673c83c", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1617,7 +1617,7 @@ "was_informed_by": "gold:Gp0321269", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:3f1eb315892bb62126887cce05bdae32", + "id": "nmdc:act-3f1eb315892bb62126887cce05bdae32", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1637,7 +1637,7 @@ "was_informed_by": "gold:Gp0321270", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:63648550d5280b9de5c61fc3d9f75f27", + "id": "nmdc:act-63648550d5280b9de5c61fc3d9f75f27", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1657,7 +1657,7 @@ "was_informed_by": "gold:Gp0321271", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:9593e1500765d71b2a9eeb87ff22cb7a", + "id": "nmdc:act-9593e1500765d71b2a9eeb87ff22cb7a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1677,7 +1677,7 @@ "was_informed_by": "gold:Gp0321272", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:8e3f1f49fdd583134060849f51c4c9b2", + "id": "nmdc:act-8e3f1f49fdd583134060849f51c4c9b2", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1697,7 +1697,7 @@ "was_informed_by": "gold:Gp0321273", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:10c34e648ade3d60e9a82c234293c3ad", + "id": "nmdc:act-10c34e648ade3d60e9a82c234293c3ad", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1717,7 +1717,7 @@ "was_informed_by": "gold:Gp0321274", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:9fb743bed2cae43e0c86553b046e1ec3", + "id": "nmdc:act-9fb743bed2cae43e0c86553b046e1ec3", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1737,7 +1737,7 @@ "was_informed_by": "gold:Gp0321275", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:43eaacb2ce2ac16f5ac67ccecfcd66be", + "id": "nmdc:act-43eaacb2ce2ac16f5ac67ccecfcd66be", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1757,7 +1757,7 @@ "was_informed_by": "gold:Gp0321276", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:b4656c5f9122aab8e12e40bc24bec749", + "id": "nmdc:act-b4656c5f9122aab8e12e40bc24bec749", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1777,7 +1777,7 @@ "was_informed_by": "gold:Gp0321277", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:aa45b2e1b2a903ffe1861ff6c2afcb51", + "id": "nmdc:act-aa45b2e1b2a903ffe1861ff6c2afcb51", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1797,7 +1797,7 @@ "was_informed_by": "gold:Gp0321278", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:7f6f6431a81d831ade7a2c66ec675f3a", + "id": "nmdc:act-7f6f6431a81d831ade7a2c66ec675f3a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1817,7 +1817,7 @@ "was_informed_by": "gold:Gp0321279", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:642b62309801412cc0020f1b9e02f2bf", + "id": "nmdc:act-642b62309801412cc0020f1b9e02f2bf", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1837,7 +1837,7 @@ "was_informed_by": "gold:Gp0321280", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:b51eda7aa71887b5c3d87a88ae9ef886", + "id": "nmdc:act-b51eda7aa71887b5c3d87a88ae9ef886", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1857,7 +1857,7 @@ "was_informed_by": "gold:Gp0321281", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:24cc70779dc20ddcb8472360e94c1adb", + "id": "nmdc:act-24cc70779dc20ddcb8472360e94c1adb", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1877,7 +1877,7 @@ "was_informed_by": "gold:Gp0321282", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:3c9a77593015e132a0fcb47e32077c78", + "id": "nmdc:act-3c9a77593015e132a0fcb47e32077c78", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1897,7 +1897,7 @@ "was_informed_by": "gold:Gp0321283", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:86ebdd0ce08264d2642a571956d686db", + "id": "nmdc:act-86ebdd0ce08264d2642a571956d686db", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1917,7 +1917,7 @@ "was_informed_by": "gold:Gp0321284", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:8c0f927607c2b240824a5c52800d4c04", + "id": "nmdc:act-8c0f927607c2b240824a5c52800d4c04", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1937,7 +1937,7 @@ "was_informed_by": "gold:Gp0321285", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:030d8c58a26cc8164ce629b8e988532a", + "id": "nmdc:act-030d8c58a26cc8164ce629b8e988532a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1957,7 +1957,7 @@ "was_informed_by": "gold:Gp0321286", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:132d4df2f27d60ae8fb093248975462f", + "id": "nmdc:act-132d4df2f27d60ae8fb093248975462f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1977,7 +1977,7 @@ "was_informed_by": "gold:Gp0321287", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:6dfbdbcd7ab18ee7b2d213124e239cf6", + "id": "nmdc:act-6dfbdbcd7ab18ee7b2d213124e239cf6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1997,7 +1997,7 @@ "was_informed_by": "gold:Gp0321288", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:1f8036641fc942724894de3ed94df671", + "id": "nmdc:act-1f8036641fc942724894de3ed94df671", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2017,7 +2017,7 @@ "was_informed_by": "gold:Gp0321289", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:9b38ed417fe51b52f3afbe0ac56b25c1", + "id": "nmdc:act-9b38ed417fe51b52f3afbe0ac56b25c1", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2037,7 +2037,7 @@ "was_informed_by": "gold:Gp0321290", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:4e839407423180f709d7d5a81e6f070f", + "id": "nmdc:act-4e839407423180f709d7d5a81e6f070f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2057,7 +2057,7 @@ "was_informed_by": "gold:Gp0321291", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:65a4e2c6d56914ab2e923aedd3441c4d", + "id": "nmdc:act-65a4e2c6d56914ab2e923aedd3441c4d", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2077,7 +2077,7 @@ "was_informed_by": "gold:Gp0321292", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:5e2e998dfbfbfde7091237749c8d9028", + "id": "nmdc:act-5e2e998dfbfbfde7091237749c8d9028", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2097,7 +2097,7 @@ "was_informed_by": "gold:Gp0321293", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:1d1f5b339f19cc457782e86e04688b9f", + "id": "nmdc:act-1d1f5b339f19cc457782e86e04688b9f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2117,7 +2117,7 @@ "was_informed_by": "gold:Gp0321294", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:fd71f805d1e05eae9f38d7d16de66299", + "id": "nmdc:act-fd71f805d1e05eae9f38d7d16de66299", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2137,7 +2137,7 @@ "was_informed_by": "gold:Gp0321295", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:7fbff9ac4fe3633f9f762069ed572b1c", + "id": "nmdc:act-7fbff9ac4fe3633f9f762069ed572b1c", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2157,7 +2157,7 @@ "was_informed_by": "gold:Gp0321296", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:327db9baa82cc3d9de443613cea1ee35", + "id": "nmdc:act-327db9baa82cc3d9de443613cea1ee35", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2177,7 +2177,7 @@ "was_informed_by": "gold:Gp0321297", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:6b8a96eb366ae631aa86badd9d11e9ae", + "id": "nmdc:act-6b8a96eb366ae631aa86badd9d11e9ae", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2197,7 +2197,7 @@ "was_informed_by": "gold:Gp0321298", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:17fadd9c29b2374dbee61bd95e3f0a02", + "id": "nmdc:act-17fadd9c29b2374dbee61bd95e3f0a02", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2217,7 +2217,7 @@ "was_informed_by": "gold:Gp0321299", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:8456c04883daa652cd3c8ef61440c602", + "id": "nmdc:act-8456c04883daa652cd3c8ef61440c602", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2237,7 +2237,7 @@ "was_informed_by": "gold:Gp0321300", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:724f98d56bbda5686819251b3d35b3bb", + "id": "nmdc:act-724f98d56bbda5686819251b3d35b3bb", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2257,7 +2257,7 @@ "was_informed_by": "gold:Gp0321301", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:b8865de68b6a30e28e9232a1184e4703", + "id": "nmdc:act-b8865de68b6a30e28e9232a1184e4703", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2277,7 +2277,7 @@ "was_informed_by": "gold:Gp0321302", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:449b5471dff17853621e8dcd4e46d790", + "id": "nmdc:act-449b5471dff17853621e8dcd4e46d790", "ended_at_time": "2021-01-12T00:00:00+00:00" } ] diff --git a/test/data/mg_assembly_activities_test.json b/test/data/mg_assembly_activities_test.json index 286a38984e..02f194ec6f 100644 --- a/test/data/mg_assembly_activities_test.json +++ b/test/data/mg_assembly_activities_test.json @@ -1,7 +1,7 @@ { "metagenome_assembly_set": [ { - "id": "nmdc:f404cb05d4c1458b659ae2232245c45d", + "id": "nmdc:act-f404cb05d4c1458b659ae2232245c45d", "name": "Metagenome assembly 1472_51277", "was_informed_by": "gold:Gp0061273", "started_at_time": "2020-03-24T00:00:00+00:00", @@ -48,7 +48,7 @@ "num_aligned_reads": 63046103 }, { - "id": "nmdc:e7d3e1551ad9439505b522d5b1768c97", + "id": "nmdc:act-e7d3e1551ad9439505b522d5b1768c97", "name": "Metagenome assembly 1472_51278", "was_informed_by": "gold:Gp0061274", "started_at_time": "2020-03-25T00:00:00+00:00", @@ -95,7 +95,7 @@ "num_aligned_reads": 95369019 }, { - "id": "nmdc:9a2a0778e003977d594c93e54fcef3e6", + "id": "nmdc:act-9a2a0778e003977d594c93e54fcef3e6", "name": "Metagenome assembly 1472_51279", "was_informed_by": "gold:Gp0061275", "started_at_time": "2020-03-25T00:00:00+00:00", From 13eb10a397327e23b548e81b909c74fce970b39f Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 09:04:44 -0500 Subject: [PATCH 23/60] AnalyticalSample typecode added, no test? --- src/schema/core.yaml | 7 +++++++ src/schema/nmdc.yaml | 2 +- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/src/schema/core.yaml b/src/schema/core.yaml index 84d7c9ac52..cfc6b0fa51 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -111,6 +111,13 @@ classes: AnalyticalSample: is_a: MaterialEntity title: Analytical Sample + slot_usage: + id: + pattern: '^nmdc:ansm' + structured_pattern: + syntax: "{id_nmdc_prefix}:ansm-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false Site: is_a: MaterialEntity diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index d8ad7bbbd1..a6f125c69a 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -105,7 +105,7 @@ settings: id_typecode_biosample_processing: "bsmprc" id_typecode_omics_processing: "omprc" id_typecode_dataobject: "dobj" - id_typecode_activity: "acty" +# id_typecode_activity: "acty" id_typecode_named_thing: "nt" From 4ccfe201b4a11395b0ceee88bff706ac72c5953e Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 09:14:58 -0500 Subject: [PATCH 24/60] Biosample typecode updated inc tests --- src/schema/nmdc.yaml | 10 ++++------ test/data/biosample_test.json | 8 ++++---- test/data/biosamples_to_sites.json | 12 ++++++------ test/data/invalid_data/biosample_invalid_range.json | 6 +++--- .../data/invalid_data/biosample_undeclared_slot.json | 6 +++--- test/data/nmdc_example_database.json | 6 +++--- 6 files changed, 23 insertions(+), 25 deletions(-) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index a6f125c69a..56b0d77292 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -100,12 +100,12 @@ settings: id_version: "(\\.[A-Za-z0-9]{1,})*" id_locus: "(_[A-Za-z0-9_\\.-]+)?$" # class to typecode associations - id_typecode_biosample: "bsm" + # id_typecode_biosample: "bsm" id_typecode_study: "sty" id_typecode_biosample_processing: "bsmprc" id_typecode_omics_processing: "omprc" id_typecode_dataobject: "dobj" -# id_typecode_activity: "acty" + # id_typecode_activity: "acty" id_typecode_named_thing: "nt" @@ -504,11 +504,9 @@ classes: id: description: An NMDC assigned unique identifier for a biosample submitted to NMDC. required: true - pattern: '^nmdc:' + pattern: '^nmdc:bsm' structured_pattern: - todos: - - remove the static pattern once the minter can generate ids that satisfy this structured_pattern - syntax: "{id_nmdc_prefix}:{id_typecode_biosample}-{id_shoulder}-{id_blade}{id_version}{id_locus}" + syntax: "{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false diff --git a/test/data/biosample_test.json b/test/data/biosample_test.json index 23ab5c9046..d8a1948f07 100644 --- a/test/data/biosample_test.json +++ b/test/data/biosample_test.json @@ -1,7 +1,7 @@ { "biosample_set": [ { - "id": "nmdc:6057d02c-664c-41c9-8486-3624ca845747", + "id": "nmdc:bsm-6057d02c-664c-41c9-8486-3624ca845747", "gold_biosample_identifiers": [ "gold:Gb0101224" ], @@ -51,7 +51,7 @@ "sample_collection_site": "Lithgow State Coal Mine" }, { - "id": "nmdc:6057d02c-664c-41c9-8486-3624ca845747", + "id": "nmdc:bsm-bsm-6057d02c-664c-41c9-8486-3624ca845747", "gold_biosample_identifiers": [ "gold:Gb0101224" ], @@ -105,7 +105,7 @@ "sample_collection_site": "Lithgow State Coal Mine" }, { - "id": "nmdc:e924072f-98b5-4f88-a796-a7ba1d8ddd92", + "id": "nmdc:bsm-bsm-e924072f-98b5-4f88-a796-a7ba1d8ddd92", "gold_biosample_identifiers": [ "gold:Gb0101225" ], @@ -155,7 +155,7 @@ "sample_collection_site": "Lithgow State Coal Mine" }, { - "id": "nmdc:61c3332d-f654-4db8-8d2f-59475894daa5", + "id": "nmdc:bsm-bsm-61c3332d-f654-4db8-8d2f-59475894daa5", "gold_biosample_identifiers": [ "gold:Gb0101226" ], diff --git a/test/data/biosamples_to_sites.json b/test/data/biosamples_to_sites.json index 59a81c8582..d0e789839c 100644 --- a/test/data/biosamples_to_sites.json +++ b/test/data/biosamples_to_sites.json @@ -1,7 +1,7 @@ { "biosample_set": [ { - "id": "nmdc:biosample_placeholder_1", + "id": "nmdc:bsm-biosample_placeholder_1", "name": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33 endosphere", "description": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA", "collected_from": "GOLD:BESC-13-CL1_35_33", @@ -31,7 +31,7 @@ } }, { - "id": "nmdc:biosample_placeholder_2", + "id": "nmdc:bsm-biosample_placeholder_2", "name": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33", "description": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", "collected_from": "GOLD:BESC-13-CL1_35_33", @@ -61,7 +61,7 @@ } }, { - "id": "nmdc:biosample_placeholder_3", + "id": "nmdc:bsm-biosample_placeholder_3", "name": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33", "description": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", "collected_from": "GOLD:BESC-13-CL1_35_33", @@ -91,7 +91,7 @@ } }, { - "id": "nmdc:biosample_placeholder_4", + "id": "nmdc:bsm-biosample_placeholder_4", "name": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29 endosphere", "description": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA", "collected_from": "GOLD:BESC-13-CL2_39_29", @@ -121,7 +121,7 @@ } }, { - "id": "nmdc:study_placeholder", + "id": "nmdc:bsm-study_placeholder", "name": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29", "description": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", "collected_from": "GOLD:BESC-13-CL2_39_29", @@ -151,7 +151,7 @@ } }, { - "id": "nmdc:biosample_placeholder_6", + "id": "nmdc:bsm-biosample_placeholder_6", "name": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29", "description": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", "collected_from": "GOLD:BESC-13-CL2_39_29", diff --git a/test/data/invalid_data/biosample_invalid_range.json b/test/data/invalid_data/biosample_invalid_range.json index 98def01cf6..a81166e0f9 100644 --- a/test/data/invalid_data/biosample_invalid_range.json +++ b/test/data/invalid_data/biosample_invalid_range.json @@ -1,7 +1,7 @@ { "biosample_set": [ { - "id": "nmdc:6057d02c-664c-41c9-8486-3624ca845747", + "id": "nmdc:bsm-6057d02c-664c-41c9-8486-3624ca845747", "gold_biosample_identifiers": [ "gold:Gb0101224" ], @@ -51,7 +51,7 @@ "sample_collection_site": "Lithgow State Coal Mine" }, { - "id": "nmdc:e924072f-98b5-4f88-a796-a7ba1d8ddd92", + "id": "nmdc:bsm-e924072f-98b5-4f88-a796-a7ba1d8ddd92", "gold_biosample_identifiers": [ "gold:Gb0101225" ], @@ -101,7 +101,7 @@ "sample_collection_site": "Lithgow State Coal Mine" }, { - "id": "nmdc:61c3332d-f654-4db8-8d2f-59475894daa5", + "id": "nmdc:bsm-61c3332d-f654-4db8-8d2f-59475894daa5", "gold_biosample_identifiers": [ "gold:Gb0101226" ], diff --git a/test/data/invalid_data/biosample_undeclared_slot.json b/test/data/invalid_data/biosample_undeclared_slot.json index 5d2b172da8..dba46e3b3d 100644 --- a/test/data/invalid_data/biosample_undeclared_slot.json +++ b/test/data/invalid_data/biosample_undeclared_slot.json @@ -2,7 +2,7 @@ "biosample_set": [ { "foo": "bar", - "id": "nmdc:6057d02c-664c-41c9-8486-3624ca845747", + "id": "nmdc:bsm-6057d02c-664c-41c9-8486-3624ca845747", "gold_biosample_identifiers": [ "gold:Gb0101224" ], @@ -52,7 +52,7 @@ "sample_collection_site": "Lithgow State Coal Mine" }, { - "id": "nmdc:e924072f-98b5-4f88-a796-a7ba1d8ddd92", + "id": "nmdc:bsm-e924072f-98b5-4f88-a796-a7ba1d8ddd92", "gold_biosample_identifiers": [ "gold:Gb0101225" ], @@ -102,7 +102,7 @@ "sample_collection_site": "Lithgow State Coal Mine" }, { - "id": "nmdc:61c3332d-f654-4db8-8d2f-59475894daa5", + "id": "nmdc:bsm-61c3332d-f654-4db8-8d2f-59475894daa5", "gold_biosample_identifiers": [ "gold:Gb0101226" ], diff --git a/test/data/nmdc_example_database.json b/test/data/nmdc_example_database.json index 15a71fdf1f..7550394ea4 100644 --- a/test/data/nmdc_example_database.json +++ b/test/data/nmdc_example_database.json @@ -122,7 +122,7 @@ ], "biosample_set": [ { - "id": "nmdc:c6eb9f01-796b-4bd6-8ed4-74e221eed7c1", + "id": "nmdc:bsm-c6eb9f01-796b-4bd6-8ed4-74e221eed7c1", "gold_biosample_identifiers": [ "gold:Gb0150408" ], @@ -176,7 +176,7 @@ "sample_collection_site": "Mire fen" }, { - "id": "nmdc:87698d0e-13b5-488a-9324-53846a6e332d", + "id": "nmdc:bsm-87698d0e-13b5-488a-9324-53846a6e332d", "gold_biosample_identifiers": [ "gold:Gb0157174" ], @@ -230,7 +230,7 @@ "sample_collection_site": "forest soil" }, { - "id": "nmdc:9a4f0882-49b2-46ed-8951-0ee2ea019df7", + "id": "nmdc:bsm-9a4f0882-49b2-46ed-8951-0ee2ea019df7", "gold_biosample_identifiers": [ "gold:Gb0188037" ], From 178001322ca2422a24713e38a27acd4dce9d274f Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 09:40:48 -0500 Subject: [PATCH 25/60] BiosampleProcessing typecode updated inc tests --- src/schema/nmdc.yaml | 7 +++---- test/data/gold_project_test.json | 15 ++++++++++++--- test/data/nmdc_example_database.json | 15 ++++++++++++--- 3 files changed, 27 insertions(+), 10 deletions(-) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 56b0d77292..d4e5cdbf59 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -102,7 +102,7 @@ settings: # class to typecode associations # id_typecode_biosample: "bsm" id_typecode_study: "sty" - id_typecode_biosample_processing: "bsmprc" + # id_typecode_biosample_processing: "bsmprc" id_typecode_omics_processing: "omprc" id_typecode_dataobject: "dobj" # id_typecode_activity: "acty" @@ -711,10 +711,9 @@ classes: - has_input slot_usage: id: + pattern: '^nmdc:bsmprc' structured_pattern: - todos: - - remove any static pattern once the minter can generate ids that satisfy this structured_pattern - syntax: "{id_nmdc_prefix}:{id_typecode_biosample_processing}-{id_shoulder}-{id_blade}{id_version}{id_locus}" + syntax: "{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false has_input: diff --git a/test/data/gold_project_test.json b/test/data/gold_project_test.json index 373f4e6537..77fcf8b03b 100644 --- a/test/data/gold_project_test.json +++ b/test/data/gold_project_test.json @@ -1,7 +1,10 @@ { "omics_processing_set": [ { - "id": "gold:Gp0108335", + "id": "nmdc:bsmprc-93312e7f-79f2-4861-b108-3aa8ccb86c9b", + "alternative_identifiers": [ + "gold:Gp0108335" + ], "name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D", "has_input": [ "gold:Gb0108335" @@ -22,7 +25,10 @@ "type": "nmdc:OmicsProcessing" }, { - "id": "gold:Gp0108340", + "id": "nmdc:bsmprc-68fa114f-6709-4e4c-bd2b-c53fd5ee51da", + "alternative_identifiers": [ + "gold:Gp0108340" + ], "name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 612S3M", "has_input": [ "gold:Gb0108340" @@ -43,7 +49,10 @@ "type": "nmdc:OmicsProcessing" }, { - "id": "gold:Gp0108341", + "id": "nmdc:bsmprc-32604e07-bfa6-4d43-a998-3f1cde25bf4f", + "alternative_identifiers": [ + "gold:Gp0108341" + ], "name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712S3S", "has_input": [ "gold:Gb0108341" diff --git a/test/data/nmdc_example_database.json b/test/data/nmdc_example_database.json index 7550394ea4..fead25d8f0 100644 --- a/test/data/nmdc_example_database.json +++ b/test/data/nmdc_example_database.json @@ -54,7 +54,10 @@ ], "omics_processing_set": [ { - "id": "gold:Gp0225767", + "id": "nmdc:bsmprc-45fc7de7-3610-4f15-b95e-d19462c98469", + "alternative_identifiers": [ + "gold:Gp0225767" + ], "name": "Forest soil microbial communities from Barre Woods Harvard Forest LTER site, Petersham, Massachusetts, United States - Inc-BW-C-14-O", "description": "Forest soil from Barre Woods Harvard Forest LTER site was incubated at 10C with heavy water. Sample is from a control plot at ambient soil temperature, organic horizon - top 4cm of soil", "has_input": [ @@ -76,7 +79,10 @@ "type": "nmdc:OmicsProcessing" }, { - "id": "gold:Gp0208560", + "id": "nmdc:bsmprc-50a0ab53-cd00-476e-9ca1-f178843b4a30", + "alternative_identifiers": [ + "gold:Gp0208560" + ], "name": "Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG", "description": "Permafrost microbial communities from Stordalen Mire, Sweden", "has_input": [ @@ -98,7 +104,10 @@ "type": "nmdc:OmicsProcessing" }, { - "id": "gold:Gp0306221", + "id": "nmdc:bsmprc-ed3f3c3a-8916-4fc8-8d98-40a8399719e3", + "alternative_identifiers": [ + "gold:Gp0306221" + ], "name": "Rhizosphere microbial communities from Carex aquatilis grown in University of Washington, Seatle, WA, United States - 4-1-23 metaG", "description": "Rhizosphere microbial communities from Carex aquatilis grown in submerged peat from a thermokarst bog, University of Washington, Seatle, WA, United States", "has_input": [ From dd0f1f33a1ef3b0f471d457689564c15626336fe Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 10:05:45 -0500 Subject: [PATCH 26/60] undo ChemicalEntity and OntologyClass typecodes --- src/schema/core.yaml | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/src/schema/core.yaml b/src/schema/core.yaml index cfc6b0fa51..ec50829361 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -138,6 +138,15 @@ classes: OntologyClass: is_a: NamedThing + notes: + - The identifiers for terms from external ontologies can't have their ids constrained to the nmdc namespace + # slot_usage: + # id: + # pattern: '^nmdc:ontc' + # structured_pattern: + # syntax: "{id_nmdc_prefix}:ontc-{id_shoulder}-{id_blade}{id_version}{id_locus}" + # interpolated: true + # partial_match: false EnvironmentalMaterialTerm: is_a: OntologyClass @@ -373,7 +382,15 @@ classes: description: >- An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states + comments: + - As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode to this class. slot_usage: + # id: + # pattern: '^nmdc:cheme' + # structured_pattern: + # syntax: "{id_nmdc_prefix}:cheme-{id_shoulder}-{id_blade}{id_version}{id_locus}" + # interpolated: true + # partial_match: false inchi: key: false multivalued: false From 75a1e6aabc7e85ca07d490b740850f541a3bc402 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 10:13:20 -0500 Subject: [PATCH 27/60] CollectingBiosamplesFromSite typecode and tests --- src/schema/nmdc.yaml | 6 ++++++ test/data/biosamples_to_sites.json | 4 ++-- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index d4e5cdbf59..b19d1275d1 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -192,6 +192,12 @@ classes: has_outputs: range: Biosample required: true + id: + pattern: '^nmdc:clsite' + structured_pattern: + syntax: "{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false DataObject: diff --git a/test/data/biosamples_to_sites.json b/test/data/biosamples_to_sites.json index d0e789839c..0d210827d0 100644 --- a/test/data/biosamples_to_sites.json +++ b/test/data/biosamples_to_sites.json @@ -193,7 +193,7 @@ ], "collecting_biosamples_from_site_set": [ { - "id": "cleanroom_schema:cbfs1", + "id": "nmdc:clsite-4ff95e3a-e5e1-4a85-96b2-acf3fb242004", "name": "Collection of biosamples from BESC-13-CL1_35_33", "has_inputs": [ "GOLD:BESC-13-CL1_35_33" @@ -205,7 +205,7 @@ ] }, { - "id": "cleanroom_schema:cbfs2", + "id": "nmdc:clsite-87c6ff79-4d89-4362-be87-67766356b1ce", "name": "Collection of biosamples from BESC-13-CL2_39_29", "has_inputs": [ "GOLD:BESC-13-CL2_39_29" From 8dbcfd6a17c95bebed23c8839120e7fbd03dbd06 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 10:19:59 -0500 Subject: [PATCH 28/60] DataObject typecode and tests --- src/schema/nmdc.yaml | 8 +++----- test/data/mg_assembly_data_objects_test.json | 6 +++--- test/data/nmdc_example_database.json | 6 +++--- 3 files changed, 9 insertions(+), 11 deletions(-) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index b19d1275d1..133feba4fc 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -104,7 +104,7 @@ settings: id_typecode_study: "sty" # id_typecode_biosample_processing: "bsmprc" id_typecode_omics_processing: "omprc" - id_typecode_dataobject: "dobj" + # id_typecode_dataobject: "dobj" # id_typecode_activity: "acty" id_typecode_named_thing: "nt" @@ -220,11 +220,9 @@ classes: description: required: true id: - pattern: '^nmdc:' + pattern: '^nmdc:dobj' structured_pattern: - todos: - - remove the static pattern once the minter can generate ids that satisfy this structured_pattern - syntax: "{id_nmdc_prefix}:{id_typecode_dataobject}-{id_shoulder}-{id_blade}{id_version}{id_locus}" + syntax: "{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false id_prefixes: diff --git a/test/data/mg_assembly_data_objects_test.json b/test/data/mg_assembly_data_objects_test.json index 78f0299a36..09e7768f66 100644 --- a/test/data/mg_assembly_data_objects_test.json +++ b/test/data/mg_assembly_data_objects_test.json @@ -1,21 +1,21 @@ { "data_object_set": [ { - "id": "nmdc:8ecc9e4fe4c74d7a58b02fd8954555b9", + "id": "nmdc:dobj-8ecc9e4fe4c74d7a58b02fd8954555b9", "name": "mapping_stats.txt", "description": "Metagenome Contig Coverage Stats for gold:Gp0061273", "file_size_bytes": 32787380, "type": "nmdc:DataObject" }, { - "id": "nmdc:3f85e34d2c32b65e33e4abd2431dfbe8", + "id": "nmdc:dobj-3f85e34d2c32b65e33e4abd2431dfbe8", "name": "assembly_contigs.fna", "description": "Assembled contigs fasta for gold:Gp0061273", "file_size_bytes": 206578499, "type": "nmdc:DataObject" }, { - "id": "nmdc:3c892f96e847b0b524d5d4e50611b5fd", + "id": "nmdc:dobj-3c892f96e847b0b524d5d4e50611b5fd", "name": "assembly_scaffolds.fna", "description": "Assembled scaffold fasta for gold:Gp0061273", "file_size_bytes": 205297945, diff --git a/test/data/nmdc_example_database.json b/test/data/nmdc_example_database.json index fead25d8f0..f76d531e58 100644 --- a/test/data/nmdc_example_database.json +++ b/test/data/nmdc_example_database.json @@ -296,21 +296,21 @@ ], "data_object_set": [ { - "id": "nmdc:161afbd2-0d43-48ba-bc96-47697de83fbb", + "id": "nmdc:dobj-161afbd2-0d43-48ba-bc96-47697de83fbb", "name": "11340.8.202049.GTCTCCT-AAGGAGA.fastq.gz", "description": "Raw sequencer read data", "file_size_bytes": 9208349052.0, "type": "nmdc:DataObject" }, { - "id": "nmdc:80224019-2607-4610-8981-11ba7ef871fc", + "id": "nmdc:dobj-80224019-2607-4610-8981-11ba7ef871fc", "name": "11839.4.222578.GAGCTCA-TTGAGCT.fastq.gz", "description": "Raw sequencer read data", "file_size_bytes": 34243309819.0, "type": "nmdc:DataObject" }, { - "id": "nmdc:5fd558d1-38d3-4f70-8fca-023fff2a035e", + "id": "nmdc:dobj-5fd558d1-38d3-4f70-8fca-023fff2a035e", "name": "12660.4.274923.GATCGTAC-GTACGATC.fastq.gz", "description": "Raw sequencer read data", "file_size_bytes": 7580035314.0, From 589278e5bf787611768b03830ba684fca52001f0 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 10:36:15 -0500 Subject: [PATCH 29/60] FieldResearchSite typecode and tests --- src/schema/nmdc.yaml | 7 +++++++ test/data/biosamples_to_sites.json | 14 ++++++++------ 2 files changed, 15 insertions(+), 6 deletions(-) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 133feba4fc..c13526436d 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -175,6 +175,13 @@ classes: the same plant were obtained at the same site. In this case, the site would correspond to one tree. - "might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833" + slot_usage: + id: + pattern: '^nmdc:frsite' + structured_pattern: + syntax: "{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false CollectingBiosamplesFromSite: is_a: PlannedProcess diff --git a/test/data/biosamples_to_sites.json b/test/data/biosamples_to_sites.json index 0d210827d0..558625ce7a 100644 --- a/test/data/biosamples_to_sites.json +++ b/test/data/biosamples_to_sites.json @@ -4,7 +4,7 @@ "id": "nmdc:bsm-biosample_placeholder_1", "name": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33 endosphere", "description": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA", - "collected_from": "GOLD:BESC-13-CL1_35_33", + "collected_from": "nmdc:frsite-2ec2ebde-857f-4dc5-ab5e-881c3eb337ce", "gold_biosample_identifiers": [ "GOLD:Gb0305833" ], @@ -34,7 +34,7 @@ "id": "nmdc:bsm-biosample_placeholder_2", "name": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33", "description": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", - "collected_from": "GOLD:BESC-13-CL1_35_33", + "collected_from": "nmdc:frsite-2ec2ebde-857f-4dc5-ab5e-881c3eb337ce", "gold_biosample_identifiers": [ "GOLD:Gb0291692" ], @@ -64,7 +64,7 @@ "id": "nmdc:bsm-biosample_placeholder_3", "name": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33", "description": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", - "collected_from": "GOLD:BESC-13-CL1_35_33", + "collected_from": "nmdc:frsite-2ec2ebde-857f-4dc5-ab5e-881c3eb337ce", "gold_biosample_identifiers": [ "GOLD:Gb0291582" ], @@ -183,11 +183,13 @@ ], "field_research_site_set": [ { - "id": "GOLD:BESC-13-CL1_35_33", + "id": "nmdc:frsite-2ec2ebde-857f-4dc5-ab5e-881c3eb337ce", + "name": "BESC-13-CL1_35_33", "description": "Bioscales tree BESC-13-CL1_35_33" }, { - "id": "GOLD:BESC-13-CL2_39_29", + "id": "nmdc:frsite-10e5281b-504b-4f56-80fe-2e50d7d00521", + "name": "BESC-13-CL2_39_29", "description": "Bioscales tree BESC-13-CL2_39_29" } ], @@ -196,7 +198,7 @@ "id": "nmdc:clsite-4ff95e3a-e5e1-4a85-96b2-acf3fb242004", "name": "Collection of biosamples from BESC-13-CL1_35_33", "has_inputs": [ - "GOLD:BESC-13-CL1_35_33" + "nmdc:frsite-2ec2ebde-857f-4dc5-ab5e-881c3eb337ce" ], "has_outputs": [ "GOLD:Gb0305833", From b74b14f9741734da292e124d5eb4b55d3a9286d2 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 11:08:31 -0500 Subject: [PATCH 30/60] Instrument typecode and tests --- src/schema/core.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/schema/core.yaml b/src/schema/core.yaml index ec50829361..34dcf48402 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -300,6 +300,13 @@ classes: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI]. exact_mappings: - OBI:0000485 + slot_usage: + id: + pattern: '^nmdc:inst' + structured_pattern: + syntax: "{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false MetaboliteQuantification: description: >- From f1abc94316b3e9402f985b7bbd1f45120959ed27 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 11:19:08 -0500 Subject: [PATCH 31/60] MagsAnalysisActivity typecode and tests --- src/schema/workflow_execution_activity.yaml | 9 ++++++++- test/data/MAGs_activity.json | 4 ++-- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index 67e14c9707..7550879009 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -187,6 +187,13 @@ classes: - low_depth_contig_num - unbinned_contig_num - mags_list + slot_usage: + id: + pattern: '^nmdc:wfmag' + structured_pattern: + syntax: "{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false ReadQcAnalysisActivity: description: A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal @@ -200,7 +207,7 @@ classes: - input_base_count - output_read_count - output_base_count -# - version + # - version slot_usage: input_read_bases: range: float diff --git a/test/data/MAGs_activity.json b/test/data/MAGs_activity.json index bca9143a3f..368fd50774 100644 --- a/test/data/MAGs_activity.json +++ b/test/data/MAGs_activity.json @@ -1,7 +1,7 @@ { "mags_activity_set": [ { - "id": "nmdc:act-f2fc8f5aade3092ea97769f0a892d2a9", + "id": "nmdc:wfmag-f2fc8f5aade3092ea97769f0a892d2a9", "name": "MAGs activiity 1781_86101", "was_informed_by": "gold:Gp0115663", "started_at_time": "2021-01-10T00:00:00+00:00", @@ -65,7 +65,7 @@ ] }, { - "id": "nmdc:act-a0ca0743a49e4bf12db9b5d933c4e76a", + "id": "nmdc:wfmag-a0ca0743a49e4bf12db9b5d933c4e76a", "name": "MAGs activiity 1781_86089", "was_informed_by": "gold:Gp0115664", "started_at_time": "2021-01-10T00:00:00+00:00", From a8eff2b8eb19c78bc4be2c068a9ca9520182d282 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 12:18:03 -0500 Subject: [PATCH 32/60] MaterialSample typecode and tests --- src/schema/core.yaml | 7 +++++++ src/schema/sample_prep.yaml | 9 ++++++++- test/data/samp_prep_db.json | 27 ++++++++++++++++----------- 3 files changed, 31 insertions(+), 12 deletions(-) diff --git a/src/schema/core.yaml b/src/schema/core.yaml index 34dcf48402..c9328d02da 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -107,6 +107,13 @@ classes: - Physical entity is_a: NamedThing title: Material Entity + slot_usage: + id: + pattern: '^nmdc:mate' + structured_pattern: + syntax: "{id_nmdc_prefix}:mate-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false AnalyticalSample: is_a: MaterialEntity diff --git a/src/schema/sample_prep.yaml b/src/schema/sample_prep.yaml index ef30bd78d3..48994809bc 100644 --- a/src/schema/sample_prep.yaml +++ b/src/schema/sample_prep.yaml @@ -266,10 +266,17 @@ classes: MaterialSample: name: MaterialSample title: Material sample - aliases: - Material entity is_a: NamedThing + slot_usage: + id: + pattern: '^nmdc:matsm' + structured_pattern: + syntax: "{id_nmdc_prefix}:matsm-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false + MaterialSamplingActivity: name: MaterialSamplingActivity title: Material sampling activity diff --git a/test/data/samp_prep_db.json b/test/data/samp_prep_db.json index 354435a83c..ef66d713a3 100644 --- a/test/data/samp_prep_db.json +++ b/test/data/samp_prep_db.json @@ -24,29 +24,34 @@ }, "container_type": "screw_top_conical" }, - "material_input": "monet_data:somextract_6", - "material_output": "monet_data:somextract_7" + "material_input": "nmdc:matsm-b1fb4ff1-e59b-4e2b-a8f9-b95ea6ba4135", + "material_output": "nmdc:matsm-181a7a0a-4b04-4a22-9b89-db53e2ccdc99" } ], "material_sample_set": [ { - "id": "monet_data:soil_1", + "name": "monet_data:soil_1", + "id": "nmdc:matsm-bfc5b458-1c62-44e7-886a-dd3a2cc7ad67", "description": "a soil biosample" }, { - "id": "monet_data:somextract_6", + "name": "nmdc:matsm-b1fb4ff1-e59b-4e2b-a8f9-b95ea6ba4135", + "id": "nmdc:matsm-b1fb4ff1-e59b-4e2b-a8f9-b95ea6ba4135", "description": "a 6 gram aliquot of monet_data:soil_1" }, { - "id": "monet_data:somextract_7", + "name": "monet_data:somextract_7", + "id": "nmdc:matsm-181a7a0a-4b04-4a22-9b89-db53e2ccdc99", "description": "monet_data:somextract_6 dissolved in 30 mL of water" }, { - "id": "monet_data:derive_4", + "name": "monet_data:derive_4", + "id": "nmdc:matsm-31380f3c-cea3-4f68-a8c6-cd84efa5e622", "description": "something at the beginning of a reaction" }, { - "id": "monet_data:derive_5", + "name": "monet_data:derive_5", + "id": "nmdc:matsm-9fe9277b-454a-4257-a825-3b4725df665e", "description": "something at the end of a reaction" } ], @@ -63,15 +68,15 @@ }, "container_type": "screw_top_conical" }, - "biosample_input": "monet_data:soil_1", - "material_output": "monet_data:somextract_6", + "biosample_input": "nmdc:matsm-bfc5b458-1c62-44e7-886a-dd3a2cc7ad67", + "material_output": "nmdc:matsm-b1fb4ff1-e59b-4e2b-a8f9-b95ea6ba4135", "sampling_method": "weighing" } ], "reaction_activity_set": [ { - "material_input": "monet_data:derive_4", - "material_output": "monet_data:derive_5", + "material_input": "nmdc:matsm-31380f3c-cea3-4f68-a8c6-cd84efa5e622", + "material_output": "nmdc:matsm-9fe9277b-454a-4257-a825-3b4725df665e", "reaction_aided_by": { "device_type": "thermomixer", "activity_temperature": { From 2f5120a06e952ca4672c3990f6169d93b07cdfad Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 12:23:15 -0500 Subject: [PATCH 33/60] MetabolomicsAnalysisActivity typecode but untested --- src/schema/workflow_execution_activity.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index 7550879009..182def9655 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -250,6 +250,12 @@ classes: has_calibration: description: >- TODO: Yuri to fill in + id: + pattern: '^nmdc:wfmb' + structured_pattern: + syntax: "{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false MetaproteomicsAnalysisActivity: is_a: WorkflowExecutionActivity From 6b4d0dc657bf66eb42a8d3bdbfd9fb92860fbe9b Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 12:28:53 -0500 Subject: [PATCH 34/60] MetagenomeAnnotationActivity typecode but untested --- src/schema/workflow_execution_activity.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index 182def9655..619dc6f1a0 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -154,6 +154,13 @@ classes: - gold_analysis_project_identifiers in_subset: - workflow subset + slot_usage: + id: + pattern: '^nmdc:wfmgan' + structured_pattern: + syntax: "{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false MetatranscriptomeAnnotationActivity: is_a: WorkflowExecutionActivity From 37f1f0a78cd9999996501b0e01a4e1847f2e2329 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 12:33:54 -0500 Subject: [PATCH 35/60] MetagenomeAssembly typecode but untested --- src/schema/workflow_execution_activity.yaml | 7 +++++++ test/data/mg_assembly_activities_test.json | 6 +++--- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index 619dc6f1a0..014665ee92 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -111,6 +111,13 @@ classes: - num_input_reads - num_aligned_reads - insdc_assembly_identifiers + slot_usage: + id: + pattern: '^nmdc:wfmgas' + structured_pattern: + syntax: "{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false MetatranscriptomeAssembly: is_a: WorkflowExecutionActivity diff --git a/test/data/mg_assembly_activities_test.json b/test/data/mg_assembly_activities_test.json index 02f194ec6f..50e0bf230b 100644 --- a/test/data/mg_assembly_activities_test.json +++ b/test/data/mg_assembly_activities_test.json @@ -1,7 +1,7 @@ { "metagenome_assembly_set": [ { - "id": "nmdc:act-f404cb05d4c1458b659ae2232245c45d", + "id": "nmdc:wfmgas-f404cb05d4c1458b659ae2232245c45d", "name": "Metagenome assembly 1472_51277", "was_informed_by": "gold:Gp0061273", "started_at_time": "2020-03-24T00:00:00+00:00", @@ -48,7 +48,7 @@ "num_aligned_reads": 63046103 }, { - "id": "nmdc:act-e7d3e1551ad9439505b522d5b1768c97", + "id": "nmdc:wfmgas-e7d3e1551ad9439505b522d5b1768c97", "name": "Metagenome assembly 1472_51278", "was_informed_by": "gold:Gp0061274", "started_at_time": "2020-03-25T00:00:00+00:00", @@ -95,7 +95,7 @@ "num_aligned_reads": 95369019 }, { - "id": "nmdc:act-9a2a0778e003977d594c93e54fcef3e6", + "id": "nmdc:wfmgas-9a2a0778e003977d594c93e54fcef3e6", "name": "Metagenome assembly 1472_51279", "was_informed_by": "gold:Gp0061275", "started_at_time": "2020-03-25T00:00:00+00:00", From 5be35e9a7b308bb934beb8d1e98c5ad35fb64e3c Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 12:37:39 -0500 Subject: [PATCH 36/60] MetaproteomicsAnalysisActivity typecode but untested --- src/schema/workflow_execution_activity.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index 014665ee92..231a802806 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -286,6 +286,12 @@ classes: has_peptide_quantifications: range: PeptideQuantification multivalued: true + id: + pattern: '^nmdc:wfmp' + structured_pattern: + syntax: "{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false NomAnalysisActivity: is_a: WorkflowExecutionActivity From f9417f54450d41dbaa0cde6dbda0ac20c9d56b58 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 12:43:43 -0500 Subject: [PATCH 37/60] MetatranscriptomeActivity typecode but untested --- src/schema/workflow_execution_activity.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index 231a802806..23ded4c1f9 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -185,6 +185,13 @@ classes: - workflow subset slots: - type + slot_usage: + id: + pattern: '^nmdc:wfmt' + structured_pattern: + syntax: "{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false MagsAnalysisActivity: From 00fcdc30a772ebc2b6267755e84a2c1461a753a1 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 12:46:59 -0500 Subject: [PATCH 38/60] MetatranscriptomeAnnotationActivity typecode but untested --- src/schema/workflow_execution_activity.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index 23ded4c1f9..46cd30049b 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -176,6 +176,13 @@ classes: - gold_analysis_project_identifiers in_subset: - workflow subset + slot_usage: + id: + pattern: '^nmdc:wfmtan' + structured_pattern: + syntax: "{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false MetatranscriptomeActivity: is_a: WorkflowExecutionActivity From c84f3f201b083f125f7d5afbb7b5ac251d3c2b76 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 12:50:34 -0500 Subject: [PATCH 39/60] MetatranscriptomeAssembly typecode but untested --- src/schema/workflow_execution_activity.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index 46cd30049b..e0fcef4639 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -152,6 +152,13 @@ classes: - num_input_reads - num_aligned_reads - insdc_assembly_identifiers + slot_usage: + id: + pattern: '^nmdc:wfmtas' + structured_pattern: + syntax: "{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false MetagenomeAnnotationActivity: description: A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs From c6bd285f4da2b1a45c5a4ea2027855c902ad8084 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 12:55:25 -0500 Subject: [PATCH 40/60] NomAnalysisActivity typecode but untested --- src/schema/workflow_execution_activity.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index e0fcef4639..815807a7ab 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -330,6 +330,13 @@ classes: range: string description: >- A reference to a file that holds calibration information. + id: + pattern: '^nmdc:wfnom' + structured_pattern: + syntax: "{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false + slots: From a57f3d4bd76984a5cc784121a24c5a0c2ed9ddbf Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 13:01:05 -0500 Subject: [PATCH 41/60] OmicsProcessing typecode but untested --- src/schema/nmdc.yaml | 6 +++--- test/data/gold_project_test.json | 6 +++--- test/data/nmdc_example_database.json | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index c13526436d..39711ca948 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -771,12 +771,12 @@ classes: - seq_meth - seq_quality_check - chimera_check + slot_usage: id: + pattern: '^nmdc:omprc' structured_pattern: - todos: - - remove any static pattern once the minter can generate ids that satisfy this structured_pattern - syntax: "{id_nmdc_prefix}:{id_typecode_omics_processing}-{id_shoulder}-{id_blade}{id_version}{id_locus}" + syntax: "{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false has_input: diff --git a/test/data/gold_project_test.json b/test/data/gold_project_test.json index 77fcf8b03b..9d743bc457 100644 --- a/test/data/gold_project_test.json +++ b/test/data/gold_project_test.json @@ -1,7 +1,7 @@ { "omics_processing_set": [ { - "id": "nmdc:bsmprc-93312e7f-79f2-4861-b108-3aa8ccb86c9b", + "id": "nmdc:omprc-93312e7f-79f2-4861-b108-3aa8ccb86c9b", "alternative_identifiers": [ "gold:Gp0108335" ], @@ -25,7 +25,7 @@ "type": "nmdc:OmicsProcessing" }, { - "id": "nmdc:bsmprc-68fa114f-6709-4e4c-bd2b-c53fd5ee51da", + "id": "nmdc:omprc-68fa114f-6709-4e4c-bd2b-c53fd5ee51da", "alternative_identifiers": [ "gold:Gp0108340" ], @@ -49,7 +49,7 @@ "type": "nmdc:OmicsProcessing" }, { - "id": "nmdc:bsmprc-32604e07-bfa6-4d43-a998-3f1cde25bf4f", + "id": "nmdc:omprc-32604e07-bfa6-4d43-a998-3f1cde25bf4f", "alternative_identifiers": [ "gold:Gp0108341" ], diff --git a/test/data/nmdc_example_database.json b/test/data/nmdc_example_database.json index f76d531e58..6760016c22 100644 --- a/test/data/nmdc_example_database.json +++ b/test/data/nmdc_example_database.json @@ -54,7 +54,7 @@ ], "omics_processing_set": [ { - "id": "nmdc:bsmprc-45fc7de7-3610-4f15-b95e-d19462c98469", + "id": "nmdc:omprc-45fc7de7-3610-4f15-b95e-d19462c98469", "alternative_identifiers": [ "gold:Gp0225767" ], @@ -79,7 +79,7 @@ "type": "nmdc:OmicsProcessing" }, { - "id": "nmdc:bsmprc-50a0ab53-cd00-476e-9ca1-f178843b4a30", + "id": "nmdc:omprc-50a0ab53-cd00-476e-9ca1-f178843b4a30", "alternative_identifiers": [ "gold:Gp0208560" ], @@ -104,7 +104,7 @@ "type": "nmdc:OmicsProcessing" }, { - "id": "nmdc:bsmprc-ed3f3c3a-8916-4fc8-8d98-40a8399719e3", + "id": "nmdc:omprc-ed3f3c3a-8916-4fc8-8d98-40a8399719e3", "alternative_identifiers": [ "gold:Gp0306221" ], From a84d7593858647026598cbf62325c0ac55e97049 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 13:07:39 -0500 Subject: [PATCH 42/60] made PlannedProcess abstract see also PersonValue --- src/schema/core.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/schema/core.yaml b/src/schema/core.yaml index c9328d02da..c049772de9 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -135,6 +135,7 @@ classes: PlannedProcess: + abstract: true class_uri: OBI:0000011 is_a: NamedThing title: Planned Process From b34b72eaeab3c82493a16405ed57fdfbb43edeba Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 13:11:38 -0500 Subject: [PATCH 43/60] ReadBasedTaxonomyAnalysisActivity typecode but untested --- src/schema/workflow_execution_activity.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index 815807a7ab..601d9da4f1 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -265,6 +265,13 @@ classes: - workflow subset slots: - type + slot_usage: + id: + pattern: '^nmdc:wfrbt' + structured_pattern: + syntax: "{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false MetabolomicsAnalysisActivity: From 325c8be91dfccef80d43474278f4bce9da7fbcc6 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 13:16:12 -0500 Subject: [PATCH 44/60] ReadQcAnalysisActivity typecode but untested --- src/schema/workflow_execution_activity.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index 601d9da4f1..dedff3af53 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -256,6 +256,12 @@ classes: inlined: false has_output: inlined: false + id: + pattern: '^nmdc:wfrqc' + structured_pattern: + syntax: "{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false ReadBasedTaxonomyAnalysisActivity: description: A workflow execution activity that performs taxonomy classification using sequencing reads From 7806fa31fc5bda334f7688c858de275124313e34 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 13:19:44 -0500 Subject: [PATCH 45/60] Site typecode but untested --- src/schema/core.yaml | 9 +++++++-- src/schema/nmdc.yaml | 2 +- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/src/schema/core.yaml b/src/schema/core.yaml index c049772de9..c702745599 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -131,8 +131,13 @@ classes: title: Site comments: - BCO sample collection site ? - - + slot_usage: + id: + pattern: '^nmdc:site' + structured_pattern: + syntax: "{id_nmdc_prefix}:site-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false PlannedProcess: abstract: true diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 39711ca948..359a5ce614 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -103,7 +103,7 @@ settings: # id_typecode_biosample: "bsm" id_typecode_study: "sty" # id_typecode_biosample_processing: "bsmprc" - id_typecode_omics_processing: "omprc" +# id_typecode_omics_processing: "omprc" # id_typecode_dataobject: "dobj" # id_typecode_activity: "acty" id_typecode_named_thing: "nt" From 61200cc5eccbfdf4e817e3036e7b090ee4ff1243 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 13:28:15 -0500 Subject: [PATCH 46/60] WorkflowExecutionActivity typecode with tests --- src/schema/workflow_execution_activity.yaml | 6 + test/data/img_mg_annotation_objects.json | 228 ++++++++++---------- 2 files changed, 120 insertions(+), 114 deletions(-) diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index dedff3af53..b6db29eeaf 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -73,6 +73,12 @@ classes: execution_resource: required: true type: { } + id: + pattern: '^nmdc:wf' + structured_pattern: + syntax: "{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false MetagenomeAssembly: description: A workflow execution activity that converts sequencing reads into an assembled metagenome. diff --git a/test/data/img_mg_annotation_objects.json b/test/data/img_mg_annotation_objects.json index f5d4fe59e6..3d78849ab5 100644 --- a/test/data/img_mg_annotation_objects.json +++ b/test/data/img_mg_annotation_objects.json @@ -17,7 +17,7 @@ "was_informed_by": "gold:Gp0153825", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-9076b6e2b334532d7be4e48b25ca80dd", + "id": "nmdc:wf-9076b6e2b334532d7be4e48b25ca80dd", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -37,7 +37,7 @@ "was_informed_by": "gold:Gp0119849", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-bf16723c3a2b226747c6b40085f51cc2", + "id": "nmdc:wf-bf16723c3a2b226747c6b40085f51cc2", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -57,7 +57,7 @@ "was_informed_by": "gold:Gp0119850", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-c77fe920a664d4e174d413ec89f040a3", + "id": "nmdc:wf-c77fe920a664d4e174d413ec89f040a3", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -77,7 +77,7 @@ "was_informed_by": "gold:Gp0119851", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-6c5858d2b28e1de316120d410ed62544", + "id": "nmdc:wf-6c5858d2b28e1de316120d410ed62544", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -97,7 +97,7 @@ "was_informed_by": "gold:Gp0119852", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-879e7ff3374deee6054684076a882649", + "id": "nmdc:wf-879e7ff3374deee6054684076a882649", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -117,7 +117,7 @@ "was_informed_by": "gold:Gp0119853", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-608cc16c1e395be8f7f56f123b88d17a", + "id": "nmdc:wf-608cc16c1e395be8f7f56f123b88d17a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -137,7 +137,7 @@ "was_informed_by": "gold:Gp0119854", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-db089a3971603b130cc25c9edf29a951", + "id": "nmdc:wf-db089a3971603b130cc25c9edf29a951", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -157,7 +157,7 @@ "was_informed_by": "gold:Gp0119855", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-1762bbeb64674af6e394ee1323391833", + "id": "nmdc:wf-1762bbeb64674af6e394ee1323391833", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -177,7 +177,7 @@ "was_informed_by": "gold:Gp0119856", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-4794bbc1dc72807df92a30088cf4551b", + "id": "nmdc:wf-4794bbc1dc72807df92a30088cf4551b", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -197,7 +197,7 @@ "was_informed_by": "gold:Gp0119857", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-9cb27d7fe967ed437acf43b7cb5f01ee", + "id": "nmdc:wf-9cb27d7fe967ed437acf43b7cb5f01ee", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -217,7 +217,7 @@ "was_informed_by": "gold:Gp0119858", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-b52fd6e2d28c922c305849b2e6e29246", + "id": "nmdc:wf-b52fd6e2d28c922c305849b2e6e29246", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -237,7 +237,7 @@ "was_informed_by": "gold:Gp0119859", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-f23f9cd69666b01795e4c43bacb9ae62", + "id": "nmdc:wf-f23f9cd69666b01795e4c43bacb9ae62", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -257,7 +257,7 @@ "was_informed_by": "gold:Gp0119860", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-9278b29bb5c234046a11937991a3a652", + "id": "nmdc:wf-9278b29bb5c234046a11937991a3a652", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -277,7 +277,7 @@ "was_informed_by": "gold:Gp0119861", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-67d82e4c6f9796611f5a2234596eb6a2", + "id": "nmdc:wf-67d82e4c6f9796611f5a2234596eb6a2", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -297,7 +297,7 @@ "was_informed_by": "gold:Gp0119862", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-9e9c8643f496b6472ddb602aff30021d", + "id": "nmdc:wf-9e9c8643f496b6472ddb602aff30021d", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -317,7 +317,7 @@ "was_informed_by": "gold:Gp0119863", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-facd1cd7880760c4d227237d8142d60b", + "id": "nmdc:wf-facd1cd7880760c4d227237d8142d60b", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -337,7 +337,7 @@ "was_informed_by": "gold:Gp0119864", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-6c6eff8448b4782e31363eb7a783ef16", + "id": "nmdc:wf-6c6eff8448b4782e31363eb7a783ef16", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -357,7 +357,7 @@ "was_informed_by": "gold:Gp0119865", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-3d2d6fbece4298a34798a5cdc28fccbc", + "id": "nmdc:wf-3d2d6fbece4298a34798a5cdc28fccbc", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -377,7 +377,7 @@ "was_informed_by": "gold:Gp0119866", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-993f0fb1fb43a8db2c04f6a6064d1e91", + "id": "nmdc:wf-993f0fb1fb43a8db2c04f6a6064d1e91", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -397,7 +397,7 @@ "was_informed_by": "gold:Gp0119867", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-8a43ec3baf8aafe09d96eb7fbf58c916", + "id": "nmdc:wf-8a43ec3baf8aafe09d96eb7fbf58c916", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -417,7 +417,7 @@ "was_informed_by": "gold:Gp0119868", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-57e9c4e31f9c612633325bbe5c6c2f87", + "id": "nmdc:wf-57e9c4e31f9c612633325bbe5c6c2f87", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -437,7 +437,7 @@ "was_informed_by": "gold:Gp0119869", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-60c965c51b96153a9cffa6f4dd62a2e6", + "id": "nmdc:wf-60c965c51b96153a9cffa6f4dd62a2e6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -457,7 +457,7 @@ "was_informed_by": "gold:Gp0119870", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-42addbcd527a65d01a4d2fbd2da7758a", + "id": "nmdc:wf-42addbcd527a65d01a4d2fbd2da7758a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -477,7 +477,7 @@ "was_informed_by": "gold:Gp0119871", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-3204b453fe3471a5c6babce54398d9af", + "id": "nmdc:wf-3204b453fe3471a5c6babce54398d9af", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -497,7 +497,7 @@ "was_informed_by": "gold:Gp0127623", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-92070449b2ee66f6ec04125edc8ae30a", + "id": "nmdc:wf-92070449b2ee66f6ec04125edc8ae30a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -517,7 +517,7 @@ "was_informed_by": "gold:Gp0127624", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-f0773e35f29db6c8c9ec2354b6560c5f", + "id": "nmdc:wf-f0773e35f29db6c8c9ec2354b6560c5f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -537,7 +537,7 @@ "was_informed_by": "gold:Gp0127625", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-dfbc92d67d6307fc16059f858f8d81f6", + "id": "nmdc:wf-dfbc92d67d6307fc16059f858f8d81f6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -557,7 +557,7 @@ "was_informed_by": "gold:Gp0127626", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-b17f7734657148a50baf5216849b3b2f", + "id": "nmdc:wf-b17f7734657148a50baf5216849b3b2f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -577,7 +577,7 @@ "was_informed_by": "gold:Gp0127627", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-4b54a8416db39168fa6403d6832476e6", + "id": "nmdc:wf-4b54a8416db39168fa6403d6832476e6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -597,7 +597,7 @@ "was_informed_by": "gold:Gp0127628", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-689781c3f0a680b05f9a0a9b377b0ed9", + "id": "nmdc:wf-689781c3f0a680b05f9a0a9b377b0ed9", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -617,7 +617,7 @@ "was_informed_by": "gold:Gp0127629", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-d8af769e0dd753e86ef1f545536f3024", + "id": "nmdc:wf-d8af769e0dd753e86ef1f545536f3024", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -637,7 +637,7 @@ "was_informed_by": "gold:Gp0127630", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-b579670a8b80fd02e453d5ac031a574e", + "id": "nmdc:wf-b579670a8b80fd02e453d5ac031a574e", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -657,7 +657,7 @@ "was_informed_by": "gold:Gp0127631", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-406be722709ec331037987b30acc6b18", + "id": "nmdc:wf-406be722709ec331037987b30acc6b18", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -677,7 +677,7 @@ "was_informed_by": "gold:Gp0127632", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-163dfd2463186259deeae10b15d25119", + "id": "nmdc:wf-163dfd2463186259deeae10b15d25119", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -697,7 +697,7 @@ "was_informed_by": "gold:Gp0127633", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-act-ac967b73a027cfac522a742ddbbf9521", + "id": "nmdc:wf-ac967b73a027cfac522a742ddbbf9521", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -717,7 +717,7 @@ "was_informed_by": "gold:Gp0127634", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-8287ea44a458b50606a04fe82ceb83b1", + "id": "nmdc:wf-8287ea44a458b50606a04fe82ceb83b1", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -737,7 +737,7 @@ "was_informed_by": "gold:Gp0127635", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-e763e255fa74e2629d7d86e10f838d4b", + "id": "nmdc:wf-e763e255fa74e2629d7d86e10f838d4b", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -757,7 +757,7 @@ "was_informed_by": "gold:Gp0127636", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-89dde14d6545e93e749ffeae6fc3bdd6", + "id": "nmdc:wf-89dde14d6545e93e749ffeae6fc3bdd6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -777,7 +777,7 @@ "was_informed_by": "gold:Gp0127637", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-507c53e61a3c02d763b05d2a5eb2bda5", + "id": "nmdc:wf-507c53e61a3c02d763b05d2a5eb2bda5", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -797,7 +797,7 @@ "was_informed_by": "gold:Gp0127638", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-93656c96853f97524040c44f4b346d75", + "id": "nmdc:wf-93656c96853f97524040c44f4b346d75", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -817,7 +817,7 @@ "was_informed_by": "gold:Gp0127639", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-78ec466d9918b7fa1cbc033b19a37a10", + "id": "nmdc:wf-78ec466d9918b7fa1cbc033b19a37a10", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -837,7 +837,7 @@ "was_informed_by": "gold:Gp0127640", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-5ac74427da62d00b8493cf6bc7c8e43d", + "id": "nmdc:wf-5ac74427da62d00b8493cf6bc7c8e43d", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -857,7 +857,7 @@ "was_informed_by": "gold:Gp0127641", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-6808e9a6d7450f02019691d89c57ff1f", + "id": "nmdc:wf-6808e9a6d7450f02019691d89c57ff1f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -877,7 +877,7 @@ "was_informed_by": "gold:Gp0127642", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-45f4a9d66e8d45a534fc2067670bf012", + "id": "nmdc:wf-45f4a9d66e8d45a534fc2067670bf012", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -897,7 +897,7 @@ "was_informed_by": "gold:Gp0127643", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-b59602d74d9ee08ccd285a7ac2e5f6b2", + "id": "nmdc:wf-b59602d74d9ee08ccd285a7ac2e5f6b2", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -917,7 +917,7 @@ "was_informed_by": "gold:Gp0127644", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-339e8f1e41b780e4e565ce53067bc9bb", + "id": "nmdc:wf-339e8f1e41b780e4e565ce53067bc9bb", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -937,7 +937,7 @@ "was_informed_by": "gold:Gp0127645", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-e148a2d4befa290bbd216b6654371606", + "id": "nmdc:wf-e148a2d4befa290bbd216b6654371606", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -957,7 +957,7 @@ "was_informed_by": "gold:Gp0127646", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-02aca43c6efc414d5971e8a179bbbcf0", + "id": "nmdc:wf-02aca43c6efc414d5971e8a179bbbcf0", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -977,7 +977,7 @@ "was_informed_by": "gold:Gp0127647", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-4488991684ed07f2b9a2bb5b8b1a59a9", + "id": "nmdc:wf-4488991684ed07f2b9a2bb5b8b1a59a9", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -997,7 +997,7 @@ "was_informed_by": "gold:Gp0127648", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-ca2cac5f3de8db080031d727ff4db8ec", + "id": "nmdc:wf-ca2cac5f3de8db080031d727ff4db8ec", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1017,7 +1017,7 @@ "was_informed_by": "gold:Gp0127649", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-1524a48694d670c26a1b55238d9f1949", + "id": "nmdc:wf-1524a48694d670c26a1b55238d9f1949", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1037,7 +1037,7 @@ "was_informed_by": "gold:Gp0127651", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-e96dba76c7c388aebab7ad759b2a5694", + "id": "nmdc:wf-e96dba76c7c388aebab7ad759b2a5694", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1057,7 +1057,7 @@ "was_informed_by": "gold:Gp0127652", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-5e21f299a395e845341500a334e94ff2", + "id": "nmdc:wf-5e21f299a395e845341500a334e94ff2", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1077,7 +1077,7 @@ "was_informed_by": "gold:Gp0127653", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-d6f99d25d421ab54908e603b016df20f", + "id": "nmdc:wf-d6f99d25d421ab54908e603b016df20f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1097,7 +1097,7 @@ "was_informed_by": "gold:Gp0127654", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-405d59d65f666d1bb1f44393bf6b3c1a", + "id": "nmdc:wf-405d59d65f666d1bb1f44393bf6b3c1a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1117,7 +1117,7 @@ "was_informed_by": "gold:Gp0127655", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-82124fe8afc73ce5f61011ba9520ae38", + "id": "nmdc:wf-82124fe8afc73ce5f61011ba9520ae38", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1137,7 +1137,7 @@ "was_informed_by": "gold:Gp0127656", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-9bdf633bcd7d5b9bb1bf95ccd26349cd", + "id": "nmdc:wf-9bdf633bcd7d5b9bb1bf95ccd26349cd", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1157,7 +1157,7 @@ "was_informed_by": "gold:Gp0115664", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-686818cb31dc45d3d4482847ec007584", + "id": "nmdc:wf-686818cb31dc45d3d4482847ec007584", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1177,7 +1177,7 @@ "was_informed_by": "gold:Gp0115675", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-2e10913bdcfacfeeab4d9f7a0aa2af8f", + "id": "nmdc:wf-2e10913bdcfacfeeab4d9f7a0aa2af8f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1197,7 +1197,7 @@ "was_informed_by": "gold:Gp0115673", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-b3bd170070e9c37f535de92c9f37b2b4", + "id": "nmdc:wf-b3bd170070e9c37f535de92c9f37b2b4", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1217,7 +1217,7 @@ "was_informed_by": "gold:Gp0115677", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-fdd5f518cea894505f0bd6ac02205ba3", + "id": "nmdc:wf-fdd5f518cea894505f0bd6ac02205ba3", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1237,7 +1237,7 @@ "was_informed_by": "gold:Gp0115678", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-42613f7c1fa860e847e2c93e2462b6f7", + "id": "nmdc:wf-42613f7c1fa860e847e2c93e2462b6f7", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1257,7 +1257,7 @@ "was_informed_by": "gold:Gp0115665", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-9b6144e11b277a1f020c54da4ee79bac", + "id": "nmdc:wf-9b6144e11b277a1f020c54da4ee79bac", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1277,7 +1277,7 @@ "was_informed_by": "gold:Gp0115671", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-c65521ed98ca6f569686debc46ea274d", + "id": "nmdc:wf-c65521ed98ca6f569686debc46ea274d", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1297,7 +1297,7 @@ "was_informed_by": "gold:Gp0115666", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-638923494b08b936cefdac95ef58c558", + "id": "nmdc:wf-638923494b08b936cefdac95ef58c558", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1317,7 +1317,7 @@ "was_informed_by": "gold:Gp0115669", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-73840751bf8835b680aff13d0eb2335a", + "id": "nmdc:wf-73840751bf8835b680aff13d0eb2335a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1337,7 +1337,7 @@ "was_informed_by": "gold:Gp0115667", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-7b684248db11762d14a95ebdda7e8a81", + "id": "nmdc:wf-7b684248db11762d14a95ebdda7e8a81", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1357,7 +1357,7 @@ "was_informed_by": "gold:Gp0115676", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-87eb3326bcc84557dc334eff00d4a0bf", + "id": "nmdc:wf-87eb3326bcc84557dc334eff00d4a0bf", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1377,7 +1377,7 @@ "was_informed_by": "gold:Gp0115668", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-87de8edb421c5364ee75c172715292cc", + "id": "nmdc:wf-87de8edb421c5364ee75c172715292cc", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1397,7 +1397,7 @@ "was_informed_by": "gold:Gp0115663", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-2d9a6d5e57ab455c257d8c3424331113", + "id": "nmdc:wf-2d9a6d5e57ab455c257d8c3424331113", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1417,7 +1417,7 @@ "was_informed_by": "gold:Gp0115670", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-9994a8414976fd6b56935648246493b5", + "id": "nmdc:wf-9994a8414976fd6b56935648246493b5", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1437,7 +1437,7 @@ "was_informed_by": "gold:Gp0115672", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-932040eace29833c2b528f4279446285", + "id": "nmdc:wf-932040eace29833c2b528f4279446285", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1457,7 +1457,7 @@ "was_informed_by": "gold:Gp0115674", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-5981c6f73f7cdc963866091b0101a9b7", + "id": "nmdc:wf-5981c6f73f7cdc963866091b0101a9b7", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1477,7 +1477,7 @@ "was_informed_by": "gold:Gp0115679", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-9fcee63f77040c2b8cc0726b15f9f068", + "id": "nmdc:wf-9fcee63f77040c2b8cc0726b15f9f068", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1497,7 +1497,7 @@ "was_informed_by": "gold:Gp0321263", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-8d355d3c7070686b0beb20e39d17e172", + "id": "nmdc:wf-8d355d3c7070686b0beb20e39d17e172", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1517,7 +1517,7 @@ "was_informed_by": "gold:Gp0321264", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-9269f143d88b7d5ff3c61897cfef80a7", + "id": "nmdc:wf-9269f143d88b7d5ff3c61897cfef80a7", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1537,7 +1537,7 @@ "was_informed_by": "gold:Gp0321265", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-36f15e6f9d8426dbc49ea6928b6b4bb6", + "id": "nmdc:wf-36f15e6f9d8426dbc49ea6928b6b4bb6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1557,7 +1557,7 @@ "was_informed_by": "gold:Gp0321266", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-c6acdfbb7449a3faf079ec67396af96b", + "id": "nmdc:wf-c6acdfbb7449a3faf079ec67396af96b", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1577,7 +1577,7 @@ "was_informed_by": "gold:Gp0321267", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-739891753f88a2359b78191f41c19ad0", + "id": "nmdc:wf-739891753f88a2359b78191f41c19ad0", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1597,7 +1597,7 @@ "was_informed_by": "gold:Gp0321268", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-428a67c345a48187f0924d3af673c83c", + "id": "nmdc:wf-428a67c345a48187f0924d3af673c83c", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1617,7 +1617,7 @@ "was_informed_by": "gold:Gp0321269", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-3f1eb315892bb62126887cce05bdae32", + "id": "nmdc:wf-3f1eb315892bb62126887cce05bdae32", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1637,7 +1637,7 @@ "was_informed_by": "gold:Gp0321270", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-63648550d5280b9de5c61fc3d9f75f27", + "id": "nmdc:wf-63648550d5280b9de5c61fc3d9f75f27", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1657,7 +1657,7 @@ "was_informed_by": "gold:Gp0321271", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-9593e1500765d71b2a9eeb87ff22cb7a", + "id": "nmdc:wf-9593e1500765d71b2a9eeb87ff22cb7a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1677,7 +1677,7 @@ "was_informed_by": "gold:Gp0321272", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-8e3f1f49fdd583134060849f51c4c9b2", + "id": "nmdc:wf-8e3f1f49fdd583134060849f51c4c9b2", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1697,7 +1697,7 @@ "was_informed_by": "gold:Gp0321273", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-10c34e648ade3d60e9a82c234293c3ad", + "id": "nmdc:wf-10c34e648ade3d60e9a82c234293c3ad", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1717,7 +1717,7 @@ "was_informed_by": "gold:Gp0321274", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-9fb743bed2cae43e0c86553b046e1ec3", + "id": "nmdc:wf-9fb743bed2cae43e0c86553b046e1ec3", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1737,7 +1737,7 @@ "was_informed_by": "gold:Gp0321275", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-43eaacb2ce2ac16f5ac67ccecfcd66be", + "id": "nmdc:wf-43eaacb2ce2ac16f5ac67ccecfcd66be", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1757,7 +1757,7 @@ "was_informed_by": "gold:Gp0321276", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-b4656c5f9122aab8e12e40bc24bec749", + "id": "nmdc:wf-b4656c5f9122aab8e12e40bc24bec749", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1777,7 +1777,7 @@ "was_informed_by": "gold:Gp0321277", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-aa45b2e1b2a903ffe1861ff6c2afcb51", + "id": "nmdc:wf-aa45b2e1b2a903ffe1861ff6c2afcb51", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1797,7 +1797,7 @@ "was_informed_by": "gold:Gp0321278", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-7f6f6431a81d831ade7a2c66ec675f3a", + "id": "nmdc:wf-7f6f6431a81d831ade7a2c66ec675f3a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1817,7 +1817,7 @@ "was_informed_by": "gold:Gp0321279", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-642b62309801412cc0020f1b9e02f2bf", + "id": "nmdc:wf-642b62309801412cc0020f1b9e02f2bf", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1837,7 +1837,7 @@ "was_informed_by": "gold:Gp0321280", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-b51eda7aa71887b5c3d87a88ae9ef886", + "id": "nmdc:wf-b51eda7aa71887b5c3d87a88ae9ef886", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1857,7 +1857,7 @@ "was_informed_by": "gold:Gp0321281", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-24cc70779dc20ddcb8472360e94c1adb", + "id": "nmdc:wf-24cc70779dc20ddcb8472360e94c1adb", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1877,7 +1877,7 @@ "was_informed_by": "gold:Gp0321282", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-3c9a77593015e132a0fcb47e32077c78", + "id": "nmdc:wf-3c9a77593015e132a0fcb47e32077c78", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1897,7 +1897,7 @@ "was_informed_by": "gold:Gp0321283", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-86ebdd0ce08264d2642a571956d686db", + "id": "nmdc:wf-86ebdd0ce08264d2642a571956d686db", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1917,7 +1917,7 @@ "was_informed_by": "gold:Gp0321284", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-8c0f927607c2b240824a5c52800d4c04", + "id": "nmdc:wf-8c0f927607c2b240824a5c52800d4c04", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1937,7 +1937,7 @@ "was_informed_by": "gold:Gp0321285", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-030d8c58a26cc8164ce629b8e988532a", + "id": "nmdc:wf-030d8c58a26cc8164ce629b8e988532a", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1957,7 +1957,7 @@ "was_informed_by": "gold:Gp0321286", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-132d4df2f27d60ae8fb093248975462f", + "id": "nmdc:wf-132d4df2f27d60ae8fb093248975462f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1977,7 +1977,7 @@ "was_informed_by": "gold:Gp0321287", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-6dfbdbcd7ab18ee7b2d213124e239cf6", + "id": "nmdc:wf-6dfbdbcd7ab18ee7b2d213124e239cf6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1997,7 +1997,7 @@ "was_informed_by": "gold:Gp0321288", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-1f8036641fc942724894de3ed94df671", + "id": "nmdc:wf-1f8036641fc942724894de3ed94df671", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2017,7 +2017,7 @@ "was_informed_by": "gold:Gp0321289", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-9b38ed417fe51b52f3afbe0ac56b25c1", + "id": "nmdc:wf-9b38ed417fe51b52f3afbe0ac56b25c1", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2037,7 +2037,7 @@ "was_informed_by": "gold:Gp0321290", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-4e839407423180f709d7d5a81e6f070f", + "id": "nmdc:wf-4e839407423180f709d7d5a81e6f070f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2057,7 +2057,7 @@ "was_informed_by": "gold:Gp0321291", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-65a4e2c6d56914ab2e923aedd3441c4d", + "id": "nmdc:wf-65a4e2c6d56914ab2e923aedd3441c4d", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2077,7 +2077,7 @@ "was_informed_by": "gold:Gp0321292", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-5e2e998dfbfbfde7091237749c8d9028", + "id": "nmdc:wf-5e2e998dfbfbfde7091237749c8d9028", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2097,7 +2097,7 @@ "was_informed_by": "gold:Gp0321293", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-1d1f5b339f19cc457782e86e04688b9f", + "id": "nmdc:wf-1d1f5b339f19cc457782e86e04688b9f", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2117,7 +2117,7 @@ "was_informed_by": "gold:Gp0321294", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-fd71f805d1e05eae9f38d7d16de66299", + "id": "nmdc:wf-fd71f805d1e05eae9f38d7d16de66299", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2137,7 +2137,7 @@ "was_informed_by": "gold:Gp0321295", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-7fbff9ac4fe3633f9f762069ed572b1c", + "id": "nmdc:wf-7fbff9ac4fe3633f9f762069ed572b1c", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2157,7 +2157,7 @@ "was_informed_by": "gold:Gp0321296", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-327db9baa82cc3d9de443613cea1ee35", + "id": "nmdc:wf-327db9baa82cc3d9de443613cea1ee35", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2177,7 +2177,7 @@ "was_informed_by": "gold:Gp0321297", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-6b8a96eb366ae631aa86badd9d11e9ae", + "id": "nmdc:wf-6b8a96eb366ae631aa86badd9d11e9ae", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2197,7 +2197,7 @@ "was_informed_by": "gold:Gp0321298", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-17fadd9c29b2374dbee61bd95e3f0a02", + "id": "nmdc:wf-17fadd9c29b2374dbee61bd95e3f0a02", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2217,7 +2217,7 @@ "was_informed_by": "gold:Gp0321299", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-8456c04883daa652cd3c8ef61440c602", + "id": "nmdc:wf-8456c04883daa652cd3c8ef61440c602", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2237,7 +2237,7 @@ "was_informed_by": "gold:Gp0321300", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-724f98d56bbda5686819251b3d35b3bb", + "id": "nmdc:wf-724f98d56bbda5686819251b3d35b3bb", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2257,7 +2257,7 @@ "was_informed_by": "gold:Gp0321301", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-b8865de68b6a30e28e9232a1184e4703", + "id": "nmdc:wf-b8865de68b6a30e28e9232a1184e4703", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2277,7 +2277,7 @@ "was_informed_by": "gold:Gp0321302", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:act-449b5471dff17853621e8dcd4e46d790", + "id": "nmdc:wf-449b5471dff17853621e8dcd4e46d790", "ended_at_time": "2021-01-12T00:00:00+00:00" } ] From 49a09a4fcc7e65ddc27705f52c57d8a40c2ee0f2 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 13:34:51 -0500 Subject: [PATCH 47/60] NamedThing id pattern and typecode removal --- src/schema/core.yaml | 14 +++++++------- src/schema/nmdc.yaml | 6 ++---- 2 files changed, 9 insertions(+), 11 deletions(-) diff --git a/src/schema/core.yaml b/src/schema/core.yaml index c702745599..e3e6ef6ea4 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -92,13 +92,13 @@ classes: - name - description - alternative_identifiers - slot_usage: - id: - structured_pattern: - todos: - syntax: "{id_nmdc_prefix}:{id_typecode_named_thing}-{id_shoulder}-{id_blade}{id_version}{id_locus}" - interpolated: true - partial_match: false +# slot_usage: +# id: +# structured_pattern: +# todos: +# syntax: "{id_nmdc_prefix}:{id_typecode_named_thing}-{id_shoulder}-{id_blade}{id_version}{id_locus}" +# interpolated: true +# partial_match: false MaterialEntity: diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 359a5ce614..d737c1b70d 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -103,12 +103,10 @@ settings: # id_typecode_biosample: "bsm" id_typecode_study: "sty" # id_typecode_biosample_processing: "bsmprc" -# id_typecode_omics_processing: "omprc" + # id_typecode_omics_processing: "omprc" # id_typecode_dataobject: "dobj" # id_typecode_activity: "acty" - id_typecode_named_thing: "nt" - - + # id_typecode_named_thing: "nt" subsets: sample subset: From 349aac993f69f6a80f38f724ae13c82168c05082 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 13:53:05 -0500 Subject: [PATCH 48/60] Study typecode with tests --- src/schema/nmdc.yaml | 7 +++---- test/data/nmdc_example_database.json | 15 ++++++++++++--- test/data/study_credit_test.json | 2 +- test/data/study_test.json | 15 ++++++++++++--- 4 files changed, 28 insertions(+), 11 deletions(-) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index d737c1b70d..249fa3b55e 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -619,13 +619,12 @@ classes: - study_image slot_usage: id: - description: An NMDC assigned unique identifier for a study submitted to NMDC. + pattern: '^nmdc:sty' structured_pattern: - todos: - - remove any static pattern once the minter can generate ids that satisfy this structured_pattern - syntax: "{id_nmdc_prefix}:{id_typecode_study}-{id_shoulder}-{id_blade}{id_version}{id_locus}" + syntax: "{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false + doi: description: >- The dataset citation for this study diff --git a/test/data/nmdc_example_database.json b/test/data/nmdc_example_database.json index 6760016c22..c93471a411 100644 --- a/test/data/nmdc_example_database.json +++ b/test/data/nmdc_example_database.json @@ -1,7 +1,10 @@ { "study_set": [ { - "id": "gold:Gs0128849", + "id": "nmdc:sty-19f024bb-8f6a-42e9-846b-beff8e417cbd", + "gold_study_identifiers": [ + "gold:Gs0128849" + ], "name": "Permafrost microbial communities from Stordalen Mire, Sweden", "description": "Thawing permafrost is one of the largest soil carbon pools on the planet. The goal of this project is to study microbial communities that participate in the soil carbon cycle.", "ecosystem": "Environmental", @@ -18,7 +21,10 @@ "type": "nmdc:Study" }, { - "id": "gold:Gs0130354", + "id": "nmdc:sty-d9a5431e-0ae0-4953-b00a-945fc5d94cd9", + "gold_study_identifiers": [ + "gold:Gs0130354" + ], "name": "Forest soil microbial communities from Barre Woods Harvard Forest LTER site, Petersham, Massachusetts, United States", "description": "The goal of this study is to learn the molecular mechanisms underlying changes in the temperature sensitive respiration response of forest soils to long-term experimental warming", "ecosystem": "Environmental", @@ -35,7 +41,10 @@ "type": "nmdc:Study" }, { - "id": "gold:Gs0134277", + "id": "nmdc:sty-2e9e3439-06e1-4ebb-ae97-20a198272831", + "gold_study_identifiers": [ + "gold:Gs0134277" + ], "name": "Rhizosphere microbial communities from Carex aquatilis grown in University of Washington, Seatle, WA, United States", "description": "The goal of this study is to advance understanding of the response of methane production and methane oxidation to changes in plant productivity so that modeled representations of these processes and interactions can be improved.", "ecosystem": "Host-associated", diff --git a/test/data/study_credit_test.json b/test/data/study_credit_test.json index 4e0a892775..56c7e0cbad 100644 --- a/test/data/study_credit_test.json +++ b/test/data/study_credit_test.json @@ -1,7 +1,7 @@ { "study_set": [ { - "id": "example:123", + "id": "nmdc:sty-b08d8a6a-0940-4d36-939f-7320d672f051", "has_credit_associations": [ { "applied_roles": [ diff --git a/test/data/study_test.json b/test/data/study_test.json index cf79262a92..ce5c7e528b 100644 --- a/test/data/study_test.json +++ b/test/data/study_test.json @@ -1,7 +1,10 @@ { "study_set": [ { - "id": "gold:Gs0110115", + "id": "nmdc:sty-da4abee8-23df-4c65-8ac4-48db0f3aa4e5", + "gold_study_identifiers": [ + "gold:Gs0110115" + ], "name": "Avena fatua rhizosphere microbial communities from Hopland, California, USA, for root-enhanced decomposition of organic matter studies", "description": "Using analytical expertise at both the JGI and EMSL, we plan to follow successional patterns of protein expression by root-associated microorganisms. This work builds on foundational research we are conducting with the common California grassland plant, Avena fatua, grown in Hopland, CA soil (FOA DE-PS02-09ER09-25). Using our 16-chamber 13C labeling facility at UC Berkeley, we have shown that elevated CO2 increased the amount of C allocated belowground, and increased the yield of root biomass. The rhizosphere microbial community undergoes a succession as the root grows, senesces, and dies. In elevated CO2 treatments, we also detect a greater amount of root-derived 13C in the mineral-associated heavy fraction of the soil, which is commonly assumed to reflect longer term stabilization. \\n \\nIn our JGI-EMSL project, we will follow over time how roots impact the functional capacity of the rhizosphere microbiome to enzymatically mediate decomposition processes. We hypothesize that root-exudate stimulation of soil microbial populations results in elevated expression of biomolecules (transcripts, enzymes, metabolites) for the decomposition of macromolecular C compounds.", "ecosystem": "Host-associated", @@ -18,7 +21,10 @@ "type": "nmdc:Study" }, { - "id": "gold:Gs0110132", + "id": "nmdc:sty-2da265bf-ebfe-43b0-84d9-e33fcec8f852", + "gold_study_identifiers": [ + "gold:Gs0110132" + ], "name": "Cyanobacterial communities from the Joint Genome Institute, California, USA", "description": "We propose to utilize the unique resources at EMSL and the JGI to obtain a better understanding of the phylogenetic and functional diversity of cyanobacteria that have been collected from DOE mission relevant environments (e.g. alkaline and acidic hot springs, and hypersaline terrestrial and water habitats) and deposited in a culture collection that contains >1,200 strains. The Cyanobacteria are one of the most metabolically and morphologically diverse bacterial phyla and it has been hypothesized that they are the origin of oxygenic photosynthesis. The project proposed here would complement and utilize the genomic information that was generated during JGI\u2019s GEBA Cyano project to add valuable insights about the metabolic processes that are active in members of this phylum and that have been - and still are - key factors in shaping our planet. In contrast to the GEBA Cyano project, the project proposed here include mixed cultures of organisms that are recalcitrant to separation. A comprehensive omics approach of these simple consortia will allow us to develop tools for Systems Microbiology and for analyzing microbe-microbe and microbe-climate interactions and the single-cell and whole system level. Phylogenomics: We will request 16S rRNA data from our culture collections to classify phenotypes that are most promising for addressing questions related to carbon and nitrogen cycling and developing new chassis for biofuel production strains. To obtain a complete 16S rRNA-based inventory of the Cyanobacteria collection we would request ~40 Gb of iTag data from the JGI. In addition, we would request Fluorescence in situ hybridization (FISH) microscopy from EMSL for selected samples that contain more than one phylotype, to obtain a better understanding of the special organization within mixed populations. We will request an additional ~10 Gb of iTag data to monitor phylogenetic changes in mixed cultures with phenotypes that are in particular relevant to carbon and nitrogen cycling. Single Cell Genomics and Metagenomics: We will request sorting of mixed cultures targeting ~100 single cells and genomic sequencing of the obtained isolates using JGI's PacBio pipeline (total of ~50 Gb genomic data). For mixed cultured from which no ? or only a fraction of the community - can be isolated as single cell, we will request a total of ~50 Gb of metagenomics data. This will provide us with the genomic data that will be necessary to reconstruct metabolic pathways of hitherto uncultured cyanobacteria and to identify the key factors that make the individual members of these mixed cultures recalcitrant to cultivation under axenic conditions. Physiology and chemistry: To determine the physical and chemical changes that occur during Cyanobacteria mediated carbon and nitrogen cycling, we will request access to cryo-transmission electron microscopy, scanning electron microscopy coupled with focused ion beam, X ray spectroscopy and electron diffraction analyses, confocal microscopy, Raman spectroscopy, synchrotron-based computed x-ray microtomography, nano secondary ion mass spectrometry, and high field Fourier transform ion cyclotron resonance mass spectrometry at EMSL. Functional dynamics: To determine the dynamics of the genetic modules that are being transcribed into mRNA during Cyanobacteria mediated carbon and nitrogen cycling, we propose to generate expression profiles from 10 selected axenic and 10 mixed cultures. We will request a total of ~10 Gb and ~50 Gb of transcriptome and metatranscriptomic data from the JGI, respectively. To determine the dynamics of genetic modules being translated and converted into proteins and metabolites during Cyanobacteria mediated carbon and nitrogen cycling, we will generate metaproteomic and metametabolomic data from 10 selected axenic and 10 mixed cultures. We will request access and support to and with mass spectrometry, NMR spectrometry, and computation time on Chinook from EMSL.", "ecosystem": "Host-associated", @@ -35,7 +41,10 @@ "type": "nmdc:Study" }, { - "id": "gold:Gs0112340", + "id": "nmdc:sty-602bc5a4-14bf-48f5-96bf-a2b7236d0a04", + "gold_study_identifiers": [ + "gold:Gs0112340" + ], "name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations", "description": "A fundamental challenge of microbial environmental science is to understand how earth systems will respond to climate change. A parallel challenge in biology is to unverstand how information encoded in organismal genes manifests as biogeochemical processes at ecosystem-to-global scales. These grand challenges intersect in the need to understand the glocal carbon (C) cycle, which is both mediated by biological processes and a key driver of climate through the greenhouse gases carbon dioxide (CO2) and methane (CH4). A key aspect of these challenges is the C cycle implications of the predicted dramatic shrinkage in northern permafrost in the coming century. ", "ecosystem": "Environmental", From 1173043ff6b218fa69e298540409120b5eb4a063 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 14:25:36 -0500 Subject: [PATCH 49/60] more abstracts; fewer id_prefixes --- src/schema/core.yaml | 16 +++++++++------- src/schema/nmdc.yaml | 26 +++++++++++++++----------- test/test_credit_associations.py | 2 +- 3 files changed, 25 insertions(+), 19 deletions(-) diff --git a/src/schema/core.yaml b/src/schema/core.yaml index e3e6ef6ea4..7ca5891fd2 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -92,16 +92,17 @@ classes: - name - description - alternative_identifiers -# slot_usage: -# id: -# structured_pattern: -# todos: -# syntax: "{id_nmdc_prefix}:{id_typecode_named_thing}-{id_shoulder}-{id_blade}{id_version}{id_locus}" -# interpolated: true -# partial_match: false + # slot_usage: + # id: + # structured_pattern: + # todos: + # syntax: "{id_nmdc_prefix}:{id_typecode_named_thing}-{id_shoulder}-{id_blade}{id_version}{id_locus}" + # interpolated: true + # partial_match: false MaterialEntity: + abstract: true aliases: - Material - Physical entity @@ -127,6 +128,7 @@ classes: partial_match: false Site: + abstract: true is_a: MaterialEntity title: Site comments: diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 249fa3b55e..41116c1d72 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -7,7 +7,7 @@ notes: - "removed/commented out the comfusing 'identifier' slot" - "removed/commented out all mentions and definitions of depth2 and subsurface_depth2" - "depth2 should now be migrated to the has_maximum_value part of depth" - - "slots requested for Bioscales, but already available for Biosample: tot_phosp, tot_carb, tot_nitro_content, pH" + - "slots requested for Bioscales, but already available for Biosample : tot_phosp, tot_carb, tot_nitro_content, pH" - "informal ## section delimiters should be replaced with subsets ?" - "commented out insdc_biosample_identifiers insdc_secondary_sample_identifiers... need better understanding of id patterns (at least)" - "commented out several MIxS terms assigned to Biosample because the definitions of those terms were commented out in mixs.yaml dues to shared slot uris" @@ -210,7 +210,9 @@ classes: in_subset: - data object subset description: 'An object that primarily consists of symbols that represent information. Files, - records, and omics data are examples of data objects. ' + records, and omics data are examples of data objects.' + notes: + - removed previous id_prefixes value of GOLD, since we are now using pattern-based id validation slots: - file_size_bytes - md5_checksum @@ -230,8 +232,8 @@ classes: syntax: "{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false - id_prefixes: - - GOLD + # id_prefixes: + # - GOLD Biosample: is_a: MaterialEntity @@ -246,6 +248,8 @@ classes: Biological source material which can be characterized by an experiment. todos: - could add GOLD and EBI's biosample definitions to the alt_descriptions? + notes: + - removed previous id_prefixes value of GOLD, since we are now using pattern-based id validation alt_descriptions: embl.ena: A sample contains information about the sequenced source material. Samples are associated with checklists, which define the fields used to annotate @@ -555,9 +559,8 @@ classes: tag: expected_value value: date, string range: string - - id_prefixes: - - GOLD + # id_prefixes: + # - GOLD exact_mappings: - OBI:0000747 - NCIT:C43412 @@ -699,14 +702,15 @@ classes: - determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor - project_name is redundant with name, so excluding it - id_prefixes: - - GOLD - - insdc.srs - - mgnify + # id_prefixes: + # - GOLD + # - insdc.srs + # - mgnify notes: - "sample GOLD link https://identifiers.org/gold:Gs0110115" - "sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?" - "sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757" + - "GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers, but no longer for the Study.id" BiosampleProcessing: aliases: diff --git a/test/test_credit_associations.py b/test/test_credit_associations.py index 4782d2f597..fe5ff1f5e9 100644 --- a/test/test_credit_associations.py +++ b/test/test_credit_associations.py @@ -23,7 +23,7 @@ def test_sum(self): ca1 = CreditAssociation(applies_to_person=pv1, applied_roles=["Supervision", "Validation"]) ca2 = CreditAssociation(applies_to_person=pv2, applied_roles=["Investigation"]) - s = Study(id="abc") + s = Study(id="nmdc:sty-e3e05c16-8c9a-421e-ade5-cde4e5a435fa") # # why is schema loaded each time? validator.validate_object(ca1, target_class=CreditAssociation) From 0812ff4a640f8afcb8ed62b5101b9b16b842336a Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 14:41:25 -0500 Subject: [PATCH 50/60] comment out id_typecode_study setting --- src/schema/nmdc.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 41116c1d72..f9ed2aeb2e 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -101,7 +101,7 @@ settings: id_locus: "(_[A-Za-z0-9_\\.-]+)?$" # class to typecode associations # id_typecode_biosample: "bsm" - id_typecode_study: "sty" + # id_typecode_study: "sty" # id_typecode_biosample_processing: "bsmprc" # id_typecode_omics_processing: "omprc" # id_typecode_dataobject: "dobj" From 1654683389f3725de1001f7335ff04d391a25103 Mon Sep 17 00:00:00 2001 From: Sujay Patil Date: Thu, 19 Jan 2023 12:25:43 -0800 Subject: [PATCH 51/60] add samp_taxon_id slot to MIxS schema and asset on Biosample class --- src/schema/mixs.yaml | 24 +++++++++++++++++++++++- src/schema/nmdc.yaml | 1 + 2 files changed, 24 insertions(+), 1 deletion(-) diff --git a/src/schema/mixs.yaml b/src/schema/mixs.yaml index 8f31a732cd..350a496d89 100644 --- a/src/schema/mixs.yaml +++ b/src/schema/mixs.yaml @@ -14,7 +14,7 @@ notes: prefixes: nmdc: https://w3id.org/nmdc/ mixs: https://w3id.org/mixs/ - + NCBITaxon: https://ontobee.org/ontology/NCBITaxon default_prefix: nmdc @@ -7335,6 +7335,10 @@ slots: slot_uri: mixs:0000813 multivalued: false range: TextValue + investigation field: + abstract: true + description: field describing aspect of the investigation/study to which the sample + belongs iw_bt_date_well: name: iw_bt_date_well aliases: @@ -10882,6 +10886,24 @@ slots: slot_uri: mixs:0000999 multivalued: false range: TextValue + samp_taxon_id: + is_a: investigation field + title: Taxonomy ID of DNA sample + description: "NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa\ + \ sample. Use 'synthetic metagenome\u2019 for mock community/positive controls,\ + \ or 'blank sample' for negative controls." + range: string + multivalued: false + examples: + - value: soil metagenome [NCBITaxon:410658] + comments: [] + todos: + - "structured pattern: {text} [NCBITaxon:{integer}]" + aliases: + - Taxonomy ID of DNA sample + annotations: + expected_value: Taxonomy ID + slot_uri: mixs:0001320 samp_time_out: name: samp_time_out aliases: diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index d8ad7bbbd1..e25637c9d6 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -350,6 +350,7 @@ classes: - samp_mat_process - samp_store_dur - samp_store_loc + - samp_taxon_id - samp_store_temp - samp_vol_we_dna_ext - season_temp From ef238bf8e8182ad9d87e76bef097f59652b48d2a Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 15:28:51 -0500 Subject: [PATCH 52/60] review responses 20230119 1528 ET removed suplicated typecodes in sample data ids; improved referential integrity in biosamples_to_sites.json; commented out id pattern for MaterialEntity --- src/schema/core.yaml | 14 +++++----- test/data/biosample_test.json | 6 ++--- test/data/biosamples_to_sites.json | 43 +++++++++++++++--------------- 3 files changed, 31 insertions(+), 32 deletions(-) diff --git a/src/schema/core.yaml b/src/schema/core.yaml index 7ca5891fd2..74a62cd4b3 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -108,13 +108,13 @@ classes: - Physical entity is_a: NamedThing title: Material Entity - slot_usage: - id: - pattern: '^nmdc:mate' - structured_pattern: - syntax: "{id_nmdc_prefix}:mate-{id_shoulder}-{id_blade}{id_version}{id_locus}" - interpolated: true - partial_match: false + # slot_usage: + # id: + # pattern: '^nmdc:mate' + # structured_pattern: + # syntax: "{id_nmdc_prefix}:mate-{id_shoulder}-{id_blade}{id_version}{id_locus}" + # interpolated: true + # partial_match: false AnalyticalSample: is_a: MaterialEntity diff --git a/test/data/biosample_test.json b/test/data/biosample_test.json index d8a1948f07..f91172b1d5 100644 --- a/test/data/biosample_test.json +++ b/test/data/biosample_test.json @@ -51,7 +51,7 @@ "sample_collection_site": "Lithgow State Coal Mine" }, { - "id": "nmdc:bsm-bsm-6057d02c-664c-41c9-8486-3624ca845747", + "id": "nmdc:bsm-6057d02c-664c-41c9-8486-3624ca845747", "gold_biosample_identifiers": [ "gold:Gb0101224" ], @@ -105,7 +105,7 @@ "sample_collection_site": "Lithgow State Coal Mine" }, { - "id": "nmdc:bsm-bsm-e924072f-98b5-4f88-a796-a7ba1d8ddd92", + "id": "nmdc:bsm-e924072f-98b5-4f88-a796-a7ba1d8ddd92", "gold_biosample_identifiers": [ "gold:Gb0101225" ], @@ -155,7 +155,7 @@ "sample_collection_site": "Lithgow State Coal Mine" }, { - "id": "nmdc:bsm-bsm-61c3332d-f654-4db8-8d2f-59475894daa5", + "id": "nmdc:bsm-61c3332d-f654-4db8-8d2f-59475894daa5", "gold_biosample_identifiers": [ "gold:Gb0101226" ], diff --git a/test/data/biosamples_to_sites.json b/test/data/biosamples_to_sites.json index 558625ce7a..3d1cfda19f 100644 --- a/test/data/biosamples_to_sites.json +++ b/test/data/biosamples_to_sites.json @@ -1,7 +1,7 @@ { "biosample_set": [ { - "id": "nmdc:bsm-biosample_placeholder_1", + "id": "nmdc:bsm-ad9d77a0-52d7-43fe-ba66-6fd33b6946d2", "name": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33 endosphere", "description": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA", "collected_from": "nmdc:frsite-2ec2ebde-857f-4dc5-ab5e-881c3eb337ce", @@ -9,7 +9,7 @@ "GOLD:Gb0305833" ], "part_of": [ - "nmdc:study_placeholder" + "nmdc:sty-8f2bf526-5fe2-4bc0-aa75-82a9f0b868a5" ], "env_broad_scale": { "has_raw_value": "ENVO:00002030", @@ -31,7 +31,7 @@ } }, { - "id": "nmdc:bsm-biosample_placeholder_2", + "id": "nmdc:bsm-2a85c34d-ef39-4160-8959-ce831b26c1fa", "name": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33", "description": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", "collected_from": "nmdc:frsite-2ec2ebde-857f-4dc5-ab5e-881c3eb337ce", @@ -39,7 +39,7 @@ "GOLD:Gb0291692" ], "part_of": [ - "nmdc:study_placeholder" + "nmdc:sty-8f2bf526-5fe2-4bc0-aa75-82a9f0b868a5" ], "env_broad_scale": { "has_raw_value": "ENVO:00002030", @@ -61,7 +61,7 @@ } }, { - "id": "nmdc:bsm-biosample_placeholder_3", + "id": "nmdc:bsm-c253f1e2-d532-4fdb-9bd3-32b611dcb680", "name": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33", "description": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", "collected_from": "nmdc:frsite-2ec2ebde-857f-4dc5-ab5e-881c3eb337ce", @@ -69,7 +69,7 @@ "GOLD:Gb0291582" ], "part_of": [ - "nmdc:study_placeholder" + "nmdc:sty-8f2bf526-5fe2-4bc0-aa75-82a9f0b868a5" ], "env_broad_scale": { "has_raw_value": "ENVO:00002030", @@ -91,15 +91,15 @@ } }, { - "id": "nmdc:bsm-biosample_placeholder_4", + "id": "nmdc:bsm-f34aa0dd-1fbf-4c46-aa16-713d41cfdc64", "name": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29 endosphere", "description": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA", - "collected_from": "GOLD:BESC-13-CL2_39_29", + "collected_from": "nmdc:frsite-10e5281b-504b-4f56-80fe-2e50d7d00521", "gold_biosample_identifiers": [ "GOLD:Gb0305834" ], "part_of": [ - "nmdc:study_placeholder" + "nmdc:sty-8f2bf526-5fe2-4bc0-aa75-82a9f0b868a5" ], "env_broad_scale": { "has_raw_value": "ENVO:00002030", @@ -121,15 +121,15 @@ } }, { - "id": "nmdc:bsm-study_placeholder", + "id": "nmdc:bsm-32dea169-9135-4e9b-bce2-2286ac10ac0b", "name": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29", "description": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", - "collected_from": "GOLD:BESC-13-CL2_39_29", + "collected_from": "nmdc:frsite-10e5281b-504b-4f56-80fe-2e50d7d00521", "gold_biosample_identifiers": [ "GOLD:Gb0291693" ], "part_of": [ - "nmdc:study_placeholder" + "nmdc:sty-8f2bf526-5fe2-4bc0-aa75-82a9f0b868a5" ], "env_broad_scale": { "has_raw_value": "ENVO:00002030", @@ -151,15 +151,15 @@ } }, { - "id": "nmdc:bsm-biosample_placeholder_6", + "id": "nmdc:bsm-0e948efc-15bb-48b5-b312-d87fafe5ba9a", "name": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29", "description": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", - "collected_from": "GOLD:BESC-13-CL2_39_29", + "collected_from": "nmdc:frsite-10e5281b-504b-4f56-80fe-2e50d7d00521", "gold_biosample_identifiers": [ "GOLD:Gb0291583" ], "part_of": [ - "nmdc:study_placeholder" + "nmdc:sty-8f2bf526-5fe2-4bc0-aa75-82a9f0b868a5" ], "env_broad_scale": { "has_raw_value": "ENVO:00002030", @@ -201,21 +201,20 @@ "nmdc:frsite-2ec2ebde-857f-4dc5-ab5e-881c3eb337ce" ], "has_outputs": [ - "GOLD:Gb0305833", - "GOLD:Gb0291692", - "GOLD:Gb0291582" + "nmdc:bsm-ad9d77a0-52d7-43fe-ba66-6fd33b6946d2", + "nmdc:bsm-2a85c34d-ef39-4160-8959-ce831b26c1fa", + "nmdc:bsm-c253f1e2-d532-4fdb-9bd3-32b611dcb680" ] }, { "id": "nmdc:clsite-87c6ff79-4d89-4362-be87-67766356b1ce", "name": "Collection of biosamples from BESC-13-CL2_39_29", "has_inputs": [ - "GOLD:BESC-13-CL2_39_29" + "nmdc:frsite-10e5281b-504b-4f56-80fe-2e50d7d00521" ], "has_outputs": [ - "GOLD:Gb0305834", - "GOLD:Gb0291693", - "GOLD:Gb0291583" + "nmdc:bsm-f34aa0dd-1fbf-4c46-aa16-713d41cfdc64", + "nmdc:bsm-32dea169-9135-4e9b-bce2-2286ac10ac0b" ] } ] From 76c9cef9cf7bd04d4afde50c532a267b390f837c Mon Sep 17 00:00:00 2001 From: Sujay Patil Date: Thu, 19 Jan 2023 12:58:36 -0800 Subject: [PATCH 53/60] add samp_taxon_id slot on biosample test instance data --- test/data/biosample_test.json | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/test/data/biosample_test.json b/test/data/biosample_test.json index 23ab5c9046..1f1c19c3d4 100644 --- a/test/data/biosample_test.json +++ b/test/data/biosample_test.json @@ -48,6 +48,7 @@ "location": "from the Lithgow State Coal Mine, New South Wales, Australia", "mod_date": "26-AUG-16 01.50.27.000000000 PM", "ncbi_taxonomy_name": "coal metagenome", + "samp_taxon_id": "coal metagenome [NCBITaxon:1260732]", "sample_collection_site": "Lithgow State Coal Mine" }, { @@ -102,6 +103,7 @@ "location": "from the Lithgow State Coal Mine, New South Wales, Australia", "mod_date": "26-AUG-16 01.50.27.000000000 PM", "ncbi_taxonomy_name": "coal metagenome", + "samp_taxon_id": "coal metagenome [NCBITaxon:1260732]", "sample_collection_site": "Lithgow State Coal Mine" }, { @@ -152,6 +154,7 @@ "location": "from the Lithgow State Coal Mine, New South Wales, Australia", "mod_date": "26-AUG-16 01.50.27.000000000 PM", "ncbi_taxonomy_name": "coal metagenome", + "samp_taxon_id": "coal metagenome [NCBITaxon:1260732]", "sample_collection_site": "Lithgow State Coal Mine" }, { @@ -202,6 +205,7 @@ "location": "from the Lithgow State Coal Mine, New South Wales, Australia", "mod_date": "26-AUG-16 01.50.27.000000000 PM", "ncbi_taxonomy_name": "coal metagenome", + "samp_taxon_id": "coal metagenome [NCBITaxon:1260732]", "sample_collection_site": "Lithgow State Coal Mine" } ] From 47db2bba93ee6d0cae952bce60688d449816b6b3 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Thu, 19 Jan 2023 16:30:19 -0500 Subject: [PATCH 54/60] all biosamples are the output of a collection biosamples_to_sites.json --- test/data/biosamples_to_sites.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/data/biosamples_to_sites.json b/test/data/biosamples_to_sites.json index 3d1cfda19f..52b4acaf0d 100644 --- a/test/data/biosamples_to_sites.json +++ b/test/data/biosamples_to_sites.json @@ -214,7 +214,8 @@ ], "has_outputs": [ "nmdc:bsm-f34aa0dd-1fbf-4c46-aa16-713d41cfdc64", - "nmdc:bsm-32dea169-9135-4e9b-bce2-2286ac10ac0b" + "nmdc:bsm-32dea169-9135-4e9b-bce2-2286ac10ac0b", + "nmdc:bsm-0e948efc-15bb-48b5-b312-d87fafe5ba9a" ] } ] From 7f9d2c24fb1b8a4c7aa136019ac0050fcd1bd46e Mon Sep 17 00:00:00 2001 From: Sujay Patil Date: Fri, 20 Jan 2023 09:28:34 -0800 Subject: [PATCH 55/60] remove backslashes, unicode from samp_taxon_id desc --- src/schema/mixs.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/schema/mixs.yaml b/src/schema/mixs.yaml index 350a496d89..2ddd09990c 100644 --- a/src/schema/mixs.yaml +++ b/src/schema/mixs.yaml @@ -10889,9 +10889,9 @@ slots: samp_taxon_id: is_a: investigation field title: Taxonomy ID of DNA sample - description: "NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa\ - \ sample. Use 'synthetic metagenome\u2019 for mock community/positive controls,\ - \ or 'blank sample' for negative controls." + description: NCBI taxon id of the sample. May be a single taxon or mixed taxa + sample. Use 'synthetic metagenome' for mock community/positive controls, + or 'blank sample' for negative controls. range: string multivalued: false examples: From 876a6224083398b0af1b9d4bf32d947e1af27c60 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Fri, 20 Jan 2023 12:45:20 -0500 Subject: [PATCH 56/60] #625 materialized -> jsonschema with updated test data --- Makefile | 16 +- poetry.lock | 1330 ++++++++++-------- src/schema/nmdc.yaml | 2 +- test/data/MAGs_activity.json | 4 +- test/data/biosample_test.json | 8 +- test/data/biosamples_to_sites.json | 60 +- test/data/gold_project_test.json | 6 +- test/data/img_mg_annotation_objects.json | 228 +-- test/data/mg_assembly_activities_test.json | 6 +- test/data/mg_assembly_data_objects_test.json | 6 +- test/data/nmdc_example_database.json | 24 +- test/data/samp_prep_db.json | 10 +- test/data/study_credit_test.json | 2 +- test/data/study_test.json | 6 +- 14 files changed, 956 insertions(+), 752 deletions(-) diff --git a/Makefile b/Makefile index 2279ff3584..431dd4f1dd 100644 --- a/Makefile +++ b/Makefile @@ -116,7 +116,19 @@ target/graphql/%.graphql: $(SCHEMA_DIR)/%.yaml tdir-graphql gen-jsonschema: target/jsonschema/$(SCHEMA_NAME).schema.json .PHONY: gen-jsonschema target/jsonschema/%.schema.json: $(SCHEMA_DIR)/%.yaml tdir-jsonschema - $(RUN) gen-json-schema $(GEN_OPTS) --closed -t database $< > $@ + #$(RUN) gen-json-schema $(GEN_OPTS) --closed -t database $< > $@ + # pre-materialize the patterns before jsonschema generation + # should be doing that for all of the generated artifacts + $(RUN) gen-linkml \ + -o target/nmdc_generated.yaml \ + --materialize-patterns \ + --no-materialize-attributes \ + --format yaml \ + --mergeimports $(SCHEMA_SRC) + $(RUN) gen-json-schema $(GEN_OPTS) \ + --closed \ + -t database target/nmdc_generated.yaml > $@ + rm -rf target/nmdc_generated.yaml ### -- JSONLD Context -- gen-jsonld-context: target/jsonld-context/$(SCHEMA_NAME).context.jsonld @@ -213,9 +225,9 @@ delete-poetry-env: # datasets used test/validate the schema # SCHEMA_TEST_EXAMPLES := \ - biosamples_to_sites \ MAGs_activity \ biosample_test \ + biosamples_to_sites \ functional_annotation_set \ gold_project_test \ img_mg_annotation_objects \ diff --git a/poetry.lock b/poetry.lock index 6db471dc6c..519096bbc4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,14 +2,14 @@ [[package]] name = "alabaster" -version = "0.7.12" +version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.6" files = [ - {file = "alabaster-0.7.12-py2.py3-none-any.whl", hash = "sha256:446438bdcca0e05bd45ea2de1668c1d9b032e1a9154c2c259092d77031ddd359"}, - {file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"}, + {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, + {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, ] [[package]] @@ -409,19 +409,102 @@ files = [ [[package]] name = "charset-normalizer" -version = "2.1.1" +version = "3.0.1" description = "The Real First Universal Charset Detector. 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"nmdc:wfmag-f2fc8f5aade3092ea97769f0a892d2a9", + "id": "nmdc:wfmag-99-5MiDJM", "name": "MAGs activiity 1781_86101", "was_informed_by": "gold:Gp0115663", "started_at_time": "2021-01-10T00:00:00+00:00", @@ -65,7 +65,7 @@ ] }, { - "id": "nmdc:wfmag-a0ca0743a49e4bf12db9b5d933c4e76a", + "id": "nmdc:wfmag-99-VOgM5i", "name": "MAGs activiity 1781_86089", "was_informed_by": "gold:Gp0115664", "started_at_time": "2021-01-10T00:00:00+00:00", diff --git a/test/data/biosample_test.json b/test/data/biosample_test.json index f91172b1d5..280b1ed20c 100644 --- a/test/data/biosample_test.json +++ b/test/data/biosample_test.json @@ -1,7 +1,7 @@ { "biosample_set": [ { - "id": "nmdc:bsm-6057d02c-664c-41c9-8486-3624ca845747", + "id": "nmdc:bsm-99-dtTMNb", "gold_biosample_identifiers": [ "gold:Gb0101224" ], @@ -51,7 +51,7 @@ "sample_collection_site": "Lithgow State Coal Mine" }, { - "id": "nmdc:bsm-6057d02c-664c-41c9-8486-3624ca845747", + "id": "nmdc:bsm-99-AtTUOs", "gold_biosample_identifiers": [ 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Oregon, USA", - "collected_from": "nmdc:frsite-2ec2ebde-857f-4dc5-ab5e-881c3eb337ce", + "collected_from": "nmdc:frsite-99-SPreao", "gold_biosample_identifiers": [ "GOLD:Gb0305833" ], "part_of": [ - "nmdc:sty-8f2bf526-5fe2-4bc0-aa75-82a9f0b868a5" + "nmdc:sty-99-U21mUX" ], "env_broad_scale": { "has_raw_value": "ENVO:00002030", @@ -31,15 +31,15 @@ } }, { - "id": "nmdc:bsm-2a85c34d-ef39-4160-8959-ce831b26c1fa", + "id": "nmdc:bsm-99-BdlWdQ", "name": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33", "description": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", - "collected_from": "nmdc:frsite-2ec2ebde-857f-4dc5-ab5e-881c3eb337ce", + "collected_from": "nmdc:frsite-99-SPreao", "gold_biosample_identifiers": [ "GOLD:Gb0291692" ], "part_of": [ - "nmdc:sty-8f2bf526-5fe2-4bc0-aa75-82a9f0b868a5" + "nmdc:sty-99-U21mUX" ], "env_broad_scale": { "has_raw_value": "ENVO:00002030", @@ -61,15 +61,15 @@ } }, { - "id": "nmdc:bsm-c253f1e2-d532-4fdb-9bd3-32b611dcb680", + "id": "nmdc:bsm-99-vn74Wq", "name": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33", "description": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", - "collected_from": "nmdc:frsite-2ec2ebde-857f-4dc5-ab5e-881c3eb337ce", + "collected_from": "nmdc:frsite-99-SPreao", "gold_biosample_identifiers": [ "GOLD:Gb0291582" ], "part_of": [ - "nmdc:sty-8f2bf526-5fe2-4bc0-aa75-82a9f0b868a5" + "nmdc:sty-99-U21mUX" ], "env_broad_scale": { "has_raw_value": "ENVO:00002030", @@ -91,15 +91,15 @@ } }, { - "id": "nmdc:bsm-f34aa0dd-1fbf-4c46-aa16-713d41cfdc64", + "id": "nmdc:bsm-99-P8FdpS", "name": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29 endosphere", "description": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA", - "collected_from": "nmdc:frsite-10e5281b-504b-4f56-80fe-2e50d7d00521", + "collected_from": "nmdc:frsite-99-h2mYFG", "gold_biosample_identifiers": [ "GOLD:Gb0305834" ], "part_of": [ - "nmdc:sty-8f2bf526-5fe2-4bc0-aa75-82a9f0b868a5" + "nmdc:sty-99-U21mUX" ], "env_broad_scale": { "has_raw_value": "ENVO:00002030", @@ -121,15 +121,15 @@ } }, { - "id": "nmdc:bsm-32dea169-9135-4e9b-bce2-2286ac10ac0b", + "id": "nmdc:bsm-99-ugBwz3", "name": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29", "description": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", - "collected_from": "nmdc:frsite-10e5281b-504b-4f56-80fe-2e50d7d00521", + "collected_from": "nmdc:frsite-99-h2mYFG", "gold_biosample_identifiers": [ "GOLD:Gb0291693" ], "part_of": [ - "nmdc:sty-8f2bf526-5fe2-4bc0-aa75-82a9f0b868a5" + "nmdc:sty-99-U21mUX" ], "env_broad_scale": { "has_raw_value": "ENVO:00002030", @@ -151,15 +151,15 @@ } }, { - "id": "nmdc:bsm-0e948efc-15bb-48b5-b312-d87fafe5ba9a", + "id": "nmdc:bsm-99-tN5lxM", "name": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29", "description": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", - "collected_from": "nmdc:frsite-10e5281b-504b-4f56-80fe-2e50d7d00521", + "collected_from": "nmdc:frsite-99-h2mYFG", "gold_biosample_identifiers": [ "GOLD:Gb0291583" ], "part_of": [ - "nmdc:sty-8f2bf526-5fe2-4bc0-aa75-82a9f0b868a5" + "nmdc:sty-99-U21mUX" ], "env_broad_scale": { "has_raw_value": "ENVO:00002030", @@ -183,39 +183,39 @@ ], "field_research_site_set": [ { - "id": "nmdc:frsite-2ec2ebde-857f-4dc5-ab5e-881c3eb337ce", + "id": "nmdc:frsite-99-SPreao", "name": "BESC-13-CL1_35_33", "description": "Bioscales tree BESC-13-CL1_35_33" }, { - "id": "nmdc:frsite-10e5281b-504b-4f56-80fe-2e50d7d00521", + "id": "nmdc:frsite-99-h2mYFG", "name": "BESC-13-CL2_39_29", "description": "Bioscales tree BESC-13-CL2_39_29" } ], "collecting_biosamples_from_site_set": [ { - "id": "nmdc:clsite-4ff95e3a-e5e1-4a85-96b2-acf3fb242004", + "id": "nmdc:clsite-99-Cq00d1", "name": "Collection of biosamples from BESC-13-CL1_35_33", "has_inputs": [ - "nmdc:frsite-2ec2ebde-857f-4dc5-ab5e-881c3eb337ce" + "nmdc:frsite-99-SPreao" ], "has_outputs": [ - "nmdc:bsm-ad9d77a0-52d7-43fe-ba66-6fd33b6946d2", - "nmdc:bsm-2a85c34d-ef39-4160-8959-ce831b26c1fa", - "nmdc:bsm-c253f1e2-d532-4fdb-9bd3-32b611dcb680" + "nmdc:bsm-99-J9FcnC", + "nmdc:bsm-99-BdlWdQ", + "nmdc:bsm-99-vn74Wq" ] }, { - "id": "nmdc:clsite-87c6ff79-4d89-4362-be87-67766356b1ce", + "id": "nmdc:clsite-99-yzmLBN", "name": "Collection of biosamples from BESC-13-CL2_39_29", "has_inputs": [ - "nmdc:frsite-10e5281b-504b-4f56-80fe-2e50d7d00521" + "nmdc:frsite-99-h2mYFG" ], "has_outputs": [ - "nmdc:bsm-f34aa0dd-1fbf-4c46-aa16-713d41cfdc64", - "nmdc:bsm-32dea169-9135-4e9b-bce2-2286ac10ac0b", - "nmdc:bsm-0e948efc-15bb-48b5-b312-d87fafe5ba9a" + "nmdc:bsm-99-P8FdpS", + "nmdc:bsm-99-ugBwz3", + "nmdc:bsm-99-tN5lxM" ] } ] diff --git a/test/data/gold_project_test.json b/test/data/gold_project_test.json index 9d743bc457..917fa0e69d 100644 --- a/test/data/gold_project_test.json +++ b/test/data/gold_project_test.json @@ -1,7 +1,7 @@ { "omics_processing_set": [ { - "id": "nmdc:omprc-93312e7f-79f2-4861-b108-3aa8ccb86c9b", + "id": "nmdc:omprc-99-zUCd5N", "alternative_identifiers": [ "gold:Gp0108335" ], @@ -25,7 +25,7 @@ "type": "nmdc:OmicsProcessing" }, { - "id": "nmdc:omprc-68fa114f-6709-4e4c-bd2b-c53fd5ee51da", + "id": "nmdc:omprc-99-gKlQlF", "alternative_identifiers": [ "gold:Gp0108340" ], @@ -49,7 +49,7 @@ "type": "nmdc:OmicsProcessing" }, { - "id": "nmdc:omprc-32604e07-bfa6-4d43-a998-3f1cde25bf4f", + "id": "nmdc:omprc-99-5kgIJR", "alternative_identifiers": [ "gold:Gp0108341" ], diff --git a/test/data/img_mg_annotation_objects.json b/test/data/img_mg_annotation_objects.json index 3d78849ab5..14afcb915c 100644 --- a/test/data/img_mg_annotation_objects.json +++ b/test/data/img_mg_annotation_objects.json @@ -17,7 +17,7 @@ "was_informed_by": "gold:Gp0153825", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-9076b6e2b334532d7be4e48b25ca80dd", + "id": "nmdc:wf-99-v7tNhU", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -37,7 +37,7 @@ "was_informed_by": "gold:Gp0119849", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-bf16723c3a2b226747c6b40085f51cc2", + "id": "nmdc:wf-99-bzS2v1", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -57,7 +57,7 @@ "was_informed_by": "gold:Gp0119850", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-c77fe920a664d4e174d413ec89f040a3", + "id": "nmdc:wf-99-sXZVjh", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -77,7 +77,7 @@ "was_informed_by": "gold:Gp0119851", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-6c5858d2b28e1de316120d410ed62544", + "id": "nmdc:wf-99-3fBeJp", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -97,7 +97,7 @@ "was_informed_by": "gold:Gp0119852", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-879e7ff3374deee6054684076a882649", + "id": "nmdc:wf-99-F6E55A", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -117,7 +117,7 @@ "was_informed_by": "gold:Gp0119853", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-608cc16c1e395be8f7f56f123b88d17a", + "id": "nmdc:wf-99-Zrij2v", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -137,7 +137,7 @@ "was_informed_by": "gold:Gp0119854", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-db089a3971603b130cc25c9edf29a951", + "id": "nmdc:wf-99-swlzri", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -157,7 +157,7 @@ "was_informed_by": "gold:Gp0119855", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-1762bbeb64674af6e394ee1323391833", + "id": "nmdc:wf-99-k15Id6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -177,7 +177,7 @@ "was_informed_by": "gold:Gp0119856", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-4794bbc1dc72807df92a30088cf4551b", + "id": "nmdc:wf-99-phL8rY", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -197,7 +197,7 @@ "was_informed_by": "gold:Gp0119857", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-9cb27d7fe967ed437acf43b7cb5f01ee", + "id": "nmdc:wf-99-rIKnPj", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -217,7 +217,7 @@ "was_informed_by": "gold:Gp0119858", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-b52fd6e2d28c922c305849b2e6e29246", + "id": "nmdc:wf-99-NHVre9", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -237,7 +237,7 @@ "was_informed_by": "gold:Gp0119859", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-f23f9cd69666b01795e4c43bacb9ae62", + "id": "nmdc:wf-99-n84Tew", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -257,7 +257,7 @@ "was_informed_by": "gold:Gp0119860", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-9278b29bb5c234046a11937991a3a652", + "id": "nmdc:wf-99-6IBBqL", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -277,7 +277,7 @@ "was_informed_by": "gold:Gp0119861", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-67d82e4c6f9796611f5a2234596eb6a2", + "id": "nmdc:wf-99-sCL9p6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -297,7 +297,7 @@ "was_informed_by": "gold:Gp0119862", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-9e9c8643f496b6472ddb602aff30021d", + "id": "nmdc:wf-99-xtaqhx", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -317,7 +317,7 @@ "was_informed_by": "gold:Gp0119863", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-facd1cd7880760c4d227237d8142d60b", + "id": "nmdc:wf-99-cnpEPb", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -337,7 +337,7 @@ "was_informed_by": "gold:Gp0119864", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-6c6eff8448b4782e31363eb7a783ef16", + "id": "nmdc:wf-99-bFWXyt", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -357,7 +357,7 @@ "was_informed_by": "gold:Gp0119865", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-3d2d6fbece4298a34798a5cdc28fccbc", + "id": "nmdc:wf-99-H9y4oj", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -377,7 +377,7 @@ "was_informed_by": "gold:Gp0119866", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-993f0fb1fb43a8db2c04f6a6064d1e91", + "id": "nmdc:wf-99-exEkWs", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -397,7 +397,7 @@ "was_informed_by": "gold:Gp0119867", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-8a43ec3baf8aafe09d96eb7fbf58c916", + "id": "nmdc:wf-99-GzdjHY", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -417,7 +417,7 @@ "was_informed_by": "gold:Gp0119868", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-57e9c4e31f9c612633325bbe5c6c2f87", + "id": "nmdc:wf-99-4V6suA", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -437,7 +437,7 @@ "was_informed_by": "gold:Gp0119869", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-60c965c51b96153a9cffa6f4dd62a2e6", + "id": "nmdc:wf-99-JoTrst", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -457,7 +457,7 @@ "was_informed_by": "gold:Gp0119870", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-42addbcd527a65d01a4d2fbd2da7758a", + "id": "nmdc:wf-99-WMxKQm", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -477,7 +477,7 @@ "was_informed_by": "gold:Gp0119871", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-3204b453fe3471a5c6babce54398d9af", + "id": "nmdc:wf-99-KNca8B", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -497,7 +497,7 @@ "was_informed_by": "gold:Gp0127623", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-92070449b2ee66f6ec04125edc8ae30a", + "id": "nmdc:wf-99-dNish1", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -517,7 +517,7 @@ "was_informed_by": "gold:Gp0127624", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-f0773e35f29db6c8c9ec2354b6560c5f", + "id": "nmdc:wf-99-U1umHi", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -537,7 +537,7 @@ "was_informed_by": "gold:Gp0127625", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-dfbc92d67d6307fc16059f858f8d81f6", + "id": "nmdc:wf-99-Teg8kK", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -557,7 +557,7 @@ "was_informed_by": "gold:Gp0127626", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-b17f7734657148a50baf5216849b3b2f", + "id": "nmdc:wf-99-qB4hXN", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -577,7 +577,7 @@ "was_informed_by": "gold:Gp0127627", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-4b54a8416db39168fa6403d6832476e6", + "id": "nmdc:wf-99-72JIpi", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -597,7 +597,7 @@ "was_informed_by": "gold:Gp0127628", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-689781c3f0a680b05f9a0a9b377b0ed9", + "id": "nmdc:wf-99-mbF4y1", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -617,7 +617,7 @@ "was_informed_by": "gold:Gp0127629", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-d8af769e0dd753e86ef1f545536f3024", + "id": "nmdc:wf-99-ylyhlC", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -637,7 +637,7 @@ "was_informed_by": "gold:Gp0127630", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-b579670a8b80fd02e453d5ac031a574e", + "id": "nmdc:wf-99-56GrFn", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -657,7 +657,7 @@ "was_informed_by": "gold:Gp0127631", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-406be722709ec331037987b30acc6b18", + "id": "nmdc:wf-99-i3NwIC", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -677,7 +677,7 @@ "was_informed_by": "gold:Gp0127632", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-163dfd2463186259deeae10b15d25119", + "id": "nmdc:wf-99-GjHwbW", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -697,7 +697,7 @@ "was_informed_by": "gold:Gp0127633", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-ac967b73a027cfac522a742ddbbf9521", + "id": "nmdc:wf-99-wx4FsZ", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -717,7 +717,7 @@ "was_informed_by": "gold:Gp0127634", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-8287ea44a458b50606a04fe82ceb83b1", + "id": "nmdc:wf-99-av43Nc", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -737,7 +737,7 @@ "was_informed_by": "gold:Gp0127635", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-e763e255fa74e2629d7d86e10f838d4b", + "id": "nmdc:wf-99-UbQ1cX", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -757,7 +757,7 @@ "was_informed_by": "gold:Gp0127636", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-89dde14d6545e93e749ffeae6fc3bdd6", + "id": "nmdc:wf-99-43gCPe", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -777,7 +777,7 @@ "was_informed_by": "gold:Gp0127637", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-507c53e61a3c02d763b05d2a5eb2bda5", + "id": "nmdc:wf-99-226YUT", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -797,7 +797,7 @@ "was_informed_by": "gold:Gp0127638", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-93656c96853f97524040c44f4b346d75", + "id": "nmdc:wf-99-QxzAEB", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -817,7 +817,7 @@ "was_informed_by": "gold:Gp0127639", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-78ec466d9918b7fa1cbc033b19a37a10", + "id": "nmdc:wf-99-JeORrG", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -837,7 +837,7 @@ "was_informed_by": "gold:Gp0127640", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-5ac74427da62d00b8493cf6bc7c8e43d", + "id": "nmdc:wf-99-UKUKLq", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -857,7 +857,7 @@ "was_informed_by": "gold:Gp0127641", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-6808e9a6d7450f02019691d89c57ff1f", + "id": "nmdc:wf-99-QhDga7", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -877,7 +877,7 @@ "was_informed_by": "gold:Gp0127642", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-45f4a9d66e8d45a534fc2067670bf012", + "id": "nmdc:wf-99-i0BJTw", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -897,7 +897,7 @@ "was_informed_by": "gold:Gp0127643", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-b59602d74d9ee08ccd285a7ac2e5f6b2", + "id": "nmdc:wf-99-CDkOOW", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -917,7 +917,7 @@ "was_informed_by": "gold:Gp0127644", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-339e8f1e41b780e4e565ce53067bc9bb", + "id": "nmdc:wf-99-DNvmyp", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -937,7 +937,7 @@ "was_informed_by": "gold:Gp0127645", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-e148a2d4befa290bbd216b6654371606", + "id": "nmdc:wf-99-Oxm5LI", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -957,7 +957,7 @@ "was_informed_by": "gold:Gp0127646", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-02aca43c6efc414d5971e8a179bbbcf0", + "id": "nmdc:wf-99-RiJ5rZ", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -977,7 +977,7 @@ "was_informed_by": "gold:Gp0127647", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-4488991684ed07f2b9a2bb5b8b1a59a9", + "id": "nmdc:wf-99-3Xgfcz", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -997,7 +997,7 @@ "was_informed_by": "gold:Gp0127648", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-ca2cac5f3de8db080031d727ff4db8ec", + "id": "nmdc:wf-99-0gilcH", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1017,7 +1017,7 @@ "was_informed_by": "gold:Gp0127649", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-1524a48694d670c26a1b55238d9f1949", + "id": "nmdc:wf-99-3TAfCa", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1037,7 +1037,7 @@ "was_informed_by": "gold:Gp0127651", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-e96dba76c7c388aebab7ad759b2a5694", + "id": "nmdc:wf-99-Uv1aai", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1057,7 +1057,7 @@ "was_informed_by": "gold:Gp0127652", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-5e21f299a395e845341500a334e94ff2", + "id": "nmdc:wf-99-XcNXLE", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1077,7 +1077,7 @@ "was_informed_by": "gold:Gp0127653", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-d6f99d25d421ab54908e603b016df20f", + "id": "nmdc:wf-99-RGaB6W", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1097,7 +1097,7 @@ "was_informed_by": "gold:Gp0127654", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-405d59d65f666d1bb1f44393bf6b3c1a", + "id": "nmdc:wf-99-z7uO9d", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1117,7 +1117,7 @@ "was_informed_by": "gold:Gp0127655", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-82124fe8afc73ce5f61011ba9520ae38", + "id": "nmdc:wf-99-jz3us6", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1137,7 +1137,7 @@ "was_informed_by": "gold:Gp0127656", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-9bdf633bcd7d5b9bb1bf95ccd26349cd", + "id": "nmdc:wf-99-a9m4gL", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1157,7 +1157,7 @@ "was_informed_by": "gold:Gp0115664", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-686818cb31dc45d3d4482847ec007584", + "id": "nmdc:wf-99-yo16Ew", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1177,7 +1177,7 @@ "was_informed_by": "gold:Gp0115675", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-2e10913bdcfacfeeab4d9f7a0aa2af8f", + "id": "nmdc:wf-99-vhVDYB", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1197,7 +1197,7 @@ "was_informed_by": "gold:Gp0115673", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-b3bd170070e9c37f535de92c9f37b2b4", + "id": "nmdc:wf-99-nlSyxA", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1217,7 +1217,7 @@ "was_informed_by": "gold:Gp0115677", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-fdd5f518cea894505f0bd6ac02205ba3", + "id": "nmdc:wf-99-eo5wHj", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1237,7 +1237,7 @@ "was_informed_by": "gold:Gp0115678", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-42613f7c1fa860e847e2c93e2462b6f7", + "id": "nmdc:wf-99-ecPEJ8", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1257,7 +1257,7 @@ "was_informed_by": "gold:Gp0115665", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-9b6144e11b277a1f020c54da4ee79bac", + "id": "nmdc:wf-99-PTHtcy", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1277,7 +1277,7 @@ "was_informed_by": "gold:Gp0115671", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-c65521ed98ca6f569686debc46ea274d", + "id": "nmdc:wf-99-jwN3cK", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1297,7 +1297,7 @@ "was_informed_by": "gold:Gp0115666", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-638923494b08b936cefdac95ef58c558", + "id": "nmdc:wf-99-Cgtoyl", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1317,7 +1317,7 @@ "was_informed_by": "gold:Gp0115669", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-73840751bf8835b680aff13d0eb2335a", + "id": "nmdc:wf-99-EfFMDW", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1337,7 +1337,7 @@ "was_informed_by": "gold:Gp0115667", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-7b684248db11762d14a95ebdda7e8a81", + "id": "nmdc:wf-99-0AwQGw", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1357,7 +1357,7 @@ "was_informed_by": "gold:Gp0115676", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-87eb3326bcc84557dc334eff00d4a0bf", + "id": "nmdc:wf-99-CroPRX", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1377,7 +1377,7 @@ "was_informed_by": "gold:Gp0115668", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-87de8edb421c5364ee75c172715292cc", + "id": "nmdc:wf-99-HHkLNr", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1397,7 +1397,7 @@ "was_informed_by": "gold:Gp0115663", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-2d9a6d5e57ab455c257d8c3424331113", + "id": "nmdc:wf-99-VCC4zi", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1417,7 +1417,7 @@ "was_informed_by": "gold:Gp0115670", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-9994a8414976fd6b56935648246493b5", + "id": "nmdc:wf-99-w74cHl", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1437,7 +1437,7 @@ "was_informed_by": "gold:Gp0115672", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-932040eace29833c2b528f4279446285", + "id": "nmdc:wf-99-bSPq9H", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1457,7 +1457,7 @@ "was_informed_by": "gold:Gp0115674", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-5981c6f73f7cdc963866091b0101a9b7", + "id": "nmdc:wf-99-0UgR6E", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1477,7 +1477,7 @@ "was_informed_by": "gold:Gp0115679", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-9fcee63f77040c2b8cc0726b15f9f068", + "id": "nmdc:wf-99-fLwkIr", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1497,7 +1497,7 @@ "was_informed_by": "gold:Gp0321263", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-8d355d3c7070686b0beb20e39d17e172", + "id": "nmdc:wf-99-aIy9XQ", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1517,7 +1517,7 @@ "was_informed_by": "gold:Gp0321264", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-9269f143d88b7d5ff3c61897cfef80a7", + "id": "nmdc:wf-99-oWCV5s", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1537,7 +1537,7 @@ "was_informed_by": "gold:Gp0321265", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-36f15e6f9d8426dbc49ea6928b6b4bb6", + "id": "nmdc:wf-99-lEBJxj", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1557,7 +1557,7 @@ "was_informed_by": "gold:Gp0321266", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-c6acdfbb7449a3faf079ec67396af96b", + "id": "nmdc:wf-99-qlz9HX", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1577,7 +1577,7 @@ "was_informed_by": "gold:Gp0321267", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-739891753f88a2359b78191f41c19ad0", + "id": "nmdc:wf-99-2Qr8Pe", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1597,7 +1597,7 @@ "was_informed_by": "gold:Gp0321268", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-428a67c345a48187f0924d3af673c83c", + "id": "nmdc:wf-99-vlNUXC", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1617,7 +1617,7 @@ "was_informed_by": "gold:Gp0321269", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-3f1eb315892bb62126887cce05bdae32", + "id": "nmdc:wf-99-T4zSdA", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1637,7 +1637,7 @@ "was_informed_by": "gold:Gp0321270", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-63648550d5280b9de5c61fc3d9f75f27", + "id": "nmdc:wf-99-fPJH8j", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1657,7 +1657,7 @@ "was_informed_by": "gold:Gp0321271", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-9593e1500765d71b2a9eeb87ff22cb7a", + "id": "nmdc:wf-99-vvPofB", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1677,7 +1677,7 @@ "was_informed_by": "gold:Gp0321272", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-8e3f1f49fdd583134060849f51c4c9b2", + "id": "nmdc:wf-99-ulEnFz", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1697,7 +1697,7 @@ "was_informed_by": "gold:Gp0321273", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-10c34e648ade3d60e9a82c234293c3ad", + "id": "nmdc:wf-99-ltxbNs", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1717,7 +1717,7 @@ "was_informed_by": "gold:Gp0321274", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-9fb743bed2cae43e0c86553b046e1ec3", + "id": "nmdc:wf-99-eWTU43", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1737,7 +1737,7 @@ "was_informed_by": "gold:Gp0321275", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-43eaacb2ce2ac16f5ac67ccecfcd66be", + "id": "nmdc:wf-99-YDynsC", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1757,7 +1757,7 @@ "was_informed_by": "gold:Gp0321276", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-b4656c5f9122aab8e12e40bc24bec749", + "id": "nmdc:wf-99-tMBif9", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1777,7 +1777,7 @@ "was_informed_by": "gold:Gp0321277", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-aa45b2e1b2a903ffe1861ff6c2afcb51", + "id": "nmdc:wf-99-XjMQse", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1797,7 +1797,7 @@ "was_informed_by": "gold:Gp0321278", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-7f6f6431a81d831ade7a2c66ec675f3a", + "id": "nmdc:wf-99-henu5l", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1817,7 +1817,7 @@ "was_informed_by": "gold:Gp0321279", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-642b62309801412cc0020f1b9e02f2bf", + "id": "nmdc:wf-99-uw8bXm", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1837,7 +1837,7 @@ "was_informed_by": "gold:Gp0321280", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-b51eda7aa71887b5c3d87a88ae9ef886", + "id": "nmdc:wf-99-NPUIdn", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1857,7 +1857,7 @@ "was_informed_by": "gold:Gp0321281", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-24cc70779dc20ddcb8472360e94c1adb", + "id": "nmdc:wf-99-2Kolge", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1877,7 +1877,7 @@ "was_informed_by": "gold:Gp0321282", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-3c9a77593015e132a0fcb47e32077c78", + "id": "nmdc:wf-99-KIP9Ra", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1897,7 +1897,7 @@ "was_informed_by": "gold:Gp0321283", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-86ebdd0ce08264d2642a571956d686db", + "id": "nmdc:wf-99-v30BKk", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1917,7 +1917,7 @@ "was_informed_by": "gold:Gp0321284", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-8c0f927607c2b240824a5c52800d4c04", + "id": "nmdc:wf-99-ZIuifm", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1937,7 +1937,7 @@ "was_informed_by": "gold:Gp0321285", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-030d8c58a26cc8164ce629b8e988532a", + "id": "nmdc:wf-99-GGDI6V", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1957,7 +1957,7 @@ "was_informed_by": "gold:Gp0321286", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-132d4df2f27d60ae8fb093248975462f", + "id": "nmdc:wf-99-bKBOWR", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1977,7 +1977,7 @@ "was_informed_by": "gold:Gp0321287", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-6dfbdbcd7ab18ee7b2d213124e239cf6", + "id": "nmdc:wf-99-0oSxaI", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -1997,7 +1997,7 @@ "was_informed_by": "gold:Gp0321288", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-1f8036641fc942724894de3ed94df671", + "id": "nmdc:wf-99-zwlhtX", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2017,7 +2017,7 @@ "was_informed_by": "gold:Gp0321289", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-9b38ed417fe51b52f3afbe0ac56b25c1", + "id": "nmdc:wf-99-xSa1ZG", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2037,7 +2037,7 @@ "was_informed_by": "gold:Gp0321290", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-4e839407423180f709d7d5a81e6f070f", + "id": "nmdc:wf-99-nnWqhU", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2057,7 +2057,7 @@ "was_informed_by": "gold:Gp0321291", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-65a4e2c6d56914ab2e923aedd3441c4d", + "id": "nmdc:wf-99-nIFZZ2", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2077,7 +2077,7 @@ "was_informed_by": "gold:Gp0321292", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-5e2e998dfbfbfde7091237749c8d9028", + "id": "nmdc:wf-99-yOE0jd", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2097,7 +2097,7 @@ "was_informed_by": "gold:Gp0321293", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-1d1f5b339f19cc457782e86e04688b9f", + "id": "nmdc:wf-99-8LpUgc", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2117,7 +2117,7 @@ "was_informed_by": "gold:Gp0321294", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-fd71f805d1e05eae9f38d7d16de66299", + "id": "nmdc:wf-99-vJ2Mxf", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2137,7 +2137,7 @@ "was_informed_by": "gold:Gp0321295", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-7fbff9ac4fe3633f9f762069ed572b1c", + "id": "nmdc:wf-99-IIrhrj", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2157,7 +2157,7 @@ "was_informed_by": "gold:Gp0321296", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-327db9baa82cc3d9de443613cea1ee35", + "id": "nmdc:wf-99-eZmaaQ", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2177,7 +2177,7 @@ "was_informed_by": "gold:Gp0321297", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-6b8a96eb366ae631aa86badd9d11e9ae", + "id": "nmdc:wf-99-ASXJEJ", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2197,7 +2197,7 @@ "was_informed_by": "gold:Gp0321298", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-17fadd9c29b2374dbee61bd95e3f0a02", + "id": "nmdc:wf-99-J1EP4o", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2217,7 +2217,7 @@ "was_informed_by": "gold:Gp0321299", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-8456c04883daa652cd3c8ef61440c602", + "id": "nmdc:wf-99-fkLvFW", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2237,7 +2237,7 @@ "was_informed_by": "gold:Gp0321300", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-724f98d56bbda5686819251b3d35b3bb", + "id": "nmdc:wf-99-N8UcIX", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2257,7 +2257,7 @@ "was_informed_by": "gold:Gp0321301", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-b8865de68b6a30e28e9232a1184e4703", + "id": "nmdc:wf-99-vqx3jd", "ended_at_time": "2021-01-12T00:00:00+00:00" }, { @@ -2277,7 +2277,7 @@ "was_informed_by": "gold:Gp0321302", "execution_resource": "NERSC - Cori", "type": "nmdc:MetagenomeAnnotation", - "id": "nmdc:wf-449b5471dff17853621e8dcd4e46d790", + "id": "nmdc:wf-99-HV79Ao", "ended_at_time": "2021-01-12T00:00:00+00:00" } ] diff --git a/test/data/mg_assembly_activities_test.json b/test/data/mg_assembly_activities_test.json index 50e0bf230b..7275c29d7f 100644 --- a/test/data/mg_assembly_activities_test.json +++ b/test/data/mg_assembly_activities_test.json @@ -1,7 +1,7 @@ { "metagenome_assembly_set": [ { - "id": "nmdc:wfmgas-f404cb05d4c1458b659ae2232245c45d", + "id": "nmdc:wfmgas-99-B7Vogx", "name": "Metagenome assembly 1472_51277", "was_informed_by": "gold:Gp0061273", "started_at_time": "2020-03-24T00:00:00+00:00", @@ -48,7 +48,7 @@ "num_aligned_reads": 63046103 }, { - "id": "nmdc:wfmgas-e7d3e1551ad9439505b522d5b1768c97", + "id": "nmdc:wfmgas-99-CvgXTq", "name": "Metagenome assembly 1472_51278", "was_informed_by": "gold:Gp0061274", "started_at_time": "2020-03-25T00:00:00+00:00", @@ -95,7 +95,7 @@ "num_aligned_reads": 95369019 }, { - "id": "nmdc:wfmgas-9a2a0778e003977d594c93e54fcef3e6", + "id": "nmdc:wfmgas-99-L9Z34K", "name": "Metagenome assembly 1472_51279", "was_informed_by": "gold:Gp0061275", "started_at_time": "2020-03-25T00:00:00+00:00", diff --git a/test/data/mg_assembly_data_objects_test.json b/test/data/mg_assembly_data_objects_test.json index 09e7768f66..a1b9d73885 100644 --- a/test/data/mg_assembly_data_objects_test.json +++ b/test/data/mg_assembly_data_objects_test.json @@ -1,21 +1,21 @@ { "data_object_set": [ { - "id": "nmdc:dobj-8ecc9e4fe4c74d7a58b02fd8954555b9", + "id": "nmdc:dobj-99-izwYW6", "name": "mapping_stats.txt", "description": "Metagenome Contig Coverage Stats for gold:Gp0061273", "file_size_bytes": 32787380, "type": "nmdc:DataObject" }, { - "id": "nmdc:dobj-3f85e34d2c32b65e33e4abd2431dfbe8", + "id": "nmdc:dobj-99-bS0GkU", "name": "assembly_contigs.fna", "description": "Assembled contigs fasta for gold:Gp0061273", "file_size_bytes": 206578499, "type": "nmdc:DataObject" }, { - "id": "nmdc:dobj-3c892f96e847b0b524d5d4e50611b5fd", + "id": "nmdc:dobj-99-PqBJvW", "name": "assembly_scaffolds.fna", "description": "Assembled scaffold fasta for gold:Gp0061273", "file_size_bytes": 205297945, diff --git a/test/data/nmdc_example_database.json b/test/data/nmdc_example_database.json index c93471a411..8139f8ca96 100644 --- a/test/data/nmdc_example_database.json +++ b/test/data/nmdc_example_database.json @@ -1,7 +1,7 @@ { "study_set": [ { - "id": "nmdc:sty-19f024bb-8f6a-42e9-846b-beff8e417cbd", + "id": "nmdc:sty-99-FkQIsc", "gold_study_identifiers": [ "gold:Gs0128849" ], @@ -21,7 +21,7 @@ "type": "nmdc:Study" }, { - "id": "nmdc:sty-d9a5431e-0ae0-4953-b00a-945fc5d94cd9", + "id": "nmdc:sty-99-oJmAOs", "gold_study_identifiers": [ "gold:Gs0130354" ], @@ -41,7 +41,7 @@ "type": "nmdc:Study" }, { - "id": "nmdc:sty-2e9e3439-06e1-4ebb-ae97-20a198272831", + "id": "nmdc:sty-99-3bQQ4j", "gold_study_identifiers": [ "gold:Gs0134277" ], @@ -63,7 +63,7 @@ ], "omics_processing_set": [ { - "id": "nmdc:omprc-45fc7de7-3610-4f15-b95e-d19462c98469", + "id": "nmdc:omprc-99-9XUVVF", "alternative_identifiers": [ "gold:Gp0225767" ], @@ -88,7 +88,7 @@ "type": "nmdc:OmicsProcessing" }, { - "id": "nmdc:omprc-50a0ab53-cd00-476e-9ca1-f178843b4a30", + "id": "nmdc:omprc-99-dk9vgI", "alternative_identifiers": [ "gold:Gp0208560" ], @@ -113,7 +113,7 @@ "type": "nmdc:OmicsProcessing" }, { - "id": "nmdc:omprc-ed3f3c3a-8916-4fc8-8d98-40a8399719e3", + "id": "nmdc:omprc-99-MVW1FV", "alternative_identifiers": [ "gold:Gp0306221" ], @@ -140,7 +140,7 @@ ], "biosample_set": [ { - "id": "nmdc:bsm-c6eb9f01-796b-4bd6-8ed4-74e221eed7c1", + "id": "nmdc:bsm-99-isqhuW", "gold_biosample_identifiers": [ "gold:Gb0150408" ], @@ -194,7 +194,7 @@ "sample_collection_site": "Mire fen" }, { - "id": "nmdc:bsm-87698d0e-13b5-488a-9324-53846a6e332d", + "id": "nmdc:bsm-99-dge3H9", "gold_biosample_identifiers": [ "gold:Gb0157174" ], @@ -248,7 +248,7 @@ "sample_collection_site": "forest soil" }, { - "id": "nmdc:bsm-9a4f0882-49b2-46ed-8951-0ee2ea019df7", + "id": "nmdc:bsm-99-dc6tg6", "gold_biosample_identifiers": [ "gold:Gb0188037" ], @@ -305,21 +305,21 @@ ], "data_object_set": [ { - "id": "nmdc:dobj-161afbd2-0d43-48ba-bc96-47697de83fbb", + "id": "nmdc:dobj-99-dkJ8xX", "name": "11340.8.202049.GTCTCCT-AAGGAGA.fastq.gz", "description": "Raw sequencer read data", "file_size_bytes": 9208349052.0, "type": "nmdc:DataObject" }, { - "id": "nmdc:dobj-80224019-2607-4610-8981-11ba7ef871fc", + "id": "nmdc:dobj-99-7zrm55", "name": "11839.4.222578.GAGCTCA-TTGAGCT.fastq.gz", "description": "Raw sequencer read data", "file_size_bytes": 34243309819.0, "type": "nmdc:DataObject" }, { - "id": "nmdc:dobj-5fd558d1-38d3-4f70-8fca-023fff2a035e", + "id": "nmdc:dobj-99-sQQw0I", "name": "12660.4.274923.GATCGTAC-GTACGATC.fastq.gz", "description": "Raw sequencer read data", "file_size_bytes": 7580035314.0, diff --git a/test/data/samp_prep_db.json b/test/data/samp_prep_db.json index ef66d713a3..ec9d8420b2 100644 --- a/test/data/samp_prep_db.json +++ b/test/data/samp_prep_db.json @@ -31,27 +31,27 @@ "material_sample_set": [ { "name": "monet_data:soil_1", - "id": "nmdc:matsm-bfc5b458-1c62-44e7-886a-dd3a2cc7ad67", + "id": "nmdc:matsm-99-PVhTGD", "description": "a soil biosample" }, { "name": "nmdc:matsm-b1fb4ff1-e59b-4e2b-a8f9-b95ea6ba4135", - "id": "nmdc:matsm-b1fb4ff1-e59b-4e2b-a8f9-b95ea6ba4135", + "id": "nmdc:matsm-99-m7PfV8", "description": "a 6 gram aliquot of monet_data:soil_1" }, { "name": "monet_data:somextract_7", - "id": "nmdc:matsm-181a7a0a-4b04-4a22-9b89-db53e2ccdc99", + "id": "nmdc:matsm-99-j670OL", "description": "monet_data:somextract_6 dissolved in 30 mL of water" }, { "name": "monet_data:derive_4", - "id": "nmdc:matsm-31380f3c-cea3-4f68-a8c6-cd84efa5e622", + "id": "nmdc:matsm-99-KyiIwv", "description": "something at the beginning of a reaction" }, { "name": "monet_data:derive_5", - "id": "nmdc:matsm-9fe9277b-454a-4257-a825-3b4725df665e", + "id": "nmdc:matsm-99-KaZog6", "description": "something at the end of a reaction" } ], diff --git a/test/data/study_credit_test.json b/test/data/study_credit_test.json index 56c7e0cbad..74a8221c13 100644 --- a/test/data/study_credit_test.json +++ b/test/data/study_credit_test.json @@ -1,7 +1,7 @@ { "study_set": [ { - "id": "nmdc:sty-b08d8a6a-0940-4d36-939f-7320d672f051", + "id": "nmdc:sty-99-WoeqAi", "has_credit_associations": [ { "applied_roles": [ diff --git a/test/data/study_test.json b/test/data/study_test.json index ce5c7e528b..c8c4adbc01 100644 --- a/test/data/study_test.json +++ b/test/data/study_test.json @@ -1,7 +1,7 @@ { "study_set": [ { - "id": "nmdc:sty-da4abee8-23df-4c65-8ac4-48db0f3aa4e5", + "id": "nmdc:sty-99-boww8R", "gold_study_identifiers": [ "gold:Gs0110115" ], @@ -21,7 +21,7 @@ "type": "nmdc:Study" }, { - "id": "nmdc:sty-2da265bf-ebfe-43b0-84d9-e33fcec8f852", + "id": "nmdc:sty-99-hfaLvo", "gold_study_identifiers": [ "gold:Gs0110132" ], @@ -41,7 +41,7 @@ "type": "nmdc:Study" }, { - "id": "nmdc:sty-602bc5a4-14bf-48f5-96bf-a2b7236d0a04", + "id": "nmdc:sty-99-dkDZYe", "gold_study_identifiers": [ "gold:Gs0112340" ], From efbf4f03fe4cbdda86e2139c5dd7c30142d4fd25 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Fri, 20 Jan 2023 13:25:09 -0500 Subject: [PATCH 57/60] regen for #625 --- Makefile | 12 + json/nmdc.linkml.json | 49594 ++++++++++++++++++- jsonld-context/nmdc.context.jsonld | 8 +- jsonschema/nmdc.schema.json | 5574 ++- nmdc_schema/annotation.py | 80 +- nmdc_schema/basic_slots.py | 32 +- nmdc_schema/bioscales.py | 32 +- nmdc_schema/core.py | 32 +- nmdc_schema/external_identifiers.py | 32 +- nmdc_schema/mixs.py | 32 +- nmdc_schema/mixs_legacy.py | 3311 -- nmdc_schema/mixs_new.py | 4656 -- nmdc_schema/nmdc.py | 113 +- nmdc_schema/nmdc.schema.json | 5574 ++- nmdc_schema/nmdc.yaml | 74 +- nmdc_schema/prov.py | 32 +- nmdc_schema/sample_prep.py | 115 +- nmdc_schema/workflow_execution_activity.py | 80 +- python/annotation.py | 80 +- python/basic_slots.py | 32 +- python/bioscales.py | 32 +- python/core.py | 32 +- python/external_identifiers.py | 32 +- python/mixs.py | 32 +- python/mixs_legacy.py | 3311 -- python/mixs_new.py | 4656 -- python/nmdc.py | 113 +- python/portal/README.md | 3 + python/portal/emsl.py | 2 +- python/portal/jgi_metagenomics.py | 5 +- python/portal/jgi_metatranscriptomics.py | 5 +- python/portal/mixs_inspired.py | 2 +- python/portal/sample_id.py | 2 +- python/prov.py | 32 +- python/sample_prep.py | 115 +- python/workflow_execution_activity.py | 80 +- 36 files changed, 60499 insertions(+), 17450 deletions(-) delete mode 100644 nmdc_schema/mixs_legacy.py delete mode 100644 nmdc_schema/mixs_new.py delete mode 100644 python/mixs_legacy.py delete mode 100644 python/mixs_new.py create mode 100644 python/portal/README.md diff --git a/Makefile b/Makefile index 431dd4f1dd..46318f5c82 100644 --- a/Makefile +++ b/Makefile @@ -1,3 +1,7 @@ +# consider some cleanup: /assets /images /slides /util +# /doc vs /docs? +# empties: /graphql /owl /rdf /shex + SRC_DIR = src SCHEMA_DIR = $(SRC_DIR)/schema SOURCE_FILES := $(shell find $(SCHEMA_DIR) -name '*.yaml') @@ -29,6 +33,13 @@ revert-jsonschema: clean-artifacts: rm -rf target/ + rm -rf json/*.json + rm -rf jsonld-context/*.jsonld + rm -rf jsonschema/*.json + rm -rf python/*.py + rm -rf python/portal/*.py + + clean-docs: ls docs/*.md | egrep -v 'README.md|README.markdown' | xargs rm -f # keep readme files @@ -186,6 +197,7 @@ clean-package: rm -f nmdc_schema/*.json rm -f nmdc_schema/*.py rm -f nmdc_schema/*.tsv + rm -f nmdc_schema/*.yaml rm -rf dist && echo 'dist removed' rm -rf nmdc_schema.egg-info && echo 'egg-info removed' diff --git a/json/nmdc.linkml.json b/json/nmdc.linkml.json index 292826c9a8..3c0f208cd4 100644 --- a/json/nmdc.linkml.json +++ b/json/nmdc.linkml.json @@ -7,7 +7,7 @@ "removed/commented out the comfusing 'identifier' slot", "removed/commented out all mentions and definitions of depth2 and subsurface_depth2", "depth2 should now be migrated to the has_maximum_value part of depth", - "slots requested for Bioscales, but already available for Biosample: tot_phosp, tot_carb, tot_nitro_content, pH", + "slots requested for Bioscales, but already available for Biosample : tot_phosp, tot_carb, tot_nitro_content, pH", "informal ## section delimiters should be replaced with subsets ?", "commented out insdc_biosample_identifiers insdc_secondary_sample_identifiers... need better understanding of id patterns (at least)", "commented out several MIxS terms assigned to Biosample because the definitions of those terms were commented out in mixs.yaml dues to shared slot uris", @@ -15,23 +15,6 @@ ], "id": "https://microbiomedata/schema", "version": "7.0.0", - "imports": [ - "annotation", - "basic_slots", - "bioscales", - "core", - "external_identifiers", - "linkml:types", - "mixs", - "portal/emsl", - "portal/jgi_metagenomics", - "portal/jgi_metatranscriptomics", - "portal/mixs_inspired", - "portal/sample_id", - "prov", - "sample_prep", - "workflow_execution_activity" - ], "license": "https://creativecommons.org/publicdomain/zero/1.0/", "prefixes": { "COG": { @@ -165,6 +148,54 @@ "xsd": { "prefix_prefix": "xsd", "prefix_reference": "http://www.w3.org/2001/XMLSchema#" + }, + "KEGG.COMPOUND": { + "prefix_prefix": "KEGG.COMPOUND", + "prefix_reference": "http://identifiers.org/kegg.compound/" + }, + "igsnvoc": { + "prefix_prefix": "igsnvoc", + "prefix_reference": "https://igsn.org/voc/v1/" + }, + "sio": { + "prefix_prefix": "sio", + "prefix_reference": "http://semanticscience.org/resource/SIO_" + }, + "shex": { + "prefix_prefix": "shex", + "prefix_reference": "http://www.w3.org/ns/shex#" + }, + "CHEBI": { + "prefix_prefix": "CHEBI", + "prefix_reference": "http://purl.obolibrary.org/obo/CHEBI_" + }, + "CHMO": { + "prefix_prefix": "CHMO", + "prefix_reference": "http://purl.obolibrary.org/obo/CHMO_" + }, + "GO": { + "prefix_prefix": "GO", + "prefix_reference": "http://purl.obolibrary.org/obo/GO_" + }, + "KEGG_PATHWAY": { + "prefix_prefix": "KEGG_PATHWAY", + "prefix_reference": "http://identifiers.org/kegg.pathway/" + }, + "KEGG.REACTION": { + "prefix_prefix": "KEGG.REACTION", + "prefix_reference": "http://identifiers.org/kegg.reaction/" + }, + "RHEA": { + "prefix_prefix": "RHEA", + "prefix_reference": "http://identifiers.org/rhea/" + }, + "SEED": { + "prefix_prefix": "SEED", + "prefix_reference": "http://identifiers.org/seed/" + }, + "KEGG.ORTHOLOGY": { + "prefix_prefix": "KEGG.ORTHOLOGY", + "prefix_reference": "http://identifiers.org/kegg.orthology/" } }, "emit_prefixes": [ @@ -189,6 +220,210 @@ "name": "data object subset", "description": "Subset consisting of the data objects that either inputs or outputs of processes or workflows.", "from_schema": "https://microbiomedata/schema" + }, + "workflow subset": { + "name": "workflow subset", + "description": "Subset consisting of just the workflow execution activities", + "from_schema": "https://microbiomedata/schema" + }, + "environment": { + "name": "environment", + "from_schema": "https://microbiomedata/schema" + }, + "investigation": { + "name": "investigation", + "from_schema": "https://microbiomedata/schema" + }, + "mixs extension": { + "name": "mixs extension", + "from_schema": "https://microbiomedata/schema" + }, + "nucleic acid sequence source": { + "name": "nucleic acid sequence source", + "from_schema": "https://microbiomedata/schema" + }, + "sequencing": { + "name": "sequencing", + "from_schema": "https://microbiomedata/schema" + }, + "soil": { + "name": "soil", + "from_schema": "https://microbiomedata/schema" + } + }, + "types": { + "bytes": { + "name": "bytes", + "description": "An integer value that corresponds to a size in bytes", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "UO:0000233" + ], + "base": "int", + "uri": "xsd:long" + }, + "decimal degree": { + "name": "decimal degree", + "description": "A decimal degree expresses latitude or longitude as decimal fractions.", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://en.wikipedia.org/wiki/Decimal_degrees" + ], + "base": "float", + "uri": "xsd:decimal" + }, + "language code": { + "name": "language code", + "description": "A language code conforming to ISO_639-1", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://en.wikipedia.org/wiki/ISO_639-1" + ], + "base": "str", + "uri": "xsd:language" + }, + "unit": { + "name": "unit", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "qud:Unit", + "UO:0000000" + ], + "base": "str", + "uri": "xsd:string" + }, + "string": { + "name": "string", + "description": "A character string", + "from_schema": "https://microbiomedata/schema", + "base": "str", + "uri": "xsd:string" + }, + "integer": { + "name": "integer", + "description": "An integer", + "from_schema": "https://microbiomedata/schema", + "base": "int", + "uri": "xsd:integer" + }, + "boolean": { + "name": "boolean", + "description": "A binary (true or false) value", + "from_schema": "https://microbiomedata/schema", + "base": "Bool", + "uri": "xsd:boolean", + "repr": "bool" + }, + "float": { + "name": "float", + "description": "A real number that conforms to the xsd:float specification", + "from_schema": "https://microbiomedata/schema", + "base": "float", + "uri": "xsd:float" + }, + "double": { + "name": "double", + "description": "A real number that conforms to the xsd:double specification", + "from_schema": "https://microbiomedata/schema", + "base": "float", + "uri": "xsd:double" + }, + "decimal": { + "name": "decimal", + "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "from_schema": "https://microbiomedata/schema", + "base": "Decimal", + "uri": "xsd:decimal" + }, + "time": { + "name": "time", + "description": "A time object represents a (local) time of day, independent of any particular day", + "notes": [ + "URI is dateTime because OWL reasoners do not work with straight date or time" + ], + "from_schema": "https://microbiomedata/schema", + "base": "XSDTime", + "uri": "xsd:dateTime", + "repr": "str" + }, + "date": { + "name": "date", + "description": "a date (year, month and day) in an idealized calendar", + "notes": [ + "URI is dateTime because OWL reasoners don't work with straight date or time" + ], + "from_schema": "https://microbiomedata/schema", + "base": "XSDDate", + "uri": "xsd:date", + "repr": "str" + }, + "datetime": { + "name": "datetime", + "description": "The combination of a date and time", + "from_schema": "https://microbiomedata/schema", + "base": "XSDDateTime", + "uri": "xsd:dateTime", + "repr": "str" + }, + "date_or_datetime": { + "name": "date_or_datetime", + "description": "Either a date or a datetime", + "from_schema": "https://microbiomedata/schema", + "base": "str", + "uri": "linkml:DateOrDatetime", + "repr": "str" + }, + "uriorcurie": { + "name": "uriorcurie", + "description": "a URI or a CURIE", + "from_schema": "https://microbiomedata/schema", + "base": "URIorCURIE", + "uri": "xsd:anyURI", + "repr": "str" + }, + "uri": { + "name": "uri", + "description": "a complete URI", + "from_schema": "https://microbiomedata/schema", + "base": "URI", + "uri": "xsd:anyURI", + "repr": "str" + }, + "ncname": { + "name": "ncname", + "description": "Prefix part of CURIE", + "from_schema": "https://microbiomedata/schema", + "base": "NCName", + "uri": "xsd:string", + "repr": "str" + }, + "objectidentifier": { + "name": "objectidentifier", + "description": "A URI or CURIE that represents an object in the model.", + "comments": [ + "Used for inheritence and type checking" + ], + "from_schema": "https://microbiomedata/schema", + "base": "ElementIdentifier", + "uri": "shex:iri", + "repr": "str" + }, + "nodeidentifier": { + "name": "nodeidentifier", + "description": "A URI, CURIE or BNODE that represents a node in a model.", + "from_schema": "https://microbiomedata/schema", + "base": "NodeIdentifier", + "uri": "shex:nonLiteral", + "repr": "str" + }, + "external identifier": { + "name": "external identifier", + "description": "A CURIE representing an external identifier", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://microbiomedata.github.io/nmdc-schema/identifiers.html" + ], + "typeof": "uriorcurie" } }, "enums": { @@ -586,895 +821,23275 @@ ] } } - } - }, - "slots": { - "collected_from": { - "name": "collected_from", - "description": "The Site from which a Biosample was collected", - "todos": [ - "add an OBO slot_uri ?" - ], - "comments": [ - "this illustrates implementing a Biosample relation with a (binary) slot" - ], - "from_schema": "https://microbiomedata/schema", - "domain": "Biosample", - "range": "FieldResearchSite" }, - "emsl_project_identifier": { - "name": "emsl_project_identifier", - "from_schema": "https://microbiomedata/schema" + "ContainerTypeEnum": { + "name": "ContainerTypeEnum", + "title": "Container type enumeration", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "screw_top_conical": { + "text": "screw_top_conical", + "title": "Screw top conical tube", + "aliases": [ + "falcon tube" + ] + } + } }, - "img_identifiers": { - "name": "img_identifiers", - "description": "A list of identifiers that relate the biosample to records in the IMG database.", - "title": "IMG Identifiers", - "todos": [ - "add is_a or mixin modeling", - "what are the class of IMG records?!" - ], + "DeviceTypeEnum": { + "name": "DeviceTypeEnum", + "title": "Shaker type enumeration", "from_schema": "https://microbiomedata/schema", - "multivalued": true + "permissible_values": { + "orbital_shaker": { + "text": "orbital_shaker", + "title": "Orbital shaker" + }, + "thermomixer": { + "text": "thermomixer", + "title": "Thermomixer" + } + } }, - "emsl_biosample_identifiers": { - "name": "emsl_biosample_identifiers", - "description": "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.", - "title": "EMSL Biosample Identifiers", - "todos": [ - "removed \"planned\" once NEXUS is online", - "make an emsl identifiers mixin", - "determine real expansion for emsl prefix" - ], + "SamplingMethodEnum": { + "name": "SamplingMethodEnum", "from_schema": "https://microbiomedata/schema", - "is_a": "biosample_identifiers", - "multivalued": true + "permissible_values": { + "weighing": { + "text": "weighing", + "title": "Weighing" + } + } }, - "igsn_biosample_identifiers": { - "name": "igsn_biosample_identifiers", - "description": "A list of identifiers for the biosample from the IGSN database.", - "title": "IGSN Biosample Identifiers", - "todos": [ - "make an igsn identifiers mixin" - ], + "SolventEnum": { + "name": "SolventEnum", + "title": "Solvent enumeration", "from_schema": "https://microbiomedata/schema", - "is_a": "biosample_identifiers", - "multivalued": true + "permissible_values": { + "deionized_water": { + "text": "deionized_water", + "title": "Deionized water", + "broad_mappings": [ + "CHEBI:15377" + ] + }, + "methanol": { + "text": "methanol", + "meaning": "CHEBI:17790", + "title": "Methanol" + }, + "chloroform": { + "text": "chloroform", + "meaning": "CHEBI:35255", + "title": "Chloroform" + } + } }, - "biosample_categories": { - "name": "biosample_categories", - "title": "Categories the biosample belongs to", + "analysis_type_enum": { + "name": "analysis_type_enum", "from_schema": "https://microbiomedata/schema", - "multivalued": true, - "range": "biosample_category_enum" + "permissible_values": { + "metabolomics": { + "text": "metabolomics" + }, + "metagenomics": { + "text": "metagenomics" + }, + "metaproteomics": { + "text": "metaproteomics" + }, + "metatranscriptomics": { + "text": "metatranscriptomics" + }, + "natural organic matter": { + "text": "natural organic matter" + } + } }, - "date_created": { - "name": "date_created", - "description": "from database class", - "from_schema": "https://microbiomedata/schema" + "dnase_rna_enum": { + "name": "dnase_rna_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "no": { + "text": "no" + }, + "yes": { + "text": "yes" + } + } }, - "etl_software_version": { - "name": "etl_software_version", - "description": "from database class", - "from_schema": "https://microbiomedata/schema" + "rna_cont_type_enum": { + "name": "rna_cont_type_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "plate": { + "text": "plate" + }, + "tube": { + "text": "tube" + } + } }, - "related_identifiers": { - "name": "related_identifiers", - "description": "Identifiers assigned to a thing that is similar to that which is represented in NMDC. Related identifier are not an identical match and may have some variation.", - "title": "Related Identifiers", - "from_schema": "https://microbiomedata/schema" + "rna_sample_format_enum": { + "name": "rna_sample_format_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "10 mM Tris-HCl": { + "text": "10 mM Tris-HCl" + }, + "DNAStable": { + "text": "DNAStable" + }, + "Ethanol": { + "text": "Ethanol" + }, + "Low EDTA TE": { + "text": "Low EDTA TE" + }, + "MDA reaction buffer": { + "text": "MDA reaction buffer" + }, + "PBS": { + "text": "PBS" + }, + "Pellet": { + "text": "Pellet" + }, + "RNAStable": { + "text": "RNAStable" + }, + "TE": { + "text": "TE" + }, + "Water": { + "text": "Water" + }, + "Gentegra-DNA": { + "text": "Gentegra-DNA" + }, + "Gentegra-RNA": { + "text": "Gentegra-RNA" + } + } }, - "emsl_proposal_identifier": { - "name": "emsl_proposal_identifier", - "description": "The proposal number assigned to the EMSL awarded study that relates to that which is represented in NMDC.", - "title": "EMSL Proposal Identifier", - "from_schema": "https://microbiomedata/schema" + "dna_cont_type_enum": { + "name": "dna_cont_type_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "plate": { + "text": "plate" + }, + "tube": { + "text": "tube" + } + } }, - "emsl_proposal_doi": { - "name": "emsl_proposal_doi", - "description": "The proposal DOI assigned to the awarded EMSL study.", - "title": "EMSL Proposal DOI", - "from_schema": "https://microbiomedata/schema" + "dna_dnase_enum": { + "name": "dna_dnase_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "no": { + "text": "no" + }, + "yes": { + "text": "yes" + } + } }, - "notes": { - "name": "notes", - "description": "from study class", - "from_schema": "https://microbiomedata/schema" + "dna_sample_format_enum": { + "name": "dna_sample_format_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "10 mM Tris-HCl": { + "text": "10 mM Tris-HCl" + }, + "DNAStable": { + "text": "DNAStable" + }, + "Ethanol": { + "text": "Ethanol" + }, + "Low EDTA TE": { + "text": "Low EDTA TE" + }, + "MDA reaction buffer": { + "text": "MDA reaction buffer" + }, + "PBS": { + "text": "PBS" + }, + "Pellet": { + "text": "Pellet" + }, + "RNAStable": { + "text": "RNAStable" + }, + "TE": { + "text": "TE" + }, + "Water": { + "text": "Water" + }, + "Gentegra-DNA": { + "text": "Gentegra-DNA" + }, + "Gentegra-RNA": { + "text": "Gentegra-RNA" + } + } }, - "canary": { - "name": "canary", - "description": "a slot that can be added and removed as evidence that schema changes have propagated to other systems", - "from_schema": "https://microbiomedata/schema" + "sample_type_enum": { + "name": "sample_type_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "soil": { + "text": "soil" + }, + "water_extract_soil": { + "text": "water_extract_soil" + } + } }, - "ess_dive_datasets": { - "name": "ess_dive_datasets", - "description": "List of ESS-DIVE dataset DOIs", + "arch_struc_enum": { + "name": "arch_struc_enum", "from_schema": "https://microbiomedata/schema", - "multivalued": true + "permissible_values": { + "building": { + "text": "building" + }, + "shed": { + "text": "shed" + }, + "home": { + "text": "home" + } + } }, - "has_credit_associations": { - "name": "has_credit_associations", - "annotations": { - "display_hint": { - "tag": "display_hint", - "value": "Other researchers associated with this study." - } - }, - "description": "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study", - "notes": [ - "had just been \"inlined: true\"" - ], + "biol_stat_enum": { + "name": "biol_stat_enum", "from_schema": "https://microbiomedata/schema", - "domain": "Study", - "slot_uri": "prov:qualifiedAssociation", - "multivalued": true, - "range": "CreditAssociation", - "inlined_as_list": true + "permissible_values": { + "wild": { + "text": "wild" + }, + "natural": { + "text": "natural" + }, + "semi-natural": { + "text": "semi-natural" + }, + "inbred line": { + "text": "inbred line" + }, + "breeder's line": { + "text": "breeder's line" + }, + "hybrid": { + "text": "hybrid" + }, + "clonal selection": { + "text": "clonal selection" + }, + "mutant": { + "text": "mutant" + } + } }, - "study_image": { - "name": "study_image", - "description": "Links a study to one or more images.", + "biotic_relationship_enum": { + "name": "biotic_relationship_enum", "from_schema": "https://microbiomedata/schema", - "domain": "Study", - "multivalued": true, - "range": "ImageValue", - "inlined": true + "permissible_values": { + "free living": { + "text": "free living" + }, + "parasite": { + "text": "parasite" + }, + "commensal": { + "text": "commensal" + }, + "symbiont": { + "text": "symbiont" + } + } }, - "relevant_protocols": { - "name": "relevant_protocols", + "build_docs_enum": { + "name": "build_docs_enum", "from_schema": "https://microbiomedata/schema", - "multivalued": true, - "range": "string" + "permissible_values": { + "building information model": { + "text": "building information model" + }, + "commissioning report": { + "text": "commissioning report" + }, + "complaint logs": { + "text": "complaint logs" + }, + "contract administration": { + "text": "contract administration" + }, + "cost estimate": { + "text": "cost estimate" + }, + "janitorial schedules or logs": { + "text": "janitorial schedules or logs" + }, + "maintenance plans": { + "text": "maintenance plans" + }, + "schedule": { + "text": "schedule" + }, + "sections": { + "text": "sections" + }, + "shop drawings": { + "text": "shop drawings" + }, + "submittals": { + "text": "submittals" + }, + "ventilation system": { + "text": "ventilation system" + }, + "windows": { + "text": "windows" + } + } }, - "funding_sources": { - "name": "funding_sources", + "build_occup_type_enum": { + "name": "build_occup_type_enum", "from_schema": "https://microbiomedata/schema", - "multivalued": true, - "range": "string" + "permissible_values": { + "office": { + "text": "office" + }, + "market": { + "text": "market" + }, + "restaurant": { + "text": "restaurant" + }, + "residence": { + "text": "residence" + }, + "school": { + "text": "school" + }, + "residential": { + "text": "residential" + }, + "commercial": { + "text": "commercial" + }, + "low rise": { + "text": "low rise" + }, + "high rise": { + "text": "high rise" + }, + "wood framed": { + "text": "wood framed" + }, + "health care": { + "text": "health care" + }, + "airport": { + "text": "airport" + }, + "sports complex": { + "text": "sports complex" + } + } }, - "applied_role": { - "name": "applied_role", - "deprecated": "A credit association may have multiple roles. So, use the applied roles slot.", + "building_setting_enum": { + "name": "building_setting_enum", "from_schema": "https://microbiomedata/schema", - "domain": "CreditAssociation", - "slot_uri": "prov:hadRole", - "multivalued": false, - "range": "credit enum", - "required": false - }, - "applied_roles": { - "name": "applied_roles", - "annotations": { - "display_hint": { - "tag": "display_hint", - "value": "Identify all CRediT roles associated with this contributor. CRediT Information: https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/" + "permissible_values": { + "urban": { + "text": "urban" + }, + "suburban": { + "text": "suburban" + }, + "exurban": { + "text": "exurban" + }, + "rural": { + "text": "rural" } - }, - "from_schema": "https://microbiomedata/schema", - "domain": "CreditAssociation", - "multivalued": true, - "range": "credit enum", - "required": true + } }, - "applies_to_person": { - "name": "applies_to_person", - "todos": [ - "prov:agent takes an Agent object. Is a person value an Agent? Also try to relate to principal investigator slot? could include OBI:0000103 principal investigator role... do we need to define the OBI prefix?" - ], + "ceil_cond_enum": { + "name": "ceil_cond_enum", "from_schema": "https://microbiomedata/schema", - "domain": "CreditAssociation", - "slot_uri": "prov:agent", - "multivalued": false, - "range": "PersonValue", - "required": true + "permissible_values": { + "new": { + "text": "new" + }, + "visible wear": { + "text": "visible wear" + }, + "needs repair": { + "text": "needs repair" + }, + "damaged": { + "text": "damaged" + }, + "rupture": { + "text": "rupture" + } + } }, - "object_set": { - "name": "object_set", - "description": "Applies to a property that links a database object to a set of objects. This is necessary in a json document to provide context for a list, and to allow for a single json object that combines multiple object types", + "ceil_finish_mat_enum": { + "name": "ceil_finish_mat_enum", "from_schema": "https://microbiomedata/schema", - "mixin": true, - "domain": "Database", - "multivalued": true, - "inlined_as_list": true + "permissible_values": { + "drywall": { + "text": "drywall" + }, + "mineral fibre": { + "text": "mineral fibre" + }, + "tiles": { + "text": "tiles" + }, + "PVC": { + "text": "PVC" + }, + "plasterboard": { + "text": "plasterboard" + }, + "metal": { + "text": "metal" + }, + "fiberglass": { + "text": "fiberglass" + }, + "stucco": { + "text": "stucco" + }, + "mineral wool/calcium silicate": { + "text": "mineral wool/calcium silicate" + }, + "wood": { + "text": "wood" + } + } }, - "biosample_set": { - "name": "biosample_set", - "description": "This property links a database object to the set of samples within it.", + "ceil_texture_enum": { + "name": "ceil_texture_enum", "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "Biosample" + "permissible_values": { + "crows feet": { + "text": "crows feet" + }, + "crows-foot stomp": { + "text": "crows-foot stomp" + }, + "double skip": { + "text": "double skip" + }, + "hawk and trowel": { + "text": "hawk and trowel" + }, + "knockdown": { + "text": "knockdown" + }, + "popcorn": { + "text": "popcorn" + }, + "orange peel": { + "text": "orange peel" + }, + "rosebud stomp": { + "text": "rosebud stomp" + }, + "Santa-Fe texture": { + "text": "Santa-Fe texture" + }, + "skip trowel": { + "text": "skip trowel" + }, + "smooth": { + "text": "smooth" + }, + "stomp knockdown": { + "text": "stomp knockdown" + }, + "swirl": { + "text": "swirl" + } + } }, - "study_set": { - "name": "study_set", - "description": "This property links a database object to the set of studies within it.", + "ceil_type_enum": { + "name": "ceil_type_enum", "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "Study" + "permissible_values": { + "cathedral": { + "text": "cathedral" + }, + "dropped": { + "text": "dropped" + }, + "concave": { + "text": "concave" + }, + "barrel-shaped": { + "text": "barrel-shaped" + }, + "coffered": { + "text": "coffered" + }, + "cove": { + "text": "cove" + }, + "stretched": { + "text": "stretched" + } + } }, - "field_research_site_set": { - "name": "field_research_site_set", + "cur_land_use_enum": { + "name": "cur_land_use_enum", "from_schema": "https://microbiomedata/schema", - "domain": "Database", - "multivalued": true, - "range": "FieldResearchSite", - "inlined_as_list": true + "permissible_values": { + "cities": { + "text": "cities" + }, + "farmstead": { + "text": "farmstead" + }, + "industrial areas": { + "text": "industrial areas" + }, + "roads/railroads": { + "text": "roads/railroads" + }, + "rock": { + "text": "rock" + }, + "sand": { + "text": "sand" + }, + "gravel": { + "text": "gravel" + }, + "mudflats": { + "text": "mudflats" + }, + "salt flats": { + "text": "salt flats" + }, + "badlands": { + "text": "badlands" + }, + "permanent snow or ice": { + "text": "permanent snow or ice" + }, + "saline seeps": { + "text": "saline seeps" + }, + "mines/quarries": { + "text": "mines/quarries" + }, + "oil waste areas": { + "text": "oil waste areas" + }, + "small grains": { + "text": "small grains" + }, + "row crops": { + "text": "row crops" + }, + "vegetable crops": { + "text": "vegetable crops" + }, + "horticultural plants (e.g. tulips)": { + "text": "horticultural plants (e.g. tulips)" + }, + "marshlands (grass,sedges,rushes)": { + "text": "marshlands (grass,sedges,rushes)" + }, + "tundra (mosses,lichens)": { + "text": "tundra (mosses,lichens)" + }, + "rangeland": { + "text": "rangeland" + }, + "pastureland (grasslands used for livestock grazing)": { + "text": "pastureland (grasslands used for livestock grazing)" + }, + "hayland": { + "text": "hayland" + }, + "meadows (grasses,alfalfa,fescue,bromegrass,timothy)": { + "text": "meadows (grasses,alfalfa,fescue,bromegrass,timothy)" + }, + "shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)": { + "text": "shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)" + }, + "successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)": { + "text": "successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)" + }, + "shrub crops (blueberries,nursery ornamentals,filberts)": { + "text": "shrub crops (blueberries,nursery ornamentals,filberts)" + }, + "vine crops (grapes)": { + "text": "vine crops (grapes)" + }, + "conifers (e.g. pine,spruce,fir,cypress)": { + "text": "conifers (e.g. pine,spruce,fir,cypress)" + }, + "hardwoods (e.g. oak,hickory,elm,aspen)": { + "text": "hardwoods (e.g. oak,hickory,elm,aspen)" + }, + "intermixed hardwood and conifers": { + "text": "intermixed hardwood and conifers" + }, + "tropical (e.g. mangrove,palms)": { + "text": "tropical (e.g. mangrove,palms)" + }, + "rainforest (evergreen forest receiving greater than 406 cm annual rainfall)": { + "text": "rainforest (evergreen forest receiving greater than 406 cm annual rainfall)" + }, + "swamp (permanent or semi-permanent water body dominated by woody plants)": { + "text": "swamp (permanent or semi-permanent water body dominated by woody plants)" + }, + "crop trees (nuts,fruit,christmas trees,nursery trees)": { + "text": "crop trees (nuts,fruit,christmas trees,nursery trees)" + } + } }, - "collecting_biosamples_from_site_set": { - "name": "collecting_biosamples_from_site_set", + "depos_env_enum": { + "name": "depos_env_enum", "from_schema": "https://microbiomedata/schema", - "domain": "Database", - "multivalued": true, - "range": "CollectingBiosamplesFromSite", - "inlined_as_list": true + "permissible_values": { + "Continental - Alluvial": { + "text": "Continental - Alluvial" + }, + "Continental - Aeolian": { + "text": "Continental - Aeolian" + }, + "Continental - Fluvial": { + "text": "Continental - Fluvial" + }, + "Continental - Lacustrine": { + "text": "Continental - Lacustrine" + }, + "Transitional - Deltaic": { + "text": "Transitional - Deltaic" + }, + "Transitional - Tidal": { + "text": "Transitional - Tidal" + }, + "Transitional - Lagoonal": { + "text": "Transitional - Lagoonal" + }, + "Transitional - Beach": { + "text": "Transitional - Beach" + }, + "Transitional - Lake": { + "text": "Transitional - Lake" + }, + "Marine - Shallow": { + "text": "Marine - Shallow" + }, + "Marine - Deep": { + "text": "Marine - Deep" + }, + "Marine - Reef": { + "text": "Marine - Reef" + }, + "Other - Evaporite": { + "text": "Other - Evaporite" + }, + "Other - Glacial": { + "text": "Other - Glacial" + }, + "Other - Volcanic": { + "text": "Other - Volcanic" + }, + "other": { + "text": "other" + } + } }, - "data_object_set": { - "name": "data_object_set", - "description": "This property links a database object to the set of data objects within it.", + "door_comp_type_enum": { + "name": "door_comp_type_enum", "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "DataObject" - }, - "genome_feature_set": { - "name": "genome_feature_set", - "description": "This property links a database object to the set of all features", - "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "GenomeFeature" - }, - "functional_annotation_set": { - "name": "functional_annotation_set", - "description": "This property links a database object to the set of all functional annotations", - "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "FunctionalAnnotation" + "permissible_values": { + "metal covered": { + "text": "metal covered" + }, + "revolving": { + "text": "revolving" + }, + "sliding": { + "text": "sliding" + }, + "telescopic": { + "text": "telescopic" + } + } }, - "activity_set": { - "name": "activity_set", - "description": "This property links a database object to the set of workflow activities.", + "door_cond_enum": { + "name": "door_cond_enum", "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "WorkflowExecutionActivity" + "permissible_values": { + "damaged": { + "text": "damaged" + }, + "needs repair": { + "text": "needs repair" + }, + "new": { + "text": "new" + }, + "rupture": { + "text": "rupture" + }, + "visible wear": { + "text": "visible wear" + } + } }, - "mags_activity_set": { - "name": "mags_activity_set", - "description": "This property links a database object to the set of MAGs analysis activities.", + "door_direct_enum": { + "name": "door_direct_enum", "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "MagsAnalysisActivity" + "permissible_values": { + "inward": { + "text": "inward" + }, + "outward": { + "text": "outward" + }, + "sideways": { + "text": "sideways" + } + } }, - "metabolomics_analysis_activity_set": { - "name": "metabolomics_analysis_activity_set", - "description": "This property links a database object to the set of metabolomics analysis activities.", + "door_loc_enum": { + "name": "door_loc_enum", "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "MetabolomicsAnalysisActivity" + "permissible_values": { + "north": { + "text": "north" + }, + "south": { + "text": "south" + }, + "east": { + "text": "east" + }, + "west": { + "text": "west" + } + } }, - "metaproteomics_analysis_activity_set": { - "name": "metaproteomics_analysis_activity_set", - "description": "This property links a database object to the set of metaproteomics analysis activities.", + "door_mat_enum": { + "name": "door_mat_enum", "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "MetaproteomicsAnalysisActivity" + "permissible_values": { + "aluminum": { + "text": "aluminum" + }, + "cellular PVC": { + "text": "cellular PVC" + }, + "engineered plastic": { + "text": "engineered plastic" + }, + "fiberboard": { + "text": "fiberboard" + }, + "fiberglass": { + "text": "fiberglass" + }, + "metal": { + "text": "metal" + }, + "thermoplastic alloy": { + "text": "thermoplastic alloy" + }, + "vinyl": { + "text": "vinyl" + }, + "wood": { + "text": "wood" + }, + "wood/plastic composite": { + "text": "wood/plastic composite" + } + } }, - "metagenome_annotation_activity_set": { - "name": "metagenome_annotation_activity_set", - "description": "This property links a database object to the set of metagenome annotation activities.", + "door_move_enum": { + "name": "door_move_enum", "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "MetagenomeAnnotationActivity" + "permissible_values": { + "collapsible": { + "text": "collapsible" + }, + "folding": { + "text": "folding" + }, + "revolving": { + "text": "revolving" + }, + "rolling shutter": { + "text": "rolling shutter" + }, + "sliding": { + "text": "sliding" + }, + "swinging": { + "text": "swinging" + } + } }, - "metagenome_assembly_set": { - "name": "metagenome_assembly_set", - "description": "This property links a database object to the set of metagenome assembly activities.", + "door_type_enum": { + "name": "door_type_enum", "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "MetagenomeAssembly" + "permissible_values": { + "composite": { + "text": "composite" + }, + "metal": { + "text": "metal" + }, + "wooden": { + "text": "wooden" + } + } }, - "metatranscriptome_activity_set": { - "name": "metatranscriptome_activity_set", - "description": "This property links a database object to the set of metatranscriptome analysis activities.", + "door_type_metal_enum": { + "name": "door_type_metal_enum", "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "MetatranscriptomeActivity" + "permissible_values": { + "collapsible": { + "text": "collapsible" + }, + "corrugated steel": { + "text": "corrugated steel" + }, + "hollow": { + "text": "hollow" + }, + "rolling shutters": { + "text": "rolling shutters" + }, + "steel plate": { + "text": "steel plate" + } + } }, - "read_qc_analysis_activity_set": { - "name": "read_qc_analysis_activity_set", - "description": "This property links a database object to the set of read QC analysis activities.", + "door_type_wood_enum": { + "name": "door_type_wood_enum", "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "ReadQcAnalysisActivity" + "permissible_values": { + "bettened and ledged": { + "text": "bettened and ledged" + }, + "battened": { + "text": "battened" + }, + "ledged and braced": { + "text": "ledged and braced" + }, + "ledged and framed": { + "text": "ledged and framed" + }, + "ledged, braced and frame": { + "text": "ledged, braced and frame" + }, + "framed and paneled": { + "text": "framed and paneled" + }, + "glashed or sash": { + "text": "glashed or sash" + }, + "flush": { + "text": "flush" + }, + "louvered": { + "text": "louvered" + }, + "wire gauged": { + "text": "wire gauged" + } + } }, - "read_based_taxonomy_analysis_activity_set": { - "name": "read_based_taxonomy_analysis_activity_set", - "description": "This property links a database object to the set of read based analysis activities.", + "drainage_class_enum": { + "name": "drainage_class_enum", "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "ReadBasedTaxonomyAnalysisActivity" + "permissible_values": { + "very poorly": { + "text": "very poorly" + }, + "poorly": { + "text": "poorly" + }, + "somewhat poorly": { + "text": "somewhat poorly" + }, + "moderately well": { + "text": "moderately well" + }, + "well": { + "text": "well" + }, + "excessively drained": { + "text": "excessively drained" + } + } }, - "nom_analysis_activity_set": { - "name": "nom_analysis_activity_set", - "description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", + "drawings_enum": { + "name": "drawings_enum", "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "NomAnalysisActivity" + "permissible_values": { + "operation": { + "text": "operation" + }, + "as built": { + "text": "as built" + }, + "construction": { + "text": "construction" + }, + "bid": { + "text": "bid" + }, + "design": { + "text": "design" + }, + "building navigation map": { + "text": "building navigation map" + }, + "diagram": { + "text": "diagram" + }, + "sketch": { + "text": "sketch" + } + } }, - "omics_processing_set": { - "name": "omics_processing_set", - "description": "This property links a database object to the set of omics processings within it.", + "ext_wall_orient_enum": { + "name": "ext_wall_orient_enum", "from_schema": "https://microbiomedata/schema", - "mixins": [ - "object_set" - ], - "domain": "Database", - "multivalued": true, - "range": "OmicsProcessing" - }, - "omics_type": { - "name": "omics_type", - "description": "The type of omics data", - "notes": [ - "was the range string at one point? the values in MongoDB don't look like NMDC classes" - ], - "examples": [ - { - "value": "metatranscriptome" + "permissible_values": { + "north": { + "text": "north" }, - { - "value": "metagenome" + "south": { + "text": "south" + }, + "east": { + "text": "east" + }, + "west": { + "text": "west" + }, + "northeast": { + "text": "northeast" + }, + "southeast": { + "text": "southeast" + }, + "southwest": { + "text": "southwest" + }, + "northwest": { + "text": "northwest" } - ], - "from_schema": "https://microbiomedata/schema", - "range": "ControlledTermValue" + } }, - "data_object_type": { - "name": "data_object_type", - "description": "The type of file represented by the data object.", - "examples": [ - { - "value": "FT ICR-MS Analysis Results" + "ext_window_orient_enum": { + "name": "ext_window_orient_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "north": { + "text": "north" }, - { - "value": "GC-MS Metabolomics Results" + "south": { + "text": "south" + }, + "east": { + "text": "east" + }, + "west": { + "text": "west" + }, + "northeast": { + "text": "northeast" + }, + "southeast": { + "text": "southeast" + }, + "southwest": { + "text": "southwest" + }, + "northwest": { + "text": "northwest" } - ], - "from_schema": "https://microbiomedata/schema", - "range": "file type enum" + } }, - "compression_type": { - "name": "compression_type", - "description": "If provided, specifies the compression type", - "todos": [ - "consider enum" - ], - "examples": [ - { - "value": "gzip" - } - ], + "fao_class_enum": { + "name": "fao_class_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" - }, - "instrument_name": { - "name": "instrument_name", - "description": "The name of the instrument that was used for processing the sample.", - "from_schema": "https://microbiomedata/schema" + "permissible_values": { + "Acrisols": { + "text": "Acrisols" + }, + "Andosols": { + "text": "Andosols" + }, + "Arenosols": { + "text": "Arenosols" + }, + "Cambisols": { + "text": "Cambisols" + }, + "Chernozems": { + "text": "Chernozems" + }, + "Ferralsols": { + "text": "Ferralsols" + }, + "Fluvisols": { + "text": "Fluvisols" + }, + "Gleysols": { + "text": "Gleysols" + }, + "Greyzems": { + "text": "Greyzems" + }, + "Gypsisols": { + "text": "Gypsisols" + }, + "Histosols": { + "text": "Histosols" + }, + "Kastanozems": { + "text": "Kastanozems" + }, + "Lithosols": { + "text": "Lithosols" + }, + "Luvisols": { + "text": "Luvisols" + }, + "Nitosols": { + "text": "Nitosols" + }, + "Phaeozems": { + "text": "Phaeozems" + }, + "Planosols": { + "text": "Planosols" + }, + "Podzols": { + "text": "Podzols" + }, + "Podzoluvisols": { + "text": "Podzoluvisols" + }, + "Rankers": { + "text": "Rankers" + }, + "Regosols": { + "text": "Regosols" + }, + "Rendzinas": { + "text": "Rendzinas" + }, + "Solonchaks": { + "text": "Solonchaks" + }, + "Solonetz": { + "text": "Solonetz" + }, + "Vertisols": { + "text": "Vertisols" + }, + "Yermosols": { + "text": "Yermosols" + } + } }, - "gold_path_field": { - "name": "gold_path_field", - "description": "This is a grouping for any of the gold path fields", + "filter_type_enum": { + "name": "filter_type_enum", "from_schema": "https://microbiomedata/schema", - "is_a": "attribute", - "abstract": true, - "range": "string" + "permissible_values": { + "particulate air filter": { + "text": "particulate air filter" + }, + "chemical air filter": { + "text": "chemical air filter" + }, + "low-MERV pleated media": { + "text": "low-MERV pleated media" + }, + "HEPA": { + "text": "HEPA" + }, + "electrostatic": { + "text": "electrostatic" + }, + "gas-phase or ultraviolet air treatments": { + "text": "gas-phase or ultraviolet air treatments" + } + } }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], + "floor_cond_enum": { + "name": "floor_cond_enum", "from_schema": "https://microbiomedata/schema", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "is_a": "gold_path_field" + "permissible_values": { + "new": { + "text": "new" + }, + "visible wear": { + "text": "visible wear" + }, + "needs repair": { + "text": "needs repair" + }, + "damaged": { + "text": "damaged" + }, + "rupture": { + "text": "rupture" + } + } }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], + "floor_finish_mat_enum": { + "name": "floor_finish_mat_enum", "from_schema": "https://microbiomedata/schema", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "is_a": "gold_path_field" + "permissible_values": { + "tile": { + "text": "tile" + }, + "wood strip or parquet": { + "text": "wood strip or parquet" + }, + "carpet": { + "text": "carpet" + }, + "rug": { + "text": "rug" + }, + "laminate wood": { + "text": "laminate wood" + }, + "lineoleum": { + "text": "lineoleum" + }, + "vinyl composition tile": { + "text": "vinyl composition tile" + }, + "sheet vinyl": { + "text": "sheet vinyl" + }, + "stone": { + "text": "stone" + }, + "bamboo": { + "text": "bamboo" + }, + "cork": { + "text": "cork" + }, + "terrazo": { + "text": "terrazo" + }, + "concrete": { + "text": "concrete" + }, + "none": { + "text": "none" + }, + "sealed": { + "text": "sealed" + }, + "clear finish": { + "text": "clear finish" + }, + "paint": { + "text": "paint" + }, + "none or unfinished": { + "text": "none or unfinished" + } + } }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], + "floor_struc_enum": { + "name": "floor_struc_enum", "from_schema": "https://microbiomedata/schema", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "is_a": "gold_path_field" + "permissible_values": { + "balcony": { + "text": "balcony" + }, + "floating floor": { + "text": "floating floor" + }, + "glass floor": { + "text": "glass floor" + }, + "raised floor": { + "text": "raised floor" + }, + "sprung floor": { + "text": "sprung floor" + }, + "wood-framed": { + "text": "wood-framed" + }, + "concrete": { + "text": "concrete" + } + } }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], + "floor_water_mold_enum": { + "name": "floor_water_mold_enum", "from_schema": "https://microbiomedata/schema", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "is_a": "gold_path_field" + "permissible_values": { + "mold odor": { + "text": "mold odor" + }, + "wet floor": { + "text": "wet floor" + }, + "water stains": { + "text": "water stains" + }, + "wall discoloration": { + "text": "wall discoloration" + }, + "floor discoloration": { + "text": "floor discoloration" + }, + "ceiling discoloration": { + "text": "ceiling discoloration" + }, + "peeling paint or wallpaper": { + "text": "peeling paint or wallpaper" + }, + "bulging walls": { + "text": "bulging walls" + }, + "condensation": { + "text": "condensation" + } + } }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], + "freq_clean_enum": { + "name": "freq_clean_enum", "from_schema": "https://microbiomedata/schema", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "is_a": "gold_path_field" + "permissible_values": { + "Daily": { + "text": "Daily" + }, + "Weekly": { + "text": "Weekly" + }, + "Monthly": { + "text": "Monthly" + }, + "Quarterly": { + "text": "Quarterly" + }, + "Annually": { + "text": "Annually" + }, + "other": { + "text": "other" + } + } }, - "principal_investigator": { - "name": "principal_investigator", - "description": "Principal Investigator who led the study and/or generated the dataset.", + "furniture_enum": { + "name": "furniture_enum", "from_schema": "https://microbiomedata/schema", - "aliases": [ - "PI" - ], - "is_a": "attribute", - "range": "PersonValue" + "permissible_values": { + "cabinet": { + "text": "cabinet" + }, + "chair": { + "text": "chair" + }, + "desks": { + "text": "desks" + } + } }, - "doi": { - "name": "doi", + "gender_restroom_enum": { + "name": "gender_restroom_enum", "from_schema": "https://microbiomedata/schema", - "is_a": "attribute", - "range": "AttributeValue" + "permissible_values": { + "all gender": { + "text": "all gender" + }, + "female": { + "text": "female" + }, + "gender neurtral": { + "text": "gender neurtral" + }, + "male": { + "text": "male" + }, + "male and female": { + "text": "male and female" + }, + "unisex": { + "text": "unisex" + } + } }, - "add_date": { - "name": "add_date", - "description": "The date on which the information was added to the database.", + "growth_habit_enum": { + "name": "growth_habit_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" + "permissible_values": { + "erect": { + "text": "erect" + }, + "semi-erect": { + "text": "semi-erect" + }, + "spreading": { + "text": "spreading" + }, + "prostrate": { + "text": "prostrate" + } + } }, - "mod_date": { - "name": "mod_date", - "description": "The last date on which the database information was modified.", + "handidness_enum": { + "name": "handidness_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" + "permissible_values": { + "ambidexterity": { + "text": "ambidexterity" + }, + "left handedness": { + "text": "left handedness" + }, + "mixed-handedness": { + "text": "mixed-handedness" + }, + "right handedness": { + "text": "right handedness" + } + } }, - "ecosystem_path_id": { - "name": "ecosystem_path_id", - "description": "A unique id representing the GOLD classifers associated with a sample.", + "hc_produced_enum": { + "name": "hc_produced_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" + "permissible_values": { + "Oil": { + "text": "Oil" + }, + "Gas-Condensate": { + "text": "Gas-Condensate" + }, + "Gas": { + "text": "Gas" + }, + "Bitumen": { + "text": "Bitumen" + }, + "Coalbed Methane": { + "text": "Coalbed Methane" + }, + "other": { + "text": "other" + } + } }, - "habitat": { - "name": "habitat", + "hcr_enum": { + "name": "hcr_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" + "permissible_values": { + "Oil Reservoir": { + "text": "Oil Reservoir" + }, + "Gas Reservoir": { + "text": "Gas Reservoir" + }, + "Oil Sand": { + "text": "Oil Sand" + }, + "Coalbed": { + "text": "Coalbed" + }, + "Shale": { + "text": "Shale" + }, + "Tight Oil Reservoir": { + "text": "Tight Oil Reservoir" + }, + "Tight Gas Reservoir": { + "text": "Tight Gas Reservoir" + }, + "other": { + "text": "other" + } + } }, - "location": { - "name": "location", + "hcr_geol_age_enum": { + "name": "hcr_geol_age_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" + "permissible_values": { + "Archean": { + "text": "Archean" + }, + "Cambrian": { + "text": "Cambrian" + }, + "Carboniferous": { + "text": "Carboniferous" + }, + "Cenozoic": { + "text": "Cenozoic" + }, + "Cretaceous": { + "text": "Cretaceous" + }, + "Devonian": { + "text": "Devonian" + }, + "Jurassic": { + "text": "Jurassic" + }, + "Mesozoic": { + "text": "Mesozoic" + }, + "Neogene": { + "text": "Neogene" + }, + "Ordovician": { + "text": "Ordovician" + }, + "Paleogene": { + "text": "Paleogene" + }, + "Paleozoic": { + "text": "Paleozoic" + }, + "Permian": { + "text": "Permian" + }, + "Precambrian": { + "text": "Precambrian" + }, + "Proterozoic": { + "text": "Proterozoic" + }, + "Silurian": { + "text": "Silurian" + }, + "Triassic": { + "text": "Triassic" + }, + "other": { + "text": "other" + } + } }, - "community": { - "name": "community", + "heat_cool_type_enum": { + "name": "heat_cool_type_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" - }, - "ncbi_taxonomy_name": { - "name": "ncbi_taxonomy_name", + "permissible_values": { + "radiant system": { + "text": "radiant system" + }, + "heat pump": { + "text": "heat pump" + }, + "forced air system": { + "text": "forced air system" + }, + "steam forced heat": { + "text": "steam forced heat" + }, + "wood stove": { + "text": "wood stove" + } + } + }, + "heat_deliv_loc_enum": { + "name": "heat_deliv_loc_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" + "permissible_values": { + "north": { + "text": "north" + }, + "south": { + "text": "south" + }, + "east": { + "text": "east" + }, + "west": { + "text": "west" + } + } }, - "ncbi_project_name": { - "name": "ncbi_project_name", + "horizon_enum": { + "name": "horizon_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" + "permissible_values": { + "O horizon": { + "text": "O horizon" + }, + "A horizon": { + "text": "A horizon" + }, + "E horizon": { + "text": "E horizon" + }, + "B horizon": { + "text": "B horizon" + }, + "C horizon": { + "text": "C horizon" + }, + "R layer": { + "text": "R layer" + }, + "Permafrost": { + "text": "Permafrost" + } + } }, - "sample_collection_site": { - "name": "sample_collection_site", + "host_sex_enum": { + "name": "host_sex_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" + "permissible_values": { + "female": { + "text": "female" + }, + "hermaphrodite": { + "text": "hermaphrodite" + }, + "male": { + "text": "male" + }, + "neuter": { + "text": "neuter" + } + } }, - "sample_collection_year": { - "name": "sample_collection_year", + "indoor_space_enum": { + "name": "indoor_space_enum", "from_schema": "https://microbiomedata/schema", - "range": "integer" + "permissible_values": { + "bedroom": { + "text": "bedroom" + }, + "office": { + "text": "office" + }, + "bathroom": { + "text": "bathroom" + }, + "foyer": { + "text": "foyer" + }, + "kitchen": { + "text": "kitchen" + }, + "locker room": { + "text": "locker room" + }, + "hallway": { + "text": "hallway" + }, + "elevator": { + "text": "elevator" + } + } }, - "sample_collection_month": { - "name": "sample_collection_month", + "indoor_surf_enum": { + "name": "indoor_surf_enum", "from_schema": "https://microbiomedata/schema", - "range": "integer" + "permissible_values": { + "cabinet": { + "text": "cabinet" + }, + "ceiling": { + "text": "ceiling" + }, + "counter top": { + "text": "counter top" + }, + "door": { + "text": "door" + }, + "shelving": { + "text": "shelving" + }, + "vent cover": { + "text": "vent cover" + }, + "window": { + "text": "window" + }, + "wall": { + "text": "wall" + } + } }, - "sample_collection_day": { - "name": "sample_collection_day", + "int_wall_cond_enum": { + "name": "int_wall_cond_enum", "from_schema": "https://microbiomedata/schema", - "range": "integer" + "permissible_values": { + "new": { + "text": "new" + }, + "visible wear": { + "text": "visible wear" + }, + "needs repair": { + "text": "needs repair" + }, + "damaged": { + "text": "damaged" + }, + "rupture": { + "text": "rupture" + } + } }, - "sample_collection_hour": { - "name": "sample_collection_hour", + "light_type_enum": { + "name": "light_type_enum", "from_schema": "https://microbiomedata/schema", - "range": "integer" + "permissible_values": { + "natural light": { + "text": "natural light" + }, + "electric light": { + "text": "electric light" + }, + "desk lamp": { + "text": "desk lamp" + }, + "flourescent lights": { + "text": "flourescent lights" + }, + "none": { + "text": "none" + } + } }, - "sample_collection_minute": { - "name": "sample_collection_minute", + "lithology_enum": { + "name": "lithology_enum", "from_schema": "https://microbiomedata/schema", - "range": "integer" + "permissible_values": { + "Basement": { + "text": "Basement" + }, + "Chalk": { + "text": "Chalk" + }, + "Chert": { + "text": "Chert" + }, + "Coal": { + "text": "Coal" + }, + "Conglomerate": { + "text": "Conglomerate" + }, + "Diatomite": { + "text": "Diatomite" + }, + "Dolomite": { + "text": "Dolomite" + }, + "Limestone": { + "text": "Limestone" + }, + "Sandstone": { + "text": "Sandstone" + }, + "Shale": { + "text": "Shale" + }, + "Siltstone": { + "text": "Siltstone" + }, + "Volcanic": { + "text": "Volcanic" + }, + "other": { + "text": "other" + } + } }, - "salinity_category": { - "name": "salinity_category", - "description": "Categorcial description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline", - "notes": [ - "maps to gold:salinity" - ], + "mech_struc_enum": { + "name": "mech_struc_enum", "from_schema": "https://microbiomedata/schema", - "see_also": [ - "https://github.com/microbiomedata/nmdc-metadata/pull/297" - ], - "range": "string" + "permissible_values": { + "subway": { + "text": "subway" + }, + "coach": { + "text": "coach" + }, + "carriage": { + "text": "carriage" + }, + "elevator": { + "text": "elevator" + }, + "escalator": { + "text": "escalator" + }, + "boat": { + "text": "boat" + }, + "train": { + "text": "train" + }, + "car": { + "text": "car" + }, + "bus": { + "text": "bus" + } + } }, - "soluble_iron_micromol": { - "name": "soluble_iron_micromol", + "occup_document_enum": { + "name": "occup_document_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" + "permissible_values": { + "automated count": { + "text": "automated count" + }, + "estimate": { + "text": "estimate" + }, + "manual count": { + "text": "manual count" + }, + "videos": { + "text": "videos" + } + } }, - "host_name": { - "name": "host_name", + "organism_count_enum": { + "name": "organism_count_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" + "permissible_values": { + "ATP": { + "text": "ATP" + }, + "MPN": { + "text": "MPN" + }, + "other": { + "text": "other" + } + } }, - "subsurface_depth": { - "name": "subsurface_depth", + "oxy_stat_samp_enum": { + "name": "oxy_stat_samp_enum", "from_schema": "https://microbiomedata/schema", - "range": "QuantityValue" + "permissible_values": { + "aerobic": { + "text": "aerobic" + }, + "anaerobic": { + "text": "anaerobic" + }, + "other": { + "text": "other" + } + } }, - "proport_woa_temperature": { - "name": "proport_woa_temperature", + "plant_growth_med_enum": { + "name": "plant_growth_med_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" + "permissible_values": { + "other artificial liquid medium": { + "text": "other artificial liquid medium" + }, + "other artificial solid medium": { + "text": "other artificial solid medium" + }, + "peat moss": { + "text": "peat moss" + }, + "perlite": { + "text": "perlite" + }, + "pumice": { + "text": "pumice" + }, + "sand": { + "text": "sand" + }, + "soil": { + "text": "soil" + }, + "vermiculite": { + "text": "vermiculite" + }, + "water": { + "text": "water" + } + } }, - "biogas_temperature": { - "name": "biogas_temperature", + "plant_sex_enum": { + "name": "plant_sex_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" + "permissible_values": { + "Androdioecious": { + "text": "Androdioecious" + }, + "Androecious": { + "text": "Androecious" + }, + "Androgynous": { + "text": "Androgynous" + }, + "Androgynomonoecious": { + "text": "Androgynomonoecious" + }, + "Andromonoecious": { + "text": "Andromonoecious" + }, + "Bisexual": { + "text": "Bisexual" + }, + "Dichogamous": { + "text": "Dichogamous" + }, + "Diclinous": { + "text": "Diclinous" + }, + "Dioecious": { + "text": "Dioecious" + }, + "Gynodioecious": { + "text": "Gynodioecious" + }, + "Gynoecious": { + "text": "Gynoecious" + }, + "Gynomonoecious": { + "text": "Gynomonoecious" + }, + "Hermaphroditic": { + "text": "Hermaphroditic" + }, + "Imperfect": { + "text": "Imperfect" + }, + "Monoclinous": { + "text": "Monoclinous" + }, + "Monoecious": { + "text": "Monoecious" + }, + "Perfect": { + "text": "Perfect" + }, + "Polygamodioecious": { + "text": "Polygamodioecious" + }, + "Polygamomonoecious": { + "text": "Polygamomonoecious" + }, + "Polygamous": { + "text": "Polygamous" + }, + "Protandrous": { + "text": "Protandrous" + }, + "Protogynous": { + "text": "Protogynous" + }, + "Subandroecious": { + "text": "Subandroecious" + }, + "Subdioecious": { + "text": "Subdioecious" + }, + "Subgynoecious": { + "text": "Subgynoecious" + }, + "Synoecious": { + "text": "Synoecious" + }, + "Trimonoecious": { + "text": "Trimonoecious" + }, + "Trioecious": { + "text": "Trioecious" + }, + "Unisexual": { + "text": "Unisexual" + } + } }, - "soil_annual_season_temp": { - "name": "soil_annual_season_temp", + "profile_position_enum": { + "name": "profile_position_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" + "permissible_values": { + "summit": { + "text": "summit" + }, + "shoulder": { + "text": "shoulder" + }, + "backslope": { + "text": "backslope" + }, + "footslope": { + "text": "footslope" + }, + "toeslope": { + "text": "toeslope" + } + } }, - "biogas_retention_time": { - "name": "biogas_retention_time", + "quad_pos_enum": { + "name": "quad_pos_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" + "permissible_values": { + "North side": { + "text": "North side" + }, + "West side": { + "text": "West side" + }, + "South side": { + "text": "South side" + }, + "East side": { + "text": "East side" + } + } }, - "processing_institution": { - "name": "processing_institution", - "description": "The organization that processed the sample.", + "rel_samp_loc_enum": { + "name": "rel_samp_loc_enum", "from_schema": "https://microbiomedata/schema", - "range": "processing_institution_enum" + "permissible_values": { + "edge of car": { + "text": "edge of car" + }, + "center of car": { + "text": "center of car" + }, + "under a seat": { + "text": "under a seat" + } + } }, - "completion_date": { - "name": "completion_date", + "rel_to_oxygen_enum": { + "name": "rel_to_oxygen_enum", "from_schema": "https://microbiomedata/schema", - "range": "string" - } - }, - "classes": { - "Database": { - "name": "Database", - "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest", + "permissible_values": { + "aerobe": { + "text": "aerobe" + }, + "anaerobe": { + "text": "anaerobe" + }, + "facultative": { + "text": "facultative" + }, + "microaerophilic": { + "text": "microaerophilic" + }, + "microanaerobe": { + "text": "microanaerobe" + }, + "obligate aerobe": { + "text": "obligate aerobe" + }, + "obligate anaerobe": { + "text": "obligate anaerobe" + } + } + }, + "room_condt_enum": { + "name": "room_condt_enum", "from_schema": "https://microbiomedata/schema", - "aliases": [ - "NMDC metadata object" - ], - "slots": [ - "activity_set", - "biosample_set", - "data_object_set", - "dissolving_activity_set", - "functional_annotation_set", - "genome_feature_set", - "mags_activity_set", - "material_sample_set", - "material_sampling_activity_set", - "metabolomics_analysis_activity_set", - "metagenome_annotation_activity_set", - "metagenome_assembly_set", - "metaproteomics_analysis_activity_set", - "metatranscriptome_activity_set", - "nom_analysis_activity_set", - "omics_processing_set", - "reaction_activity_set", - "read_qc_analysis_activity_set", - "read_based_taxonomy_analysis_activity_set", - "study_set", - "field_research_site_set", - "collecting_biosamples_from_site_set" - ], - "slot_usage": { - "date_created": { - "name": "date_created", - "description": "TODO" + "permissible_values": { + "new": { + "text": "new" }, - "etl_software_version": { - "name": "etl_software_version", - "description": "TODO" + "visible wear": { + "text": "visible wear" }, - "metatranscriptome_activity_set": { - "name": "metatranscriptome_activity_set", - "description": "TODO" + "needs repair": { + "text": "needs repair" + }, + "damaged": { + "text": "damaged" + }, + "rupture": { + "text": "rupture" + }, + "visible signs of mold/mildew": { + "text": "visible signs of mold/mildew" } - }, - "tree_root": true + } }, - "FieldResearchSite": { - "name": "FieldResearchSite", - "description": "A site, outside of a laboratory, from which biosamples may be collected.", - "title": "Field Research Site", - "comments": [ - "Provides grouping of biosamples at level that's more specific than belonging to the same study", - "be very clear that this could be part of a larger site", - "In Bioscales, one might say that rhizosphere soil and bulk soil from around the same plant were obtained at the same site. In this case, the site would correspond to one tree.", - "might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833" - ], + "room_connected_enum": { + "name": "room_connected_enum", "from_schema": "https://microbiomedata/schema", - "aliases": [ - "research plot" - ], - "is_a": "Site" + "permissible_values": { + "attic": { + "text": "attic" + }, + "bathroom": { + "text": "bathroom" + }, + "closet": { + "text": "closet" + }, + "conference room": { + "text": "conference room" + }, + "elevator": { + "text": "elevator" + }, + "examining room": { + "text": "examining room" + }, + "hallway": { + "text": "hallway" + }, + "kitchen": { + "text": "kitchen" + }, + "mail room": { + "text": "mail room" + }, + "office": { + "text": "office" + }, + "stairwell": { + "text": "stairwell" + } + } }, - "CollectingBiosamplesFromSite": { - "name": "CollectingBiosamplesFromSite", - "title": "Collecting Biosamples From Site", - "comments": [ - "this illustrates implementing a Biosample relation with a process class" - ], + "room_loc_enum": { + "name": "room_loc_enum", "from_schema": "https://microbiomedata/schema", - "is_a": "PlannedProcess", - "slots": [ - "has_inputs", - "has_outputs" - ], - "slot_usage": { - "has_inputs": { - "name": "has_inputs", - "range": "Site", - "required": true + "permissible_values": { + "corner room": { + "text": "corner room" }, - "has_outputs": { - "name": "has_outputs", - "range": "Biosample", - "required": true + "interior room": { + "text": "interior room" + }, + "exterior wall": { + "text": "exterior wall" } } }, - "DataObject": { - "name": "DataObject", - "id_prefixes": [ - "GOLD" - ], - "description": "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects. ", - "in_subset": [ - "data object subset" - ], + "room_samp_pos_enum": { + "name": "room_samp_pos_enum", "from_schema": "https://microbiomedata/schema", - "is_a": "NamedThing", - "slots": [ - "file_size_bytes", - "md5_checksum", - "data_object_type", - "compression_type", - "was_generated_by", - "url", - "type" - ], - "slot_usage": { - "name": { - "name": "name", - "required": true + "permissible_values": { + "north corner": { + "text": "north corner" }, - "description": { - "name": "description", - "required": true + "south corner": { + "text": "south corner" + }, + "west corner": { + "text": "west corner" + }, + "east corner": { + "text": "east corner" + }, + "northeast corner": { + "text": "northeast corner" + }, + "northwest corner": { + "text": "northwest corner" + }, + "southeast corner": { + "text": "southeast corner" + }, + "southwest corner": { + "text": "southwest corner" + }, + "center": { + "text": "center" } } }, - "Biosample": { - "name": "Biosample", - "id_prefixes": [ - "GOLD" - ], - "description": "Biological source material which can be characterized by an experiment.", - "alt_descriptions": { - "embl.ena": { - "source": "embl.ena", - "description": "A sample contains information about the sequenced source material. Samples are associated with checklists, which define the fields used to annotate the samples. Samples are always associated with a taxon." + "room_type_enum": { + "name": "room_type_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "attic": { + "text": "attic" + }, + "bathroom": { + "text": "bathroom" + }, + "closet": { + "text": "closet" + }, + "conference room": { + "text": "conference room" + }, + "elevator": { + "text": "elevator" + }, + "examining room": { + "text": "examining room" + }, + "hallway": { + "text": "hallway" + }, + "kitchen": { + "text": "kitchen" + }, + "mail room": { + "text": "mail room" + }, + "private office": { + "text": "private office" + }, + "open office": { + "text": "open office" + }, + "stairwell": { + "text": "stairwell" + }, + ",restroom": { + "text": ",restroom" + }, + "lobby": { + "text": "lobby" + }, + "vestibule": { + "text": "vestibule" + }, + "mechanical or electrical room": { + "text": "mechanical or electrical room" + }, + "data center": { + "text": "data center" + }, + "laboratory_wet": { + "text": "laboratory_wet" + }, + "laboratory_dry": { + "text": "laboratory_dry" + }, + "gymnasium": { + "text": "gymnasium" + }, + "natatorium": { + "text": "natatorium" + }, + "auditorium": { + "text": "auditorium" + }, + "lockers": { + "text": "lockers" + }, + "cafe": { + "text": "cafe" + }, + "warehouse": { + "text": "warehouse" } - }, - "todos": [ - "could add GOLD and EBI's biosample definitions to the alt_descriptions?" - ], - "in_subset": [ - "sample subset" - ], + } + }, + "samp_capt_status_enum": { + "name": "samp_capt_status_enum", "from_schema": "https://microbiomedata/schema", - "aliases": [ - "sample", - "material sample", - "specimen", - "biospecimen" - ], - "exact_mappings": [ - "OBI:0000747", - "NCIT:C43412", - "http://purl.obolibrary.org/obo/FBcv_0003024" - ], - "is_a": "MaterialEntity", - "slots": [ - "collected_from", - "type", - "img_identifiers", - "samp_name", - "biosample_categories", - "type", - "part_of", - "id", - "alternative_identifiers", - "gold_biosample_identifiers", - "insdc_biosample_identifiers", - "emsl_biosample_identifiers", - "igsn_biosample_identifiers", - "agrochem_addition", - "alkalinity", - "alkalinity_method", - "alkyl_diethers", - "alt", - "al_sat", - "al_sat_meth", - "aminopept_act", - "ammonium", - "annual_precpt", - "annual_temp", - "bacteria_carb_prod", - "bishomohopanol", - "bromide", - "calcium", - "carb_nitro_ratio", - "chem_administration", - "chloride", - "chlorophyll", - "collection_date", - "cur_land_use", - "cur_vegetation", - "cur_vegetation_meth", - "crop_rotation", - "density", - "depth", - "diss_carb_dioxide", - "diss_hydrogen", - "diss_inorg_carb", - "diss_inorg_phosp", - "diss_org_carb", - "diss_org_nitro", - "diss_oxygen", - "drainage_class", - "elev", - "env_package", - "env_broad_scale", - "env_local_scale", - "env_medium", - "extreme_event", - "fao_class", - "fire", - "flooding", - "geo_loc_name", - "glucosidase_act", - "heavy_metals", - "heavy_metals_meth", - "lat_lon", - "link_addit_analys", - "link_class_info", - "link_climate_info", - "local_class", - "local_class_meth", - "magnesium", - "mean_frict_vel", - "mean_peak_frict_vel", - "misc_param", - "n_alkanes", - "nitrate", - "nitrite", - "org_matter", - "org_nitro", - "organism_count", - "oxy_stat_samp", - "part_org_carb", - "perturbation", - "petroleum_hydrocarb", - "ph", - "ph_meth", - "phaeopigments", - "phosplipid_fatt_acid", - "pool_dna_extracts", - "potassium", - "pressure", - "profile_position", + "permissible_values": { + "active surveillance in response to an outbreak": { + "text": "active surveillance in response to an outbreak" + }, + "active surveillance not initiated by an outbreak": { + "text": "active surveillance not initiated by an outbreak" + }, + "farm sample": { + "text": "farm sample" + }, + "market sample": { + "text": "market sample" + }, + "other": { + "text": "other" + } + } + }, + "samp_collect_point_enum": { + "name": "samp_collect_point_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "well": { + "text": "well" + }, + "test well": { + "text": "test well" + }, + "drilling rig": { + "text": "drilling rig" + }, + "wellhead": { + "text": "wellhead" + }, + "separator": { + "text": "separator" + }, + "storage tank": { + "text": "storage tank" + }, + "other": { + "text": "other" + } + } + }, + "samp_dis_stage_enum": { + "name": "samp_dis_stage_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "dissemination": { + "text": "dissemination" + }, + "growth and reproduction": { + "text": "growth and reproduction" + }, + "infection": { + "text": "infection" + }, + "inoculation": { + "text": "inoculation" + }, + "penetration": { + "text": "penetration" + }, + "other": { + "text": "other" + } + } + }, + "samp_floor_enum": { + "name": "samp_floor_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "1st floor": { + "text": "1st floor" + }, + "2nd floor": { + "text": "2nd floor" + }, + "basement": { + "text": "basement" + }, + "lobby": { + "text": "lobby" + } + } + }, + "samp_md_enum": { + "name": "samp_md_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "DF": { + "text": "DF" + }, + "RT": { + "text": "RT" + }, + "KB": { + "text": "KB" + }, + "MSL": { + "text": "MSL" + }, + "other": { + "text": "other" + } + } + }, + "samp_subtype_enum": { + "name": "samp_subtype_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "oil phase": { + "text": "oil phase" + }, + "water phase": { + "text": "water phase" + }, + "biofilm": { + "text": "biofilm" + }, + "not applicable": { + "text": "not applicable" + }, + "other": { + "text": "other" + } + } + }, + "samp_weather_enum": { + "name": "samp_weather_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "clear sky": { + "text": "clear sky" + }, + "cloudy": { + "text": "cloudy" + }, + "foggy": { + "text": "foggy" + }, + "hail": { + "text": "hail" + }, + "rain": { + "text": "rain" + }, + "snow": { + "text": "snow" + }, + "sleet": { + "text": "sleet" + }, + "sunny": { + "text": "sunny" + }, + "windy": { + "text": "windy" + } + } + }, + "season_use_enum": { + "name": "season_use_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "Spring": { + "text": "Spring" + }, + "Summer": { + "text": "Summer" + }, + "Fall": { + "text": "Fall" + }, + "Winter": { + "text": "Winter" + } + } + }, + "sediment_type_enum": { + "name": "sediment_type_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "biogenous": { + "text": "biogenous" + }, + "cosmogenous": { + "text": "cosmogenous" + }, + "hydrogenous": { + "text": "hydrogenous" + }, + "lithogenous": { + "text": "lithogenous" + } + } + }, + "shading_device_cond_enum": { + "name": "shading_device_cond_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "damaged": { + "text": "damaged" + }, + "needs repair": { + "text": "needs repair" + }, + "new": { + "text": "new" + }, + "rupture": { + "text": "rupture" + }, + "visible wear": { + "text": "visible wear" + } + } + }, + "shading_device_type_enum": { + "name": "shading_device_type_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "bahama shutters": { + "text": "bahama shutters" + }, + "exterior roll blind": { + "text": "exterior roll blind" + }, + "gambrel awning": { + "text": "gambrel awning" + }, + "hood awning": { + "text": "hood awning" + }, + "porchroller awning": { + "text": "porchroller awning" + }, + "sarasota shutters": { + "text": "sarasota shutters" + }, + "slatted aluminum": { + "text": "slatted aluminum" + }, + "solid aluminum awning": { + "text": "solid aluminum awning" + }, + "sun screen": { + "text": "sun screen" + }, + "tree": { + "text": "tree" + }, + "trellis": { + "text": "trellis" + }, + "venetian awning": { + "text": "venetian awning" + } + } + }, + "soil_horizon_enum": { + "name": "soil_horizon_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "O horizon": { + "text": "O horizon" + }, + "A horizon": { + "text": "A horizon" + }, + "E horizon": { + "text": "E horizon" + }, + "B horizon": { + "text": "B horizon" + }, + "C horizon": { + "text": "C horizon" + }, + "R layer": { + "text": "R layer" + }, + "Permafrost": { + "text": "Permafrost" + } + } + }, + "specific_enum": { + "name": "specific_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "operation": { + "text": "operation" + }, + "as built": { + "text": "as built" + }, + "construction": { + "text": "construction" + }, + "bid": { + "text": "bid" + }, + "design": { + "text": "design" + }, + "photos": { + "text": "photos" + } + } + }, + "sr_dep_env_enum": { + "name": "sr_dep_env_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "Lacustine": { + "text": "Lacustine" + }, + "Fluvioldeltaic": { + "text": "Fluvioldeltaic" + }, + "Fluviomarine": { + "text": "Fluviomarine" + }, + "Marine": { + "text": "Marine" + }, + "other": { + "text": "other" + } + } + }, + "sr_geol_age_enum": { + "name": "sr_geol_age_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "Archean": { + "text": "Archean" + }, + "Cambrian": { + "text": "Cambrian" + }, + "Carboniferous": { + "text": "Carboniferous" + }, + "Cenozoic": { + "text": "Cenozoic" + }, + "Cretaceous": { + "text": "Cretaceous" + }, + "Devonian": { + "text": "Devonian" + }, + "Jurassic": { + "text": "Jurassic" + }, + "Mesozoic": { + "text": "Mesozoic" + }, + "Neogene": { + "text": "Neogene" + }, + "Ordovician": { + "text": "Ordovician" + }, + "Paleogene": { + "text": "Paleogene" + }, + "Paleozoic": { + "text": "Paleozoic" + }, + "Permian": { + "text": "Permian" + }, + "Precambrian": { + "text": "Precambrian" + }, + "Proterozoic": { + "text": "Proterozoic" + }, + "Silurian": { + "text": "Silurian" + }, + "Triassic": { + "text": "Triassic" + }, + "other": { + "text": "other" + } + } + }, + "sr_kerog_type_enum": { + "name": "sr_kerog_type_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "Type I": { + "text": "Type I" + }, + "Type II": { + "text": "Type II" + }, + "Type III": { + "text": "Type III" + }, + "Type IV": { + "text": "Type IV" + }, + "other": { + "text": "other" + } + } + }, + "sr_lithology_enum": { + "name": "sr_lithology_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "Clastic": { + "text": "Clastic" + }, + "Carbonate": { + "text": "Carbonate" + }, + "Coal": { + "text": "Coal" + }, + "Biosilicieous": { + "text": "Biosilicieous" + }, + "other": { + "text": "other" + } + } + }, + "substructure_type_enum": { + "name": "substructure_type_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "crawlspace": { + "text": "crawlspace" + }, + "slab on grade": { + "text": "slab on grade" + }, + "basement": { + "text": "basement" + } + } + }, + "surf_air_cont_enum": { + "name": "surf_air_cont_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "dust": { + "text": "dust" + }, + "organic matter": { + "text": "organic matter" + }, + "particulate matter": { + "text": "particulate matter" + }, + "volatile organic compounds": { + "text": "volatile organic compounds" + }, + "biological contaminants": { + "text": "biological contaminants" + }, + "radon": { + "text": "radon" + }, + "nutrients": { + "text": "nutrients" + }, + "biocides": { + "text": "biocides" + } + } + }, + "surf_material_enum": { + "name": "surf_material_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "adobe": { + "text": "adobe" + }, + "carpet": { + "text": "carpet" + }, + "cinder blocks": { + "text": "cinder blocks" + }, + "concrete": { + "text": "concrete" + }, + "hay bales": { + "text": "hay bales" + }, + "glass": { + "text": "glass" + }, + "metal": { + "text": "metal" + }, + "paint": { + "text": "paint" + }, + "plastic": { + "text": "plastic" + }, + "stainless steel": { + "text": "stainless steel" + }, + "stone": { + "text": "stone" + }, + "stucco": { + "text": "stucco" + }, + "tile": { + "text": "tile" + }, + "vinyl": { + "text": "vinyl" + }, + "wood": { + "text": "wood" + } + } + }, + "tidal_stage_enum": { + "name": "tidal_stage_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "low tide": { + "text": "low tide" + }, + "ebb tide": { + "text": "ebb tide" + }, + "flood tide": { + "text": "flood tide" + }, + "high tide": { + "text": "high tide" + } + } + }, + "tillage_enum": { + "name": "tillage_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "drill": { + "text": "drill" + }, + "cutting disc": { + "text": "cutting disc" + }, + "ridge till": { + "text": "ridge till" + }, + "strip tillage": { + "text": "strip tillage" + }, + "zonal tillage": { + "text": "zonal tillage" + }, + "chisel": { + "text": "chisel" + }, + "tined": { + "text": "tined" + }, + "mouldboard": { + "text": "mouldboard" + }, + "disc plough": { + "text": "disc plough" + } + } + }, + "train_line_enum": { + "name": "train_line_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "red": { + "text": "red" + }, + "green": { + "text": "green" + }, + "orange": { + "text": "orange" + } + } + }, + "train_stat_loc_enum": { + "name": "train_stat_loc_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "south station above ground": { + "text": "south station above ground" + }, + "south station underground": { + "text": "south station underground" + }, + "south station amtrak": { + "text": "south station amtrak" + }, + "forest hills": { + "text": "forest hills" + }, + "riverside": { + "text": "riverside" + } + } + }, + "train_stop_loc_enum": { + "name": "train_stop_loc_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "end": { + "text": "end" + }, + "mid": { + "text": "mid" + }, + "downtown": { + "text": "downtown" + } + } + }, + "vis_media_enum": { + "name": "vis_media_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "photos": { + "text": "photos" + }, + "videos": { + "text": "videos" + }, + "commonly of the building": { + "text": "commonly of the building" + }, + "site context (adjacent buildings, vegetation, terrain, streets)": { + "text": "site context (adjacent buildings, vegetation, terrain, streets)" + }, + "interiors": { + "text": "interiors" + }, + "equipment": { + "text": "equipment" + }, + "3D scans": { + "text": "3D scans" + } + } + }, + "wall_const_type_enum": { + "name": "wall_const_type_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "frame construction": { + "text": "frame construction" + }, + "joisted masonry": { + "text": "joisted masonry" + }, + "light noncombustible": { + "text": "light noncombustible" + }, + "masonry noncombustible": { + "text": "masonry noncombustible" + }, + "modified fire resistive": { + "text": "modified fire resistive" + }, + "fire resistive": { + "text": "fire resistive" + } + } + }, + "wall_finish_mat_enum": { + "name": "wall_finish_mat_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "plaster": { + "text": "plaster" + }, + "gypsum plaster": { + "text": "gypsum plaster" + }, + "veneer plaster": { + "text": "veneer plaster" + }, + "gypsum board": { + "text": "gypsum board" + }, + "tile": { + "text": "tile" + }, + "terrazzo": { + "text": "terrazzo" + }, + "stone facing": { + "text": "stone facing" + }, + "acoustical treatment": { + "text": "acoustical treatment" + }, + "wood": { + "text": "wood" + }, + "metal": { + "text": "metal" + }, + "masonry": { + "text": "masonry" + } + } + }, + "wall_loc_enum": { + "name": "wall_loc_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "north": { + "text": "north" + }, + "south": { + "text": "south" + }, + "east": { + "text": "east" + }, + "west": { + "text": "west" + } + } + }, + "wall_surf_treatment_enum": { + "name": "wall_surf_treatment_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "painted": { + "text": "painted" + }, + "wall paper": { + "text": "wall paper" + }, + "no treatment": { + "text": "no treatment" + }, + "paneling": { + "text": "paneling" + }, + "stucco": { + "text": "stucco" + }, + "fabric": { + "text": "fabric" + } + } + }, + "wall_texture_enum": { + "name": "wall_texture_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "crows feet": { + "text": "crows feet" + }, + "crows-foot stomp": { + "text": "crows-foot stomp", + "notes": [ + "removed '?' and '' as PVs" + ] + }, + "double skip": { + "text": "double skip" + }, + "hawk and trowel": { + "text": "hawk and trowel" + }, + "knockdown": { + "text": "knockdown" + }, + "popcorn": { + "text": "popcorn" + }, + "orange peel": { + "text": "orange peel" + }, + "rosebud stomp": { + "text": "rosebud stomp" + }, + "Santa-Fe texture": { + "text": "Santa-Fe texture" + }, + "skip trowel": { + "text": "skip trowel" + }, + "smooth": { + "text": "smooth" + }, + "stomp knockdown": { + "text": "stomp knockdown" + }, + "swirl": { + "text": "swirl" + } + } + }, + "water_feat_type_enum": { + "name": "water_feat_type_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "fountain": { + "text": "fountain" + }, + "pool": { + "text": "pool" + }, + "standing feature": { + "text": "standing feature" + }, + "stream": { + "text": "stream" + }, + "waterfall": { + "text": "waterfall" + } + } + }, + "weekday_enum": { + "name": "weekday_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "Monday": { + "text": "Monday" + }, + "Tuesday": { + "text": "Tuesday" + }, + "Wednesday": { + "text": "Wednesday" + }, + "Thursday": { + "text": "Thursday" + }, + "Friday": { + "text": "Friday" + }, + "Saturday": { + "text": "Saturday" + }, + "Sunday": { + "text": "Sunday" + } + } + }, + "window_cond_enum": { + "name": "window_cond_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "damaged": { + "text": "damaged" + }, + "needs repair": { + "text": "needs repair" + }, + "new": { + "text": "new" + }, + "rupture": { + "text": "rupture" + }, + "visible wear": { + "text": "visible wear" + } + } + }, + "window_cover_enum": { + "name": "window_cover_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "blinds": { + "text": "blinds" + }, + "curtains": { + "text": "curtains" + }, + "none": { + "text": "none" + } + } + }, + "window_horiz_pos_enum": { + "name": "window_horiz_pos_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "left": { + "text": "left" + }, + "middle": { + "text": "middle" + }, + "right": { + "text": "right" + } + } + }, + "window_loc_enum": { + "name": "window_loc_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "north": { + "text": "north" + }, + "south": { + "text": "south" + }, + "east": { + "text": "east" + }, + "west": { + "text": "west" + } + } + }, + "window_mat_enum": { + "name": "window_mat_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "clad": { + "text": "clad" + }, + "fiberglass": { + "text": "fiberglass" + }, + "metal": { + "text": "metal" + }, + "vinyl": { + "text": "vinyl" + }, + "wood": { + "text": "wood" + } + } + }, + "window_type_enum": { + "name": "window_type_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "single-hung sash window": { + "text": "single-hung sash window" + }, + "horizontal sash window": { + "text": "horizontal sash window" + }, + "fixed window": { + "text": "fixed window" + } + } + }, + "window_vert_pos_enum": { + "name": "window_vert_pos_enum", + "from_schema": "https://microbiomedata/schema", + "permissible_values": { + "bottom": { + "text": "bottom" + }, + "middle": { + "text": "middle" + }, + "top": { + "text": "top" + }, + "low": { + "text": "low" + }, + "high": { + "text": "high" + } + } + } + }, + "slots": { + "collected_from": { + "name": "collected_from", + "description": "The Site from which a Biosample was collected", + "todos": [ + "add an OBO slot_uri ?" + ], + "comments": [ + "this illustrates implementing a Biosample relation with a (binary) slot" + ], + "from_schema": "https://microbiomedata/schema", + "domain": "Biosample", + "range": "FieldResearchSite" + }, + "emsl_project_identifier": { + "name": "emsl_project_identifier", + "from_schema": "https://microbiomedata/schema" + }, + "img_identifiers": { + "name": "img_identifiers", + "description": "A list of identifiers that relate the biosample to records in the IMG database.", + "title": "IMG Identifiers", + "todos": [ + "add is_a or mixin modeling", + "what are the class of IMG records?!" + ], + "from_schema": "https://microbiomedata/schema", + "multivalued": true + }, + "emsl_biosample_identifiers": { + "name": "emsl_biosample_identifiers", + "description": "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.", + "title": "EMSL Biosample Identifiers", + "todos": [ + "removed \"planned\" once NEXUS is online", + "make an emsl identifiers mixin", + "determine real expansion for emsl prefix" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "biosample_identifiers", + "multivalued": true + }, + "igsn_biosample_identifiers": { + "name": "igsn_biosample_identifiers", + "description": "A list of identifiers for the biosample from the IGSN database.", + "title": "IGSN Biosample Identifiers", + "todos": [ + "make an igsn identifiers mixin" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "biosample_identifiers", + "multivalued": true + }, + "biosample_categories": { + "name": "biosample_categories", + "title": "Categories the biosample belongs to", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "range": "biosample_category_enum" + }, + "date_created": { + "name": "date_created", + "description": "from database class", + "from_schema": "https://microbiomedata/schema" + }, + "etl_software_version": { + "name": "etl_software_version", + "description": "from database class", + "from_schema": "https://microbiomedata/schema" + }, + "related_identifiers": { + "name": "related_identifiers", + "description": "Identifiers assigned to a thing that is similar to that which is represented in NMDC. Related identifier are not an identical match and may have some variation.", + "title": "Related Identifiers", + "from_schema": "https://microbiomedata/schema" + }, + "emsl_proposal_identifier": { + "name": "emsl_proposal_identifier", + "description": "The proposal number assigned to the EMSL awarded study that relates to that which is represented in NMDC.", + "title": "EMSL Proposal Identifier", + "from_schema": "https://microbiomedata/schema" + }, + "emsl_proposal_doi": { + "name": "emsl_proposal_doi", + "description": "The proposal DOI assigned to the awarded EMSL study.", + "title": "EMSL Proposal DOI", + "from_schema": "https://microbiomedata/schema" + }, + "notes": { + "name": "notes", + "description": "from study class", + "from_schema": "https://microbiomedata/schema" + }, + "canary": { + "name": "canary", + "description": "a slot that can be added and removed as evidence that schema changes have propagated to other systems", + "from_schema": "https://microbiomedata/schema" + }, + "ess_dive_datasets": { + "name": "ess_dive_datasets", + "description": "List of ESS-DIVE dataset DOIs", + "from_schema": "https://microbiomedata/schema", + "multivalued": true + }, + "has_credit_associations": { + "name": "has_credit_associations", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Other researchers associated with this study." + } + }, + "description": "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study", + "notes": [ + "had just been \"inlined: true\"" + ], + "from_schema": "https://microbiomedata/schema", + "domain": "Study", + "slot_uri": "prov:qualifiedAssociation", + "multivalued": true, + "range": "CreditAssociation", + "inlined": true, + "inlined_as_list": true + }, + "study_image": { + "name": "study_image", + "description": "Links a study to one or more images.", + "from_schema": "https://microbiomedata/schema", + "domain": "Study", + "multivalued": true, + "range": "ImageValue", + "inlined": true + }, + "relevant_protocols": { + "name": "relevant_protocols", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "range": "string" + }, + "funding_sources": { + "name": "funding_sources", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "range": "string" + }, + "applied_role": { + "name": "applied_role", + "deprecated": "A credit association may have multiple roles. So, use the applied roles slot.", + "from_schema": "https://microbiomedata/schema", + "domain": "CreditAssociation", + "slot_uri": "prov:hadRole", + "multivalued": false, + "range": "credit enum", + "required": false + }, + "applied_roles": { + "name": "applied_roles", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Identify all CRediT roles associated with this contributor. CRediT Information: https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/" + } + }, + "from_schema": "https://microbiomedata/schema", + "domain": "CreditAssociation", + "multivalued": true, + "range": "credit enum", + "required": true + }, + "applies_to_person": { + "name": "applies_to_person", + "todos": [ + "prov:agent takes an Agent object. Is a person value an Agent? Also try to relate to principal investigator slot? could include OBI:0000103 principal investigator role... do we need to define the OBI prefix?" + ], + "from_schema": "https://microbiomedata/schema", + "domain": "CreditAssociation", + "slot_uri": "prov:agent", + "multivalued": false, + "range": "PersonValue", + "required": true + }, + "object_set": { + "name": "object_set", + "description": "Applies to a property that links a database object to a set of objects. This is necessary in a json document to provide context for a list, and to allow for a single json object that combines multiple object types", + "from_schema": "https://microbiomedata/schema", + "mixin": true, + "domain": "Database", + "multivalued": true, + "inlined_as_list": true + }, + "biosample_set": { + "name": "biosample_set", + "description": "This property links a database object to the set of samples within it.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "Biosample" + }, + "study_set": { + "name": "study_set", + "description": "This property links a database object to the set of studies within it.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "Study" + }, + "field_research_site_set": { + "name": "field_research_site_set", + "from_schema": "https://microbiomedata/schema", + "domain": "Database", + "multivalued": true, + "range": "FieldResearchSite", + "inlined": true, + "inlined_as_list": true + }, + "collecting_biosamples_from_site_set": { + "name": "collecting_biosamples_from_site_set", + "from_schema": "https://microbiomedata/schema", + "domain": "Database", + "multivalued": true, + "range": "CollectingBiosamplesFromSite", + "inlined": true, + "inlined_as_list": true + }, + "data_object_set": { + "name": "data_object_set", + "description": "This property links a database object to the set of data objects within it.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "DataObject" + }, + "genome_feature_set": { + "name": "genome_feature_set", + "description": "This property links a database object to the set of all features", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "GenomeFeature" + }, + "functional_annotation_set": { + "name": "functional_annotation_set", + "description": "This property links a database object to the set of all functional annotations", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "FunctionalAnnotation" + }, + "activity_set": { + "name": "activity_set", + "description": "This property links a database object to the set of workflow activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "WorkflowExecutionActivity" + }, + "mags_activity_set": { + "name": "mags_activity_set", + "description": "This property links a database object to the set of MAGs analysis activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "MagsAnalysisActivity" + }, + "metabolomics_analysis_activity_set": { + "name": "metabolomics_analysis_activity_set", + "description": "This property links a database object to the set of metabolomics analysis activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "MetabolomicsAnalysisActivity" + }, + "metaproteomics_analysis_activity_set": { + "name": "metaproteomics_analysis_activity_set", + "description": "This property links a database object to the set of metaproteomics analysis activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "MetaproteomicsAnalysisActivity" + }, + "metagenome_annotation_activity_set": { + "name": "metagenome_annotation_activity_set", + "description": "This property links a database object to the set of metagenome annotation activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "MetagenomeAnnotationActivity" + }, + "metagenome_assembly_set": { + "name": "metagenome_assembly_set", + "description": "This property links a database object to the set of metagenome assembly activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "MetagenomeAssembly" + }, + "metatranscriptome_activity_set": { + "name": "metatranscriptome_activity_set", + "description": "This property links a database object to the set of metatranscriptome analysis activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "MetatranscriptomeActivity" + }, + "read_qc_analysis_activity_set": { + "name": "read_qc_analysis_activity_set", + "description": "This property links a database object to the set of read QC analysis activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "ReadQcAnalysisActivity" + }, + "read_based_taxonomy_analysis_activity_set": { + "name": "read_based_taxonomy_analysis_activity_set", + "description": "This property links a database object to the set of read based analysis activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "ReadBasedTaxonomyAnalysisActivity" + }, + "nom_analysis_activity_set": { + "name": "nom_analysis_activity_set", + "description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "NomAnalysisActivity" + }, + "omics_processing_set": { + "name": "omics_processing_set", + "description": "This property links a database object to the set of omics processings within it.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "range": "OmicsProcessing" + }, + "omics_type": { + "name": "omics_type", + "description": "The type of omics data", + "notes": [ + "was the range string at one point? the values in MongoDB don't look like NMDC classes" + ], + "examples": [ + { + "value": "metatranscriptome" + }, + { + "value": "metagenome" + } + ], + "from_schema": "https://microbiomedata/schema", + "range": "ControlledTermValue" + }, + "data_object_type": { + "name": "data_object_type", + "description": "The type of file represented by the data object.", + "examples": [ + { + "value": "FT ICR-MS Analysis Results" + }, + { + "value": "GC-MS Metabolomics Results" + } + ], + "from_schema": "https://microbiomedata/schema", + "range": "file type enum" + }, + "compression_type": { + "name": "compression_type", + "description": "If provided, specifies the compression type", + "todos": [ + "consider enum" + ], + "examples": [ + { + "value": "gzip" + } + ], + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "instrument_name": { + "name": "instrument_name", + "description": "The name of the instrument that was used for processing the sample.", + "from_schema": "https://microbiomedata/schema" + }, + "gold_path_field": { + "name": "gold_path_field", + "description": "This is a grouping for any of the gold path fields", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "abstract": true, + "range": "string" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field" + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field" + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field" + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field" + }, + "principal_investigator": { + "name": "principal_investigator", + "description": "Principal Investigator who led the study and/or generated the dataset.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "PI" + ], + "is_a": "attribute", + "range": "PersonValue" + }, + "doi": { + "name": "doi", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "range": "AttributeValue" + }, + "add_date": { + "name": "add_date", + "description": "The date on which the information was added to the database.", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "mod_date": { + "name": "mod_date", + "description": "The last date on which the database information was modified.", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "ecosystem_path_id": { + "name": "ecosystem_path_id", + "description": "A unique id representing the GOLD classifers associated with a sample.", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "habitat": { + "name": "habitat", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "location": { + "name": "location", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "community": { + "name": "community", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "ncbi_taxonomy_name": { + "name": "ncbi_taxonomy_name", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "ncbi_project_name": { + "name": "ncbi_project_name", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "sample_collection_site": { + "name": "sample_collection_site", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "sample_collection_year": { + "name": "sample_collection_year", + "from_schema": "https://microbiomedata/schema", + "range": "integer" + }, + "sample_collection_month": { + "name": "sample_collection_month", + "from_schema": "https://microbiomedata/schema", + "range": "integer" + }, + "sample_collection_day": { + "name": "sample_collection_day", + "from_schema": "https://microbiomedata/schema", + "range": "integer" + }, + "sample_collection_hour": { + "name": "sample_collection_hour", + "from_schema": "https://microbiomedata/schema", + "range": "integer" + }, + "sample_collection_minute": { + "name": "sample_collection_minute", + "from_schema": "https://microbiomedata/schema", + "range": "integer" + }, + "salinity_category": { + "name": "salinity_category", + "description": "Categorcial description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline", + "notes": [ + "maps to gold:salinity" + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://github.com/microbiomedata/nmdc-metadata/pull/297" + ], + "range": "string" + }, + "soluble_iron_micromol": { + "name": "soluble_iron_micromol", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "host_name": { + "name": "host_name", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "subsurface_depth": { + "name": "subsurface_depth", + "from_schema": "https://microbiomedata/schema", + "range": "QuantityValue" + }, + "proport_woa_temperature": { + "name": "proport_woa_temperature", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "biogas_temperature": { + "name": "biogas_temperature", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "soil_annual_season_temp": { + "name": "soil_annual_season_temp", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "biogas_retention_time": { + "name": "biogas_retention_time", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "processing_institution": { + "name": "processing_institution", + "description": "The organization that processed the sample.", + "from_schema": "https://microbiomedata/schema", + "range": "processing_institution_enum" + }, + "completion_date": { + "name": "completion_date", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "metagenome_assembly_parameter": { + "name": "metagenome_assembly_parameter", + "from_schema": "https://microbiomedata/schema" + }, + "has_peptide_quantifications": { + "name": "has_peptide_quantifications", + "from_schema": "https://microbiomedata/schema" + }, + "asm_score": { + "name": "asm_score", + "description": "A score for comparing metagenomic assembly quality from same sample.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "scaffolds": { + "name": "scaffolds", + "description": "Total sequence count of all scaffolds.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "scaf_logsum": { + "name": "scaf_logsum", + "description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "scaf_powsum": { + "name": "scaf_powsum", + "description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "scaf_max": { + "name": "scaf_max", + "description": "Maximum scaffold length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "scaf_bp": { + "name": "scaf_bp", + "description": "Total size in bp of all scaffolds.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "scaf_n50": { + "name": "scaf_n50", + "description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "scaf_n90": { + "name": "scaf_n90", + "description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "scaf_l50": { + "name": "scaf_l50", + "description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "scaf_l90": { + "name": "scaf_l90", + "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "scaf_n_gt50k": { + "name": "scaf_n_gt50k", + "description": "Total sequence count of scaffolds greater than 50 KB.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "scaf_l_gt50k": { + "name": "scaf_l_gt50k", + "description": "Total size in bp of all scaffolds greater than 50 KB.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "scaf_pct_gt50k": { + "name": "scaf_pct_gt50k", + "description": "Total sequence size percentage of scaffolds greater than 50 KB.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "contigs": { + "name": "contigs", + "description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "contig_bp": { + "name": "contig_bp", + "description": "Total size in bp of all contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "ctg_n50": { + "name": "ctg_n50", + "description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "ctg_l50": { + "name": "ctg_l50", + "description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "ctg_n90": { + "name": "ctg_n90", + "description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "ctg_l90": { + "name": "ctg_l90", + "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "ctg_logsum": { + "name": "ctg_logsum", + "description": "Maximum contig length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "ctg_powsum": { + "name": "ctg_powsum", + "description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "ctg_max": { + "name": "ctg_max", + "description": "Maximum contig length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "gap_pct": { + "name": "gap_pct", + "description": "The gap size percentage of all scaffolds.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "gc_std": { + "name": "gc_std", + "description": "Standard deviation of GC content of all contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "gc_avg": { + "name": "gc_avg", + "description": "Average of GC content of all contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "num_input_reads": { + "name": "num_input_reads", + "description": "The sequence count number of input reads for assembly.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "num_aligned_reads": { + "name": "num_aligned_reads", + "description": "The sequence count number of input reads aligned to assembled contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "range": "float" + }, + "read_qc_analysis_statistic": { + "name": "read_qc_analysis_statistic", + "from_schema": "https://microbiomedata/schema" + }, + "mags_list": { + "name": "mags_list", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "range": "MagBin" + }, + "too_short_contig_num": { + "name": "too_short_contig_num", + "from_schema": "https://microbiomedata/schema", + "range": "integer" + }, + "binned_contig_num": { + "name": "binned_contig_num", + "from_schema": "https://microbiomedata/schema", + "range": "integer" + }, + "input_contig_num": { + "name": "input_contig_num", + "from_schema": "https://microbiomedata/schema", + "range": "integer" + }, + "unbinned_contig_num": { + "name": "unbinned_contig_num", + "from_schema": "https://microbiomedata/schema", + "range": "integer" + }, + "low_depth_contig_num": { + "name": "low_depth_contig_num", + "from_schema": "https://microbiomedata/schema", + "range": "integer" + }, + "input_read_count": { + "name": "input_read_count", + "description": "The sequence count number of input reads for QC analysis.", + "from_schema": "https://microbiomedata/schema", + "is_a": "read_qc_analysis_statistic", + "range": "float" + }, + "input_base_count": { + "name": "input_base_count", + "description": "The nucleotide base count number of input reads for QC analysis.", + "from_schema": "https://microbiomedata/schema", + "is_a": "read_qc_analysis_statistic", + "range": "float" + }, + "output_read_count": { + "name": "output_read_count", + "description": "After QC analysis sequence count number.", + "from_schema": "https://microbiomedata/schema", + "is_a": "read_qc_analysis_statistic", + "range": "float" + }, + "output_base_count": { + "name": "output_base_count", + "description": "After QC analysis nucleotide base count number.", + "from_schema": "https://microbiomedata/schema", + "is_a": "read_qc_analysis_statistic", + "range": "float" + }, + "has_calibration": { + "name": "has_calibration", + "from_schema": "https://microbiomedata/schema" + }, + "has_metabolite_quantifications": { + "name": "has_metabolite_quantifications", + "from_schema": "https://microbiomedata/schema" + }, + "input_read_bases": { + "name": "input_read_bases", + "from_schema": "https://microbiomedata/schema" + }, + "output_read_bases": { + "name": "output_read_bases", + "from_schema": "https://microbiomedata/schema" + }, + "started_at_time": { + "name": "started_at_time", + "notes": [ + "The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/ It may not be complete, but it is good enough for now." + ], + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:startedAtTime" + ], + "range": "datetime", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "ended_at_time": { + "name": "ended_at_time", + "notes": [ + "The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/ It may not be complete, but it is good enough for now." + ], + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:endedAtTime" + ], + "range": "datetime", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasInformedBy" + ], + "range": "Activity" + }, + "was_associated_with": { + "name": "was_associated_with", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasAssociatedWith" + ], + "range": "Agent" + }, + "acted_on_behalf_of": { + "name": "acted_on_behalf_of", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:actedOnBehalfOf" + ], + "range": "Agent" + }, + "was_generated_by": { + "name": "was_generated_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasGeneratedBy" + ], + "range": "Activity" + }, + "used": { + "name": "used", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:used" + ], + "domain": "Activity" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "notes": [ + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", + "minting authority shoulders should probably be enumerated and checked in the pattern" + ], + "examples": [ + { + "value": "nmdc:mgmag-00-x012.1_7_c1", + "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" + } + ], + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "range": "string" + }, + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "examples": [ + { + "value": "nmdc:Biosample" + }, + { + "value": "nmdc:Study" + } + ], + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "title": { + "name": "title", + "description": "A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.", + "from_schema": "https://microbiomedata/schema", + "exact_mappings": [ + "dcterms:title" + ], + "multivalued": false, + "range": "string" + }, + "alternative_titles": { + "name": "alternative_titles", + "description": "A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.", + "from_schema": "https://microbiomedata/schema", + "exact_mappings": [ + "dcterms:alternative" + ], + "multivalued": true, + "range": "string" + }, + "alternative_names": { + "name": "alternative_names", + "description": "A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.", + "from_schema": "https://microbiomedata/schema", + "exact_mappings": [ + "dcterms:alternative", + "skos:altLabel" + ], + "multivalued": true, + "range": "string" + }, + "alternative_descriptions": { + "name": "alternative_descriptions", + "description": "A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "range": "string" + }, + "has_inputs": { + "name": "has_inputs", + "from_schema": "https://microbiomedata/schema", + "domain": "PlannedProcess", + "multivalued": true, + "range": "NamedThing" + }, + "has_outputs": { + "name": "has_outputs", + "from_schema": "https://microbiomedata/schema", + "domain": "PlannedProcess", + "multivalued": true, + "range": "NamedThing" + }, + "participating_agent": { + "name": "participating_agent", + "from_schema": "https://microbiomedata/schema", + "domain": "PlannedProcess", + "range": "Agent" + }, + "language": { + "name": "language", + "description": "Should use ISO 639-1 code e.g. \"en\", \"fr\"", + "from_schema": "https://microbiomedata/schema", + "range": "language code" + }, + "attribute": { + "name": "attribute", + "description": "A attribute of a biosample. Examples: depth, habitat, material. For NMDC, attributes SHOULD be mapped to terms within a MIxS template", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "field", + "property", + "template field", + "key", + "characteristic" + ], + "abstract": true + }, + "has_raw_value": { + "name": "has_raw_value", + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "from_schema": "https://microbiomedata/schema", + "domain": "AttributeValue", + "multivalued": false, + "range": "string", + "required": false + }, + "has_unit": { + "name": "has_unit", + "description": "Links a QuantityValue to a unit", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "scale" + ], + "mappings": [ + "qud:unit", + "schema:unitCode" + ], + "range": "unit" + }, + "has_numeric_value": { + "name": "has_numeric_value", + "description": "Links a quantity value to a number", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "qud:quantityValue", + "schema:value" + ], + "multivalued": false, + "range": "float" + }, + "has_minimum_numeric_value": { + "name": "has_minimum_numeric_value", + "description": "The minimum value part, expressed as number, of the quantity value when the value covers a range.", + "from_schema": "https://microbiomedata/schema", + "is_a": "has_numeric_value" + }, + "has_maximum_numeric_value": { + "name": "has_maximum_numeric_value", + "description": "The maximum value part, expressed as number, of the quantity value when the value covers a range.", + "from_schema": "https://microbiomedata/schema", + "is_a": "has_numeric_value" + }, + "has_boolean_value": { + "name": "has_boolean_value", + "description": "Links a quantity value to a boolean", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "range": "boolean" + }, + "latitude": { + "name": "latitude", + "description": "latitude", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "schema:latitude" + ], + "domain": "GeolocationValue", + "slot_uri": "wgs84:lat", + "range": "decimal degree" + }, + "longitude": { + "name": "longitude", + "description": "longitude", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "schema:longitude" + ], + "domain": "GeolocationValue", + "slot_uri": "wgs84:long", + "range": "decimal degree" + }, + "term": { + "name": "term", + "description": "pointer to an ontology class", + "notes": [ + "removed 'slot_uri: rdf:type'" + ], + "from_schema": "https://microbiomedata/schema", + "domain": "ControlledTermValue", + "range": "OntologyClass", + "inlined": true + }, + "orcid": { + "name": "orcid", + "description": "The ORCID of a person.", + "from_schema": "https://microbiomedata/schema", + "domain": "PersonValue", + "range": "string" + }, + "email": { + "name": "email", + "description": "An email address for an entity such as a person. This should be the primarly email address used.", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "schema:email", + "range": "string" + }, + "alternate_emails": { + "name": "alternate_emails", + "description": "One or more other email addresses for an entity.", + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "profile_image_url": { + "name": "profile_image_url", + "description": "A url that points to an image of a person.", + "from_schema": "https://microbiomedata/schema", + "domain": "PersonValue", + "range": "string" + }, + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "input" + ], + "domain": "NamedThing", + "multivalued": true, + "range": "NamedThing" + }, + "has_output": { + "name": "has_output", + "description": "An output biosample to a processing step", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "output" + ], + "domain": "NamedThing", + "multivalued": true, + "range": "NamedThing" + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "is part of" + ], + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "range": "NamedThing" + }, + "execution_resource": { + "name": "execution_resource", + "description": "Example: NERSC-Cori", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute" + }, + "url": { + "name": "url", + "notes": [ + "See issue 207 - this clashes with the mixs field" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "range": "string" + }, + "display_order": { + "name": "display_order", + "description": "When rendering information, this attribute to specify the order in which the information should be rendered.", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute" + }, + "git_url": { + "name": "git_url", + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "range": "string" + }, + "file_size_bytes": { + "name": "file_size_bytes", + "description": "Size of the file in bytes", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "range": "bytes" + }, + "md5_checksum": { + "name": "md5_checksum", + "description": "MD5 checksum of file (pre-compressed)", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "range": "string" + }, + "abstract": { + "name": "abstract", + "description": "The abstract of manuscript/grant associated with the entity; i.e., a summary of the resource.", + "from_schema": "https://microbiomedata/schema", + "exact_mappings": [ + "dcterms:abstract" + ], + "range": "string" + }, + "keywords": { + "name": "keywords", + "description": "A list of keywords that used to associate the entity. Keywords SHOULD come from controlled vocabularies, including MESH, ENVO.", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "dcterms:subject" + ], + "multivalued": true, + "range": "string" + }, + "objective": { + "name": "objective", + "description": "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "sio:000337" + ], + "multivalued": false, + "range": "string" + }, + "websites": { + "name": "websites", + "description": "A list of websites that are associated with the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "range": "string" + }, + "publications": { + "name": "publications", + "description": "A list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "range": "string" + }, + "all_proteins": { + "name": "all_proteins", + "from_schema": "https://microbiomedata/schema" + }, + "best_protein": { + "name": "best_protein", + "from_schema": "https://microbiomedata/schema" + }, + "chemical_formula": { + "name": "chemical_formula", + "from_schema": "https://microbiomedata/schema" + }, + "inchi_key": { + "name": "inchi_key", + "notes": [ + "key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental testing. J Cheminform. 4:12" + ], + "from_schema": "https://microbiomedata/schema" + }, + "inchi": { + "name": "inchi", + "from_schema": "https://microbiomedata/schema" + }, + "min_q_value": { + "name": "min_q_value", + "from_schema": "https://microbiomedata/schema" + }, + "peptide_sequence": { + "name": "peptide_sequence", + "from_schema": "https://microbiomedata/schema" + }, + "peptide_sequence_count": { + "name": "peptide_sequence_count", + "from_schema": "https://microbiomedata/schema" + }, + "peptide_spectral_count": { + "name": "peptide_spectral_count", + "from_schema": "https://microbiomedata/schema" + }, + "peptide_sum_masic_abundance": { + "name": "peptide_sum_masic_abundance", + "from_schema": "https://microbiomedata/schema" + }, + "protein_spectral_count": { + "name": "protein_spectral_count", + "from_schema": "https://microbiomedata/schema" + }, + "protein_sum_masic_abundance": { + "name": "protein_sum_masic_abundance", + "from_schema": "https://microbiomedata/schema" + }, + "smiles": { + "name": "smiles", + "from_schema": "https://microbiomedata/schema" + }, + "metabolite_quantified": { + "name": "metabolite_quantified", + "from_schema": "https://microbiomedata/schema" + }, + "highest_similarity_score": { + "name": "highest_similarity_score", + "from_schema": "https://microbiomedata/schema" + }, + "external_database_identifiers": { + "name": "external_database_identifiers", + "description": "Link to corresponding identifier in external database", + "notes": [ + "had tried ranges of external identifier and string" + ], + "comments": [ + "The value of this field is always a registered CURIE" + ], + "from_schema": "https://microbiomedata/schema", + "close_mappings": [ + "skos:closeMatch" + ], + "is_a": "alternative_identifiers", + "abstract": true, + "multivalued": true, + "range": "uriorcurie" + }, + "gold_identifiers": { + "name": "gold_identifiers", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/" + ], + "mixin": true + }, + "mgnify_identifiers": { + "name": "mgnify_identifiers", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ebi.ac.uk/metagenomics/" + ], + "mixin": true + }, + "insdc_identifiers": { + "name": "insdc_identifiers", + "description": "Any identifier covered by the International Nucleotide Sequence Database Collaboration", + "comments": [ + "note that we deliberately abstract over which of the partner databases accepted the initial submission", + "the first letter of the accession indicates which partner accepted the initial submission: E for ENA, D for DDBJ, or S or N for NCBI." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.insdc.org/", + "https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html" + ], + "aliases": [ + "EBI identifiers", + "NCBI identifiers", + "DDBJ identifiers" + ], + "mixin": true + }, + "study_identifiers": { + "name": "study_identifiers", + "from_schema": "https://microbiomedata/schema", + "is_a": "external_database_identifiers", + "abstract": true + }, + "insdc_sra_ena_study_identifiers": { + "name": "insdc_sra_ena_study_identifiers", + "description": "identifiers for corresponding project in INSDC SRA / ENA", + "examples": [ + { + "value": "https://identifiers.org/insdc.sra:SRP121659", + "description": "Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://github.com/bioregistry/bioregistry/issues/109", + "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies", + "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies" + ], + "aliases": [ + "EBI ENA study identifiers", + "NCBI SRA identifiers", + "DDBJ SRA identifiers" + ], + "is_a": "study_identifiers", + "mixins": [ + "insdc_identifiers" + ], + "multivalued": true, + "pattern": "^insdc.sra:(E|D|S)RP[0-9]{6,}$" + }, + "insdc_bioproject_identifiers": { + "name": "insdc_bioproject_identifiers", + "description": "identifiers for corresponding project in INSDC Bioproject", + "comments": [ + "these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?) one to one" + ], + "examples": [ + { + "value": "https://identifiers.org/bioproject:PRJNA366857", + "description": "Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ncbi.nlm.nih.gov/bioproject/", + "https://www.ddbj.nig.ac.jp/bioproject/index-e.html" + ], + "aliases": [ + "NCBI bioproject identifiers", + "DDBJ bioproject identifiers" + ], + "is_a": "insdc_identifiers", + "mixins": [ + "insdc_identifiers" + ], + "pattern": "^bioproject:PRJ[DEN][A-Z][0-9]+$" + }, + "gold_study_identifiers": { + "name": "gold_study_identifiers", + "description": "identifiers for corresponding project(s) in GOLD", + "title": "GOLD Study Identifiers", + "comments": [ + "uses the prefix GS (but possibly in a different case)" + ], + "examples": [ + { + "value": "https://identifiers.org/gold:Gs0110115" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/studies" + ], + "is_a": "study_identifiers", + "mixins": [ + "gold_identifiers" + ], + "multivalued": true, + "pattern": "^GOLD:Gs[0-9]+$" + }, + "mgnify_project_identifiers": { + "name": "mgnify_project_identifiers", + "description": "identifiers for corresponding project in MGnify", + "examples": [ + { + "value": "https://identifiers.org/mgnify.proj:MGYS00005757" + } + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "insdc_identifiers", + "pattern": "^mgnify.proj:[A-Z]+[0-9]+$" + }, + "biosample_identifiers": { + "name": "biosample_identifiers", + "from_schema": "https://microbiomedata/schema", + "is_a": "external_database_identifiers", + "abstract": true + }, + "gold_biosample_identifiers": { + "name": "gold_biosample_identifiers", + "description": "identifiers for corresponding sample in GOLD", + "examples": [ + { + "value": "https://identifiers.org/gold:Gb0312930" + } + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "biosample_identifiers", + "mixins": [ + "gold_identifiers" + ], + "multivalued": true, + "pattern": "^GOLD:Gb[0-9]+$" + }, + "insdc_biosample_identifiers": { + "name": "insdc_biosample_identifiers", + "description": "identifiers for corresponding sample in INSDC", + "examples": [ + { + "value": "https://identifiers.org/biosample:SAMEA5989477" + }, + { + "value": "https://identifiers.org/biosample:SAMD00212331", + "description": "I13_N_5-10 sample from Soil fungal diversity along elevational gradients" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://github.com/bioregistry/bioregistry/issues/108", + "https://www.ebi.ac.uk/biosamples/", + "https://www.ncbi.nlm.nih.gov/biosample", + "https://www.ddbj.nig.ac.jp/biosample/index-e.html" + ], + "aliases": [ + "EBI biosample identifiers", + "NCBI biosample identifiers", + "DDBJ biosample identifiers" + ], + "is_a": "biosample_identifiers", + "mixins": [ + "insdc_identifiers" + ], + "multivalued": true, + "pattern": "^biosample:SAM[NED]([A-Z])?[0-9]+$" + }, + "insdc_secondary_sample_identifiers": { + "name": "insdc_secondary_sample_identifiers", + "description": "secondary identifiers for corresponding sample in INSDC", + "comments": [ + "ENA redirects these to primary IDs, e.g. https://www.ebi.ac.uk/ena/browser/view/DRS166340 -> SAMD00212331", + "MGnify uses these as their primary sample IDs" + ], + "examples": [ + { + "value": "https://identifiers.org/insdc.sra:DRS166340", + "description": "I13_N_5-10 sample from Soil fungal diversity along elevational gradients" + } + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "biosample_identifiers", + "mixins": [ + "insdc_identifiers" + ], + "pattern": "^biosample:(E|D|S)RS[0-9]{6,}$" + }, + "omics_processing_identifiers": { + "name": "omics_processing_identifiers", + "from_schema": "https://microbiomedata/schema", + "is_a": "external_database_identifiers", + "abstract": true + }, + "gold_sequencing_project_identifiers": { + "name": "gold_sequencing_project_identifiers", + "description": "identifiers for corresponding sequencing project in GOLD", + "examples": [ + { + "value": "https://identifiers.org/gold:Gp0108335" + } + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "omics_processing_identifiers", + "mixins": [ + "gold_identifiers" + ], + "multivalued": true, + "pattern": "^GOLD:Gp[0-9]+$" + }, + "insdc_experiment_identifiers": { + "name": "insdc_experiment_identifiers", + "from_schema": "https://microbiomedata/schema", + "is_a": "external_database_identifiers", + "mixins": [ + "insdc_identifiers" + ], + "pattern": "^insdc.sra:(E|D|S)RX[0-9]{6,}$" + }, + "analysis_identifiers": { + "name": "analysis_identifiers", + "from_schema": "https://microbiomedata/schema", + "is_a": "external_database_identifiers", + "abstract": true + }, + "gold_analysis_project_identifiers": { + "name": "gold_analysis_project_identifiers", + "description": "identifiers for corresponding analysis project in GOLD", + "examples": [ + { + "value": "https://identifiers.org/gold:Ga0526289" + } + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "analysis_identifiers", + "mixins": [ + "gold_identifiers" + ], + "multivalued": true, + "pattern": "^GOLD:Ga[0-9]+$" + }, + "insdc_analysis_identifiers": { + "name": "insdc_analysis_identifiers", + "comments": [ + "in INSDC this is a run but it corresponds to a GOLD analysis" + ], + "examples": [ + { + "value": "https://www.ebi.ac.uk/metagenomics/runs/DRR218479", + "description": "Illumina MiSeq paired end sequencing of SAMD00212331" + }, + { + "value": "https://www.ebi.ac.uk/ena/browser/view/ERR436051" + } + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "analysis_identifiers", + "mixins": [ + "insdc_identifiers" + ], + "pattern": "^insdc.sra:(E|D|S)RR[0-9]{6,}$" + }, + "mgnify_analysis_identifiers": { + "name": "mgnify_analysis_identifiers", + "notes": [ + "removed pattern: \"^mgnify:MGYA[0-9]+$\" ## TODO https://github.com/bioregistry/bioregistry/issues/109" + ], + "examples": [ + { + "value": "https://www.ebi.ac.uk/metagenomics/analyses/MGYA00002270", + "description": "combined analyses (taxonomic, functional) of sample ERS438107" + } + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "analysis_identifiers", + "mixins": [ + "mgnify_identifiers" + ] + }, + "assembly_identifiers": { + "name": "assembly_identifiers", + "from_schema": "https://microbiomedata/schema", + "abstract": true + }, + "insdc_assembly_identifiers": { + "name": "insdc_assembly_identifiers", + "from_schema": "https://microbiomedata/schema", + "is_a": "assembly_identifiers", + "mixins": [ + "insdc_identifiers" + ], + "pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$" + }, + "dissolving_activity_set": { + "name": "dissolving_activity_set", + "title": "dissolving activity set", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "range": "DissolvingActivity", + "inlined": true, + "inlined_as_list": true + }, + "material_sample_set": { + "name": "material_sample_set", + "title": "material sample set", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "range": "MaterialSample", + "inlined": true, + "inlined_as_list": true + }, + "material_sampling_activity_set": { + "name": "material_sampling_activity_set", + "title": "material sampling activity set", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "range": "MaterialSamplingActivity", + "inlined": true, + "inlined_as_list": true + }, + "reaction_activity_set": { + "name": "reaction_activity_set", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "range": "ReactionActivity", + "inlined": true, + "inlined_as_list": true + }, + "dissolution_aided_by": { + "name": "dissolution_aided_by", + "title": "dissolution aided by", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "shaker" + ], + "range": "LabDevice", + "inlined": true + }, + "dissolution_reagent": { + "name": "dissolution_reagent", + "title": "dissolution reagent", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "solvent" + ], + "range": "SolventEnum" + }, + "dissolution_volume": { + "name": "dissolution_volume", + "title": "dissolution volume", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "volume" + ], + "range": "QuantityValue", + "inlined": true + }, + "dissolved_in": { + "name": "dissolved_in", + "title": "dissolved in", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "container" + ], + "range": "MaterialContainer", + "inlined": true + }, + "biosample_input": { + "name": "biosample_input", + "title": "biosample input", + "from_schema": "https://microbiomedata/schema", + "range": "Biosample" + }, + "material_input": { + "name": "material_input", + "title": "material input", + "from_schema": "https://microbiomedata/schema", + "range": "MaterialSample" + }, + "material_output": { + "name": "material_output", + "title": "material output", + "from_schema": "https://microbiomedata/schema", + "range": "MaterialSample" + }, + "device_type": { + "name": "device_type", + "title": "device type", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "shaker type" + ], + "range": "DeviceTypeEnum" + }, + "activity_speed": { + "name": "activity_speed", + "title": "activity speed", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "shake_speed" + ], + "range": "QuantityValue", + "inlined": true + }, + "activity_temperature": { + "name": "activity_temperature", + "todos": [ + "constrain units" + ], + "from_schema": "https://microbiomedata/schema", + "range": "QuantityValue", + "inlined": true + }, + "activity_time": { + "name": "activity_time", + "title": "activity time", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "shake_time" + ], + "range": "QuantityValue", + "inlined": true + }, + "container_size": { + "name": "container_size", + "title": "container size", + "from_schema": "https://microbiomedata/schema", + "range": "QuantityValue", + "inlined": true + }, + "container_type": { + "name": "container_type", + "title": "container type", + "from_schema": "https://microbiomedata/schema", + "range": "ContainerTypeEnum" + }, + "amount_collected": { + "name": "amount_collected", + "title": "amount collected", + "from_schema": "https://microbiomedata/schema", + "range": "QuantityValue", + "inlined": true + }, + "collected_into": { + "name": "collected_into", + "title": "collected into", + "from_schema": "https://microbiomedata/schema" + }, + "sampling_method": { + "name": "sampling_method", + "title": "sampling method", + "from_schema": "https://microbiomedata/schema", + "range": "SamplingMethodEnum" + }, + "reaction_aided_by": { + "name": "reaction_aided_by", + "title": "reaction aided by", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "shaker" + ], + "range": "LabDevice", + "inlined": true + }, + "reaction_temperature": { + "name": "reaction_temperature", + "from_schema": "https://microbiomedata/schema" + }, + "reaction_time": { + "name": "reaction_time", + "from_schema": "https://microbiomedata/schema" + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "multivalued": true, + "slot_group": "Sample ID", + "range": "analysis_type_enum", + "required": false, + "recommended": true + }, + "sample_link": { + "name": "sample_link", + "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", + "title": "sample linkage", + "comments": [ + "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" + ], + "examples": [ + { + "value": "IGSN:DSJ0284" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 5, + "string_serialization": "{text}:{text}", + "multivalued": true, + "slot_group": "Sample ID", + "recommended": true + }, + "collection_date_inc": { + "name": "collection_date_inc", + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:collection_date" + ], + "rank": 2, + "string_serialization": "{date, arbitrary precision}", + "slot_group": "MIxS Inspired", + "recommended": true + }, + "collection_time": { + "name": "collection_time", + "description": "The time of sampling, either as an instance (single point) or interval.", + "title": "collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:collection_date" + ], + "rank": 1, + "string_serialization": "{time, seconds optional}", + "slot_group": "MIxS Inspired", + "recommended": true + }, + "collection_time_inc": { + "name": "collection_time_inc", + "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:collection_date" + ], + "rank": 3, + "string_serialization": "{time, seconds optional}", + "slot_group": "MIxS Inspired", + "recommended": true + }, + "experimental_factor_other": { + "name": "experimental_factor_other", + "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", + "title": "experimental factor- other", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:experimental_factor|additional_info" + ], + "rank": 7, + "string_serialization": "{text}", + "slot_group": "MIxS Inspired", + "recommended": true + }, + "filter_method": { + "name": "filter_method", + "description": "Type of filter used or how the sample was filtered", + "title": "filter method", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:filter_type" + ], + "rank": 6, + "string_serialization": "{text}", + "slot_group": "MIxS Inspired", + "recommended": true + }, + "isotope_exposure": { + "name": "isotope_exposure", + "description": "List isotope exposure or addition applied to your sample.", + "title": "isotope exposure/addition", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:chem_administration" + ], + "rank": 16, + "string_serialization": "{termLabel} {[termID]}; {timestamp}", + "slot_group": "MIxS Inspired", + "recommended": true + }, + "micro_biomass_c_meth": { + "name": "micro_biomass_c_meth", + "description": "Reference or method used in determining microbial biomass", + "title": "microbial biomass carbon method", + "comments": [ + "required if \"microbial_biomass_c\" is provided" + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:micro_biomass_meth" + ], + "rank": 11, + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_group": "MIxS Inspired", + "recommended": true + }, + "micro_biomass_n_meth": { + "name": "micro_biomass_n_meth", + "description": "Reference or method used in determining microbial biomass nitrogen", + "title": "microbial biomass nitrogen method", + "comments": [ + "required if \"microbial_biomass_n\" is provided" + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:micro_biomass_meth" + ], + "rank": 13, + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_group": "MIxS Inspired" + }, + "microbial_biomass_c": { + "name": "microbial_biomass_c", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "title": "microbial biomass carbon", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:microbial_biomass" + ], + "rank": 10, + "string_serialization": "{float} {unit}", + "slot_group": "MIxS Inspired" + }, + "microbial_biomass_n": { + "name": "microbial_biomass_n", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "title": "microbial biomass nitrogen", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:microbial_biomass" + ], + "rank": 12, + "string_serialization": "{float} {unit}", + "slot_group": "MIxS Inspired" + }, + "non_microb_biomass": { + "name": "non_microb_biomass", + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", + "title": "non-microbial biomass", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:biomass|microbial_biomass" + ], + "rank": 8, + "string_serialization": "{text};{float} {unit}", + "slot_group": "MIxS Inspired" + }, + "non_microb_biomass_method": { + "name": "non_microb_biomass_method", + "description": "Reference or method used in determining biomass", + "title": "non-microbial biomass method", + "comments": [ + "required if \"non-microbial biomass\" is provided" + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:microbial_biomass" + ], + "rank": 9, + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_group": "MIxS Inspired" + }, + "org_nitro_method": { + "name": "org_nitro_method", + "description": "Method used for obtaining organic nitrogen", + "title": "organic nitrogen method", + "comments": [ + "required if \"org_nitro\" is provided" + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:org_nitro|tot_nitro_cont_meth" + ], + "rank": 14, + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_group": "MIxS Inspired" + }, + "other_treatment": { + "name": "other_treatment", + "description": "Other treatments applied to your samples that are not applicable to the provided fields", + "title": "other treatments", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:additional_info" + ], + "rank": 15, + "string_serialization": "{text}", + "slot_group": "MIxS Inspired", + "recommended": true + }, + "start_date_inc": { + "name": "start_date_inc", + "description": "Date the incubation was started. Only relevant for incubation samples.", + "title": "incubation start date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:collection_date" + ], + "rank": 4, + "string_serialization": "{date, arbitrary precision}", + "slot_group": "MIxS Inspired", + "recommended": true + }, + "start_time_inc": { + "name": "start_time_inc", + "description": "Time the incubation was started. Only relevant for incubation samples.", + "title": "incubation start time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:collection_date" + ], + "rank": 5, + "string_serialization": "{time, seconds optional}", + "slot_group": "MIxS Inspired", + "recommended": true + }, + "dnase_rna": { + "name": "dnase_rna", + "title": "DNase treated", + "comments": [ + "Note DNAse treatment is required for all RNA samples." + ], + "examples": [ + { + "value": "no" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 13, + "slot_group": "JGI-Metatranscriptomics", + "range": "dnase_rna_enum", + "required": false, + "recommended": true + }, + "proposal_rna": { + "name": "proposal_rna", + "title": "RNA proposal ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "504000" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 19, + "string_serialization": "{text}", + "slot_group": "JGI-Metatranscriptomics", + "required": false, + "recommended": true + }, + "rna_absorb1": { + "name": "rna_absorb1", + "description": "260/280 measurement of RNA sample purity", + "title": "RNA absorbance 260/280", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 7, + "string_serialization": "{float}", + "slot_group": "JGI-Metatranscriptomics", + "recommended": true + }, + "rna_absorb2": { + "name": "rna_absorb2", + "description": "260/230 measurement of RNA sample purity", + "title": "RNA absorbance 260/230", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 8, + "string_serialization": "{float}", + "slot_group": "JGI-Metatranscriptomics", + "recommended": true + }, + "rna_collect_site": { + "name": "rna_collect_site", + "description": "Provide information on the site your RNA sample was collected from", + "title": "RNA collection site", + "examples": [ + { + "value": "untreated pond water" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 15, + "string_serialization": "{text}", + "slot_group": "JGI-Metatranscriptomics", + "required": false, + "recommended": true + }, + "rna_concentration": { + "name": "rna_concentration", + "title": "RNA concentration in ng/ul", + "comments": [ + "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 5, + "string_serialization": "{float}", + "slot_group": "JGI-Metatranscriptomics", + "required": false, + "recommended": true, + "minimum_value": 0, + "maximum_value": 1000 + }, + "rna_cont_type": { + "name": "rna_cont_type", + "description": "Tube or plate (96-well)", + "title": "RNA container type", + "examples": [ + { + "value": "plate" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 10, + "slot_group": "JGI-Metatranscriptomics", + "range": "rna_cont_type_enum", + "required": false, + "recommended": true + }, + "rna_cont_well": { + "name": "rna_cont_well", + "title": "RNA plate position", + "comments": [ + "Required when 'plate' is selected for container type.", + "Leave blank if the sample will be shipped in a tube.", + "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", + "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." + ], + "examples": [ + { + "value": "B2" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 11, + "string_serialization": "{96 well plate pos}", + "slot_group": "JGI-Metatranscriptomics", + "required": false, + "recommended": true, + "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" + }, + "rna_container_id": { + "name": "rna_container_id", + "title": "RNA container label", + "comments": [ + "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." + ], + "examples": [ + { + "value": "Pond_MT_041618" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 9, + "string_serialization": "{text}", + "slot_group": "JGI-Metatranscriptomics", + "required": false, + "recommended": true + }, + "rna_isolate_meth": { + "name": "rna_isolate_meth", + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "title": "RNA isolation method", + "examples": [ + { + "value": "phenol/chloroform extraction" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 16, + "string_serialization": "{text}", + "slot_group": "JGI-Metatranscriptomics", + "required": false, + "recommended": true + }, + "rna_organisms": { + "name": "rna_organisms", + "description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", + "title": "RNA expected organisms", + "examples": [ + { + "value": "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 14, + "string_serialization": "{text}", + "slot_group": "JGI-Metatranscriptomics", + "recommended": true + }, + "rna_project_contact": { + "name": "rna_project_contact", + "title": "RNA seq project contact", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "John Jones" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 18, + "string_serialization": "{text}", + "slot_group": "JGI-Metatranscriptomics", + "required": false, + "recommended": true + }, + "rna_samp_id": { + "name": "rna_samp_id", + "title": "RNA sample ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "187654" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 3, + "string_serialization": "{text}", + "slot_group": "JGI-Metatranscriptomics", + "required": false, + "recommended": true + }, + "rna_sample_format": { + "name": "rna_sample_format", + "description": "Solution in which the RNA sample has been suspended", + "title": "RNA sample format", + "examples": [ + { + "value": "Water" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 12, + "slot_group": "JGI-Metatranscriptomics", + "range": "rna_sample_format_enum", + "required": false, + "recommended": true + }, + "rna_sample_name": { + "name": "rna_sample_name", + "description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "title": "RNA sample name", + "examples": [ + { + "value": "JGI_pond_041618" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 4, + "string_serialization": "{text}", + "slot_group": "JGI-Metatranscriptomics", + "required": false, + "recommended": true, + "minimum_value": 0, + "maximum_value": 2000 + }, + "rna_seq_project": { + "name": "rna_seq_project", + "title": "RNA seq project ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "1191234" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 1, + "string_serialization": "{text}", + "slot_group": "JGI-Metatranscriptomics", + "required": false, + "recommended": true + }, + "rna_seq_project_pi": { + "name": "rna_seq_project_pi", + "title": "RNA seq project PI", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "Jane Johnson" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 17, + "string_serialization": "{text}", + "slot_group": "JGI-Metatranscriptomics", + "required": false, + "recommended": true + }, + "rna_seq_project_name": { + "name": "rna_seq_project_name", + "title": "RNA seq project name", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "JGI Pond metatranscriptomics" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 2, + "string_serialization": "{text}", + "slot_group": "JGI-Metatranscriptomics", + "required": false, + "recommended": true + }, + "rna_volume": { + "name": "rna_volume", + "title": "RNA volume in ul", + "comments": [ + "Units must be in uL. Enter the numerical part only. Value must 0-1000. Values <25 by special permission only." + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 6, + "string_serialization": "{float}", + "slot_group": "JGI-Metatranscriptomics", + "required": false, + "recommended": true + }, + "dna_absorb1": { + "name": "dna_absorb1", + "description": "260/280 measurement of DNA sample purity", + "title": "DNA absorbance 260/280", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 7, + "string_serialization": "{float}", + "slot_group": "JGI-Metagenomics", + "recommended": true + }, + "dna_absorb2": { + "name": "dna_absorb2", + "description": "260/230 measurement of DNA sample purity", + "title": "DNA absorbance 260/230", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 8, + "string_serialization": "{float}", + "slot_group": "JGI-Metagenomics", + "recommended": true + }, + "dna_collect_site": { + "name": "dna_collect_site", + "description": "Provide information on the site your DNA sample was collected from", + "title": "DNA collection site", + "examples": [ + { + "value": "untreated pond water" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 15, + "string_serialization": "{text}", + "slot_group": "JGI-Metagenomics", + "required": false, + "recommended": true + }, + "dna_concentration": { + "name": "dna_concentration", + "title": "DNA concentration in ng/ul", + "comments": [ + "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 5, + "string_serialization": "{float}", + "slot_group": "JGI-Metagenomics", + "required": false, + "recommended": true, + "minimum_value": 0, + "maximum_value": 2000 + }, + "dna_cont_type": { + "name": "dna_cont_type", + "description": "Tube or plate (96-well)", + "title": "DNA container type", + "examples": [ + { + "value": "plate" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 10, + "slot_group": "JGI-Metagenomics", + "range": "dna_cont_type_enum", + "required": false, + "recommended": true + }, + "dna_cont_well": { + "name": "dna_cont_well", + "title": "DNA plate position", + "comments": [ + "Required when 'plate' is selected for container type.", + "Leave blank if the sample will be shipped in a tube.", + "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", + "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." + ], + "examples": [ + { + "value": "B2" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 11, + "string_serialization": "{96 well plate pos}", + "slot_group": "JGI-Metagenomics", + "required": false, + "recommended": true, + "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" + }, + "dna_container_id": { + "name": "dna_container_id", + "title": "DNA container label", + "comments": [ + "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." + ], + "examples": [ + { + "value": "Pond_MT_041618" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 9, + "string_serialization": "{text < 20 characters}", + "slot_group": "JGI-Metagenomics", + "required": false, + "recommended": true + }, + "dna_dnase": { + "name": "dna_dnase", + "title": "DNase treatment DNA", + "comments": [ + "Note DNAse treatment is required for all RNA samples." + ], + "examples": [ + { + "value": "no" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 13, + "slot_group": "JGI-Metagenomics", + "range": "dna_dnase_enum", + "required": false, + "recommended": true + }, + "dna_isolate_meth": { + "name": "dna_isolate_meth", + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "title": "DNA isolation method", + "examples": [ + { + "value": "phenol/chloroform extraction" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 16, + "string_serialization": "{text}", + "slot_group": "JGI-Metagenomics", + "required": false, + "recommended": true + }, + "dna_organisms": { + "name": "dna_organisms", + "description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", + "title": "DNA expected organisms", + "examples": [ + { + "value": "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 14, + "string_serialization": "{text}", + "slot_group": "JGI-Metagenomics", + "recommended": true + }, + "dna_project_contact": { + "name": "dna_project_contact", + "title": "DNA seq project contact", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "John Jones" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 18, + "string_serialization": "{text}", + "slot_group": "JGI-Metagenomics", + "required": false, + "recommended": true + }, + "dna_samp_id": { + "name": "dna_samp_id", + "title": "DNA sample ID", + "todos": [ + "Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled?" + ], + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "187654" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 3, + "string_serialization": "{text}", + "slot_group": "JGI-Metagenomics", + "required": false, + "recommended": true + }, + "dna_sample_format": { + "name": "dna_sample_format", + "description": "Solution in which the DNA sample has been suspended", + "title": "DNA sample format", + "examples": [ + { + "value": "Water" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 12, + "slot_group": "JGI-Metagenomics", + "range": "dna_sample_format_enum", + "required": false, + "recommended": true + }, + "dna_sample_name": { + "name": "dna_sample_name", + "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "title": "DNA sample name", + "examples": [ + { + "value": "JGI_pond_041618" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 4, + "string_serialization": "{text}", + "slot_group": "JGI-Metagenomics", + "required": false, + "recommended": true + }, + "dna_seq_project": { + "name": "dna_seq_project", + "title": "DNA seq project ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "1191234" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 1, + "string_serialization": "{text}", + "slot_group": "JGI-Metagenomics", + "required": false, + "recommended": true + }, + "dna_seq_project_pi": { + "name": "dna_seq_project_pi", + "title": "DNA seq project PI", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "Jane Johnson" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 17, + "string_serialization": "{text}", + "slot_group": "JGI-Metagenomics", + "required": false, + "recommended": true + }, + "dna_seq_project_name": { + "name": "dna_seq_project_name", + "title": "DNA seq project name", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "JGI Pond metagenomics" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 2, + "string_serialization": "{text}", + "slot_group": "JGI-Metagenomics", + "required": false, + "recommended": true + }, + "dna_volume": { + "name": "dna_volume", + "title": "DNA volume in ul", + "comments": [ + "Units must be in uL. Enter the numerical part only. Value must 0-1000. Values <25 by special permission only." + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 6, + "string_serialization": "{float}", + "slot_group": "JGI-Metagenomics", + "required": false, + "recommended": true, + "minimum_value": 0, + "maximum_value": 1000 + }, + "proposal_dna": { + "name": "proposal_dna", + "title": "DNA proposal ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "504000" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 19, + "string_serialization": "{text}", + "slot_group": "JGI-Metagenomics", + "required": false, + "recommended": true + }, + "emsl_store_temp": { + "name": "emsl_store_temp", + "description": "The temperature at which the sample should be stored upon delivery to EMSL", + "title": "EMSL sample storage temperature, deg. C", + "todos": [ + "add 'see_alsos' with link to NEXUS info" + ], + "comments": [ + "Enter a temperature in celsius. Numeric portion only." + ], + "examples": [ + { + "value": "-80" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 4, + "string_serialization": "{float}", + "slot_group": "EMSL", + "required": false, + "recommended": true + }, + "project_id": { + "name": "project_id", + "description": "Proposal IDs or names associated with dataset", + "title": "project ID", + "from_schema": "https://microbiomedata/schema", + "rank": 1, + "string_serialization": "{text}", + "slot_group": "EMSL", + "required": false, + "recommended": true + }, + "replicate_number": { + "name": "replicate_number", + "description": "If sending biological replicates, indicate the rep number here.", + "title": "replicate number", + "comments": [ + "This will guide staff in ensuring your samples are block & randomized correctly" + ], + "from_schema": "https://microbiomedata/schema", + "rank": 6, + "string_serialization": "{integer}", + "slot_group": "EMSL", + "recommended": true + }, + "sample_shipped": { + "name": "sample_shipped", + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL", + "title": "sample shipped amount", + "from_schema": "https://microbiomedata/schema", + "rank": 3, + "string_serialization": "{float} {unit}", + "slot_group": "EMSL", + "required": false, + "recommended": true + }, + "sample_type": { + "name": "sample_type", + "description": "Type of sample being submitted", + "title": "sample type", + "comments": [ + "This can vary from 'environmental package' if the sample is an extraction." + ], + "examples": [ + { + "value": "water extracted soil" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 2, + "slot_group": "EMSL", + "range": "sample_type_enum", + "required": false, + "recommended": true + }, + "technical_reps": { + "name": "technical_reps", + "description": "If sending multiple technical replicates of the same sample, indicate how many replicates are being sent", + "title": "number technical replicate", + "from_schema": "https://microbiomedata/schema", + "rank": 5, + "string_serialization": "{integer}", + "slot_group": "EMSL", + "recommended": true + }, + "abs_air_humidity": { + "name": "abs_air_humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per gram, kilogram per kilogram, kilogram, pound" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Actual mass of water vapor - mh20 - present in the air water vapor mixture", + "title": "absolute air humidity", + "examples": [ + { + "value": "9 gram per gram" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "absolute air humidity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000122", + "multivalued": false, + "range": "QuantityValue" + }, + "core_field": { + "name": "core_field", + "description": "basic fields", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "abstract": true + }, + "add_recov_method": { + "name": "add_recov_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "secondary and tertiary recovery methods and start date", + "examples": [ + { + "value": "Polymer Addition;2018-06-21T14:30Z" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "secondary and tertiary recovery methods and start date" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001009", + "multivalued": false, + "range": "TextValue" + }, + "additional_info": { + "name": "additional_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary", + "title": "additional info", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "additional info" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000300", + "multivalued": false, + "range": "TextValue" + }, + "address": { + "name": "address", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The street name and building number where the sampling occurred.", + "title": "address", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "address" + ], + "is_a": "attribute", + "string_serialization": "{integer}{text}", + "slot_uri": "mixs:0000218", + "multivalued": false, + "range": "TextValue" + }, + "adj_room": { + "name": "adj_room", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of rooms (room number, room name) immediately adjacent to the sampling room", + "title": "adjacent rooms", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "adjacent rooms" + ], + "is_a": "attribute", + "string_serialization": "{text};{integer}", + "slot_uri": "mixs:0000219", + "multivalued": false, + "range": "TextValue" + }, + "aero_struc": { + "name": "aero_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together", + "title": "aerospace structure", + "examples": [ + { + "value": "plane" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "aerospace structure" + ], + "is_a": "attribute", + "string_serialization": "[plane|glider]", + "slot_uri": "mixs:0000773", + "multivalued": false, + "range": "TextValue" + }, + "agrochem_addition": { + "name": "agrochem_addition", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "agrochemical name;agrochemical amount;timestamp" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications", + "title": "history/agrochemical additions", + "examples": [ + { + "value": "roundup;5 milligram per liter;2018-06-21" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "history/agrochemical additions" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{timestamp}", + "slot_uri": "mixs:0000639", + "multivalued": false, + "range": "QuantityValue" + }, + "air_temp": { + "name": "air_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature of the air at the time of sampling", + "title": "air temperature", + "examples": [ + { + "value": "20 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "air temperature" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000124", + "multivalued": false, + "range": "QuantityValue" + }, + "air_temp_regm": { + "name": "air_temp_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "temperature value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", + "title": "air temperature regimen", + "examples": [ + { + "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "air temperature regimen" + ], + "is_a": "attribute", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000551", + "multivalued": false, + "range": "QuantityValue" + }, + "al_sat": { + "name": "al_sat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Aluminum saturation (esp. For tropical soils)", + "title": "extreme_unusual_properties/Al saturation", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "extreme_unusual_properties/Al saturation" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000607", + "multivalued": false, + "range": "QuantityValue" + }, + "al_sat_meth": { + "name": "al_sat_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or URL" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining Al saturation", + "title": "extreme_unusual_properties/Al saturation method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "extreme_unusual_properties/Al saturation method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000324", + "multivalued": false, + "range": "TextValue" + }, + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "alkalinity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000421", + "multivalued": false, + "range": "QuantityValue" + }, + "alkalinity_method": { + "name": "alkalinity_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "description of method" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method used for alkalinity measurement", + "title": "alkalinity method", + "examples": [ + { + "value": "titration" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "alkalinity method" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000298", + "multivalued": false, + "range": "TextValue" + }, + "alkyl_diethers": { + "name": "alkyl_diethers", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of alkyl diethers", + "title": "alkyl diethers", + "examples": [ + { + "value": "0.005 mole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "alkyl diethers" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000490", + "multivalued": false, + "range": "QuantityValue" + }, + "alt": { + "name": "alt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "title": "altitude", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "altitude" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000094", + "multivalued": false, + "range": "QuantityValue" + }, + "environment_field": { + "name": "environment_field", + "description": "field describing environmental aspect of a sample", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "abstract": true + }, + "aminopept_act": { + "name": "aminopept_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of aminopeptidase activity", + "title": "aminopeptidase activity", + "examples": [ + { + "value": "0.269 mole per liter per hour" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "aminopeptidase activity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000172", + "multivalued": false, + "range": "QuantityValue" + }, + "ammonium": { + "name": "ammonium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium in the sample", + "title": "ammonium", + "examples": [ + { + "value": "1.5 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "ammonium" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000427", + "multivalued": false, + "range": "QuantityValue" + }, + "amount_light": { + "name": "amount_light", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux, lumens per square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The unit of illuminance and luminous emittance, measuring luminous flux per unit area", + "title": "amount of light", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "amount of light" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000140", + "multivalued": false, + "range": "QuantityValue" + }, + "ances_data": { + "name": "ances_data", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)", + "title": "ancestral data", + "examples": [ + { + "value": "A/3*B" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "ancestral data" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000247", + "multivalued": false, + "range": "TextValue" + }, + "annual_precpt": { + "name": "annual_precpt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", + "title": "mean annual precipitation", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mean annual precipitation" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000644", + "multivalued": false, + "range": "QuantityValue" + }, + "annual_temp": { + "name": "annual_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Mean annual temperature", + "title": "mean annual temperature", + "examples": [ + { + "value": "12.5 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mean annual temperature" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000642", + "multivalued": false, + "range": "QuantityValue" + }, + "antibiotic_regm": { + "name": "antibiotic_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "antibiotic name;antibiotic amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens", + "title": "antibiotic regimen", + "examples": [ + { + "value": "penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "antibiotic regimen" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000553", + "multivalued": false, + "range": "QuantityValue" + }, + "api": { + "name": "api", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degrees API" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API)", + "title": "API gravity", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "API gravity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000157", + "multivalued": false, + "range": "QuantityValue" + }, + "arch_struc": { + "name": "arch_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "An architectural structure is a human-made, free-standing, immobile outdoor construction", + "title": "architectural structure", + "examples": [ + { + "value": "shed" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "architectural structure" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000774", + "multivalued": false, + "range": "TextValue" + }, + "aromatics_pc": { + "name": "aromatics_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "aromatics wt%", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "aromatics wt%" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000133", + "multivalued": false, + "range": "QuantityValue" + }, + "asphaltenes_pc": { + "name": "asphaltenes_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "asphaltenes wt%", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "asphaltenes wt%" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000135", + "multivalued": false, + "range": "QuantityValue" + }, + "atmospheric_data": { + "name": "atmospheric_data", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "atmospheric data name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Measurement of atmospheric data; can include multiple data", + "title": "atmospheric data", + "examples": [ + { + "value": "wind speed;9 knots" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "atmospheric data" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0001097", + "multivalued": false, + "range": "QuantityValue" + }, + "avg_dew_point": { + "name": "avg_dew_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day", + "title": "average dew point", + "examples": [ + { + "value": "25.5 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "average dew point" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000141", + "multivalued": false, + "range": "QuantityValue" + }, + "avg_occup": { + "name": "avg_occup", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.", + "title": "average daily occupancy", + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "average daily occupancy" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000775", + "multivalued": false, + "range": "TextValue" + }, + "avg_temp": { + "name": "avg_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day", + "title": "average temperature", + "examples": [ + { + "value": "12.5 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "average temperature" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000142", + "multivalued": false, + "range": "QuantityValue" + }, + "bac_prod": { + "name": "bac_prod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter per day" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Bacterial production in the water column measured by isotope uptake", + "title": "bacterial production", + "examples": [ + { + "value": "5 milligram per cubic meter per day" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "bacterial production" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000683", + "multivalued": false, + "range": "QuantityValue" + }, + "bac_resp": { + "name": "bac_resp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter per day, micromole oxygen per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of bacterial respiration in the water column", + "title": "bacterial respiration", + "examples": [ + { + "value": "300 micromole oxygen per liter per hour" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "bacterial respiration" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000684", + "multivalued": false, + "range": "QuantityValue" + }, + "bacteria_carb_prod": { + "name": "bacteria_carb_prod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of bacterial carbon production", + "title": "bacterial carbon production", + "examples": [ + { + "value": "2.53 microgram per liter per hour" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "bacterial carbon production" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000173", + "multivalued": false, + "range": "QuantityValue" + }, + "barometric_press": { + "name": "barometric_press", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millibar" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Force per unit area exerted against a surface by the weight of air above that surface", + "title": "barometric pressure", + "examples": [ + { + "value": "5 millibar" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "barometric pressure" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000096", + "multivalued": false, + "range": "QuantityValue" + }, + "basin": { + "name": "basin", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the basin (e.g. Campos)", + "title": "basin name", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "basin name" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000290", + "multivalued": false, + "range": "TextValue" + }, + "bathroom_count": { + "name": "bathroom_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of bathrooms in the building", + "title": "bathroom count", + "examples": [ + { + "value": "1" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "bathroom count" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000776", + "multivalued": false, + "range": "TextValue" + }, + "bedroom_count": { + "name": "bedroom_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of bedrooms in the building", + "title": "bedroom count", + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "bedroom count" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000777", + "multivalued": false, + "range": "TextValue" + }, + "benzene": { + "name": "benzene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of benzene in the sample", + "title": "benzene", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "benzene" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000153", + "multivalued": false, + "range": "QuantityValue" + }, + "biochem_oxygen_dem": { + "name": "biochem_oxygen_dem", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period", + "title": "biochemical oxygen demand", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "biochemical oxygen demand" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000653", + "multivalued": false, + "range": "QuantityValue" + }, + "biocide": { + "name": "biocide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;name;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of biocides (commercial name of product and supplier) and date of administration", + "title": "biocide administration", + "examples": [ + { + "value": "ALPHA 1427;Baker Hughes;2008-01-23" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "biocide administration" + ], + "is_a": "attribute", + "string_serialization": "{text};{text};{timestamp}", + "slot_uri": "mixs:0001011", + "multivalued": false, + "range": "TextValue" + }, + "biocide_admin_method": { + "name": "biocide_admin_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;frequency;duration;duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)", + "title": "biocide administration method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "biocide administration method" + ], + "is_a": "attribute", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration};{duration}", + "slot_uri": "mixs:0000456", + "multivalued": false, + "range": "QuantityValue" + }, + "biol_stat": { + "name": "biol_stat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The level of genome modification.", + "title": "biological status", + "examples": [ + { + "value": "natural" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "biological status" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000858", + "multivalued": false, + "range": "TextValue" + }, + "biomass": { + "name": "biomass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "biomass type;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ton, kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", + "title": "biomass", + "examples": [ + { + "value": "total;20 gram" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "biomass" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000174", + "multivalued": false, + "range": "QuantityValue" + }, + "biotic_regm": { + "name": "biotic_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", + "title": "biotic regimen", + "examples": [ + { + "value": "sample inoculated with Rhizobium spp. Culture" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "biotic regimen" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0001038", + "multivalued": false, + "range": "TextValue" + }, + "biotic_relationship": { + "name": "biotic_relationship", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + } + }, + "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object", + "title": "observed biotic relationship", + "examples": [ + { + "value": "free living" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "observed biotic relationship" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000028", + "multivalued": false, + "range": "TextValue" + }, + "nucleic_acid_sequence_source_field": { + "name": "nucleic_acid_sequence_source_field", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "abstract": true + }, + "bishomohopanol": { + "name": "bishomohopanol", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, microgram per gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of bishomohopanol", + "title": "bishomohopanol", + "examples": [ + { + "value": "14 microgram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "bishomohopanol" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000175", + "multivalued": false, + "range": "QuantityValue" + }, + "blood_press_diast": { + "name": "blood_press_diast", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter mercury" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Resting diastolic blood pressure, measured as mm mercury", + "title": "host blood pressure diastolic", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host blood pressure diastolic" + ], + "is_a": "core_field", + "slot_uri": "mixs:0000258", + "multivalued": false, + "range": "QuantityValue" + }, + "blood_press_syst": { + "name": "blood_press_syst", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter mercury" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Resting systolic blood pressure, measured as mm mercury", + "title": "host blood pressure systolic", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host blood pressure systolic" + ], + "is_a": "core_field", + "slot_uri": "mixs:0000259", + "multivalued": false, + "range": "QuantityValue" + }, + "bromide": { + "name": "bromide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of bromide", + "title": "bromide", + "examples": [ + { + "value": "0.05 parts per million" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "bromide" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000176", + "multivalued": false, + "range": "QuantityValue" + }, + "build_docs": { + "name": "build_docs", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The building design, construction and operation documents", + "title": "design, construction, and operation documents", + "examples": [ + { + "value": "maintenance plans" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "design, construction, and operation documents" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000787", + "multivalued": false, + "range": "TextValue" + }, + "build_occup_type": { + "name": "build_occup_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "The primary function for which a building or discrete part of a building is intended to be used", + "title": "building occupancy type", + "examples": [ + { + "value": "market" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "building occupancy type" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000761", + "multivalued": false, + "range": "TextValue" + }, + "building_setting": { + "name": "building_setting", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A location (geography) where a building is set", + "title": "building setting", + "examples": [ + { + "value": "rural" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "building setting" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000768", + "multivalued": false, + "range": "TextValue" + }, + "built_struc_age": { + "name": "built_struc_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "year" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The age of the built structure since construction", + "title": "built structure age", + "examples": [ + { + "value": "15" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "built structure age" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000145", + "multivalued": false, + "range": "QuantityValue" + }, + "built_struc_set": { + "name": "built_struc_set", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The characterization of the location of the built structure as high or low human density", + "title": "built structure setting", + "examples": [ + { + "value": "rural" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "built structure setting" + ], + "is_a": "attribute", + "string_serialization": "[urban|rural]", + "slot_uri": "mixs:0000778", + "multivalued": false, + "range": "TextValue" + }, + "built_struc_type": { + "name": "built_struc_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads", + "title": "built structure type", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "built structure type" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000721", + "multivalued": false, + "range": "TextValue" + }, + "calcium": { + "name": "calcium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of calcium in the sample", + "title": "calcium", + "examples": [ + { + "value": "0.2 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "calcium" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000432", + "multivalued": false, + "range": "QuantityValue" + }, + "carb_dioxide": { + "name": "carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Carbon dioxide (gas) amount or concentration at the time of sampling", + "title": "carbon dioxide", + "examples": [ + { + "value": "410 parts per million" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "carbon dioxide" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000097", + "multivalued": false, + "range": "QuantityValue" + }, + "carb_monoxide": { + "name": "carb_monoxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Carbon monoxide (gas) amount or concentration at the time of sampling", + "title": "carbon monoxide", + "examples": [ + { + "value": "0.1 parts per million" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "carbon monoxide" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000098", + "multivalued": false, + "range": "QuantityValue" + }, + "carb_nitro_ratio": { + "name": "carb_nitro_ratio", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ratio of amount or concentrations of carbon to nitrogen", + "title": "carbon/nitrogen ratio", + "examples": [ + { + "value": "0.417361111" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "carbon/nitrogen ratio" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000310", + "multivalued": false, + "range": "QuantityValue" + }, + "ceil_area": { + "name": "ceil_area", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The area of the ceiling space within the room", + "title": "ceiling area", + "examples": [ + { + "value": "25 square meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "ceiling area" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000148", + "multivalued": false, + "range": "QuantityValue" + }, + "ceil_cond": { + "name": "ceil_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", + "title": "ceiling condition", + "examples": [ + { + "value": "damaged" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "ceiling condition" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000779", + "multivalued": false, + "range": "TextValue" + }, + "ceil_finish_mat": { + "name": "ceil_finish_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of material used to finish a ceiling", + "title": "ceiling finish material", + "examples": [ + { + "value": "stucco" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "ceiling finish material" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000780", + "multivalued": false, + "range": "TextValue" + }, + "ceil_struc": { + "name": "ceil_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The construction format of the ceiling", + "title": "ceiling structure", + "examples": [ + { + "value": "concrete" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "ceiling structure" + ], + "is_a": "attribute", + "string_serialization": "[wood frame|concrete]", + "slot_uri": "mixs:0000782", + "multivalued": false, + "range": "TextValue" + }, + "ceil_texture": { + "name": "ceil_texture", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The feel, appearance, or consistency of a ceiling surface", + "title": "ceiling texture", + "examples": [ + { + "value": "popcorn" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "ceiling texture" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000783", + "multivalued": false, + "range": "TextValue" + }, + "ceil_thermal_mass": { + "name": "ceil_thermal_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "joule per degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow", + "title": "ceiling thermal mass", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "ceiling thermal mass" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000143", + "multivalued": false, + "range": "QuantityValue" + }, + "ceil_type": { + "name": "ceil_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of ceiling according to the ceiling's appearance or construction", + "title": "ceiling type", + "examples": [ + { + "value": "coffered" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "ceiling type" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000784", + "multivalued": false, + "range": "TextValue" + }, + "ceil_water_mold": { + "name": "ceil_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on the ceiling", + "title": "ceiling signs of water/mold", + "examples": [ + { + "value": "presence of mold visible" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "ceiling signs of water/mold" + ], + "is_a": "attribute", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "mixs:0000781", + "multivalued": false, + "range": "TextValue" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11T20:00Z" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "chemical administration" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "mixs:0000751", + "multivalued": false, + "range": "ControlledTermValue" + }, + "chem_mutagen": { + "name": "chem_mutagen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "mutagen name;mutagen amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens", + "title": "chemical mutagen", + "examples": [ + { + "value": "nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "chemical mutagen" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000555", + "multivalued": false, + "range": "QuantityValue" + }, + "chem_oxygen_dem": { + "name": "chem_oxygen_dem", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite", + "title": "chemical oxygen demand", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "chemical oxygen demand" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000656", + "multivalued": false, + "range": "QuantityValue" + }, + "chem_treat_method": { + "name": "chem_treat_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;frequency;duration;duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)", + "title": "chemical treatment method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "chemical treatment method" + ], + "is_a": "core_field", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}", + "slot_uri": "mixs:0000457", + "multivalued": false, + "range": "string" + }, + "chem_treatment": { + "name": "chem_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;name;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included", + "title": "chemical treatment", + "examples": [ + { + "value": "ACCENT 1125;DOW;2010-11-17" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "chemical treatment" + ], + "is_a": "attribute", + "string_serialization": "{text};{text};{timestamp}", + "slot_uri": "mixs:0001012", + "multivalued": false, + "range": "TextValue" + }, + "chimera_check": { + "name": "chimera_check", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name and version of software, parameters used" + } + }, + "description": "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.", + "title": "chimera check software", + "examples": [ + { + "value": "uchime;v4.1;default parameters" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "chimera check software" + ], + "is_a": "attribute", + "string_serialization": "{software};{version};{parameters}", + "slot_uri": "mixs:0000052", + "multivalued": false, + "range": "TextValue" + }, + "sequencing_field": { + "name": "sequencing_field", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "abstract": true + }, + "chloride": { + "name": "chloride", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chloride in the sample", + "title": "chloride", + "examples": [ + { + "value": "5000 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "chloride" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000429", + "multivalued": false, + "range": "QuantityValue" + }, + "chlorophyll": { + "name": "chlorophyll", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter, microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chlorophyll", + "title": "chlorophyll", + "examples": [ + { + "value": "5 milligram per cubic meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "chlorophyll" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000177", + "multivalued": false, + "range": "QuantityValue" + }, + "climate_environment": { + "name": "climate_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "climate name;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", + "title": "climate environment", + "examples": [ + { + "value": "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "climate environment" + ], + "is_a": "attribute", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0001040", + "multivalued": false, + "range": "TextValue" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant", + "title": "collection date", + "examples": [ + { + "value": "2018-05-11T10:00:00+01:00; 2018-05-11" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "collection date" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000011", + "multivalued": false, + "range": "TimestampValue" + }, + "conduc": { + "name": "conduc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliSiemens per centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Electrical conductivity of water", + "title": "conductivity", + "examples": [ + { + "value": "10 milliSiemens per centimeter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "conductivity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000692", + "multivalued": false, + "range": "QuantityValue" + }, + "cool_syst_id": { + "name": "cool_syst_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "unique identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The cooling system identifier", + "title": "cooling system identifier", + "examples": [ + { + "value": "12345" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "cooling system identifier" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000785", + "multivalued": false, + "range": "TextValue" + }, + "crop_rotation": { + "name": "crop_rotation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "crop rotation status;schedule" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Whether or not crop is rotated, and if yes, rotation schedule", + "title": "history/crop rotation", + "examples": [ + { + "value": "yes;R2/2017-01-01/2018-12-31/P6M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "history/crop rotation" + ], + "is_a": "attribute", + "string_serialization": "{boolean};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000318", + "multivalued": false, + "range": "TextValue" + }, + "cult_root_med": { + "name": "cult_root_med", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name, PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors.", + "title": "culture rooting medium", + "examples": [ + { + "value": "http://himedialabs.com/TD/PT158.pdf" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "culture rooting medium" + ], + "is_a": "attribute", + "string_serialization": "{text}|{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0001041", + "multivalued": false, + "range": "TextValue" + }, + "cur_land_use": { + "name": "cur_land_use", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Present state of sample site", + "title": "current land use", + "examples": [ + { + "value": "conifers" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "current land use" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001080", + "multivalued": false, + "range": "TextValue" + }, + "cur_vegetation": { + "name": "cur_vegetation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "current vegetation type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Vegetation classification from one or more standard classification systems, or agricultural crop", + "title": "current vegetation", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "current vegetation" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000312", + "multivalued": false, + "range": "TextValue" + }, + "cur_vegetation_meth": { + "name": "cur_vegetation_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in vegetation classification", + "title": "current vegetation method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "current vegetation method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000314", + "multivalued": false, + "range": "TextValue" + }, + "date_last_rain": { + "name": "date_last_rain", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The date of the last time it rained", + "title": "date last rain", + "examples": [ + { + "value": "2018-05-11:T14:30Z" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "date last rain" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000786", + "multivalued": false, + "range": "TimestampValue" + }, + "density": { + "name": "density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter, gram per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "title": "density", + "examples": [ + { + "value": "1000 kilogram per cubic meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "density" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000435", + "multivalued": false, + "range": "QuantityValue" + }, + "depos_env": { + "name": "depos_env", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "depositional environment", + "examples": [ + { + "value": "Continental - Alluvial" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "depositional environment" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000992", + "multivalued": false, + "range": "TextValue" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth", + "examples": [ + { + "value": "10 meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "depth" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000018", + "multivalued": false, + "range": "QuantityValue" + }, + "dew_point": { + "name": "dew_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.", + "title": "dew point", + "examples": [ + { + "value": "22 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "dew point" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000129", + "multivalued": false, + "range": "QuantityValue" + }, + "diether_lipids": { + "name": "diether_lipids", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "diether lipid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of diether lipids; can include multiple types of diether lipids", + "title": "diether lipids", + "examples": [ + { + "value": "0.2 nanogram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "diether lipids" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000178", + "multivalued": false, + "range": "QuantityValue" + }, + "diss_carb_dioxide": { + "name": "diss_carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "title": "dissolved carbon dioxide", + "examples": [ + { + "value": "5 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + 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"mixs:0001085", + "multivalued": false, + "range": "TextValue" + }, + "drawings": { + "name": "drawings", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents", + "title": "drawings", + "examples": [ + { + "value": "sketch" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "drawings" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000798", + "multivalued": false, + "range": "TextValue" + }, + "efficiency_percent": { + "name": "efficiency_percent", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Percentage of volatile solids removed from the anaerobic digestor", + "title": "efficiency percent", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "efficiency percent" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000657", + "multivalued": false, + "range": "QuantityValue" + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "elevation" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000093", + "multivalued": false, + "range": "QuantityValue" + }, + "elevator": { + "name": "elevator", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of elevators within the built structure", + "title": "elevator count", + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "elevator count" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000799", + "multivalued": false, + "range": "TextValue" + }, + "emulsions": { + "name": "emulsions", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "emulsion name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types", + "title": "emulsions", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "emulsions" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000660", + "multivalued": false, + "range": "QuantityValue" + }, + "env_broad_scale": { + "name": "env_broad_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." + } + }, + "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS", + "title": "broad-scale environmental context", + "examples": [ + { + "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "broad-scale environmental context" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "mixs:0000012", + "multivalued": false, + "range": "ControlledIdentifiedTermValue" + }, + "env_local_scale": { + "name": "env_local_scale", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Environmental entities having causal influences upon the entity at time of sampling." + } + }, + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "examples": [ + { + "value": "litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]." + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "local environmental context" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "mixs:0000013", + "multivalued": false, + "range": "ControlledIdentifiedTermValue" + }, + "env_medium": { + "name": "env_medium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." + } + }, + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "examples": [ + { + "value": "soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "environmental medium" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "mixs:0000014", + "multivalued": false, + "range": "ControlledIdentifiedTermValue" + }, + "escalator": { + "name": "escalator", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of escalators within the built structure", + "title": "escalator count", + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "escalator count" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000800", + "multivalued": false, + "range": "TextValue" + }, + "ethylbenzene": { + "name": "ethylbenzene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ethylbenzene in the sample", + "title": "ethylbenzene", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "ethylbenzene" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000155", + "multivalued": false, + "range": "QuantityValue" + }, + "exp_duct": { + "name": "exp_duct", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The amount of exposed ductwork in the room", + "title": "exposed ductwork", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "exposed ductwork" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000144", + "multivalued": false, + "range": "QuantityValue" + }, + "exp_pipe": { + "name": "exp_pipe", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of exposed pipes in the room", + "title": "exposed pipes", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "exposed pipes" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000220", + "multivalued": false, + "range": "QuantityValue" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "experimental factor" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "mixs:0000008", + "multivalued": false, + "range": "ControlledTermValue" + }, + "investigation_field": { + "name": "investigation_field", + "description": "field describing aspect of the investigation/study to which the sample belongs", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "abstract": true + }, + "ext_door": { + "name": "ext_door", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of exterior doors in the built structure", + "title": "exterior door count", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "exterior door count" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000170", + "multivalued": false, + "range": "TextValue" + }, + "ext_wall_orient": { + "name": "ext_wall_orient", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The orientation of the exterior wall", + "title": "orientations of exterior wall", + "examples": [ + { + "value": "northwest" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "orientations of exterior wall" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000817", + "multivalued": false, + "range": "TextValue" + }, + "ext_window_orient": { + "name": "ext_window_orient", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The compass direction the exterior window of the room is facing", + "title": "orientations of exterior window", + "examples": [ + { + "value": "southwest" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "orientations of exterior window" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000818", + "multivalued": false, + "range": "TextValue" + }, + "extreme_event": { + "name": "extreme_event", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Unusual physical events that may have affected microbial populations", + "title": "history/extreme events", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "history/extreme events" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000320", + "multivalued": false, + "range": "TimestampValue" + }, + "fao_class": { + "name": "fao_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups", + "title": "soil_taxonomic/FAO classification", + "examples": [ + { + "value": "Luvisols" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "soil_taxonomic/FAO classification" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001083", + "multivalued": false, + "range": "TextValue" + }, + "fertilizer_regm": { + "name": "fertilizer_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "fertilizer name;fertilizer amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens", + "title": "fertilizer regimen", + "examples": [ + { + "value": "urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "fertilizer regimen" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000556", + "multivalued": false, + "range": "QuantityValue" + }, + "field": { + "name": "field", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the hydrocarbon field (e.g. Albacora)", + "title": "field name", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "field name" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000291", + "multivalued": false, + "range": "TextValue" + }, + "filter_type": { + "name": "filter_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "A device which removes solid particulates or airborne molecular contaminants", + "title": "filter type", + "examples": [ + { + "value": "HEPA" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "filter type" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000765", + "multivalued": false, + "range": "TextValue" + }, + "fire": { + "name": "fire", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Historical and/or physical evidence of fire", + "title": "history/fire", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "history/fire" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001086", + "multivalued": false, + "range": "TimestampValue" + }, + "fireplace_type": { + "name": "fireplace_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A firebox with chimney", + "title": "fireplace type", + "examples": [ + { + "value": "wood burning" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "fireplace type" + ], + "is_a": "attribute", + "string_serialization": "[gas burning|wood burning]", + "slot_uri": "mixs:0000802", + "multivalued": false, + "range": "TextValue" + }, + "flooding": { + "name": "flooding", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Historical and/or physical evidence of flooding", + "title": "history/flooding", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "history/flooding" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000319", + "multivalued": false, + "range": "TimestampValue" + }, + "floor_age": { + "name": "floor_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "years, weeks, days" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The time period since installment of the carpet or flooring", + "title": "floor age", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "floor age" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000164", + "multivalued": false, + "range": "QuantityValue" + }, + "floor_area": { + "name": "floor_area", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The area of the floor space within the room", + "title": "floor area", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "floor area" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000165", + "multivalued": false, + "range": "QuantityValue" + }, + "floor_cond": { + "name": "floor_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", + "title": "floor condition", + "examples": [ + { + "value": "new" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "floor condition" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000803", + "multivalued": false, + "range": "TextValue" + }, + "floor_count": { + "name": "floor_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of floors in the building, including basements and mechanical penthouse", + "title": "floor count", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "floor count" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000225", + "multivalued": false, + "range": "TextValue" + }, + "floor_finish_mat": { + "name": "floor_finish_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The floor covering type; the finished surface that is walked on", + "title": "floor finish material", + "examples": [ + { + "value": "carpet" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "floor finish material" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000804", + "multivalued": false, + "range": "TextValue" + }, + "floor_struc": { + "name": "floor_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the structural elements and subfloor upon which the finish flooring is installed", + "title": "floor structure", + "examples": [ + { + "value": "concrete" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "floor structure" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000806", + "multivalued": false, + "range": "TextValue" + }, + "floor_thermal_mass": { + "name": "floor_thermal_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "joule per degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The ability of the floor to provide inertia against temperature fluctuations", + "title": "floor thermal mass", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "floor thermal mass" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000166", + "multivalued": false, + "range": "QuantityValue" + }, + "floor_water_mold": { + "name": "floor_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew in a room", + "title": "floor signs of water/mold", + "examples": [ + { + "value": "ceiling discoloration" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "floor signs of water/mold" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000805", + "multivalued": false, + "range": "TextValue" + }, + "fluor": { + "name": "fluor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram chlorophyll a per cubic meter, volts" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Raw or converted fluorescence of water", + "title": "fluorescence", + "examples": [ + { + "value": "2.5 volts" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "fluorescence" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000704", + "multivalued": false, + "range": "QuantityValue" + }, + "freq_clean": { + "name": "freq_clean", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration or {text}" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.", + "title": "frequency of cleaning", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "frequency of cleaning" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000226", + "multivalued": false, + "range": "QuantityValue" + }, + "freq_cook": { + "name": "freq_cook", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of times a meal is cooked per week", + "title": "frequency of cooking", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "frequency of cooking" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000227", + "multivalued": false, + "range": "QuantityValue" + }, + "fungicide_regm": { + "name": "fungicide_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "fungicide name;fungicide amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens", + "title": "fungicide regimen", + "examples": [ + { + "value": "bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "fungicide regimen" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000557", + "multivalued": false, + "range": "QuantityValue" + }, + "furniture": { + "name": "furniture", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The types of furniture present in the sampled room", + "title": "furniture", + "examples": [ + { + "value": "chair" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "furniture" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000807", + "multivalued": false, + "range": "TextValue" + }, + "gaseous_environment": { + "name": "gaseous_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous compound name;gaseous compound amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "title": "gaseous environment", + "examples": [ + { + "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "gaseous environment" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000558", + "multivalued": false, + "range": "QuantityValue" + }, + "gaseous_substances": { + "name": "gaseous_substances", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous substance name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances", + "title": "gaseous substances", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "gaseous substances" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000661", + "multivalued": false, + "range": "QuantityValue" + }, + "gender_restroom": { + "name": "gender_restroom", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The gender type of the restroom", + "title": "gender of restroom", + "examples": [ + { + "value": "male" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "gender of restroom" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000808", + "multivalued": false, + "range": "TextValue" + }, + "genetic_mod": { + "name": "genetic_mod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection", + "title": "genetic modification", + "examples": [ + { + "value": "aox1A transgenic" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "genetic modification" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "mixs:0000859", + "multivalued": false, + "range": "TextValue" + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "is_a": "attribute", + "string_serialization": "{term}: {term}, {text}", + "slot_uri": "mixs:0000010", + "multivalued": false, + "range": "TextValue" + }, + "glucosidase_act": { + "name": "glucosidase_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mol per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of glucosidase activity", + "title": "glucosidase activity", + "examples": [ + { + "value": "5 mol per liter per hour" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "glucosidase activity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000137", + "multivalued": false, + "range": "QuantityValue" + }, + "gravidity": { + "name": "gravidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gravidity status;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used", + "title": "gravidity", + "examples": [ + { + "value": "yes;due date:2018-05-11" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "gravidity" + ], + "is_a": "attribute", + "string_serialization": "{boolean};{timestamp}", + "slot_uri": "mixs:0000875", + "multivalued": false, + "range": "TextValue" + }, + "gravity": { + "name": "gravity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gravity factor value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per square second, g" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments", + "title": "gravity", + "examples": [ + { + "value": "12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "gravity" + ], + "is_a": "attribute", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000559", + "multivalued": false, + "range": "QuantityValue" + }, + "growth_facil": { + "name": "growth_facil", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text or CO" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research", + "title": "growth facility", + "examples": [ + { + "value": "Growth chamber [CO_715:0000189]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "growth facility" + ], + "is_a": "attribute", + "string_serialization": "{text}|{termLabel} {[termID]}", + "slot_uri": "mixs:0001043", + "multivalued": false, + "range": "ControlledTermValue" + }, + "growth_habit": { + "name": "growth_habit", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Characteristic shape, appearance or growth form of a plant species", + "title": "growth habit", + "examples": [ + { + "value": "spreading" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "growth habit" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001044", + "multivalued": false, + "range": "TextValue" + }, + "growth_hormone_regm": { + "name": "growth_hormone_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "growth hormone name;growth hormone amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens", + "title": "growth hormone regimen", + "examples": [ + { + "value": "abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "growth hormone regimen" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000560", + "multivalued": false, + "range": "QuantityValue" + }, + "hall_count": { + "name": "hall_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total count of hallways and cooridors in the built structure", + "title": "hallway/corridor count", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "hallway/corridor count" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000228", + "multivalued": false, + "range": "TextValue" + }, + "handidness": { + "name": "handidness", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The handidness of the individual sampled", + "title": "handidness", + "examples": [ + { + "value": "right handedness" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "handidness" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000809", + "multivalued": false, + "range": "TextValue" + }, + "hc_produced": { + "name": "hc_produced", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon type produced", + "examples": [ + { + "value": "Gas" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "hydrocarbon type produced" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000989", + "multivalued": false, + "range": "TextValue" + }, + "hcr": { + "name": "hcr", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon resource type", + "examples": [ + { + "value": "Oil Sand" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "hydrocarbon resource type" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000988", + "multivalued": false, + "range": "TextValue" + }, + "hcr_fw_salinity": { + "name": "hcr_fw_salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS", + "title": "formation water salinity", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "formation water salinity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000406", + "multivalued": false, + "range": "QuantityValue" + }, + "hcr_geol_age": { + "name": "hcr_geol_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "hydrocarbon resource geological age", + "examples": [ + { + "value": "Silurian" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "hydrocarbon resource geological age" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000993", + "multivalued": false, + "range": "TextValue" + }, + "hcr_pressure": { + "name": "hcr_pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere, kilopascal" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original pressure of the hydrocarbon resource", + "title": "hydrocarbon resource original pressure", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "hydrocarbon resource original pressure" + ], + "is_a": "attribute", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "mixs:0000395", + "multivalued": false, + "range": "QuantityValue" + }, + "hcr_temp": { + "name": "hcr_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original temperature of the hydrocarbon resource", + "title": "hydrocarbon resource original temperature", + "examples": [ + { + "value": "150-295 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "hydrocarbon resource original temperature" + ], + "is_a": "attribute", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "mixs:0000393", + "multivalued": false, + "range": "QuantityValue" + }, + "heat_cool_type": { + "name": "heat_cool_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Methods of conditioning or heating a room or building", + "title": "heating and cooling system type", + "examples": [ + { + "value": "heat pump" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "heating and cooling system type" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000766", + "multivalued": false, + "range": "TextValue" + }, + "heat_deliv_loc": { + "name": "heat_deliv_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The location of heat delivery within the room", + "title": "heating delivery locations", + "examples": [ + { + "value": "north" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "heating delivery locations" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000810", + "multivalued": false, + "range": "TextValue" + }, + "heat_sys_deliv_meth": { + "name": "heat_sys_deliv_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The method by which the heat is delivered through the system", + "title": "heating system delivery method", + "examples": [ + { + "value": "radiant" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "heating system delivery method" + ], + "is_a": "core_field", + "string_serialization": "[conductive|radiant]", + "slot_uri": "mixs:0000812", + "multivalued": false, + "range": "string" + }, + "heat_system_id": { + "name": "heat_system_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "unique identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The heating system identifier", + "title": "heating system identifier", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "heating system identifier" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000833", + "multivalued": false, + "range": "TextValue" + }, + "heavy_metals": { + "name": "heavy_metals", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "heavy metal name;measurement value unit" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field.", + "title": "extreme_unusual_properties/heavy metals", + "examples": [ + { + "value": "mercury;0.09 micrograms per gram" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "extreme_unusual_properties/heavy metals" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000652", + "multivalued": false, + "range": "QuantityValue" + }, + "heavy_metals_meth": { + "name": "heavy_metals_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining heavy metals", + "title": "extreme_unusual_properties/heavy metals method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "extreme_unusual_properties/heavy metals method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000343", + "multivalued": false, + "range": "TextValue" + }, + "height_carper_fiber": { + "name": "height_carper_fiber", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average carpet fiber height in the indoor environment", + "title": "height carpet fiber mat", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "height carpet fiber mat" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000167", + "multivalued": false, + "range": "QuantityValue" + }, + "herbicide_regm": { + "name": "herbicide_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "herbicide name;herbicide amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "herbicide regimen", + "examples": [ + { + "value": "atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "herbicide regimen" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000561", + "multivalued": false, + "range": "QuantityValue" + }, + "horizon_meth": { + "name": "horizon_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the horizon", + "title": "soil horizon method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "soil horizon method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000321", + "multivalued": false, + "range": "TextValue" + }, + "host_age": { + "name": "host_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "year, day, hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", + "title": "host age", + "examples": [ + { + "value": "10 days" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host age" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000255", + "multivalued": false, + "range": "QuantityValue" + }, + "host_body_habitat": { + "name": "host_body_habitat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original body habitat where the sample was obtained from", + "title": "host body habitat", + "examples": [ + { + "value": "nasopharynx" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host body habitat" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000866", + "multivalued": false, + "range": "TextValue" + }, + "host_body_product": { + "name": "host_body_product", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "FMA or UBERON" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon", + "title": "host body product", + "examples": [ + { + "value": "Portion of mucus [fma66938]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host body product" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "mixs:0000888", + "multivalued": false, + "range": "ControlledIdentifiedTermValue" + }, + "host_body_site": { + "name": "host_body_site", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "FMA or UBERON" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON", + "title": "host body site", + "examples": [ + { + "value": "gill [UBERON:0002535]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host body site" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "mixs:0000867", + "multivalued": false, + "range": "ControlledIdentifiedTermValue" + }, + "host_body_temp": { + "name": "host_body_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Core body temperature of the host when sample was collected", + "title": "host body temperature", + "examples": [ + { + "value": "15 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host body temperature" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000274", + "multivalued": false, + "range": "QuantityValue" + }, + "host_color": { + "name": "host_color", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "color" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The color of host", + "title": "host color", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host color" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000260", + "multivalued": false, + "range": "TextValue" + }, + "host_common_name": { + "name": "host_common_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "common name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Common name of the host.", + "title": "host common name", + "examples": [ + { + "value": "human" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host common name" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000248", + "multivalued": false, + "range": "TextValue" + }, + "host_diet": { + "name": "host_diet", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "diet type" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types", + "title": "host diet", + "examples": [ + { + "value": "herbivore" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host diet" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000869", + "multivalued": false, + "range": "TextValue" + }, + "host_dry_mass": { + "name": "host_dry_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of dry mass", + "title": "host dry mass", + "examples": [ + { + "value": "500 gram" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host dry mass" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000257", + "multivalued": false, + "range": "QuantityValue" + }, + "host_family_relation": { + "name": "host_family_relation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "relationship type;arbitrary identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Familial relationships to other hosts in the same study; can include multiple relationships", + "title": "host family relationship", + "examples": [ + { + "value": "offspring;Mussel25" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host family relationship" + ], + "is_a": "core_field", + "string_serialization": "{text};{text}", + "slot_uri": "mixs:0000872", + "multivalued": true, + "range": "string" + }, + "host_genotype": { + "name": "host_genotype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "genotype" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Observed genotype", + "title": "host genotype", + "examples": [ + { + "value": "C57BL/6" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host genotype" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000365", + "multivalued": false, + "range": "TextValue" + }, + "host_growth_cond": { + "name": "host_growth_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Literature reference giving growth conditions of the host", + "title": "host growth conditions", + "examples": [ + { + "value": "https://academic.oup.com/icesjms/article/68/2/349/617247" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host growth conditions" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "mixs:0000871", + "multivalued": false, + "range": "TextValue" + }, + "host_height": { + "name": "host_height", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter, millimeter, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The height of subject", + "title": "host height", + "examples": [ + { + "value": "0.1 meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host height" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000264", + "multivalued": false, + "range": "QuantityValue" + }, + "host_last_meal": { + "name": "host_last_meal", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "content;duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Content of last meal and time since feeding; can include multiple values", + "title": "host last meal", + "examples": [ + { + "value": "corn feed;P2H" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host last meal" + ], + "is_a": "attribute", + "string_serialization": "{text};{duration}", + "slot_uri": "mixs:0000870", + "multivalued": false, + "range": "TextValue" + }, + "host_length": { + "name": "host_length", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter, millimeter, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The length of subject", + "title": "host length", + "examples": [ + { + "value": "1 meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host length" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000256", + "multivalued": false, + "range": "QuantityValue" + }, + "host_life_stage": { + "name": "host_life_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "stage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of life stage of host", + "title": "host life stage", + "examples": [ + { + "value": "adult" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host life stage" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000251", + "multivalued": false, + "range": "TextValue" + }, + "host_phenotype": { + "name": "host_phenotype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PATO or HP" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP", + "title": "host phenotype", + "examples": [ + { + "value": "elongated [PATO:0001154]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host phenotype" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "mixs:0000874", + "multivalued": false, + "range": "ControlledIdentifiedTermValue" + }, + "host_sex": { + "name": "host_sex", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Gender or physical sex of the host.", + "title": "host sex", + "examples": [ + { + "value": "non-binary" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host sex" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000811", + "multivalued": false, + "range": "TextValue" + }, + "host_shape": { + "name": "host_shape", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "shape" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Morphological shape of host", + "title": "host shape", + "examples": [ + { + "value": "round" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host shape" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000261", + "multivalued": false, + "range": "TextValue" + }, + "host_subject_id": { + "name": "host_subject_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "unique identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A unique identifier by which each subject can be referred to, de-identified.", + "title": "host subject id", + "examples": [ + { + "value": "MPI123" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host subject id" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000861", + "multivalued": false, + "range": "TextValue" + }, + "host_subspecf_genlin": { + "name": "host_subspecf_genlin", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar." + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", + "title": "host subspecific genetic lineage", + "examples": [ + { + "value": "serovar:Newport, variety:glabrum, cultivar: Red Delicious" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host subspecific genetic lineage" + ], + "is_a": "core_field", + "string_serialization": "{rank name}:{text}", + "slot_uri": "mixs:0001318", + "multivalued": true, + "range": "string" + }, + "host_substrate": { + "name": "host_substrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "substrate name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The growth substrate of the host.", + "title": "host substrate", + "examples": [ + { + "value": "rock" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host substrate" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000252", + "multivalued": false, + "range": "TextValue" + }, + "host_symbiont": { + "name": "host_symbiont", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "species name or common name" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", + "title": "observed host symbionts", + "examples": [ + { + "value": "flukeworms" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "observed host symbionts" + ], + "is_a": "core_field", + "string_serialization": "{text}", + "slot_uri": "mixs:0001298", + "multivalued": true, + "range": "string" + }, + "host_taxid": { + "name": "host_taxid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "NCBI taxon identifier" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "NCBI taxon id of the host, e.g. 9606", + "title": "host taxid", + "examples": [ + { + "value": "7955" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host taxid" + ], + "is_a": "attribute", + "string_serialization": "{NCBI taxid}", + "slot_uri": "mixs:0000250", + "multivalued": false, + "range": "TextValue" + }, + "host_tot_mass": { + "name": "host_tot_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total mass of the host at collection, the unit depends on host", + "title": "host total mass", + "examples": [ + { + "value": "2500 gram" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host total mass" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000263", + "multivalued": false, + "range": "QuantityValue" + }, + "host_wet_mass": { + "name": "host_wet_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilogram, gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of wet mass", + "title": "host wet mass", + "examples": [ + { + "value": "1500 gram" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "host wet mass" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000567", + "multivalued": false, + "range": "QuantityValue" + }, + "humidity": { + "name": "humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Amount of water vapour in the air, at the time of sampling", + "title": "humidity", + "examples": [ + { + "value": "25 gram per cubic meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "humidity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000100", + "multivalued": false, + "range": "QuantityValue" + }, + "humidity_regm": { + "name": "humidity_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "humidity value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "humidity regimen", + "examples": [ + { + "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "humidity regimen" + ], + "is_a": "attribute", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000568", + "multivalued": false, + "range": "QuantityValue" + }, + "indoor_space": { + "name": "indoor_space", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A distinguishable space within a structure, the purpose for which discrete areas of a building is used", + "title": "indoor space", + "examples": [ + { + "value": "foyer" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "indoor space" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000763", + "multivalued": false, + "range": "TextValue" + }, + "indoor_surf": { + "name": "indoor_surf", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Type of indoor surface", + "title": "indoor surface", + "examples": [ + { + "value": "wall" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "indoor surface" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000764", + "multivalued": false, + "range": "TextValue" + }, + "indust_eff_percent": { + "name": "indust_eff_percent", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Percentage of industrial effluents received by wastewater treatment plant", + "title": "industrial effluent percent", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "industrial effluent percent" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000662", + "multivalued": false, + "range": "QuantityValue" + }, + "inorg_particles": { + "name": "inorg_particles", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "inorganic particle name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", + "title": "inorganic particles", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "inorganic particles" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000664", + "multivalued": false, + "range": "QuantityValue" + }, + "inside_lux": { + "name": "inside_lux", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilowatt per square metre" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The recorded value at sampling time (power density)", + "title": "inside lux light", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "inside lux light" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000168", + "multivalued": false, + "range": "QuantityValue" + }, + "int_wall_cond": { + "name": "int_wall_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", + "title": "interior wall condition", + "examples": [ + { + "value": "damaged" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "interior wall condition" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000813", + "multivalued": false, + "range": "TextValue" + }, + "iw_bt_date_well": { + "name": "iw_bt_date_well", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Injection water breakthrough date per well following a secondary and/or tertiary recovery", + "title": "injection water breakthrough date of specific well", + "examples": [ + { + "value": "2018-05-11" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "injection water breakthrough date of specific well" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001010", + "multivalued": false, + "range": "TimestampValue" + }, + "iwf": { + "name": "iwf", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)", + "title": "injection water fraction", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "injection water fraction" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000455", + "multivalued": false, + "range": "QuantityValue" + }, + "last_clean": { + "name": "last_clean", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The last time the floor was cleaned (swept, mopped, vacuumed)", + "title": "last time swept/mopped/vacuumed", + "examples": [ + { + "value": "2018-05-11:T14:30Z" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "last time swept/mopped/vacuumed" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000814", + "multivalued": false, + "range": "TimestampValue" + }, + "lat_lon": { + "name": "lat_lon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "decimal degrees, limit to 8 decimal points" + } + }, + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", + "title": "geographic location (latitude and longitude)", + "examples": [ + { + "value": "50.586825 6.408977" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "geographic location (latitude and longitude)" + ], + "is_a": "attribute", + "string_serialization": "{float} {float}", + "slot_uri": "mixs:0000009", + "multivalued": false, + "range": "GeolocationValue" + }, + "light_intensity": { + "name": "light_intensity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of light intensity", + "title": "light intensity", + "examples": [ + { + "value": "0.3 lux" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "light intensity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000706", + "multivalued": false, + "range": "QuantityValue" + }, + "light_regm": { + "name": "light_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "exposure type;light intensity;light quality" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux; micrometer, nanometer, angstrom" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "title": "light regimen", + "examples": [ + { + "value": "incandescant light;10 lux;450 nanometer" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "light regimen" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{float} {unit}", + "slot_uri": "mixs:0000569", + "multivalued": false, + "range": "QuantityValue" + }, + "light_type": { + "name": "light_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light", + "title": "light type", + "examples": [ + { + "value": "desk lamp" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "light type" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000769", + "multivalued": false, + "range": "TextValue" + }, + "link_addit_analys": { + "name": "link_addit_analys", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Link to additional analysis results performed on the sample", + "title": "links to additional analysis", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "links to additional analysis" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000340", + "multivalued": false, + "range": "TextValue" + }, + "link_class_info": { + "name": "link_class_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Link to digitized soil maps or other soil classification information", + "title": "link to classification information", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "link to classification information" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000329", + "multivalued": false, + "range": "TextValue" + }, + "link_climate_info": { + "name": "link_climate_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Link to climate resource", + "title": "link to climate information", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "link to climate information" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000328", + "multivalued": false, + "range": "TextValue" + }, + "lithology": { + "name": "lithology", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "lithology", + "examples": [ + { + "value": "Volcanic" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "lithology" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000990", + "multivalued": false, + "range": "TextValue" + }, + "local_class": { + "name": "local_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "local classification name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Soil classification based on local soil classification system", + "title": "soil_taxonomic/local classification", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "soil_taxonomic/local classification" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000330", + "multivalued": false, + "range": "TextValue" + }, + "local_class_meth": { + "name": "local_class_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the local soil classification", + "title": "soil_taxonomic/local classification method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "soil_taxonomic/local classification method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000331", + "multivalued": false, + "range": "TextValue" + }, + "magnesium": { + "name": "magnesium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of magnesium in the sample", + "title": "magnesium", + "examples": [ + { + "value": "52.8 micromole per kilogram" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "magnesium" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000431", + "multivalued": false, + "range": "QuantityValue" + }, + "max_occup": { + "name": "max_occup", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The maximum amount of people allowed in the indoor environment", + "title": "maximum occupancy", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "maximum occupancy" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000229", + "multivalued": false, + "range": "QuantityValue" + }, + "mean_frict_vel": { + "name": "mean_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean friction velocity", + "title": "mean friction velocity", + "examples": [ + { + "value": "0.5 meter per second" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mean friction velocity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000498", + "multivalued": false, + "range": "QuantityValue" + }, + "mean_peak_frict_vel": { + "name": "mean_peak_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean peak friction velocity", + "title": "mean peak friction velocity", + "examples": [ + { + "value": "1 meter per second" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mean peak friction velocity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000502", + "multivalued": false, + "range": "QuantityValue" + }, + "mech_struc": { + "name": "mech_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "mechanical structure: a moving structure", + "title": "mechanical structure", + "examples": [ + { + "value": "elevator" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mechanical structure" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000815", + "multivalued": false, + "range": "TextValue" + }, + "mechanical_damage": { + "name": "mechanical_damage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "damage type;body site" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about any mechanical damage exerted on the plant; can include multiple damages and sites", + "title": "mechanical damage", + "examples": [ + { + "value": "pruning;bark" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mechanical damage" + ], + "is_a": "attribute", + "string_serialization": "{text};{text}", + "slot_uri": "mixs:0001052", + "multivalued": false, + "range": "TextValue" + }, + "methane": { + "name": "methane", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, parts per billion, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Methane (gas) amount or concentration at the time of sampling", + "title": "methane", + "examples": [ + { + "value": "1800 parts per billion" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "methane" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000101", + "multivalued": false, + "range": "QuantityValue" + }, + "microbial_biomass": { + "name": "microbial_biomass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ton, kilogram, gram per kilogram soil" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "title": "microbial biomass", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "microbial biomass" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000650", + "multivalued": false, + "range": "QuantityValue" + }, + "mineral_nutr_regm": { + "name": "mineral_nutr_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "mineral nutrient name;mineral nutrient amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens", + "title": "mineral nutrient regimen", + "examples": [ + { + "value": "potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mineral nutrient regimen" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000570", + "multivalued": false, + "range": "QuantityValue" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "miscellaneous parameter" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000752", + "multivalued": false, + "range": "QuantityValue" + }, + "n_alkanes": { + "name": "n_alkanes", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "n-alkane name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of n-alkanes; can include multiple n-alkanes", + "title": "n-alkanes", + "examples": [ + { + "value": "n-hexadecane;100 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "n-alkanes" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000503", + "multivalued": false, + "range": "QuantityValue" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "nitrate" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000425", + "multivalued": false, + "range": "QuantityValue" + }, + "nitrite": { + "name": "nitrite", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite in the sample", + "title": "nitrite", + "examples": [ + { + "value": "0.5 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "nitrite" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000426", + "multivalued": false, + "range": "QuantityValue" + }, + "nitro": { + "name": "nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrogen (total)", + "title": "nitrogen", + "examples": [ + { + "value": "4.2 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "nitrogen" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000504", + "multivalued": false, + "range": "QuantityValue" + }, + "non_min_nutr_regm": { + "name": "non_min_nutr_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens", + "title": "non-mineral nutrient regimen", + "examples": [ + { + "value": "carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "non-mineral nutrient regimen" + ], + "is_a": "core_field", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000571", + "multivalued": true, + "range": "string" + }, + "nucl_acid_amp": { + "name": "nucl_acid_amp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID, DOI or URL" + } + }, + "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids", + "title": "nucleic acid amplification", + "examples": [ + { + "value": "https://phylogenomics.me/protocols/16s-pcr-protocol/" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "nucleic acid amplification" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000038", + "multivalued": false, + "range": "TextValue" + }, + "nucl_acid_ext": { + "name": "nucl_acid_ext", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID, DOI or URL" + } + }, + "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample", + "title": "nucleic acid extraction", + "examples": [ + { + "value": "https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "nucleic acid extraction" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000037", + "multivalued": false, + "range": "TextValue" + }, + "number_pets": { + "name": "number_pets", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of pets residing in the sampled space", + "title": "number of pets", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "number of pets" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000231", + "multivalued": false, + "range": "QuantityValue" + }, + "number_plants": { + "name": "number_plants", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of plant(s) in the sampling space", + "title": "number of houseplants", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "number of houseplants" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000230", + "multivalued": false, + "range": "QuantityValue" + }, + "number_resident": { + "name": "number_resident", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of individuals currently occupying in the sampling location", + "title": "number of residents", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "number of residents" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000232", + "multivalued": false, + "range": "QuantityValue" + }, + "occup_density_samp": { + "name": "occup_density_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Average number of occupants at time of sampling per square footage", + "title": "occupant density at sampling", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "occupant density at sampling" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000217", + "multivalued": false, + "range": "QuantityValue" + }, + "occup_document": { + "name": "occup_document", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of documentation of occupancy", + "title": "occupancy documentation", + "examples": [ + { + "value": "estimate" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "occupancy documentation" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000816", + "multivalued": false, + "range": "TextValue" + }, + "occup_samp": { + "name": "occup_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Number of occupants present at time of sample within the given space", + "title": "occupancy at sampling", + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "occupancy at sampling" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000772", + "multivalued": false, + "range": "QuantityValue" + }, + "org_carb": { + "name": "org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic carbon", + "title": "organic carbon", + "examples": [ + { + "value": "1.5 microgram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "organic carbon" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000508", + "multivalued": false, + "range": "QuantityValue" + }, + "org_count_qpcr_info": { + "name": "org_count_qpcr_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per gram (or ml or cm^2)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", + "title": "organism count qPCR information", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "organism count qPCR information" + ], + "is_a": "core_field", + "string_serialization": "{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles", + "slot_uri": "mixs:0000099", + "multivalued": false, + "range": "string" + }, + "org_matter": { + "name": "org_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic matter", + "title": "organic matter", + "examples": [ + { + "value": "1.75 milligram per cubic meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "organic matter" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000204", + "multivalued": false, + "range": "QuantityValue" + }, + "org_nitro": { + "name": "org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic nitrogen", + "title": "organic nitrogen", + "examples": [ + { + "value": "4 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "organic nitrogen" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000205", + "multivalued": false, + "range": "QuantityValue" + }, + "org_particles": { + "name": "org_particles", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "particle name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.", + "title": "organic particles", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "organic particles" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000665", + "multivalued": false, + "range": "QuantityValue" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "organism count" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000103", + "multivalued": false, + "range": "QuantityValue" + }, + "owc_tvdss": { + "name": "owc_tvdss", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Depth of the original oil water contact (OWC) zone (average) (m TVDSS)", + "title": "oil water contact depth", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "oil water contact depth" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000405", + "multivalued": false, + "range": "QuantityValue" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "oxygenation status of sample" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000753", + "multivalued": false, + "range": "TextValue" + }, + "oxygen": { + "name": "oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygen (gas) amount or concentration at the time of sampling", + "title": "oxygen", + "examples": [ + { + "value": "600 parts per million" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "oxygen" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000104", + "multivalued": false, + "range": "QuantityValue" + }, + "part_org_carb": { + "name": "part_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of particulate organic carbon", + "title": "particulate organic carbon", + "examples": [ + { + "value": "1.92 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "particulate organic carbon" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000515", + "multivalued": false, + "range": "QuantityValue" + }, + "part_org_nitro": { + "name": "part_org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of particulate organic nitrogen", + "title": "particulate organic nitrogen", + "examples": [ + { + "value": "0.3 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "particulate organic nitrogen" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000719", + "multivalued": false, + "range": "QuantityValue" + }, + "particle_class": { + "name": "particle_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "particle name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values", + "title": "particle classification", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "particle classification" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000206", + "multivalued": false, + "range": "QuantityValue" + }, + "pcr_cond": { + "name": "pcr_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles" + } + }, + "description": "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'", + "title": "pcr conditions", + "examples": [ + { + "value": "initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pcr conditions" + ], + "is_a": "attribute", + "string_serialization": "initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles", + "slot_uri": "mixs:0000049", + "multivalued": false, + "range": "TextValue" + }, + "pcr_primers": { + "name": "pcr_primers", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "FWD: forward primer sequence;REV:reverse primer sequence" + } + }, + "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters", + "title": "pcr primers", + "examples": [ + { + "value": "FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pcr primers" + ], + "is_a": "attribute", + "string_serialization": "FWD:{dna};REV:{dna}", + "slot_uri": "mixs:0000046", + "multivalued": false, + "range": "TextValue" + }, + "permeability": { + "name": "permeability", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mD" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))", + "title": "permeability", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "permeability" + ], + "is_a": "attribute", + "string_serialization": "{integer} - {integer} {unit}", + "slot_uri": "mixs:0000404", + "multivalued": false, + "range": "QuantityValue" + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "perturbation" + ], + "is_a": "attribute", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000754", + "multivalued": false, + "range": "TextValue" + }, + "pesticide_regm": { + "name": "pesticide_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "pesticide name;pesticide amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens", + "title": "pesticide regimen", + "examples": [ + { + "value": "pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pesticide regimen" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000573", + "multivalued": false, + "range": "QuantityValue" + }, + "petroleum_hydrocarb": { + "name": "petroleum_hydrocarb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of petroleum hydrocarbon", + "title": "petroleum hydrocarbon", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "petroleum hydrocarbon" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000516", + "multivalued": false, + "range": "QuantityValue" + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pH" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001001", + "multivalued": false, + "range": "QuantityValue" + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pH method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0001106", + "multivalued": false, + "range": "TextValue" + }, + "ph_regm": { + "name": "ph_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen", + "title": "pH regimen", + "examples": [ + { + "value": "7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pH regimen" + ], + "is_a": "attribute", + "string_serialization": "{float};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0001056", + "multivalued": false, + "range": "TextValue" + }, + "phaeopigments": { + "name": "phaeopigments", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "phaeopigment name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of phaeopigments; can include multiple phaeopigments", + "title": "phaeopigments", + "examples": [ + { + "value": "2.5 milligram per cubic meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "phaeopigments" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000180", + "multivalued": false, + "range": "QuantityValue" + }, + "phosphate": { + "name": "phosphate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of phosphate", + "title": "phosphate", + "examples": [ + { + "value": "0.7 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "phosphate" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000505", + "multivalued": false, + "range": "QuantityValue" + }, + "phosplipid_fatt_acid": { + "name": "phosplipid_fatt_acid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "phospholipid fatty acid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per gram, mole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of phospholipid fatty acids; can include multiple values", + "title": "phospholipid fatty acid", + "examples": [ + { + "value": "2.98 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "phospholipid fatty acid" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000181", + "multivalued": false, + "range": "QuantityValue" + }, + "photon_flux": { + "name": "photon_flux", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of photons per second per unit area" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of photon flux", + "title": "photon flux", + "examples": [ + { + "value": "3.926 micromole photons per second per square meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "photon flux" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000725", + "multivalued": false, + "range": "QuantityValue" + }, + "plant_growth_med": { + "name": "plant_growth_med", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "EO or enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary", + "title": "plant growth medium", + "examples": [ + { + "value": "hydroponic plant culture media [EO:0007067]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "plant growth medium" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001057", + "multivalued": false, + "range": "ControlledTermValue" + }, + "plant_product": { + "name": "plant_product", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "product name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Substance produced by the plant, where the sample was obtained from", + "title": "plant product", + "examples": [ + { + "value": "xylem sap [PO:0025539]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "plant product" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0001058", + "multivalued": false, + "range": "TextValue" + }, + "plant_sex": { + "name": "plant_sex", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite.", + "title": "plant sex", + "examples": [ + { + "value": "Hermaphroditic" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "plant sex" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001059", + "multivalued": false, + "range": "TextValue" + }, + "plant_struc": { + "name": "plant_struc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PO" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here.", + "title": "plant structure", + "examples": [ + { + "value": "epidermis [PO:0005679]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "plant structure" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "mixs:0001060", + "multivalued": false, + "range": "ControlledIdentifiedTermValue" + }, + "pollutants": { + "name": "pollutants", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "pollutant name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter, microgram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant", + "title": "pollutants", + "examples": [ + { + "value": "lead;0.15 microgram per cubic meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pollutants" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000107", + "multivalued": false, + "range": "QuantityValue" + }, + "pool_dna_extracts": { + "name": "pool_dna_extracts", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "pooling status;number of pooled extracts" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given", + "title": "pooling of DNA extracts (if done)", + "examples": [ + { + "value": "yes;5" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pooling of DNA extracts (if done)" + ], + "is_a": "attribute", + "string_serialization": "{boolean};{integer}", + "slot_uri": "mixs:0000325", + "multivalued": false, + "range": "TextValue" + }, + "porosity": { + "name": "porosity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value or range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Porosity of deposited sediment is volume of voids divided by the total volume of sample", + "title": "porosity", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "porosity" + ], + "is_a": "attribute", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "mixs:0000211", + "multivalued": false, + "range": "QuantityValue" + }, + "potassium": { + "name": "potassium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of potassium in the sample", + "title": "potassium", + "examples": [ + { + "value": "463 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "potassium" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000430", + "multivalued": false, + "range": "QuantityValue" + }, + "pour_point": { + "name": "pour_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)", + "title": "pour point", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pour point" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000127", + "multivalued": false, + "range": "QuantityValue" + }, + "pre_treatment": { + "name": "pre_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "pre-treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process of pre-treatment removes materials that can be easily collected from the raw wastewater", + "title": "pre-treatment", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pre-treatment" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000348", + "multivalued": false, + "range": "TextValue" + }, + "pres_animal_insect": { + "name": "pres_animal_insect", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration;count" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type and number of animals or insects present in the sampling space.", + "title": "presence of pets, animals, or insects", + "examples": [ + { + "value": "cat;5" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "presence of pets, animals, or insects" + ], + "is_a": "core_field", + "slot_uri": "mixs:0000819", + "multivalued": false, + "range": "string", + "pattern": "^(cat|dog|rodent|snake|other);\\d+$" + }, + "pressure": { + "name": "pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Pressure to which the sample is subject to, in atmospheres", + "title": "pressure", + "examples": [ + { + "value": "50 atmosphere" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pressure" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000412", + "multivalued": false, + "range": "QuantityValue" + }, + "previous_land_use": { + "name": "previous_land_use", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "land use name;date" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Previous land use and dates", + "title": "history/previous land use", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "history/previous land use" + ], + "is_a": "attribute", + "string_serialization": "{text};{timestamp}", + "slot_uri": "mixs:0000315", + "multivalued": false, + "range": "TextValue" + }, + "primary_prod": { + "name": "primary_prod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter per day, gram per square meter per day" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of primary production, generally measured as isotope uptake", + "title": "primary production", + "examples": [ + { + "value": "100 milligram per cubic meter per day" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "primary production" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000728", + "multivalued": false, + "range": "QuantityValue" + }, + "primary_treatment": { + "name": "primary_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "primary treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed", + "title": "primary treatment", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "primary treatment" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000349", + "multivalued": false, + "range": "TextValue" + }, + "prod_rate": { + "name": "prod_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per day" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oil and/or gas production rates per well (e.g. 524 m3 / day)", + "title": "production rate", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "production rate" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000452", + "multivalued": false, + "range": "QuantityValue" + }, + "prod_start_date": { + "name": "prod_start_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Date of field's first production", + "title": "production start date", + "examples": [ + { + "value": "2018-05-11" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "production start date" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001008", + "multivalued": false, + "range": "TimestampValue" + }, + "profile_position": { + "name": "profile_position", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas", + "title": "profile position", + "examples": [ + { + "value": "summit" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "profile position" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001084", + "multivalued": false, + "range": "TextValue" + }, + "quad_pos": { + "name": "quad_pos", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The quadrant position of the sampling room within the building", + "title": "quadrant position", + "examples": [ + { + "value": "West side" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "quadrant position" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000820", + "multivalued": false, + "range": "TextValue" + }, + "radiation_regm": { + "name": "radiation_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "radiation type name;radiation amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "rad, gray" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens", + "title": "radiation regimen", + "examples": [ + { + "value": "gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "radiation regimen" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000575", + "multivalued": false, + "range": "QuantityValue" + }, + "rainfall_regm": { + "name": "rainfall_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "rainfall regimen", + "examples": [ + { + "value": "15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "rainfall regimen" + ], + "is_a": "attribute", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000576", + "multivalued": false, + "range": "QuantityValue" + }, + "reactor_type": { + "name": "reactor_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "reactor type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage", + "title": "reactor type", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "reactor type" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000350", + "multivalued": false, + "range": "TextValue" + }, + "redox_potential": { + "name": "redox_potential", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millivolt" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", + "title": "redox potential", + "examples": [ + { + "value": "300 millivolt" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "redox potential" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000182", + "multivalued": false, + "range": "QuantityValue" + }, + "rel_air_humidity": { + "name": "rel_air_humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air", + "title": "relative air humidity", + "examples": [ + { + "value": "80%" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "relative air humidity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000121", + "multivalued": false, + "range": "QuantityValue" + }, + "rel_humidity_out": { + "name": "rel_humidity_out", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram of air, kilogram of air" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The recorded outside relative humidity value at the time of sampling", + "title": "outside relative humidity", + "examples": [ + { + "value": "12 per kilogram of air" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "outside relative humidity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000188", + "multivalued": false, + "range": "QuantityValue" + }, + "rel_samp_loc": { + "name": "rel_samp_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The sampling location within the train car", + "title": "relative sampling location", + "examples": [ + { + "value": "center of car" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "relative sampling location" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000821", + "multivalued": false, + "range": "TextValue" + }, + "rel_to_oxygen": { + "name": "rel_to_oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + } + }, + "description": "Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments", + "title": "relationship to oxygen", + "examples": [ + { + "value": "aerobe" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "relationship to oxygen" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000015", + "multivalued": false, + "range": "TextValue" + }, + "reservoir": { + "name": "reservoir", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the reservoir (e.g. Carapebus)", + "title": "reservoir name", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "reservoir name" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000303", + "multivalued": false, + "range": "TextValue" + }, + "resins_pc": { + "name": "resins_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "resins wt%", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "resins wt%" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000134", + "multivalued": false, + "range": "QuantityValue" + }, + "room_air_exch_rate": { + "name": "room_air_exch_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The rate at which outside air replaces indoor air in a given space", + "title": "room air exchange rate", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "room air exchange rate" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000169", + "multivalued": false, + "range": "QuantityValue" + }, + "room_architec_elem": { + "name": "room_architec_elem", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure", + "title": "room architectural elements", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "room architectural elements" + ], + "is_a": "core_field", + "string_serialization": "{text}", + "slot_uri": "mixs:0000233", + "multivalued": false, + "range": "string" + }, + "room_condt": { + "name": "room_condt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The condition of the room at the time of sampling", + "title": "room condition", + "examples": [ + { + "value": "new" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "room condition" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000822", + "multivalued": false, + "range": "TextValue" + }, + "room_connected": { + "name": "room_connected", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of rooms connected to the sampling room by a doorway", + "title": "rooms connected by a doorway", + "examples": [ + { + "value": "office" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "rooms connected by a doorway" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000826", + "multivalued": false, + "range": "TextValue" + }, + "room_count": { + "name": "room_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total count of rooms in the built structure including all room types", + "title": "room count", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "room count" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000234", + "multivalued": false, + "range": "TextValue" + }, + "room_dim": { + "name": "room_dim", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The length, width and height of sampling room", + "title": "room dimensions", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "room dimensions" + ], + "is_a": "attribute", + "string_serialization": "{integer} {unit} x {integer} {unit} x {integer} {unit}", + "slot_uri": "mixs:0000192", + "multivalued": false, + "range": "QuantityValue" + }, + "room_door_dist": { + "name": "room_door_dist", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Distance between doors (meters) in the hallway between the sampling room and adjacent rooms", + "title": "room door distance", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "room door distance" + ], + "is_a": "attribute", + "string_serialization": "{integer} {unit}", + "slot_uri": "mixs:0000193", + "multivalued": false, + "range": "QuantityValue" + }, + "room_door_share": { + "name": "room_door_share", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of room(s) (room number, room name) sharing a door with the sampling room", + "title": "rooms that share a door with sampling room", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "rooms that share a door with sampling room" + ], + "is_a": "attribute", + "string_serialization": "{text};{integer}", + "slot_uri": "mixs:0000242", + "multivalued": false, + "range": "TextValue" + }, + "room_hallway": { + "name": "room_hallway", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of room(s) (room number, room name) located in the same hallway as sampling room", + "title": "rooms that are on the same hallway", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "rooms that are on the same hallway" + ], + "is_a": "attribute", + "string_serialization": "{text};{integer}", + "slot_uri": "mixs:0000238", + "multivalued": false, + "range": "TextValue" + }, + "room_loc": { + "name": "room_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The position of the room within the building", + "title": "room location in building", + "examples": [ + { + "value": "interior room" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "room location in building" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000823", + "multivalued": false, + "range": "TextValue" + }, + "room_moist_dam_hist": { + "name": "room_moist_dam_hist", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed", + "title": "room moisture damage or mold history", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "room moisture damage or mold history" + ], + "is_a": "core_field", + "slot_uri": "mixs:0000235", + "multivalued": false, + "range": "integer" + }, + "room_net_area": { + "name": "room_net_area", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square feet, square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The net floor area of sampling room. Net area excludes wall thicknesses", + "title": "room net area", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "room net area" + ], + "is_a": "attribute", + "string_serialization": "{integer} {unit}", + "slot_uri": "mixs:0000194", + "multivalued": false, + "range": "QuantityValue" + }, + "room_occup": { + "name": "room_occup", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Count of room occupancy at time of sampling", + "title": "room occupancy", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "room occupancy" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000236", + "multivalued": false, + "range": "QuantityValue" + }, + "room_samp_pos": { + "name": "room_samp_pos", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The horizontal sampling position in the room relative to architectural elements", + "title": "room sampling position", + "examples": [ + { + "value": "south corner" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "room sampling position" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000824", + "multivalued": false, + "range": "TextValue" + }, + "room_type": { + "name": "room_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The main purpose or activity of the sampling room. A room is any distinguishable space within a structure", + "title": "room type", + "examples": [ + { + "value": "bathroom" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "room type" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000825", + "multivalued": false, + "range": "TextValue" + }, + "room_vol": { + "name": "room_vol", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic feet, cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Volume of sampling room", + "title": "room volume", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "room volume" + ], + "is_a": "attribute", + "string_serialization": "{integer} {unit}", + "slot_uri": "mixs:0000195", + "multivalued": false, + "range": "QuantityValue" + }, + "room_wall_share": { + "name": "room_wall_share", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "room name;room number" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "List of room(s) (room number, room name) sharing a wall with the sampling room", + "title": "rooms that share a wall with sampling room", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "rooms that share a wall with sampling room" + ], + "is_a": "attribute", + "string_serialization": "{text};{integer}", + "slot_uri": "mixs:0000243", + "multivalued": false, + "range": "TextValue" + }, + "room_window_count": { + "name": "room_window_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Number of windows in the room", + "title": "room window count", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "room window count" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000237", + "multivalued": false, + "range": "TextValue" + }, + "root_cond": { + "name": "root_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container.", + "title": "rooting conditions", + "examples": [ + { + "value": "http://himedialabs.com/TD/PT158.pdf" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "rooting conditions" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "mixs:0001061", + "multivalued": false, + "range": "TextValue" + }, + "root_med_carbon": { + "name": "root_med_carbon", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "carbon source name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Source of organic carbon in the culture rooting medium; e.g. sucrose.", + "title": "rooting medium carbon", + "examples": [ + { + "value": "sucrose" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "rooting medium carbon" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000577", + "multivalued": false, + "range": "QuantityValue" + }, + "root_med_macronutr": { + "name": "root_med_macronutr", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "macronutrient name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L).", + "title": "rooting medium macronutrients", + "examples": [ + { + "value": "KH2PO4;170¬†milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "rooting medium macronutrients" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000578", + "multivalued": false, + "range": "QuantityValue" + }, + "root_med_micronutr": { + "name": "root_med_micronutr", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "micronutrient name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L).", + "title": "rooting medium micronutrients", + "examples": [ + { + "value": "H3BO3;6.2¬†milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "rooting medium micronutrients" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000579", + "multivalued": false, + "range": "QuantityValue" + }, + "root_med_ph": { + "name": "root_med_ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "pH measurement of the culture rooting medium; e.g. 5.5.", + "title": "rooting medium pH", + "examples": [ + { + "value": "7.5" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "rooting medium pH" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001062", + "multivalued": false, + "range": "QuantityValue" + }, + "root_med_regl": { + "name": "root_med_regl", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "regulator name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA.", + "title": "rooting medium regulators", + "examples": [ + { + "value": "abscisic acid;0.75 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "rooting medium regulators" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000581", + "multivalued": false, + "range": "QuantityValue" + }, + "root_med_solid": { + "name": "root_med_solid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Specification of the solidifying agent in the culture rooting medium; e.g. agar.", + "title": "rooting medium solidifier", + "examples": [ + { + "value": "agar" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "rooting medium solidifier" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0001063", + "multivalued": false, + "range": "TextValue" + }, + "root_med_suppl": { + "name": "root_med_suppl", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "supplement name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L).", + "title": "rooting medium organic supplements", + "examples": [ + { + "value": "nicotinic acid;0.5 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "rooting medium organic supplements" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000580", + "multivalued": false, + "range": "QuantityValue" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "salinity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000183", + "multivalued": false, + "range": "QuantityValue" + }, + "salinity_meth": { + "name": "salinity_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining salinity", + "title": "salinity method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "salinity method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000341", + "multivalued": false, + "range": "TextValue" + }, + "salt_regm": { + "name": "salt_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "salt name;salt amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, mole per liter, gram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens", + "title": "salt regimen", + "examples": [ + { + "value": "NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "salt regimen" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000582", + "multivalued": false, + "range": "QuantityValue" + }, + "samp_capt_status": { + "name": "samp_capt_status", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reason for the sample", + "title": "sample capture status", + "examples": [ + { + "value": "farm sample" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample capture status" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000860", + "multivalued": false, + "range": "TextValue" + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample collection method" + ], + "is_a": "nucleic_acid_sequence_source_field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "mixs:0001225", + "multivalued": false, + "range": "string" + }, + "samp_collect_point": { + "name": "samp_collect_point", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "sample collection point", + "examples": [ + { + "value": "well" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample collection point" + ], + "is_a": "core_field", + "slot_uri": "mixs:0001015", + "multivalued": false, + "range": "samp_collect_point_enum" + }, + "samp_dis_stage": { + "name": "samp_dis_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.", + "title": "sample disease stage", + "examples": [ + { + "value": "infection" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample disease stage" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000249", + "multivalued": false, + "range": "TextValue" + }, + "samp_floor": { + "name": "samp_floor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The floor of the building, where the sampling room is located", + "title": "sampling floor", + "examples": [ + { + "value": "4th floor" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sampling floor" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000828", + "multivalued": false, + "range": "TextValue" + }, + "samp_loc_corr_rate": { + "name": "samp_loc_corr_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter per year" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays", + "title": "corrosion rate at sample location", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "corrosion rate at sample location" + ], + "is_a": "attribute", + "string_serialization": "{float} - {float} {unit}", + "slot_uri": "mixs:0000136", + "multivalued": false, + "range": "QuantityValue" + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater, storing samples in ethanol" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample material processing" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000016", + "multivalued": false, + "range": "ControlledTermValue" + }, + "samp_md": { + "name": "samp_md", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "sample measured depth", + "examples": [ + { + "value": "1534 meter;MSL" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample measured depth" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000413", + "multivalued": false, + "range": "QuantityValue" + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.", + "title": "sample name", + "examples": [ + { + "value": "ISDsoil1" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample name" + ], + "is_a": "investigation_field", + "string_serialization": "{text}", + "slot_uri": "mixs:0001107", + "multivalued": false, + "range": "string" + }, + "samp_preserv": { + "name": "samp_preserv", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliliter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)", + "title": "preservative added to sample", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "preservative added to sample" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000463", + "multivalued": false, + "range": "QuantityValue" + }, + "samp_room_id": { + "name": "samp_room_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sampling room number. This ID should be consistent with the designations on the building floor plans", + "title": "sampling room ID or name", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sampling room ID or name" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000244", + "multivalued": false, + "range": "TextValue" + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "examples": [ + { + "value": "5 liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "amount or size of sample collected" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000001", + "multivalued": false, + "range": "QuantityValue" + }, + "samp_sort_meth": { + "name": "samp_sort_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "description of method" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.", + "title": "sample size sorting method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample size sorting method" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000216", + "multivalued": false, + "range": "TextValue" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample storage duration" + ], + "is_a": "attribute", + "string_serialization": "{duration}", + "slot_uri": "mixs:0000116", + "multivalued": false, + "range": "TextValue" + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample storage location" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000755", + "multivalued": false, + "range": "TextValue" + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which sample was stored, e.g. -80 degree Celsius", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample storage temperature" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000110", + "multivalued": false, + "range": "QuantityValue" + }, + "samp_subtype": { + "name": "samp_subtype", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "sample subtype", + "examples": [ + { + "value": "biofilm" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample subtype" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000999", + "multivalued": false, + "range": "TextValue" + }, + "samp_time_out": { + "name": "samp_time_out", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "time" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The recent and long term history of outside sampling", + "title": "sampling time outside", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sampling time outside" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000196", + "multivalued": false, + "range": "TextValue" + }, + "samp_transport_cond": { + "name": "samp_transport_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "days;degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C)", + "title": "sample transport conditions", + "examples": [ + { + "value": "5 days;-20 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample transport conditions" + ], + "is_a": "attribute", + "string_serialization": "{float} {unit};{float} {unit}", + "slot_uri": "mixs:0000410", + "multivalued": false, + "range": "QuantityValue" + }, + "samp_tvdss": { + "name": "samp_tvdss", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value or measurement value range" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m", + "title": "sample true vertical depth subsea", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample true vertical depth subsea" + ], + "is_a": "attribute", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "mixs:0000409", + "multivalued": false, + "range": "QuantityValue" + }, + "samp_type": { + "name": "samp_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "GENEPIO:0001246" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).", + "title": "sample type", + "examples": [ + { + "value": "built environment sample [GENEPIO:0001248]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample type" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "mixs:0000998", + "multivalued": false, + "range": "TextValue" + }, + "samp_vol_we_dna_ext": { + "name": "samp_vol_we_dna_ext", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, square centimeter" + } + }, + "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001).", + "title": "sample volume or weight for DNA extraction", + "examples": [ + { + "value": "1500 milliliter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample volume or weight for DNA extraction" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000111", + "multivalued": false, + "range": "QuantityValue" + }, + "samp_weather": { + "name": "samp_weather", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The weather on the sampling day", + "title": "sampling day weather", + "examples": [ + { + "value": "foggy" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sampling day weather" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000827", + "multivalued": false, + "range": "TextValue" + }, + "samp_well_name": { + "name": "samp_well_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Name of the well (e.g. BXA1123) where sample was taken", + "title": "sample well name", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample well name" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000296", + "multivalued": false, + "range": "TextValue" + }, + "saturates_pc": { + "name": "saturates_pc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", + "title": "saturates wt%", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "saturates wt%" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000131", + "multivalued": false, + "range": "QuantityValue" + }, + "season": { + "name": "season", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "NCIT:C94729" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).", + "title": "season", + "examples": [ + { + "value": "autumn [NCIT:C94733]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "season" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "mixs:0000829", + "multivalued": false, + "range": "TextValue" + }, + "season_environment": { + "name": "season_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "seasonal environment name;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment", + "title": "seasonal environment", + "examples": [ + { + "value": "rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "seasonal environment" + ], + "is_a": "attribute", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0001068", + "multivalued": false, + "range": "TextValue" + }, + "season_precpt": { + "name": "season_precpt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", + "title": "mean seasonal precipitation", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mean seasonal precipitation" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000645", + "multivalued": false, + "range": "QuantityValue" + }, + "season_temp": { + "name": "season_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Mean seasonal temperature", + "title": "mean seasonal temperature", + "examples": [ + { + "value": "18 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mean seasonal temperature" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000643", + "multivalued": false, + "range": "QuantityValue" + }, + "season_use": { + "name": "season_use", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The seasons the space is occupied", + "title": "seasonal use", + "examples": [ + { + "value": "Winter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "seasonal use" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000830", + "multivalued": false, + "range": "TextValue" + }, + "secondary_treatment": { + "name": "secondary_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "secondary treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process for substantially degrading the biological content of the sewage", + "title": "secondary treatment", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "secondary treatment" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000351", + "multivalued": false, + "range": "TextValue" + }, + "sediment_type": { + "name": "sediment_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about the sediment type based on major constituents", + "title": "sediment type", + "examples": [ + { + "value": "biogenous" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sediment type" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001078", + "multivalued": false, + "range": "TextValue" + }, + "seq_meth": { + "name": "seq_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Text or OBI" + } + }, + "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", + "title": "sequencing method", + "examples": [ + { + "value": "454 Genome Sequencer FLX [OBI:0000702]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sequencing method" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "mixs:0000050", + "multivalued": false, + "range": "TextValue" + }, + "seq_quality_check": { + "name": "seq_quality_check", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "none or manually edited" + } + }, + "description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA", + "title": "sequence quality check", + "examples": [ + { + "value": "none" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sequence quality check" + ], + "is_a": "attribute", + "string_serialization": "[none|manually edited]", + "slot_uri": "mixs:0000051", + "multivalued": false, + "range": "TextValue" + }, + "sewage_type": { + "name": "sewage_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "sewage type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Type of wastewater treatment plant as municipial or industrial", + "title": "sewage type", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sewage type" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000215", + "multivalued": false, + "range": "TextValue" + }, + "shad_dev_water_mold": { + "name": "shad_dev_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on the shading device", + "title": "shading device signs of water/mold", + "examples": [ + { + "value": "no presence of mold visible" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "shading device signs of water/mold" + ], + "is_a": "core_field", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "mixs:0000834", + "multivalued": false, + "range": "string" + }, + "shading_device_cond": { + "name": "shading_device_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the shading device at the time of sampling", + "title": "shading device condition", + "examples": [ + { + "value": "new" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "shading device condition" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000831", + "multivalued": false, + "range": "TextValue" + }, + "shading_device_loc": { + "name": "shading_device_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The location of the shading device in relation to the built structure", + "title": "shading device location", + "examples": [ + { + "value": "exterior" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "shading device location" + ], + "is_a": "attribute", + "string_serialization": "[exterior|interior]", + "slot_uri": "mixs:0000832", + "multivalued": false, + "range": "TextValue" + }, + "shading_device_mat": { + "name": "shading_device_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "material name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The material the shading device is composed of", + "title": "shading device material", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "shading device material" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000245", + "multivalued": false, + "range": "TextValue" + }, + "shading_device_type": { + "name": "shading_device_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of shading device", + "title": "shading device type", + "examples": [ + { + "value": "slatted aluminum awning" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "shading device type" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000835", + "multivalued": false, + "range": "TextValue" + }, + "sieving": { + "name": "sieving", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "design name and/or size;amount" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved", + "title": "composite design/sieving", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "composite design/sieving" + ], + "is_a": "attribute", + "string_serialization": "{{text}|{float} {unit}};{float} {unit}", + "slot_uri": "mixs:0000322", + "multivalued": false, + "range": "QuantityValue" + }, + "silicate": { + "name": "silicate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of silicate", + "title": "silicate", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "silicate" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000184", + "multivalued": false, + "range": "QuantityValue" + }, + "size_frac": { + "name": "size_frac", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "filter size value range" + } + }, + "description": "Filtering pore size used in sample preparation", + "title": "size fraction selected", + "examples": [ + { + "value": "0-0.22 micrometer" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "size fraction selected" + ], + "is_a": "attribute", + "string_serialization": "{float}-{float} {unit}", + "slot_uri": "mixs:0000017", + "multivalued": false, + "range": "QuantityValue" + }, + "size_frac_low": { + "name": "size_frac_low", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample", + "title": "size-fraction lower threshold", + "examples": [ + { + "value": "0.2 micrometer" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "size-fraction lower threshold" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000735", + "multivalued": false, + "range": "QuantityValue" + }, + "size_frac_up": { + "name": "size_frac_up", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample", + "title": "size-fraction upper threshold", + "examples": [ + { + "value": "20 micrometer" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "size-fraction upper threshold" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000736", + "multivalued": false, + "range": "QuantityValue" + }, + "slope_aspect": { + "name": "slope_aspect", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.", + "title": "slope aspect", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "slope aspect" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000647", + "multivalued": false, + "range": "QuantityValue" + }, + "slope_gradient": { + "name": "slope_gradient", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer", + "title": "slope gradient", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "slope gradient" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000646", + "multivalued": false, + "range": "QuantityValue" + }, + "sludge_retent_time": { + "name": "sludge_retent_time", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "hours" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The time activated sludge remains in reactor", + "title": "sludge retention time", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sludge retention time" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000669", + "multivalued": false, + "range": "QuantityValue" + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sodium" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000428", + "multivalued": false, + "range": "QuantityValue" + }, + "soil_type": { + "name": "soil_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "ENVO_00001998" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.", + "title": "soil type", + "examples": [ + { + "value": "plinthosol [ENVO:00002250]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "soil type" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "mixs:0000332", + "multivalued": false, + "range": "TextValue" + }, + "soil_type_meth": { + "name": "soil_type_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining soil series name or other lower-level classification", + "title": "soil type method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "soil type method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000334", + "multivalued": false, + "range": "TextValue" + }, + "solar_irradiance": { + "name": "solar_irradiance", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "kilowatts per square meter per day, ergs per square centimeter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The amount of solar energy that arrives at a specific area of a surface during a specific time interval", + "title": "solar irradiance", + "examples": [ + { + "value": "1.36 kilowatts per square meter per day" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "solar irradiance" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000112", + "multivalued": false, + "range": "QuantityValue" + }, + "soluble_inorg_mat": { + "name": "soluble_inorg_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "soluble inorganic material name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, mole per liter, gram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.", + "title": "soluble inorganic material", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "soluble inorganic material" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000672", + "multivalued": false, + "range": "QuantityValue" + }, + "soluble_org_mat": { + "name": "soluble_org_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "soluble organic material name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, mole per liter, gram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.", + "title": "soluble organic material", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "soluble organic material" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000673", + "multivalued": false, + "range": "QuantityValue" + }, + "soluble_react_phosp": { + "name": "soluble_react_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of soluble reactive phosphorus", + "title": "soluble reactive phosphorus", + "examples": [ + { + "value": "0.1 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "soluble reactive phosphorus" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000738", + "multivalued": false, + "range": "QuantityValue" + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).", + "title": "source material identifiers", + "examples": [ + { + "value": "MPI012345" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "source material identifiers" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000026", + "multivalued": false, + "range": "TextValue" + }, + "space_typ_state": { + "name": "space_typ_state", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Customary or normal state of the space", + "title": "space typical state", + "examples": [ + { + "value": "typically occupied" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "space typical state" + ], + "is_a": "attribute", + "string_serialization": "[typically occupied|typically unoccupied]", + "slot_uri": "mixs:0000770", + "multivalued": false, + "range": "TextValue" + }, + "specific": { + "name": "specific", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents", + "title": "specifications", + "examples": [ + { + "value": "construction" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "specifications" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000836", + "multivalued": false, + "range": "TextValue" + }, + "specific_humidity": { + "name": "specific_humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram of air, kilogram of air" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.", + "title": "specific humidity", + "examples": [ + { + "value": "15 per kilogram of air" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "specific humidity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000214", + "multivalued": false, + "range": "QuantityValue" + }, + "sr_dep_env": { + "name": "sr_dep_env", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock depositional environment", + "examples": [ + { + "value": "Marine" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "source rock depositional environment" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000996", + "multivalued": false, + "range": "TextValue" + }, + "sr_geol_age": { + "name": "sr_geol_age", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock geological age", + "examples": [ + { + "value": "Silurian" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "source rock geological age" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000997", + "multivalued": false, + "range": "TextValue" + }, + "sr_kerog_type": { + "name": "sr_kerog_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock kerogen type", + "examples": [ + { + "value": "Type IV" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "source rock kerogen type" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000994", + "multivalued": false, + "range": "TextValue" + }, + "sr_lithology": { + "name": "sr_lithology", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field", + "title": "source rock lithology", + "examples": [ + { + "value": "Coal" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "source rock lithology" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000995", + "multivalued": false, + "range": "TextValue" + }, + "standing_water_regm": { + "name": "standing_water_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "standing water type;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "standing water regimen", + "examples": [ + { + "value": "standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "standing water regimen" + ], + "is_a": "attribute", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0001069", + "multivalued": false, + "range": "TextValue" + }, + "store_cond": { + "name": "store_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "storage condition type;duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).", + "title": "storage conditions", + "examples": [ + { + "value": "-20 degree Celsius freezer;P2Y10D" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "storage conditions" + ], + "is_a": "attribute", + "string_serialization": "{text};{duration}", + "slot_uri": "mixs:0000327", + "multivalued": false, + "range": "TextValue" + }, + "substructure_type": { + "name": "substructure_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level", + "title": "substructure type", + "examples": [ + { + "value": "basement" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "substructure type" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000767", + "multivalued": false, + "range": "TextValue" + }, + "sulfate": { + "name": "sulfate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfate in the sample", + "title": "sulfate", + "examples": [ + { + "value": "5 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sulfate" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000423", + "multivalued": false, + "range": "QuantityValue" + }, + "sulfate_fw": { + "name": "sulfate_fw", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original sulfate concentration in the hydrocarbon resource", + "title": "sulfate in formation water", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sulfate in formation water" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000407", + "multivalued": false, + "range": "QuantityValue" + }, + "sulfide": { + "name": "sulfide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfide in the sample", + "title": "sulfide", + "examples": [ + { + "value": "2 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sulfide" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000424", + "multivalued": false, + "range": "QuantityValue" + }, + "surf_air_cont": { + "name": "surf_air_cont", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Contaminant identified on surface", + "title": "surface-air contaminant", + "examples": [ + { + "value": "radon" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "surface-air contaminant" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000759", + "multivalued": false, + "range": "TextValue" + }, + "surf_humidity": { + "name": "surf_humidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Surfaces: water activity as a function of air and material moisture", + "title": "surface humidity", + "examples": [ + { + "value": "10%" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "surface humidity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000123", + "multivalued": false, + "range": "QuantityValue" + }, + "surf_material": { + "name": "surf_material", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Surface materials at the point of sampling", + "title": "surface material", + "examples": [ + { + "value": "wood" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "surface material" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000758", + "multivalued": false, + "range": "TextValue" + }, + "surf_moisture": { + "name": "surf_moisture", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "parts per million, gram per cubic meter, gram per square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Water held on a surface", + "title": "surface moisture", + "examples": [ + { + "value": "0.01 gram per square meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "surface moisture" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000128", + "multivalued": false, + "range": "QuantityValue" + }, + "surf_moisture_ph": { + "name": "surf_moisture_ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "ph measurement of surface", + "title": "surface moisture pH", + "examples": [ + { + "value": "7" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "surface moisture pH" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000760", + "multivalued": false, + "range": "QuantityValue" + }, + "surf_temp": { + "name": "surf_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature of the surface at the time of sampling", + "title": "surface temperature", + "examples": [ + { + "value": "15 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "surface temperature" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000125", + "multivalued": false, + "range": "QuantityValue" + }, + "suspend_part_matter": { + "name": "suspend_part_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of suspended particulate matter", + "title": "suspended particulate matter", + "examples": [ + { + "value": "0.5 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "suspended particulate matter" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000741", + "multivalued": false, + "range": "QuantityValue" + }, + "suspend_solids": { + "name": "suspend_solids", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "suspended solid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, microgram, milligram per liter, mole per liter, gram per liter, part per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", + "title": "suspended solids", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "suspended solids" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000150", + "multivalued": false, + "range": "QuantityValue" + }, + "tan": { + "name": "tan", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)", + "title": "total acid number", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total acid number" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000120", + "multivalued": false, + "range": "QuantityValue" + }, + "target_gene": { + "name": "target_gene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gene name" + } + }, + "description": "Targeted gene or locus name for marker gene studies", + "title": "target gene", + "examples": [ + { + "value": "16S rRNA, 18S rRNA, nif, amoA, rpo" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "target gene" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000044", + "multivalued": false, + "range": "TextValue" + }, + "target_subfragment": { + "name": "target_subfragment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gene fragment name" + } + }, + "description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA", + "title": "target subfragment", + "examples": [ + { + "value": "V6, V9, ITS" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "target subfragment" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000045", + "multivalued": false, + "range": "TextValue" + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "temperature" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000113", + "multivalued": false, + "range": "QuantityValue" + }, + "temp_out": { + "name": "temp_out", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The recorded temperature value at sampling time outside", + "title": "temperature outside house", + "examples": [ + { + "value": "5 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "temperature outside house" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000197", + "multivalued": false, + "range": "QuantityValue" + }, + "tertiary_treatment": { + "name": "tertiary_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "tertiary treatment type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment", + "title": "tertiary treatment", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "tertiary treatment" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000352", + "multivalued": false, + "range": "TextValue" + }, + "tidal_stage": { + "name": "tidal_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Stage of tide", + "title": "tidal stage", + "examples": [ + { + "value": "high tide" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "tidal stage" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000750", + "multivalued": false, + "range": "TextValue" + }, + "tillage": { + "name": "tillage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Note method(s) used for tilling", + "title": "history/tillage", + "examples": [ + { + "value": "chisel" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "history/tillage" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001081", + "multivalued": false, + "range": "TextValue" + }, + "tiss_cult_growth_med": { + "name": "tiss_cult_growth_med", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url or free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of plant tissue culture growth media used", + "title": "tissue culture growth media", + "examples": [ + { + "value": "https://link.springer.com/content/pdf/10.1007/BF02796489.pdf" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "tissue culture growth media" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "mixs:0001070", + "multivalued": false, + "range": "TextValue" + }, + "toluene": { + "name": "toluene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of toluene in the sample", + "title": "toluene", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "toluene" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000154", + "multivalued": false, + "range": "QuantityValue" + }, + "tot_carb": { + "name": "tot_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total carbon content", + "title": "total carbon", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total carbon" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000525", + "multivalued": false, + "range": "QuantityValue" + }, + "tot_depth_water_col": { + "name": "tot_depth_water_col", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of total depth of water column", + "title": "total depth of water column", + "examples": [ + { + "value": "500 meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total depth of water column" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000634", + "multivalued": false, + "range": "QuantityValue" + }, + "tot_diss_nitro": { + "name": "tot_diss_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen", + "title": "total dissolved nitrogen", + "examples": [ + { + "value": "40 microgram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total dissolved nitrogen" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000744", + "multivalued": false, + "range": "QuantityValue" + }, + "tot_inorg_nitro": { + "name": "tot_inorg_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total inorganic nitrogen content", + "title": "total inorganic nitrogen", + "examples": [ + { + "value": "40 microgram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total inorganic nitrogen" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000745", + "multivalued": false, + "range": "QuantityValue" + }, + "tot_iron": { + "name": "tot_iron", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, milligram per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of total iron in the sample", + "title": "total iron", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total iron" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000105", + "multivalued": false, + "range": "QuantityValue" + }, + "tot_nitro": { + "name": "tot_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", + "title": "total nitrogen concentration", + "examples": [ + { + "value": "50 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total nitrogen concentration" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000102", + "multivalued": false, + "range": "QuantityValue" + }, + "tot_nitro_cont_meth": { + "name": "tot_nitro_cont_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + }, + "mixs_5_name": { + "tag": "mixs_5_name", + "value": "tot_nitro_content_meth" + } + }, + "description": "Reference or method used in determining the total nitrogen", + "title": "total nitrogen content method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total nitrogen content method" + ], + "is_a": "core_field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000338", + "multivalued": false, + "range": "string" + }, + "tot_nitro_content": { + "name": "tot_nitro_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total nitrogen content of the sample", + "title": "total nitrogen content", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total nitrogen content" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000530", + "multivalued": false, + "range": "QuantityValue" + }, + "tot_org_c_meth": { + "name": "tot_org_c_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining total organic carbon", + "title": "total organic carbon method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total organic carbon method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000337", + "multivalued": false, + "range": "TextValue" + }, + "tot_org_carb": { + "name": "tot_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram Carbon per kilogram sample material" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", + "title": "total organic carbon", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total organic carbon" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000533", + "multivalued": false, + "range": "QuantityValue" + }, + "tot_part_carb": { + "name": "tot_part_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total particulate carbon content", + "title": "total particulate carbon", + "examples": [ + { + "value": "35 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total particulate carbon" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000747", + "multivalued": false, + "range": "QuantityValue" + }, + "tot_phosp": { + "name": "tot_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", + "title": "total phosphorus", + "examples": [ + { + "value": "0.03 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total phosphorus" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000117", + "multivalued": false, + "range": "QuantityValue" + }, + "tot_phosphate": { + "name": "tot_phosphate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total amount or concentration of phosphate", + "title": "total phosphate", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total phosphate" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000689", + "multivalued": false, + "range": "QuantityValue" + }, + "tot_sulfur": { + "name": "tot_sulfur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of total sulfur in the sample", + "title": "total sulfur", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total sulfur" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000419", + "multivalued": false, + "range": "QuantityValue" + }, + "train_line": { + "name": "train_line", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The subway line name", + "title": "train line", + "examples": [ + { + "value": "red" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "train line" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000837", + "multivalued": false, + "range": "TextValue" + }, + "train_stat_loc": { + "name": "train_stat_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The train station collection location", + "title": "train station collection location", + "examples": [ + { + "value": "forest hills" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "train station collection location" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000838", + "multivalued": false, + "range": "TextValue" + }, + "train_stop_loc": { + "name": "train_stop_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The train stop collection location", + "title": "train stop collection location", + "examples": [ + { + "value": "end" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "train stop collection location" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000839", + "multivalued": false, + "range": "TextValue" + }, + "turbidity": { + "name": "turbidity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "formazin turbidity unit, formazin nephelometric units" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", + "title": "turbidity", + "examples": [ + { + "value": "0.3 nephelometric turbidity units" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "turbidity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000191", + "multivalued": false, + "range": "QuantityValue" + }, + "tvdss_of_hcr_press": { + "name": "tvdss_of_hcr_press", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).", + "title": "depth (TVDSS) of hydrocarbon resource pressure", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "depth (TVDSS) of hydrocarbon resource pressure" + ], + "is_a": "core_field", + "slot_uri": "mixs:0000397", + "multivalued": false, + "range": "QuantityValue" + }, + "tvdss_of_hcr_temp": { + "name": "tvdss_of_hcr_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).", + "title": "depth (TVDSS) of hydrocarbon resource temperature", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "depth (TVDSS) of hydrocarbon resource temperature" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000394", + "multivalued": false, + "range": "QuantityValue" + }, + "typ_occup_density": { + "name": "typ_occup_density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Customary or normal density of occupants", + "title": "typical occupant density", + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "typical occupant density" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000771", + "multivalued": false, + "range": "QuantityValue" + }, + "ventilation_rate": { + "name": "ventilation_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per minute, liters per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ventilation rate of the system in the sampled premises", + "title": "ventilation rate", + "examples": [ + { + "value": "750 cubic meter per minute" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "ventilation rate" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000114", + "multivalued": false, + "range": "QuantityValue" + }, + "ventilation_type": { + "name": "ventilation_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "ventilation type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ventilation system used in the sampled premises", + "title": "ventilation type", + "examples": [ + { + "value": "Operable windows" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "ventilation type" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000756", + "multivalued": false, + "range": "TextValue" + }, + "vfa": { + "name": "vfa", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of Volatile Fatty Acids in the sample", + "title": "volatile fatty acids", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "volatile fatty acids" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000152", + "multivalued": false, + "range": "QuantityValue" + }, + "vfa_fw": { + "name": "vfa_fw", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Original volatile fatty acid concentration in the hydrocarbon resource", + "title": "vfa in formation water", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "vfa in formation water" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000408", + "multivalued": false, + "range": "QuantityValue" + }, + "vis_media": { + "name": "vis_media", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The building visual media", + "title": "visual media", + "examples": [ + { + "value": "3D scans" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "visual media" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000840", + "multivalued": false, + "range": "TextValue" + }, + "viscosity": { + "name": "viscosity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cP at degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C)", + "title": "viscosity", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "viscosity" + ], + "is_a": "attribute", + "string_serialization": "{float} {unit};{float} {unit}", + "slot_uri": "mixs:0000126", + "multivalued": false, + "range": "QuantityValue" + }, + "volatile_org_comp": { + "name": "volatile_org_comp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "volatile organic compound name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per cubic meter, parts per million, nanogram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound", + "title": "volatile organic compounds", + "examples": [ + { + "value": "formaldehyde;500 nanogram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "volatile organic compounds" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000115", + "multivalued": false, + "range": "QuantityValue" + }, + "wall_area": { + "name": "wall_area", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total area of the sampled room's walls", + "title": "wall area", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "wall area" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000198", + "multivalued": false, + "range": "QuantityValue" + }, + "wall_const_type": { + "name": "wall_const_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The building class of the wall defined by the composition of the building elements and fire-resistance rating.", + "title": "wall construction type", + "examples": [ + { + "value": "fire resistive" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "wall construction type" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000841", + "multivalued": false, + "range": "TextValue" + }, + "wall_finish_mat": { + "name": "wall_finish_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The material utilized to finish the outer most layer of the wall", + "title": "wall finish material", + "examples": [ + { + "value": "wood" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "wall finish material" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000842", + "multivalued": false, + "range": "TextValue" + }, + "wall_height": { + "name": "wall_height", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average height of the walls in the sampled room", + "title": "wall height", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "wall height" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000221", + "multivalued": false, + "range": "QuantityValue" + }, + "wall_loc": { + "name": "wall_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The relative location of the wall within the room", + "title": "wall location", + "examples": [ + { + "value": "north" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "wall location" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000843", + "multivalued": false, + "range": "TextValue" + }, + "wall_surf_treatment": { + "name": "wall_surf_treatment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The surface treatment of interior wall", + "title": "wall surface treatment", + "examples": [ + { + "value": "paneling" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "wall surface treatment" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000845", + "multivalued": false, + "range": "TextValue" + }, + "wall_texture": { + "name": "wall_texture", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The feel, appearance, or consistency of a wall surface", + "title": "wall texture", + "examples": [ + { + "value": "popcorn" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "wall texture" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000846", + "multivalued": false, + "range": "TextValue" + }, + "wall_thermal_mass": { + "name": "wall_thermal_mass", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "joule per degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint", + "title": "wall thermal mass", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "wall thermal mass" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000222", + "multivalued": false, + "range": "QuantityValue" + }, + "wall_water_mold": { + "name": "wall_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on a wall", + "title": "wall signs of water/mold", + "examples": [ + { + "value": "no presence of mold visible" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "wall signs of water/mold" + ], + "is_a": "attribute", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "mixs:0000844", + "multivalued": false, + "range": "TextValue" + }, + "wastewater_type": { + "name": "wastewater_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "wastewater type name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The origin of wastewater such as human waste, rainfall, storm drains, etc.", + "title": "wastewater type", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "wastewater type" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000353", + "multivalued": false, + "range": "TextValue" + }, + "water_cont_soil_meth": { + "name": "water_cont_soil_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + }, + "mixs_5_name": { + "tag": "mixs_5_name", + "value": "water_content_soil_meth" + } + }, + "description": "Reference or method used in determining the water content of soil", + "title": "water content method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "water content method" + ], + "is_a": "core_field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000323", + "multivalued": false, + "range": "string" + }, + "water_content": { + "name": "water_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per gram or cubic centimeter per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Water content measurement", + "title": "water content", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "water content" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000185", + "multivalued": false, + "range": "QuantityValue" + }, + "water_current": { + "name": "water_current", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per second, knots" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of magnitude and direction of flow within a fluid", + "title": "water current", + "examples": [ + { + "value": "10 cubic meter per second" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "water current" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000203", + "multivalued": false, + "range": "QuantityValue" + }, + "water_cut": { + "name": "water_cut", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percent" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Current amount of water (%) in a produced fluid stream; or the average of the combined streams", + "title": "water cut", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "water cut" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000454", + "multivalued": false, + "range": "QuantityValue" + }, + "water_feat_size": { + "name": "water_feat_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "square meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The size of the water feature", + "title": "water feature size", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "water feature size" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000223", + "multivalued": false, + "range": "QuantityValue" + }, + "water_feat_type": { + "name": "water_feat_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of water feature present within the building being sampled", + "title": "water feature type", + "examples": [ + { + "value": "stream" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "water feature_type" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000847", + "multivalued": false, + "range": "TextValue" + }, + "water_prod_rate": { + "name": "water_prod_rate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "cubic meter per day" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Water production rates per well (e.g. 987 m3 / day)", + "title": "water production rate", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "water production rate" + ], + "is_a": "core_field", + "slot_uri": "mixs:0000453", + "multivalued": false, + "range": "QuantityValue" + }, + "water_temp_regm": { + "name": "water_temp_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "water temperature regimen", + "examples": [ + { + "value": "15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "water temperature regimen" + ], + "is_a": "attribute", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000590", + "multivalued": false, + "range": "QuantityValue" + }, + "watering_regm": { + "name": "watering_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliliter, liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "watering regimen", + "examples": [ + { + "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "watering regimen" + ], + "is_a": "attribute", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000591", + "multivalued": false, + "range": "QuantityValue" + }, + "weekday": { + "name": "weekday", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The day of the week when sampling occurred", + "title": "weekday", + "examples": [ + { + "value": "Sunday" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "weekday" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000848", + "multivalued": false, + "range": "TextValue" + }, + "win": { + "name": "win", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)", + "title": "well identification number", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "well identification number" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000297", + "multivalued": false, + "range": "TextValue" + }, + "wind_direction": { + "name": "wind_direction", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "wind direction name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Wind direction is the direction from which a wind originates", + "title": "wind direction", + "examples": [ + { + "value": "Northwest" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "wind direction" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000757", + "multivalued": false, + "range": "TextValue" + }, + "wind_speed": { + "name": "wind_speed", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second, kilometer per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Speed of wind measured at the time of sampling", + "title": "wind speed", + "examples": [ + { + "value": "21 kilometer per hour" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "wind speed" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000118", + "multivalued": false, + "range": "QuantityValue" + }, + "window_cond": { + "name": "window_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The physical condition of the window at the time of sampling", + "title": "window condition", + "examples": [ + { + "value": "rupture" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "window condition" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000849", + "multivalued": false, + "range": "TextValue" + }, + "window_cover": { + "name": "window_cover", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of window covering", + "title": "window covering", + "examples": [ + { + "value": "curtains" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "window covering" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000850", + "multivalued": false, + "range": "TextValue" + }, + "window_horiz_pos": { + "name": "window_horiz_pos", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The horizontal position of the window on the wall", + "title": "window horizontal position", + "examples": [ + { + "value": "middle" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "window horizontal position" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000851", + "multivalued": false, + "range": "TextValue" + }, + "window_loc": { + "name": "window_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The relative location of the window within the room", + "title": "window location", + "examples": [ + { + "value": "west" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "window location" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000852", + "multivalued": false, + "range": "TextValue" + }, + "window_mat": { + "name": "window_mat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of material used to finish a window", + "title": "window material", + "examples": [ + { + "value": "wood" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "window material" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000853", + "multivalued": false, + "range": "TextValue" + }, + "window_open_freq": { + "name": "window_open_freq", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The number of times windows are opened per week", + "title": "window open frequency", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "window open frequency" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000246", + "multivalued": false, + "range": "TextValue" + }, + "window_size": { + "name": "window_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "inch, meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The window's length and width", + "title": "window area/size", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "window area/size" + ], + "is_a": "attribute", + "string_serialization": "{float} {unit} x {float} {unit}", + "slot_uri": "mixs:0000224", + "multivalued": false, + "range": "QuantityValue" + }, + "window_status": { + "name": "window_status", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Defines whether the windows were open or closed during environmental testing", + "title": "window status", + "examples": [ + { + "value": "open" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "window status" + ], + "is_a": "attribute", + "string_serialization": "[closed|open]", + "slot_uri": "mixs:0000855", + "multivalued": false, + "range": "TextValue" + }, + "window_type": { + "name": "window_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The type of windows", + "title": "window type", + "examples": [ + { + "value": "fixed window" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "window type" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000856", + "multivalued": false, + "range": "TextValue" + }, + "window_vert_pos": { + "name": "window_vert_pos", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The vertical position of the window on the wall", + "title": "window vertical position", + "examples": [ + { + "value": "middle" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "window vertical position" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000857", + "multivalued": false, + "range": "TextValue" + }, + "window_water_mold": { + "name": "window_water_mold", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Signs of the presence of mold or mildew on the window.", + "title": "window signs of water/mold", + "examples": [ + { + "value": "no presence of mold visible" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "window signs of water/mold" + ], + "is_a": "attribute", + "string_serialization": "[presence of mold visible|no presence of mold visible]", + "slot_uri": "mixs:0000854", + "multivalued": false, + "range": "TextValue" + }, + "xylene": { + "name": "xylene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of xylene in the sample", + "title": "xylene", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "xylene" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000156", + "multivalued": false, + "range": "QuantityValue" + }, + "env_package": { + "name": "env_package", + "description": "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported", + "in_subset": [ + "mixs extension" + ], + "from_schema": "https://microbiomedata/schema", + "source": "https://microbiomedata/schema/mixs", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "environmental package" + ], + "mappings": [ + "mixs:env_package" + ], + "is_a": "attribute", + "multivalued": false, + "range": "TextValue", + "pattern": "[air|built environment|host\\-associated|human\\-associated|human\\-skin|human\\-oral|human\\-gut|human\\-vaginal|hydrocarbon resources\\-cores|hydrocarbon resources\\-fluids\\/swabs|microbial mat\\/biofilm|misc environment|plant\\-associated|sediment|soil|wastewater\\/sludge|water]" + }, + "zinc": { + "name": "zinc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg (ppm)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of zinc in the sample", + "title": "zinc", + "examples": [ + { + "value": "2.5 mg/kg" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "zinc" + ], + "is_a": "attribute", + "multivalued": false, + "range": "QuantityValue" + }, + "manganese": { + "name": "manganese", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg (ppm)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of manganese in the sample", + "title": "manganese", + "examples": [ + { + "value": "24.7 mg/kg" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "manganese" + ], + "is_a": "attribute", + "multivalued": false, + "range": "QuantityValue" + }, + "ammonium_nitrogen": { + "name": "ammonium_nitrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium nitrogen in the sample", + "title": "ammonium nitrogen", + "examples": [ + { + "value": "2.3 mg/kg" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "ammonium_nitrogen", + "NH4-N" + ], + "is_a": "attribute", + "multivalued": false, + "range": "QuantityValue" + }, + "nitrate_nitrogen": { + "name": "nitrate_nitrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate nitrogen in the sample", + "title": "nitrate_nitrogen", + "comments": [ + "often below some specified limit of detection" + ], + "examples": [ + { + "value": "0.29 mg/kg" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "nitrate_nitrogen", + "NO3-N" + ], + "is_a": "attribute", + "multivalued": false, + "range": "QuantityValue" + }, + "nitrite_nitrogen": { + "name": "nitrite_nitrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite nitrogen in the sample", + "title": "nitrite_nitrogen", + "examples": [ + { + "value": "1.2 mg/kg" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "nitrite_nitrogen", + "NO2-N" + ], + "is_a": "attribute", + "multivalued": false, + "range": "QuantityValue" + }, + "lbc_thirty": { + "name": "lbc_thirty", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ppm CaCO3/pH" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "lime buffer capacity, determined after 30 minute incubation", + "title": "lime buffer capacity (at 30 minutes)", + "comments": [ + "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" + ], + "examples": [ + { + "value": "543 mg/kg" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0", + "https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF" + ], + "aliases": [ + "lbc_thirty", + "lbc30", + "lime buffer capacity (at 30 minutes)" + ], + "is_a": "attribute", + "multivalued": false, + "range": "QuantityValue" + }, + "lbceq": { + "name": "lbceq", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ppm CaCO3/pH" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "lime buffer capacity, determined at equilibrium after 5 day incubation", + "title": "lime buffer capacity (after 5 day incubation)", + "comments": [ + "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" + ], + "examples": [ + { + "value": "1575 mg/kg" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "lbceq", + "lime buffer capacity (at 5-day equilibrium)" + ], + "is_a": "attribute", + "multivalued": false, + "range": "QuantityValue" + }, + "has_part": { + "name": "has_part", + "from_schema": "https://microbiomedata/schema" + }, + "chemical": { + "name": "chemical", + "description": "from reaction participant class", + "from_schema": "https://microbiomedata/schema" + }, + "stoichiometry": { + "name": "stoichiometry", + "description": "from reaction participant class", + "from_schema": "https://microbiomedata/schema" + }, + "subject": { + "name": "subject", + "from_schema": "https://microbiomedata/schema", + "range": "GeneProduct" + }, + "has_function": { + "name": "has_function", + "notes": [ + "the range for has_function was asserted as functional_annotation_term/FunctionalAnnotationTerm,", + "but is actually taking string arguments in MongoDB,", + "and those are frequently fulltext, not CURIEs. MAM 2021-06-23" + ], + "from_schema": "https://microbiomedata/schema", + "range": "string" + }, + "has_participants": { + "name": "has_participants", + "from_schema": "https://microbiomedata/schema", + "exact_mappings": [ + "RO:0000057" + ], + "abstract": true + }, + "gff_coordinate": { + "name": "gff_coordinate", + "description": "A positive 1-based integer coordinate indicating start or end", + "comments": [ + "For features that cross the origin of a circular feature (e.g. most bacterial genomes, plasmids, and some viral genomes), the requirement for start to be less than or equal to end is satisfied by making end = the position of the end + the length of the landmark feature." + ], + "from_schema": "https://microbiomedata/schema", + "range": "integer", + "minimum_value": 1 + }, + "direction": { + "name": "direction", + "from_schema": "https://microbiomedata/schema" + }, + "encodes": { + "name": "encodes", + "from_schema": "https://microbiomedata/schema" + }, + "end": { + "name": "end", + "from_schema": "https://microbiomedata/schema" + }, + "feature_type": { + "name": "feature_type", + "from_schema": "https://microbiomedata/schema" + }, + "is_balanced": { + "name": "is_balanced", + "from_schema": "https://microbiomedata/schema" + }, + "is_diastereoselective": { + "name": "is_diastereoselective", + "from_schema": "https://microbiomedata/schema" + }, + "is_fully_characterized": { + "name": "is_fully_characterized", + "from_schema": "https://microbiomedata/schema" + }, + "is_stereo": { + "name": "is_stereo", + "from_schema": "https://microbiomedata/schema" + }, + "is_transport": { + "name": "is_transport", + "from_schema": "https://microbiomedata/schema" + }, + "left_participants": { + "name": "left_participants", + "from_schema": "https://microbiomedata/schema" + }, + "phase": { + "name": "phase", + "from_schema": "https://microbiomedata/schema" + }, + "right_participants": { + "name": "right_participants", + "from_schema": "https://microbiomedata/schema" + }, + "seqid": { + "name": "seqid", + "todos": [ + "change range from string to object" + ], + "from_schema": "https://microbiomedata/schema" + }, + "smarts_string": { + "name": "smarts_string", + "from_schema": "https://microbiomedata/schema" + }, + "start": { + "name": "start", + "from_schema": "https://microbiomedata/schema" + }, + "strand": { + "name": "strand", + "todos": [ + "set the range to an enum?" + ], + "from_schema": "https://microbiomedata/schema" + } + }, + "classes": { + "Database": { + "name": "Database", + "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "NMDC metadata object" + ], + "slots": [ + "activity_set", + "biosample_set", + "data_object_set", + "dissolving_activity_set", + "functional_annotation_set", + "genome_feature_set", + "mags_activity_set", + "material_sample_set", + "material_sampling_activity_set", + "metabolomics_analysis_activity_set", + "metagenome_annotation_activity_set", + "metagenome_assembly_set", + "metaproteomics_analysis_activity_set", + "metatranscriptome_activity_set", + "nom_analysis_activity_set", + "omics_processing_set", + "reaction_activity_set", + "read_qc_analysis_activity_set", + "read_based_taxonomy_analysis_activity_set", + "study_set", + "field_research_site_set", + "collecting_biosamples_from_site_set" + ], + "slot_usage": { + "date_created": { + "name": "date_created", + "description": "TODO" + }, + "etl_software_version": { + "name": "etl_software_version", + "description": "TODO" + }, + "metatranscriptome_activity_set": { + "name": "metatranscriptome_activity_set", + "description": "TODO", + "domain_of": [ + "Database" + ] + } + }, + "attributes": { + "activity_set": { + "name": "activity_set", + "description": "This property links a database object to the set of workflow activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "activity_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "WorkflowExecutionActivity", + "inlined_as_list": true + }, + "biosample_set": { + "name": "biosample_set", + "description": "This property links a database object to the set of samples within it.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "biosample_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "Biosample", + "inlined_as_list": true + }, + "data_object_set": { + "name": "data_object_set", + "description": "This property links a database object to the set of data objects within it.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "data_object_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "DataObject", + "inlined_as_list": true + }, + "dissolving_activity_set": { + "name": "dissolving_activity_set", + "title": "dissolving activity set", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "dissolving_activity_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "DissolvingActivity", + "inlined_as_list": true + }, + "functional_annotation_set": { + "name": "functional_annotation_set", + "description": "This property links a database object to the set of all functional annotations", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "functional_annotation_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "FunctionalAnnotation", + "inlined_as_list": true + }, + "genome_feature_set": { + "name": "genome_feature_set", + "description": "This property links a database object to the set of all features", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "genome_feature_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "GenomeFeature", + "inlined_as_list": true + }, + "mags_activity_set": { + "name": "mags_activity_set", + "description": "This property links a database object to the set of MAGs analysis activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "mags_activity_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "MagsAnalysisActivity", + "inlined_as_list": true + }, + "material_sample_set": { + "name": "material_sample_set", + "title": "material sample set", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "material_sample_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "MaterialSample", + "inlined_as_list": true + }, + "material_sampling_activity_set": { + "name": "material_sampling_activity_set", + "title": "material sampling activity set", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "material_sampling_activity_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "MaterialSamplingActivity", + "inlined_as_list": true + }, + "metabolomics_analysis_activity_set": { + "name": "metabolomics_analysis_activity_set", + "description": "This property links a database object to the set of metabolomics analysis activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "metabolomics_analysis_activity_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "MetabolomicsAnalysisActivity", + "inlined_as_list": true + }, + "metagenome_annotation_activity_set": { + "name": "metagenome_annotation_activity_set", + "description": "This property links a database object to the set of metagenome annotation activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "metagenome_annotation_activity_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "MetagenomeAnnotationActivity", + "inlined_as_list": true + }, + "metagenome_assembly_set": { + "name": "metagenome_assembly_set", + "description": "This property links a database object to the set of metagenome assembly activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "metagenome_assembly_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "MetagenomeAssembly", + "inlined_as_list": true + }, + "metaproteomics_analysis_activity_set": { + "name": "metaproteomics_analysis_activity_set", + "description": "This property links a database object to the set of metaproteomics analysis activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "metaproteomics_analysis_activity_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "MetaproteomicsAnalysisActivity", + "inlined_as_list": true + }, + "metatranscriptome_activity_set": { + "name": "metatranscriptome_activity_set", + "description": "TODO", + "from_schema": "https://microbiomedata/schema", + "domain": "Database", + "multivalued": true, + "alias": "metatranscriptome_activity_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "MetatranscriptomeActivity", + "inlined_as_list": true + }, + "nom_analysis_activity_set": { + "name": "nom_analysis_activity_set", + "description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "nom_analysis_activity_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "NomAnalysisActivity", + "inlined_as_list": true + }, + "omics_processing_set": { + "name": "omics_processing_set", + "description": "This property links a database object to the set of omics processings within it.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "omics_processing_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "OmicsProcessing", + "inlined_as_list": true + }, + "reaction_activity_set": { + "name": "reaction_activity_set", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "reaction_activity_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "ReactionActivity", + "inlined_as_list": true + }, + "read_qc_analysis_activity_set": { + "name": "read_qc_analysis_activity_set", + "description": "This property links a database object to the set of read QC analysis activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "read_qc_analysis_activity_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "ReadQcAnalysisActivity", + "inlined_as_list": true + }, + "read_based_taxonomy_analysis_activity_set": { + "name": "read_based_taxonomy_analysis_activity_set", + "description": "This property links a database object to the set of read based analysis activities.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "read_based_taxonomy_analysis_activity_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "ReadBasedTaxonomyAnalysisActivity", + "inlined_as_list": true + }, + "study_set": { + "name": "study_set", + "description": "This property links a database object to the set of studies within it.", + "from_schema": "https://microbiomedata/schema", + "mixins": [ + "object_set" + ], + "domain": "Database", + "multivalued": true, + "alias": "study_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "Study", + "inlined_as_list": true + }, + "field_research_site_set": { + "name": "field_research_site_set", + "from_schema": "https://microbiomedata/schema", + "domain": "Database", + "multivalued": true, + "alias": "field_research_site_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "FieldResearchSite", + "inlined_as_list": true + }, + "collecting_biosamples_from_site_set": { + "name": "collecting_biosamples_from_site_set", + "from_schema": "https://microbiomedata/schema", + "domain": "Database", + "multivalued": true, + "alias": "collecting_biosamples_from_site_set", + "owner": "Database", + "domain_of": [ + "Database" + ], + "range": "CollectingBiosamplesFromSite", + "inlined_as_list": true + } + }, + "tree_root": true + }, + "FieldResearchSite": { + "name": "FieldResearchSite", + "description": "A site, outside of a laboratory, from which biosamples may be collected.", + "title": "Field Research Site", + "comments": [ + "Provides grouping of biosamples at level that's more specific than belonging to the same study", + "be very clear that this could be part of a larger site", + "In Bioscales, one might say that rhizosphere soil and bulk soil from around the same plant were obtained at the same site. In this case, the site would correspond to one tree.", + "might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833" + ], + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "research plot" + ], + "is_a": "Site", + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "Biosample", + "Study", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:frsite", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "FieldResearchSite", + "domain_of": [ + "Biosample", + "Study", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:frsite", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "FieldResearchSite", + "domain_of": [ + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "FieldResearchSite", + "domain_of": [ + "NamedThing", + "ImageValue" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "FieldResearchSite", + "domain_of": [ + "Biosample", + "Study", + "NamedThing", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "CollectingBiosamplesFromSite": { + "name": "CollectingBiosamplesFromSite", + "title": "Collecting Biosamples From Site", + "comments": [ + "this illustrates implementing a Biosample relation with a process class" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "PlannedProcess", + "slots": [ + "has_inputs", + "has_outputs" + ], + "slot_usage": { + "has_inputs": { + "name": "has_inputs", + "domain_of": [ + "CollectingBiosamplesFromSite", + "PlannedProcess" + ], + "range": "Site", + "required": true + }, + "has_outputs": { + "name": "has_outputs", + "domain_of": [ + "CollectingBiosamplesFromSite", + "PlannedProcess" + ], + "range": "Biosample", + "required": true + }, + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "Study", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:clsite", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "has_inputs": { + "name": "has_inputs", + "from_schema": "https://microbiomedata/schema", + "domain": "PlannedProcess", + "multivalued": true, + "alias": "has_inputs", + "owner": "CollectingBiosamplesFromSite", + "domain_of": [ + "CollectingBiosamplesFromSite", + "PlannedProcess" + ], + "range": "Site", + "required": true + }, + "has_outputs": { + "name": "has_outputs", + "from_schema": "https://microbiomedata/schema", + "domain": "PlannedProcess", + "multivalued": true, + "alias": "has_outputs", + "owner": "CollectingBiosamplesFromSite", + "domain_of": [ + "CollectingBiosamplesFromSite", + "PlannedProcess" + ], + "range": "Biosample", + "required": true + }, + "participating_agent": { + "name": "participating_agent", + "from_schema": "https://microbiomedata/schema", + "domain": "PlannedProcess", + "alias": "participating_agent", + "owner": "CollectingBiosamplesFromSite", + "domain_of": [ + "PlannedProcess" + ], + "range": "Agent" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "CollectingBiosamplesFromSite", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "Study", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:clsite", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "CollectingBiosamplesFromSite", + "domain_of": [ + "FieldResearchSite", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "CollectingBiosamplesFromSite", + "domain_of": [ + "FieldResearchSite", + "NamedThing", + "ImageValue" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "CollectingBiosamplesFromSite", + "domain_of": [ + "FieldResearchSite", + "Biosample", + "Study", + "NamedThing", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "DataObject": { + "name": "DataObject", + "description": "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.", + "notes": [ + "removed previous id_prefixes value of GOLD, since we are now using pattern-based id validation" + ], + "in_subset": [ + "data object subset" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "NamedThing", + "slots": [ + "file_size_bytes", + "md5_checksum", + "data_object_type", + "compression_type", + "was_generated_by", + "url", + "type" + ], + "slot_usage": { + "name": { + "name": "name", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "Activity", + "NamedThing", + "PersonValue" + ], + "required": true + }, + "description": { + "name": "description", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "NamedThing", + "ImageValue" + ], + "required": true + }, + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "Biosample", + "Study", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:dobj", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "file_size_bytes": { + "name": "file_size_bytes", + "description": "Size of the file in bytes", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "file_size_bytes", + "owner": "DataObject", + "domain_of": [ + "DataObject" + ], + "range": "bytes" + }, + "md5_checksum": { + "name": "md5_checksum", + "description": "MD5 checksum of file (pre-compressed)", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "md5_checksum", + "owner": "DataObject", + "domain_of": [ + "DataObject" + ], + "range": "string" + }, + "data_object_type": { + "name": "data_object_type", + "description": "The type of file represented by the data object.", + "examples": [ + { + "value": "FT ICR-MS Analysis Results" + }, + { + "value": "GC-MS Metabolomics Results" + } + ], + "from_schema": "https://microbiomedata/schema", + "alias": "data_object_type", + "owner": "DataObject", + "domain_of": [ + "DataObject" + ], + "range": "file type enum" + }, + "compression_type": { + "name": "compression_type", + "description": "If provided, specifies the compression type", + "todos": [ + "consider enum" + ], + "examples": [ + { + "value": "gzip" + } + ], + "from_schema": "https://microbiomedata/schema", + "alias": "compression_type", + "owner": "DataObject", + "domain_of": [ + "DataObject" + ], + "range": "string" + }, + "was_generated_by": { + "name": "was_generated_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasGeneratedBy" + ], + "alias": "was_generated_by", + "owner": "DataObject", + "domain_of": [ + "DataObject", + "AttributeValue", + "FunctionalAnnotation" + ], + "range": "Activity" + }, + "url": { + "name": "url", + "notes": [ + "See issue 207 - this clashes with the mixs field" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "url", + "owner": "DataObject", + "domain_of": [ + "DataObject", + "ImageValue" + ], + "range": "string" + }, + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "examples": [ + { + "value": "nmdc:Biosample" + }, + { + "value": "nmdc:Study" + } + ], + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "DataObject", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "DataObject", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "Biosample", + "Study", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:dobj", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "DataObject", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string", + "required": true + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "DataObject", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "NamedThing", + "ImageValue" + ], + "range": "string", + "required": true + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "DataObject", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "Biosample", + "Study", + "NamedThing", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "Biosample": { + "name": "Biosample", + "description": "Biological source material which can be characterized by an experiment.", + "alt_descriptions": { + "embl.ena": { + "source": "embl.ena", + "description": "A sample contains information about the sequenced source material. Samples are associated with checklists, which define the fields used to annotate the samples. Samples are always associated with a taxon." + } + }, + "todos": [ + "could add GOLD and EBI's biosample definitions to the alt_descriptions?" + ], + "notes": [ + "removed previous id_prefixes value of GOLD, since we are now using pattern-based id validation" + ], + "in_subset": [ + "sample subset" + ], + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "sample", + "material sample", + "specimen", + "biospecimen" + ], + "exact_mappings": [ + "OBI:0000747", + "NCIT:C43412", + "http://purl.obolibrary.org/obo/FBcv_0003024" + ], + "is_a": "MaterialEntity", + "slots": [ + "collected_from", + "type", + "img_identifiers", + "samp_name", + "biosample_categories", + "type", + "part_of", + "id", + "alternative_identifiers", + "gold_biosample_identifiers", + "insdc_biosample_identifiers", + "emsl_biosample_identifiers", + "igsn_biosample_identifiers", + "agrochem_addition", + "alkalinity", + "alkalinity_method", + "alkyl_diethers", + "alt", + "al_sat", + "al_sat_meth", + "aminopept_act", + "ammonium", + "annual_precpt", + "annual_temp", + "bacteria_carb_prod", + "bishomohopanol", + "bromide", + "calcium", + "carb_nitro_ratio", + "chem_administration", + "chloride", + "chlorophyll", + "collection_date", + "cur_land_use", + "cur_vegetation", + "cur_vegetation_meth", + "crop_rotation", + "density", + "depth", + "diss_carb_dioxide", + "diss_hydrogen", + "diss_inorg_carb", + "diss_inorg_phosp", + "diss_org_carb", + "diss_org_nitro", + "diss_oxygen", + "drainage_class", + "elev", + "env_package", + "env_broad_scale", + "env_local_scale", + "env_medium", + "extreme_event", + "fao_class", + "fire", + "flooding", + "geo_loc_name", + "glucosidase_act", + "heavy_metals", + "heavy_metals_meth", + "lat_lon", + "link_addit_analys", + "link_class_info", + "link_climate_info", + "local_class", + "local_class_meth", + "magnesium", + "mean_frict_vel", + "mean_peak_frict_vel", + "misc_param", + "n_alkanes", + "nitrate", + "nitrite", + "org_matter", + "org_nitro", + "organism_count", + "oxy_stat_samp", + "part_org_carb", + "perturbation", + "petroleum_hydrocarb", + "ph", + "ph_meth", + "phaeopigments", + "phosplipid_fatt_acid", + "pool_dna_extracts", + "potassium", + "pressure", + "profile_position", "redox_potential", "salinity", "salinity_meth", @@ -1514,459 +24129,25148 @@ "ecosystem_type", "ecosystem_subtype", "specific_ecosystem", - "add_date", - "community", - "habitat", - "host_name", - "location", - "mod_date", - "ncbi_taxonomy_name", - "proport_woa_temperature", - "salinity_category", - "sample_collection_site", - "soluble_iron_micromol", - "subsurface_depth", - "air_temp_regm", - "biotic_regm", - "biotic_relationship", - "climate_environment", - "experimental_factor", - "gaseous_environment", - "growth_facil", - "humidity_regm", - "light_regm", - "phosphate", - "rel_to_oxygen", - "samp_collec_method", - "samp_size", - "source_mat_id", - "watering_regm", - "dna_absorb1", - "dna_absorb2", - "dna_collect_site", - "dna_concentration", - "dna_cont_type", - "dna_cont_well", - "dna_container_id", - "dna_dnase", - "dna_isolate_meth", - "dna_organisms", - "dna_project_contact", - "dna_samp_id", - "dna_sample_format", - "dna_sample_name", - "dna_seq_project", - "dna_seq_project_pi", - "dna_seq_project_name", - "dna_volume", - "proposal_dna", - "dnase_rna", - "proposal_rna", - "rna_absorb1", - "rna_absorb2", - "rna_collect_site", - "rna_concentration", - "rna_cont_type", - "rna_cont_well", - "rna_container_id", - "rna_isolate_meth", - "rna_organisms", - "rna_project_contact", - "rna_samp_id", - "rna_sample_format", - "rna_sample_name", - "rna_seq_project", - "rna_seq_project_pi", - "rna_seq_project_name", - "rna_volume", - "collection_date_inc", - "collection_time", - "collection_time_inc", - "experimental_factor_other", - "filter_method", - "isotope_exposure", - "micro_biomass_c_meth", - "micro_biomass_n_meth", - "microbial_biomass_c", - "microbial_biomass_n", - "non_microb_biomass", - "non_microb_biomass_method", - "org_nitro_method", - "other_treatment", - "start_date_inc", - "start_time_inc", - "project_id", - "replicate_number", - "sample_shipped", - "sample_type", - "technical_reps", - "analysis_type", - "sample_link", - "zinc", - "manganese", - "ammonium_nitrogen", - "nitrate_nitrogen", - "nitrite_nitrogen", - "lbc_thirty", - "lbceq" + "add_date", + "community", + "habitat", + "host_name", + "location", + "mod_date", + "ncbi_taxonomy_name", + "proport_woa_temperature", + "salinity_category", + "sample_collection_site", + "soluble_iron_micromol", + "subsurface_depth", + "air_temp_regm", + "biotic_regm", + "biotic_relationship", + "climate_environment", + "experimental_factor", + "gaseous_environment", + "growth_facil", + "humidity_regm", + "light_regm", + "phosphate", + "rel_to_oxygen", + "samp_collec_method", + "samp_size", + "source_mat_id", + "watering_regm", + "dna_absorb1", + "dna_absorb2", + "dna_collect_site", + "dna_concentration", + "dna_cont_type", + "dna_cont_well", + "dna_container_id", + "dna_dnase", + "dna_isolate_meth", + "dna_organisms", + "dna_project_contact", + "dna_samp_id", + "dna_sample_format", + "dna_sample_name", + "dna_seq_project", + "dna_seq_project_pi", + "dna_seq_project_name", + "dna_volume", + "proposal_dna", + "dnase_rna", + "proposal_rna", + "rna_absorb1", + "rna_absorb2", + "rna_collect_site", + "rna_concentration", + "rna_cont_type", + "rna_cont_well", + "rna_container_id", + "rna_isolate_meth", + "rna_organisms", + "rna_project_contact", + "rna_samp_id", + "rna_sample_format", + "rna_sample_name", + "rna_seq_project", + "rna_seq_project_pi", + "rna_seq_project_name", + "rna_volume", + "collection_date_inc", + "collection_time", + "collection_time_inc", + "experimental_factor_other", + "filter_method", + "isotope_exposure", + "micro_biomass_c_meth", + "micro_biomass_n_meth", + "microbial_biomass_c", + "microbial_biomass_n", + "non_microb_biomass", + "non_microb_biomass_method", + "org_nitro_method", + "other_treatment", + "start_date_inc", + "start_time_inc", + "project_id", + "replicate_number", + "sample_shipped", + "sample_type", + "technical_reps", + "analysis_type", + "sample_link", + "zinc", + "manganese", + "ammonium_nitrogen", + "nitrate_nitrogen", + "nitrite_nitrogen", + "lbc_thirty", + "lbceq" + ], + "slot_usage": { + "id": { + "name": "id", + "description": "An NMDC assigned unique identifier for a biosample submitted to NMDC.", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "Activity", + "NamedThing" + ], + "required": true, + "pattern": "^nmdc:bsm", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "gold_biosample_identifiers": { + "name": "gold_biosample_identifiers", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Provide the GOLD biosample IDs associated with this biosample." + } + }, + "description": "Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample", + "comments": [ + "This is the ID provided by GOLD that starts with 'GB'" + ], + "domain_of": [ + "Biosample" + ] + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "NamedThing", + "MetaboliteQuantification" + ], + "required": false + }, + "lat_lon": { + "name": "lat_lon", + "description": "This is currently a required field but it's not clear if this should be required for human hosts", + "domain_of": [ + "Biosample" + ], + "required": false + }, + "env_broad_scale": { + "name": "env_broad_scale", + "domain_of": [ + "Biosample" + ], + "required": true + }, + "env_local_scale": { + "name": "env_local_scale", + "domain_of": [ + "Biosample" + ], + "required": true + }, + "env_medium": { + "name": "env_medium", + "domain_of": [ + "Biosample" + ], + "required": true + }, + "sample_link": { + "name": "sample_link", + "description": "JsonObj()", + "domain_of": [ + "Biosample" + ], + "required": false + }, + "part_of": { + "name": "part_of", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity" + ], + "required": true + }, + "extreme_event": { + "name": "extreme_event", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date, string" + } + }, + "examples": [ + { + "value": "1980-05-18, volcanic eruption" + } + ], + "domain_of": [ + "Biosample" + ], + "range": "string" + } + }, + "attributes": { + "collected_from": { + "name": "collected_from", + "description": "The Site from which a Biosample was collected", + "todos": [ + "add an OBO slot_uri ?" + ], + "comments": [ + "this illustrates implementing a Biosample relation with a (binary) slot" + ], + "from_schema": "https://microbiomedata/schema", + "domain": "Biosample", + "alias": "collected_from", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "FieldResearchSite" + }, + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "examples": [ + { + "value": "nmdc:Biosample" + }, + { + "value": "nmdc:Study" + } + ], + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "Biosample", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "img_identifiers": { + "name": "img_identifiers", + "description": "A list of identifiers that relate the biosample to records in the IMG database.", + "title": "IMG Identifiers", + "todos": [ + "add is_a or mixin modeling", + "what are the class of IMG records?!" + ], + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "img_identifiers", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "samp_name": { + "name": "samp_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.", + "title": "sample name", + "examples": [ + { + "value": "ISDsoil1" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample name" + ], + "is_a": "investigation_field", + "string_serialization": "{text}", + "slot_uri": "mixs:0001107", + "multivalued": false, + "alias": "samp_name", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "biosample_categories": { + "name": "biosample_categories", + "title": "Categories the biosample belongs to", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "biosample_categories", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "biosample_category_enum" + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "alias": "part_of", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity" + ], + "range": "NamedThing", + "required": true + }, + "id": { + "name": "id", + "description": "An NMDC assigned unique identifier for a biosample submitted to NMDC.", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "Activity", + "NamedThing" + ], + "range": "string", + "required": true, + "pattern": "^nmdc:bsm", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "NamedThing", + "MetaboliteQuantification" + ], + "range": "string", + "required": false + }, + "gold_biosample_identifiers": { + "name": "gold_biosample_identifiers", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Provide the GOLD biosample IDs associated with this biosample." + } + }, + "description": "Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample", + "comments": [ + "This is the ID provided by GOLD that starts with 'GB'" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "biosample_identifiers", + "multivalued": true, + "alias": "gold_biosample_identifiers", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "uriorcurie", + "pattern": "^GOLD:Gb[0-9]+$" + }, + "insdc_biosample_identifiers": { + "name": "insdc_biosample_identifiers", + "description": "identifiers for corresponding sample in INSDC", + "examples": [ + { + "value": "https://identifiers.org/biosample:SAMEA5989477" + }, + { + "value": "https://identifiers.org/biosample:SAMD00212331", + "description": "I13_N_5-10 sample from Soil fungal diversity along elevational gradients" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://github.com/bioregistry/bioregistry/issues/108", + "https://www.ebi.ac.uk/biosamples/", + "https://www.ncbi.nlm.nih.gov/biosample", + "https://www.ddbj.nig.ac.jp/biosample/index-e.html" + ], + "aliases": [ + "EBI biosample identifiers", + "NCBI biosample identifiers", + "DDBJ biosample identifiers" + ], + "is_a": "biosample_identifiers", + "mixins": [ + "insdc_identifiers" + ], + "multivalued": true, + "alias": "insdc_biosample_identifiers", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "uriorcurie", + "pattern": "^biosample:SAM[NED]([A-Z])?[0-9]+$" + }, + "emsl_biosample_identifiers": { + "name": "emsl_biosample_identifiers", + "description": "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.", + "title": "EMSL Biosample Identifiers", + "todos": [ + "removed \"planned\" once NEXUS is online", + "make an emsl identifiers mixin", + "determine real expansion for emsl prefix" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "biosample_identifiers", + "multivalued": true, + "alias": "emsl_biosample_identifiers", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "uriorcurie" + }, + "igsn_biosample_identifiers": { + "name": "igsn_biosample_identifiers", + "description": "A list of identifiers for the biosample from the IGSN database.", + "title": "IGSN Biosample Identifiers", + "todos": [ + "make an igsn identifiers mixin" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "biosample_identifiers", + "multivalued": true, + "alias": "igsn_biosample_identifiers", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "uriorcurie" + }, + "agrochem_addition": { + "name": "agrochem_addition", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "agrochemical name;agrochemical amount;timestamp" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram, mole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications", + "title": "history/agrochemical additions", + "examples": [ + { + "value": "roundup;5 milligram per liter;2018-06-21" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "history/agrochemical additions" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{timestamp}", + "slot_uri": "mixs:0000639", + "multivalued": false, + "alias": "agrochem_addition", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "alkalinity": { + "name": "alkalinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliequivalent per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", + "title": "alkalinity", + "examples": [ + { + "value": "50 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "alkalinity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000421", + "multivalued": false, + "alias": "alkalinity", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "alkalinity_method": { + "name": "alkalinity_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "description of method" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Method used for alkalinity measurement", + "title": "alkalinity method", + "examples": [ + { + "value": "titration" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "alkalinity method" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000298", + "multivalued": false, + "alias": "alkalinity_method", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "alkyl_diethers": { + "name": "alkyl_diethers", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of alkyl diethers", + "title": "alkyl diethers", + "examples": [ + { + "value": "0.005 mole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "alkyl diethers" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000490", + "multivalued": false, + "alias": "alkyl_diethers", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "alt": { + "name": "alt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", + "title": "altitude", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "altitude" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000094", + "multivalued": false, + "alias": "alt", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "al_sat": { + "name": "al_sat", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Aluminum saturation (esp. For tropical soils)", + "title": "extreme_unusual_properties/Al saturation", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "extreme_unusual_properties/Al saturation" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000607", + "multivalued": false, + "alias": "al_sat", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "al_sat_meth": { + "name": "al_sat_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or URL" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining Al saturation", + "title": "extreme_unusual_properties/Al saturation method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "extreme_unusual_properties/Al saturation method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000324", + "multivalued": false, + "alias": "al_sat_meth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "aminopept_act": { + "name": "aminopept_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of aminopeptidase activity", + "title": "aminopeptidase activity", + "examples": [ + { + "value": "0.269 mole per liter per hour" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "aminopeptidase activity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000172", + "multivalued": false, + "alias": "aminopept_act", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "ammonium": { + "name": "ammonium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium in the sample", + "title": "ammonium", + "examples": [ + { + "value": "1.5 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "ammonium" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000427", + "multivalued": false, + "alias": "ammonium", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "annual_precpt": { + "name": "annual_precpt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", + "title": "mean annual precipitation", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mean annual precipitation" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000644", + "multivalued": false, + "alias": "annual_precpt", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "annual_temp": { + "name": "annual_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Mean annual temperature", + "title": "mean annual temperature", + "examples": [ + { + "value": "12.5 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mean annual temperature" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000642", + "multivalued": false, + "alias": "annual_temp", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "bacteria_carb_prod": { + "name": "bacteria_carb_prod", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "nanogram per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of bacterial carbon production", + "title": "bacterial carbon production", + "examples": [ + { + "value": "2.53 microgram per liter per hour" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "bacterial carbon production" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000173", + "multivalued": false, + "alias": "bacteria_carb_prod", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "bishomohopanol": { + "name": "bishomohopanol", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, microgram per gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of bishomohopanol", + "title": "bishomohopanol", + "examples": [ + { + "value": "14 microgram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "bishomohopanol" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000175", + "multivalued": false, + "alias": "bishomohopanol", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "bromide": { + "name": "bromide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of bromide", + "title": "bromide", + "examples": [ + { + "value": "0.05 parts per million" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "bromide" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000176", + "multivalued": false, + "alias": "bromide", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "calcium": { + "name": "calcium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, micromole per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of calcium in the sample", + "title": "calcium", + "examples": [ + { + "value": "0.2 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "calcium" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000432", + "multivalued": false, + "alias": "calcium", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "carb_nitro_ratio": { + "name": "carb_nitro_ratio", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ratio of amount or concentrations of carbon to nitrogen", + "title": "carbon/nitrogen ratio", + "examples": [ + { + "value": "0.417361111" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "carbon/nitrogen ratio" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000310", + "multivalued": false, + "alias": "carb_nitro_ratio", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "chem_administration": { + "name": "chem_administration", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "CHEBI;timestamp" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", + "title": "chemical administration", + "examples": [ + { + "value": "agar [CHEBI:2509];2018-05-11T20:00Z" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "chemical administration" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]};{timestamp}", + "slot_uri": "mixs:0000751", + "multivalued": false, + "alias": "chem_administration", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "ControlledTermValue" + }, + "chloride": { + "name": "chloride", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chloride in the sample", + "title": "chloride", + "examples": [ + { + "value": "5000 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "chloride" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000429", + "multivalued": false, + "alias": "chloride", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "chlorophyll": { + "name": "chlorophyll", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter, microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of chlorophyll", + "title": "chlorophyll", + "examples": [ + { + "value": "5 milligram per cubic meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "chlorophyll" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000177", + "multivalued": false, + "alias": "chlorophyll", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "collection_date": { + "name": "collection_date", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date and time" + } + }, + "description": "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant", + "title": "collection date", + "examples": [ + { + "value": "2018-05-11T10:00:00+01:00; 2018-05-11" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "collection date" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000011", + "multivalued": false, + "alias": "collection_date", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TimestampValue" + }, + "cur_land_use": { + "name": "cur_land_use", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Present state of sample site", + "title": "current land use", + "examples": [ + { + "value": "conifers" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "current land use" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001080", + "multivalued": false, + "alias": "cur_land_use", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "cur_vegetation": { + "name": "cur_vegetation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "current vegetation type" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Vegetation classification from one or more standard classification systems, or agricultural crop", + "title": "current vegetation", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "current vegetation" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000312", + "multivalued": false, + "alias": "cur_vegetation", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "cur_vegetation_meth": { + "name": "cur_vegetation_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in vegetation classification", + "title": "current vegetation method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "current vegetation method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000314", + "multivalued": false, + "alias": "cur_vegetation_meth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "crop_rotation": { + "name": "crop_rotation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "crop rotation status;schedule" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Whether or not crop is rotated, and if yes, rotation schedule", + "title": "history/crop rotation", + "examples": [ + { + "value": "yes;R2/2017-01-01/2018-12-31/P6M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "history/crop rotation" + ], + "is_a": "attribute", + "string_serialization": "{boolean};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000318", + "multivalued": false, + "alias": "crop_rotation", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "density": { + "name": "density", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter, gram per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", + "title": "density", + "examples": [ + { + "value": "1000 kilogram per cubic meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "density" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000435", + "multivalued": false, + "alias": "density", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "depth": { + "name": "depth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", + "title": "depth", + "examples": [ + { + "value": "10 meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "depth" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000018", + "multivalued": false, + "alias": "depth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "diss_carb_dioxide": { + "name": "diss_carb_dioxide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", + "title": "dissolved carbon dioxide", + "examples": [ + { + "value": "5 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "dissolved carbon dioxide" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000436", + "multivalued": false, + "alias": "diss_carb_dioxide", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "diss_hydrogen": { + "name": "diss_hydrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved hydrogen", + "title": "dissolved hydrogen", + "examples": [ + { + "value": "0.3 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "dissolved hydrogen" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000179", + "multivalued": false, + "alias": "diss_hydrogen", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "diss_inorg_carb": { + "name": "diss_inorg_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", + "title": "dissolved inorganic carbon", + "examples": [ + { + "value": "2059 micromole per kilogram" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "dissolved inorganic carbon" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000434", + "multivalued": false, + "alias": "diss_inorg_carb", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "diss_inorg_phosp": { + "name": "diss_inorg_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved inorganic phosphorus in the sample", + "title": "dissolved inorganic phosphorus", + "examples": [ + { + "value": "56.5 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "dissolved inorganic phosphorus" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000106", + "multivalued": false, + "alias": "diss_inorg_phosp", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "diss_org_carb": { + "name": "diss_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", + "title": "dissolved organic carbon", + "examples": [ + { + "value": "197 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "dissolved organic carbon" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000433", + "multivalued": false, + "alias": "diss_org_carb", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "diss_org_nitro": { + "name": "diss_org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", + "title": "dissolved organic nitrogen", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "dissolved organic nitrogen" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000162", + "multivalued": false, + "alias": "diss_org_nitro", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "diss_oxygen": { + "name": "diss_oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per kilogram, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of dissolved oxygen", + "title": "dissolved oxygen", + "examples": [ + { + "value": "175 micromole per kilogram" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "dissolved oxygen" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000119", + "multivalued": false, + "alias": "diss_oxygen", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "drainage_class": { + "name": "drainage_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Drainage classification from a standard system such as the USDA system", + "title": "drainage classification", + "examples": [ + { + "value": "well" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "drainage classification" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001085", + "multivalued": false, + "alias": "drainage_class", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "elev": { + "name": "elev", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + } + }, + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", + "title": "elevation", + "examples": [ + { + "value": "100 meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "elevation" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000093", + "multivalued": false, + "alias": "elev", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "env_package": { + "name": "env_package", + "description": "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported", + "in_subset": [ + "mixs extension" + ], + "from_schema": "https://microbiomedata/schema", + "source": "https://microbiomedata/schema/mixs", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "environmental package" + ], + "mappings": [ + "mixs:env_package" + ], + "is_a": "attribute", + "multivalued": false, + "alias": "env_package", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue", + "pattern": "[air|built environment|host\\-associated|human\\-associated|human\\-skin|human\\-oral|human\\-gut|human\\-vaginal|hydrocarbon resources\\-cores|hydrocarbon resources\\-fluids\\/swabs|microbial mat\\/biofilm|misc environment|plant\\-associated|sediment|soil|wastewater\\/sludge|water]" + }, + "env_broad_scale": { + "name": "env_broad_scale", + "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS", + "title": "broad-scale environmental context", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "mixs:0000012", + "multivalued": false, + "alias": "env_broad_scale", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "ControlledIdentifiedTermValue", + "required": true + }, + "env_local_scale": { + "name": "env_local_scale", + "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", + "title": "local environmental context", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "mixs:0000013", + "multivalued": false, + "alias": "env_local_scale", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "ControlledIdentifiedTermValue", + "required": true + }, + "env_medium": { + "name": "env_medium", + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", + "title": "environmental medium", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "mixs:0000014", + "multivalued": false, + "alias": "env_medium", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "ControlledIdentifiedTermValue", + "required": true + }, + "extreme_event": { + "name": "extreme_event", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date, string" + } + }, + "description": "Unusual physical events that may have affected microbial populations", + "title": "history/extreme events", + "examples": [ + { + "value": "1980-05-18, volcanic eruption" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "is_a": "attribute", + "slot_uri": "mixs:0000320", + "multivalued": false, + "alias": "extreme_event", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "fao_class": { + "name": "fao_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups", + "title": "soil_taxonomic/FAO classification", + "examples": [ + { + "value": "Luvisols" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "soil_taxonomic/FAO classification" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001083", + "multivalued": false, + "alias": "fao_class", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "fire": { + "name": "fire", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Historical and/or physical evidence of fire", + "title": "history/fire", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "history/fire" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001086", + "multivalued": false, + "alias": "fire", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TimestampValue" + }, + "flooding": { + "name": "flooding", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "date" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Historical and/or physical evidence of flooding", + "title": "history/flooding", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "history/flooding" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000319", + "multivalued": false, + "alias": "flooding", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TimestampValue" + }, + "geo_loc_name": { + "name": "geo_loc_name", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" + } + }, + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)", + "title": "geographic location (country and/or sea,region)", + "examples": [ + { + "value": "USA: Maryland, Bethesda" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "geographic location (country and/or sea,region)" + ], + "is_a": "attribute", + "string_serialization": "{term}: {term}, {text}", + "slot_uri": "mixs:0000010", + "multivalued": false, + "alias": "geo_loc_name", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "glucosidase_act": { + "name": "glucosidase_act", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mol per liter per hour" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of glucosidase activity", + "title": "glucosidase activity", + "examples": [ + { + "value": "5 mol per liter per hour" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "glucosidase activity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000137", + "multivalued": false, + "alias": "glucosidase_act", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "heavy_metals": { + "name": "heavy_metals", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "heavy metal name;measurement value unit" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per gram" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field.", + "title": "extreme_unusual_properties/heavy metals", + "examples": [ + { + "value": "mercury;0.09 micrograms per gram" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "extreme_unusual_properties/heavy metals" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000652", + "multivalued": false, + "alias": "heavy_metals", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "heavy_metals_meth": { + "name": "heavy_metals_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining heavy metals", + "title": "extreme_unusual_properties/heavy metals method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "extreme_unusual_properties/heavy metals method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000343", + "multivalued": false, + "alias": "heavy_metals_meth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "lat_lon": { + "name": "lat_lon", + "description": "This is currently a required field but it's not clear if this should be required for human hosts", + "title": "geographic location (latitude and longitude)", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "is_a": "attribute", + "string_serialization": "{float} {float}", + "slot_uri": "mixs:0000009", + "multivalued": false, + "alias": "lat_lon", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "GeolocationValue", + "required": false + }, + "link_addit_analys": { + "name": "link_addit_analys", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Link to additional analysis results performed on the sample", + "title": "links to additional analysis", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "links to additional analysis" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000340", + "multivalued": false, + "alias": "link_addit_analys", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "link_class_info": { + "name": "link_class_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Link to digitized soil maps or other soil classification information", + "title": "link to classification information", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "link to classification information" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000329", + "multivalued": false, + "alias": "link_class_info", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "link_climate_info": { + "name": "link_climate_info", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Link to climate resource", + "title": "link to climate information", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "link to climate information" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000328", + "multivalued": false, + "alias": "link_climate_info", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "local_class": { + "name": "local_class", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "local classification name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Soil classification based on local soil classification system", + "title": "soil_taxonomic/local classification", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "soil_taxonomic/local classification" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000330", + "multivalued": false, + "alias": "local_class", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "local_class_meth": { + "name": "local_class_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining the local soil classification", + "title": "soil_taxonomic/local classification method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "soil_taxonomic/local classification method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000331", + "multivalued": false, + "alias": "local_class_meth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "magnesium": { + "name": "magnesium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of magnesium in the sample", + "title": "magnesium", + "examples": [ + { + "value": "52.8 micromole per kilogram" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "magnesium" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000431", + "multivalued": false, + "alias": "magnesium", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "mean_frict_vel": { + "name": "mean_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean friction velocity", + "title": "mean friction velocity", + "examples": [ + { + "value": "0.5 meter per second" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mean friction velocity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000498", + "multivalued": false, + "alias": "mean_frict_vel", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "mean_peak_frict_vel": { + "name": "mean_peak_frict_vel", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter per second" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of mean peak friction velocity", + "title": "mean peak friction velocity", + "examples": [ + { + "value": "1 meter per second" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mean peak friction velocity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000502", + "multivalued": false, + "alias": "mean_peak_frict_vel", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "misc_param": { + "name": "misc_param", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "parameter name;measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Any other measurement performed or parameter collected, that is not listed here", + "title": "miscellaneous parameter", + "examples": [ + { + "value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "miscellaneous parameter" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000752", + "multivalued": false, + "alias": "misc_param", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "n_alkanes": { + "name": "n_alkanes", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "n-alkane name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of n-alkanes; can include multiple n-alkanes", + "title": "n-alkanes", + "examples": [ + { + "value": "n-hexadecane;100 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "n-alkanes" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000503", + "multivalued": false, + "alias": "n_alkanes", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "nitrate": { + "name": "nitrate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate in the sample", + "title": "nitrate", + "examples": [ + { + "value": "65 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "nitrate" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000425", + "multivalued": false, + "alias": "nitrate", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "nitrite": { + "name": "nitrite", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite in the sample", + "title": "nitrite", + "examples": [ + { + "value": "0.5 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "nitrite" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000426", + "multivalued": false, + "alias": "nitrite", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "org_matter": { + "name": "org_matter", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic matter", + "title": "organic matter", + "examples": [ + { + "value": "1.75 milligram per cubic meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "organic matter" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000204", + "multivalued": false, + "alias": "org_matter", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "org_nitro": { + "name": "org_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of organic nitrogen", + "title": "organic nitrogen", + "examples": [ + { + "value": "4 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "organic nitrogen" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000205", + "multivalued": false, + "alias": "org_nitro", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "organism_count": { + "name": "organism_count", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "organism name;measurement value;enumeration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", + "title": "organism count", + "examples": [ + { + "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "organism count" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000103", + "multivalued": false, + "alias": "organism_count", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "oxy_stat_samp": { + "name": "oxy_stat_samp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Oxygenation status of sample", + "title": "oxygenation status of sample", + "examples": [ + { + "value": "aerobic" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "oxygenation status of sample" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000753", + "multivalued": false, + "alias": "oxy_stat_samp", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "part_org_carb": { + "name": "part_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of particulate organic carbon", + "title": "particulate organic carbon", + "examples": [ + { + "value": "1.92 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "particulate organic carbon" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000515", + "multivalued": false, + "alias": "part_org_carb", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "perturbation": { + "name": "perturbation", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "perturbation type name;perturbation interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", + "title": "perturbation", + "examples": [ + { + "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "perturbation" + ], + "is_a": "attribute", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000754", + "multivalued": false, + "alias": "perturbation", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "petroleum_hydrocarb": { + "name": "petroleum_hydrocarb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of petroleum hydrocarbon", + "title": "petroleum hydrocarbon", + "examples": [ + { + "value": "0.05 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "petroleum hydrocarbon" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000516", + "multivalued": false, + "alias": "petroleum_hydrocarb", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "ph": { + "name": "ph", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", + "title": "pH", + "examples": [ + { + "value": "7.2" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pH" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001001", + "multivalued": false, + "alias": "ph", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "ph_meth": { + "name": "ph_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining ph", + "title": "pH method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pH method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0001106", + "multivalued": false, + "alias": "ph_meth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "phaeopigments": { + "name": "phaeopigments", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "phaeopigment name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of phaeopigments; can include multiple phaeopigments", + "title": "phaeopigments", + "examples": [ + { + "value": "2.5 milligram per cubic meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "phaeopigments" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000180", + "multivalued": false, + "alias": "phaeopigments", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "phosplipid_fatt_acid": { + "name": "phosplipid_fatt_acid", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "phospholipid fatty acid name;measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mole per gram, mole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Concentration of phospholipid fatty acids; can include multiple values", + "title": "phospholipid fatty acid", + "examples": [ + { + "value": "2.98 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "phospholipid fatty acid" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit}", + "slot_uri": "mixs:0000181", + "multivalued": false, + "alias": "phosplipid_fatt_acid", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "pool_dna_extracts": { + "name": "pool_dna_extracts", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "pooling status;number of pooled extracts" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given", + "title": "pooling of DNA extracts (if done)", + "examples": [ + { + "value": "yes;5" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pooling of DNA extracts (if done)" + ], + "is_a": "attribute", + "string_serialization": "{boolean};{integer}", + "slot_uri": "mixs:0000325", + "multivalued": false, + "alias": "pool_dna_extracts", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "potassium": { + "name": "potassium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of potassium in the sample", + "title": "potassium", + "examples": [ + { + "value": "463 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "potassium" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000430", + "multivalued": false, + "alias": "potassium", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "pressure": { + "name": "pressure", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "atmosphere" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Pressure to which the sample is subject to, in atmospheres", + "title": "pressure", + "examples": [ + { + "value": "50 atmosphere" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pressure" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000412", + "multivalued": false, + "alias": "pressure", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "profile_position": { + "name": "profile_position", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas", + "title": "profile position", + "examples": [ + { + "value": "summit" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "profile position" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001084", + "multivalued": false, + "alias": "profile_position", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "redox_potential": { + "name": "redox_potential", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millivolt" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", + "title": "redox potential", + "examples": [ + { + "value": "300 millivolt" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "redox potential" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000182", + "multivalued": false, + "alias": "redox_potential", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "salinity": { + "name": "salinity", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "practical salinity unit, percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", + "title": "salinity", + "examples": [ + { + "value": "25 practical salinity unit" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "salinity" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000183", + "multivalued": false, + "alias": "salinity", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "salinity_meth": { + "name": "salinity_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining salinity", + "title": "salinity method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "salinity method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000341", + "multivalued": false, + "alias": "salinity_meth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "samp_mat_process": { + "name": "samp_mat_process", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text" + } + }, + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", + "title": "sample material processing", + "examples": [ + { + "value": "filtering of seawater, storing samples in ethanol" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample material processing" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000016", + "multivalued": false, + "alias": "samp_mat_process", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "ControlledTermValue" + }, + "samp_store_dur": { + "name": "samp_store_dur", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Duration for which the sample was stored", + "title": "sample storage duration", + "examples": [ + { + "value": "P1Y6M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample storage duration" + ], + "is_a": "attribute", + "string_serialization": "{duration}", + "slot_uri": "mixs:0000116", + "multivalued": false, + "alias": "samp_store_dur", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "samp_store_loc": { + "name": "samp_store_loc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "location name" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Location at which sample was stored, usually name of a specific freezer/room", + "title": "sample storage location", + "examples": [ + { + "value": "Freezer no:5" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample storage location" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000755", + "multivalued": false, + "alias": "samp_store_loc", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "samp_store_temp": { + "name": "samp_store_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Temperature at which sample was stored, e.g. -80 degree Celsius", + "title": "sample storage temperature", + "examples": [ + { + "value": "-80 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample storage temperature" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000110", + "multivalued": false, + "alias": "samp_store_temp", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "samp_vol_we_dna_ext": { + "name": "samp_vol_we_dna_ext", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, square centimeter" + } + }, + "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001).", + "title": "sample volume or weight for DNA extraction", + "examples": [ + { + "value": "1500 milliliter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample volume or weight for DNA extraction" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000111", + "multivalued": false, + "alias": "samp_vol_we_dna_ext", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "OmicsProcessing" + ], + "range": "QuantityValue" + }, + "season_temp": { + "name": "season_temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Mean seasonal temperature", + "title": "mean seasonal temperature", + "examples": [ + { + "value": "18 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mean seasonal temperature" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000643", + "multivalued": false, + "alias": "season_temp", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "season_precpt": { + "name": "season_precpt", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", + "title": "mean seasonal precipitation", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "mean seasonal precipitation" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000645", + "multivalued": false, + "alias": "season_precpt", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "sieving": { + "name": "sieving", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "design name and/or size;amount" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved", + "title": "composite design/sieving", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "composite design/sieving" + ], + "is_a": "attribute", + "string_serialization": "{{text}|{float} {unit}};{float} {unit}", + "slot_uri": "mixs:0000322", + "multivalued": false, + "alias": "sieving", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "size_frac_low": { + "name": "size_frac_low", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample", + "title": "size-fraction lower threshold", + "examples": [ + { + "value": "0.2 micrometer" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "size-fraction lower threshold" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000735", + "multivalued": false, + "alias": "size_frac_low", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "size_frac_up": { + "name": "size_frac_up", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micrometer" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample", + "title": "size-fraction upper threshold", + "examples": [ + { + "value": "20 micrometer" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "size-fraction upper threshold" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000736", + "multivalued": false, + "alias": "size_frac_up", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "slope_gradient": { + "name": "slope_gradient", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "percentage" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer", + "title": "slope gradient", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "slope gradient" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000646", + "multivalued": false, + "alias": "slope_gradient", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "slope_aspect": { + "name": "slope_aspect", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.", + "title": "slope aspect", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "slope aspect" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000647", + "multivalued": false, + "alias": "slope_aspect", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "sodium": { + "name": "sodium", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Sodium concentration in the sample", + "title": "sodium", + "examples": [ + { + "value": "10.5 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sodium" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000428", + "multivalued": false, + "alias": "sodium", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "soil_type": { + "name": "soil_type", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "ENVO_00001998" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.", + "title": "soil type", + "examples": [ + { + "value": "plinthosol [ENVO:00002250]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "soil type" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}", + "slot_uri": "mixs:0000332", + "multivalued": false, + "alias": "soil_type", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "soil_type_meth": { + "name": "soil_type_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining soil series name or other lower-level classification", + "title": "soil type method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "soil type method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000334", + "multivalued": false, + "alias": "soil_type_meth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "store_cond": { + "name": "store_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "storage condition type;duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).", + "title": "storage conditions", + "examples": [ + { + "value": "-20 degree Celsius freezer;P2Y10D" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "storage conditions" + ], + "is_a": "attribute", + "string_serialization": "{text};{duration}", + "slot_uri": "mixs:0000327", + "multivalued": false, + "alias": "store_cond", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "sulfate": { + "name": "sulfate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfate in the sample", + "title": "sulfate", + "examples": [ + { + "value": "5 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sulfate" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000423", + "multivalued": false, + "alias": "sulfate", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "sulfide": { + "name": "sulfide", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of sulfide in the sample", + "title": "sulfide", + "examples": [ + { + "value": "2 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sulfide" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000424", + "multivalued": false, + "alias": "sulfide", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "temp": { + "name": "temp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "degree Celsius" + } + }, + "description": "Temperature of the sample at the time of sampling.", + "title": "temperature", + "examples": [ + { + "value": "25 degree Celsius" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "temperature" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000113", + "multivalued": false, + "alias": "temp", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "tillage": { + "name": "tillage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Note method(s) used for tilling", + "title": "history/tillage", + "examples": [ + { + "value": "chisel" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "history/tillage" + ], + "is_a": "attribute", + "slot_uri": "mixs:0001081", + "multivalued": false, + "alias": "tillage", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "tidal_stage": { + "name": "tidal_stage", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Stage of tide", + "title": "tidal stage", + "examples": [ + { + "value": "high tide" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "tidal stage" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000750", + "multivalued": false, + "alias": "tidal_stage", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "tot_carb": { + "name": "tot_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total carbon content", + "title": "total carbon", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total carbon" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000525", + "multivalued": false, + "alias": "tot_carb", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "tot_depth_water_col": { + "name": "tot_depth_water_col", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Measurement of total depth of water column", + "title": "total depth of water column", + "examples": [ + { + "value": "500 meter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total depth of water column" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000634", + "multivalued": false, + "alias": "tot_depth_water_col", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "tot_diss_nitro": { + "name": "tot_diss_nitro", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen", + "title": "total dissolved nitrogen", + "examples": [ + { + "value": "40 microgram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total dissolved nitrogen" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000744", + "multivalued": false, + "alias": "tot_diss_nitro", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "tot_org_carb": { + "name": "tot_org_carb", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram Carbon per kilogram sample material" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", + "title": "total organic carbon", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total organic carbon" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000533", + "multivalued": false, + "alias": "tot_org_carb", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "tot_org_c_meth": { + "name": "tot_org_c_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Reference or method used in determining total organic carbon", + "title": "total organic carbon method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total organic carbon method" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000337", + "multivalued": false, + "alias": "tot_org_c_meth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "tot_nitro_content": { + "name": "tot_nitro_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "microgram per liter, micromole per liter, milligram per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total nitrogen content of the sample", + "title": "total nitrogen content", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total nitrogen content" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000530", + "multivalued": false, + "alias": "tot_nitro_content", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "tot_nitro_cont_meth": { + "name": "tot_nitro_cont_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + }, + "mixs_5_name": { + "tag": "mixs_5_name", + "value": "tot_nitro_content_meth" + } + }, + "description": "Reference or method used in determining the total nitrogen", + "title": "total nitrogen content method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total nitrogen content method" + ], + "is_a": "core_field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000338", + "multivalued": false, + "alias": "tot_nitro_cont_meth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "tot_phosp": { + "name": "tot_phosp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter, milligram per liter, parts per million" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", + "title": "total phosphorus", + "examples": [ + { + "value": "0.03 milligram per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "total phosphorus" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000117", + "multivalued": false, + "alias": "tot_phosp", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "water_content": { + "name": "water_content", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per gram or cubic centimeter per cubic centimeter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Water content measurement", + "title": "water content", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "water content" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000185", + "multivalued": false, + "alias": "water_content", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "water_cont_soil_meth": { + "name": "water_cont_soil_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI or url" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + }, + "mixs_5_name": { + "tag": "mixs_5_name", + "value": "water_content_soil_meth" + } + }, + "description": "Reference or method used in determining the water content of soil", + "title": "water content method", + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "water content method" + ], + "is_a": "core_field", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000323", + "multivalued": false, + "alias": "water_cont_soil_meth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "alias": "ecosystem", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study" + ], + "range": "string" + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "alias": "ecosystem_category", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study" + ], + "range": "string" + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "alias": "ecosystem_type", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study" + ], + "range": "string" + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "alias": "ecosystem_subtype", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study" + ], + "range": "string" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "alias": "specific_ecosystem", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "Study" + ], + "range": "string" + }, + "add_date": { + "name": "add_date", + "description": "The date on which the information was added to the database.", + "from_schema": "https://microbiomedata/schema", + "alias": "add_date", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "OmicsProcessing" + ], + "range": "string" + }, + "community": { + "name": "community", + "from_schema": "https://microbiomedata/schema", + "alias": "community", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "habitat": { + "name": "habitat", + "from_schema": "https://microbiomedata/schema", + "alias": "habitat", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "host_name": { + "name": "host_name", + "from_schema": "https://microbiomedata/schema", + "alias": "host_name", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "location": { + "name": "location", + "from_schema": "https://microbiomedata/schema", + "alias": "location", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "mod_date": { + "name": "mod_date", + "description": "The last date on which the database information was modified.", + "from_schema": "https://microbiomedata/schema", + "alias": "mod_date", + "owner": "Biosample", + "domain_of": [ + "Biosample", + "OmicsProcessing" + ], + "range": "string" + }, + "ncbi_taxonomy_name": { + "name": "ncbi_taxonomy_name", + "from_schema": "https://microbiomedata/schema", + "alias": "ncbi_taxonomy_name", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "proport_woa_temperature": { + "name": "proport_woa_temperature", + "from_schema": "https://microbiomedata/schema", + "alias": "proport_woa_temperature", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "salinity_category": { + "name": "salinity_category", + "description": "Categorcial description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline", + "notes": [ + "maps to gold:salinity" + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://github.com/microbiomedata/nmdc-metadata/pull/297" + ], + "alias": "salinity_category", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "sample_collection_site": { + "name": "sample_collection_site", + "from_schema": "https://microbiomedata/schema", + "alias": "sample_collection_site", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "soluble_iron_micromol": { + "name": "soluble_iron_micromol", + "from_schema": "https://microbiomedata/schema", + "alias": "soluble_iron_micromol", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "subsurface_depth": { + "name": "subsurface_depth", + "from_schema": "https://microbiomedata/schema", + "alias": "subsurface_depth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "air_temp_regm": { + "name": "air_temp_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "temperature value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", + "title": "air temperature regimen", + "examples": [ + { + "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "air temperature regimen" + ], + "is_a": "attribute", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000551", + "multivalued": false, + "alias": "air_temp_regm", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "biotic_regm": { + "name": "biotic_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", + "title": "biotic regimen", + "examples": [ + { + "value": "sample inoculated with Rhizobium spp. Culture" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "biotic regimen" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0001038", + "multivalued": false, + "alias": "biotic_regm", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "biotic_relationship": { + "name": "biotic_relationship", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + } + }, + "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object", + "title": "observed biotic relationship", + "examples": [ + { + "value": "free living" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "observed biotic relationship" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000028", + "multivalued": false, + "alias": "biotic_relationship", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "climate_environment": { + "name": "climate_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "climate name;treatment interval and duration" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", + "title": "climate environment", + "examples": [ + { + "value": "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "climate environment" + ], + "is_a": "attribute", + "string_serialization": "{text};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0001040", + "multivalued": false, + "alias": "climate_environment", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "experimental_factor": { + "name": "experimental_factor", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "text or EFO and/or OBI" + } + }, + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", + "title": "experimental factor", + "examples": [ + { + "value": "time series design [EFO:EFO_0001779]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "experimental factor" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "mixs:0000008", + "multivalued": false, + "alias": "experimental_factor", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "ControlledTermValue" + }, + "gaseous_environment": { + "name": "gaseous_environment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gaseous compound name;gaseous compound amount;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", + "title": "gaseous environment", + "examples": [ + { + "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "gaseous environment" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000558", + "multivalued": false, + "alias": "gaseous_environment", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "growth_facil": { + "name": "growth_facil", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "free text or CO" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research", + "title": "growth facility", + "examples": [ + { + "value": "Growth chamber [CO_715:0000189]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "growth facility" + ], + "is_a": "attribute", + "string_serialization": "{text}|{termLabel} {[termID]}", + "slot_uri": "mixs:0001043", + "multivalued": false, + "alias": "growth_facil", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "ControlledTermValue" + }, + "humidity_regm": { + "name": "humidity_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "humidity value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "gram per cubic meter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "humidity regimen", + "examples": [ + { + "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "humidity regimen" + ], + "is_a": "attribute", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000568", + "multivalued": false, + "alias": "humidity_regm", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "light_regm": { + "name": "light_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "exposure type;light intensity;light quality" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "lux; micrometer, nanometer, angstrom" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", + "title": "light regimen", + "examples": [ + { + "value": "incandescant light;10 lux;450 nanometer" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "light regimen" + ], + "is_a": "attribute", + "string_serialization": "{text};{float} {unit};{float} {unit}", + "slot_uri": "mixs:0000569", + "multivalued": false, + "alias": "light_regm", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "phosphate": { + "name": "phosphate", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "micromole per liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of phosphate", + "title": "phosphate", + "examples": [ + { + "value": "0.7 micromole per liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "phosphate" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000505", + "multivalued": false, + "alias": "phosphate", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "rel_to_oxygen": { + "name": "rel_to_oxygen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "enumeration" + } + }, + "description": "Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments", + "title": "relationship to oxygen", + "examples": [ + { + "value": "aerobe" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "relationship to oxygen" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000015", + "multivalued": false, + "alias": "rel_to_oxygen", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "samp_collec_method": { + "name": "samp_collec_method", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID,DOI,url , or text" + } + }, + "description": "The method employed for collecting the sample.", + "title": "sample collection method", + "examples": [ + { + "value": "swabbing" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample collection method" + ], + "is_a": "nucleic_acid_sequence_source_field", + "string_serialization": "{PMID}|{DOI}|{URL}|{text}", + "slot_uri": "mixs:0001225", + "multivalued": false, + "alias": "samp_collec_method", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "string" + }, + "samp_size": { + "name": "samp_size", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, liter" + } + }, + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", + "title": "amount or size of sample collected", + "examples": [ + { + "value": "5 liter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "amount or size of sample collected" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000001", + "multivalued": false, + "alias": "samp_size", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "source_mat_id": { + "name": "source_mat_id", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" + } + }, + "description": "A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).", + "title": "source material identifiers", + "examples": [ + { + "value": "MPI012345" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "source material identifiers" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000026", + "multivalued": false, + "alias": "source_mat_id", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "TextValue" + }, + "watering_regm": { + "name": "watering_regm", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value;treatment interval and duration" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "milliliter, liter" + }, + "occurrence": { + "tag": "occurrence", + "value": "m" + } + }, + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", + "title": "watering regimen", + "examples": [ + { + "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "watering regimen" + ], + "is_a": "attribute", + "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", + "slot_uri": "mixs:0000591", + "multivalued": false, + "alias": "watering_regm", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "dna_absorb1": { + "name": "dna_absorb1", + "description": "260/280 measurement of DNA sample purity", + "title": "DNA absorbance 260/280", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 7, + "string_serialization": "{float}", + "alias": "dna_absorb1", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "recommended": true + }, + "dna_absorb2": { + "name": "dna_absorb2", + "description": "260/230 measurement of DNA sample purity", + "title": "DNA absorbance 260/230", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 8, + "string_serialization": "{float}", + "alias": "dna_absorb2", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "recommended": true + }, + "dna_collect_site": { + "name": "dna_collect_site", + "description": "Provide information on the site your DNA sample was collected from", + "title": "DNA collection site", + "examples": [ + { + "value": "untreated pond water" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 15, + "string_serialization": "{text}", + "alias": "dna_collect_site", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "required": false, + "recommended": true + }, + "dna_concentration": { + "name": "dna_concentration", + "title": "DNA concentration in ng/ul", + "comments": [ + "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 5, + "string_serialization": "{float}", + "alias": "dna_concentration", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "required": false, + "recommended": true, + "minimum_value": 0, + "maximum_value": 2000 + }, + "dna_cont_type": { + "name": "dna_cont_type", + "description": "Tube or plate (96-well)", + "title": "DNA container type", + "examples": [ + { + "value": "plate" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 10, + "alias": "dna_cont_type", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "dna_cont_type_enum", + "required": false, + "recommended": true + }, + "dna_cont_well": { + "name": "dna_cont_well", + "title": "DNA plate position", + "comments": [ + "Required when 'plate' is selected for container type.", + "Leave blank if the sample will be shipped in a tube.", + "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", + "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." + ], + "examples": [ + { + "value": "B2" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 11, + "string_serialization": "{96 well plate pos}", + "alias": "dna_cont_well", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "required": false, + "recommended": true, + "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" + }, + "dna_container_id": { + "name": "dna_container_id", + "title": "DNA container label", + "comments": [ + "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." + ], + "examples": [ + { + "value": "Pond_MT_041618" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 9, + "string_serialization": "{text < 20 characters}", + "alias": "dna_container_id", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "required": false, + "recommended": true + }, + "dna_dnase": { + "name": "dna_dnase", + "title": "DNase treatment DNA", + "comments": [ + "Note DNAse treatment is required for all RNA samples." + ], + "examples": [ + { + "value": "no" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 13, + "alias": "dna_dnase", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "dna_dnase_enum", + "required": false, + "recommended": true + }, + "dna_isolate_meth": { + "name": "dna_isolate_meth", + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "title": "DNA isolation method", + "examples": [ + { + "value": "phenol/chloroform extraction" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 16, + "string_serialization": "{text}", + "alias": "dna_isolate_meth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "required": false, + "recommended": true + }, + "dna_organisms": { + "name": "dna_organisms", + "description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", + "title": "DNA expected organisms", + "examples": [ + { + "value": "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 14, + "string_serialization": "{text}", + "alias": "dna_organisms", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "recommended": true + }, + "dna_project_contact": { + "name": "dna_project_contact", + "title": "DNA seq project contact", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "John Jones" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 18, + "string_serialization": "{text}", + "alias": "dna_project_contact", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "required": false, + "recommended": true + }, + "dna_samp_id": { + "name": "dna_samp_id", + "title": "DNA sample ID", + "todos": [ + "Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled?" + ], + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "187654" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 3, + "string_serialization": "{text}", + "alias": "dna_samp_id", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "required": false, + "recommended": true + }, + "dna_sample_format": { + "name": "dna_sample_format", + "description": "Solution in which the DNA sample has been suspended", + "title": "DNA sample format", + "examples": [ + { + "value": "Water" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 12, + "alias": "dna_sample_format", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "dna_sample_format_enum", + "required": false, + "recommended": true + }, + "dna_sample_name": { + "name": "dna_sample_name", + "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "title": "DNA sample name", + "examples": [ + { + "value": "JGI_pond_041618" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 4, + "string_serialization": "{text}", + "alias": "dna_sample_name", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "required": false, + "recommended": true + }, + "dna_seq_project": { + "name": "dna_seq_project", + "title": "DNA seq project ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "1191234" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 1, + "string_serialization": "{text}", + "alias": "dna_seq_project", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "required": false, + "recommended": true + }, + "dna_seq_project_pi": { + "name": "dna_seq_project_pi", + "title": "DNA seq project PI", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "Jane Johnson" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 17, + "string_serialization": "{text}", + "alias": "dna_seq_project_pi", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "required": false, + "recommended": true + }, + "dna_seq_project_name": { + "name": "dna_seq_project_name", + "title": "DNA seq project name", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "JGI Pond metagenomics" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 2, + "string_serialization": "{text}", + "alias": "dna_seq_project_name", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "required": false, + "recommended": true + }, + "dna_volume": { + "name": "dna_volume", + "title": "DNA volume in ul", + "comments": [ + "Units must be in uL. Enter the numerical part only. Value must 0-1000. Values <25 by special permission only." + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 6, + "string_serialization": "{float}", + "alias": "dna_volume", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "required": false, + "recommended": true, + "minimum_value": 0, + "maximum_value": 1000 + }, + "proposal_dna": { + "name": "proposal_dna", + "title": "DNA proposal ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "504000" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 19, + "string_serialization": "{text}", + "alias": "proposal_dna", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metagenomics", + "range": "string", + "required": false, + "recommended": true + }, + "dnase_rna": { + "name": "dnase_rna", + "title": "DNase treated", + "comments": [ + "Note DNAse treatment is required for all RNA samples." + ], + "examples": [ + { + "value": "no" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 13, + "alias": "dnase_rna", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "dnase_rna_enum", + "required": false, + "recommended": true + }, + "proposal_rna": { + "name": "proposal_rna", + "title": "RNA proposal ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "504000" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 19, + "string_serialization": "{text}", + "alias": "proposal_rna", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "required": false, + "recommended": true + }, + "rna_absorb1": { + "name": "rna_absorb1", + "description": "260/280 measurement of RNA sample purity", + "title": "RNA absorbance 260/280", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 7, + "string_serialization": "{float}", + "alias": "rna_absorb1", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "recommended": true + }, + "rna_absorb2": { + "name": "rna_absorb2", + "description": "260/230 measurement of RNA sample purity", + "title": "RNA absorbance 260/230", + "comments": [ + "Recommended value is between 1 and 3." + ], + "examples": [ + { + "value": "2.02" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 8, + "string_serialization": "{float}", + "alias": "rna_absorb2", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "recommended": true + }, + "rna_collect_site": { + "name": "rna_collect_site", + "description": "Provide information on the site your RNA sample was collected from", + "title": "RNA collection site", + "examples": [ + { + "value": "untreated pond water" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 15, + "string_serialization": "{text}", + "alias": "rna_collect_site", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "required": false, + "recommended": true + }, + "rna_concentration": { + "name": "rna_concentration", + "title": "RNA concentration in ng/ul", + "comments": [ + "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 5, + "string_serialization": "{float}", + "alias": "rna_concentration", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "required": false, + "recommended": true, + "minimum_value": 0, + "maximum_value": 1000 + }, + "rna_cont_type": { + "name": "rna_cont_type", + "description": "Tube or plate (96-well)", + "title": "RNA container type", + "examples": [ + { + "value": "plate" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 10, + "alias": "rna_cont_type", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "rna_cont_type_enum", + "required": false, + "recommended": true + }, + "rna_cont_well": { + "name": "rna_cont_well", + "title": "RNA plate position", + "comments": [ + "Required when 'plate' is selected for container type.", + "Leave blank if the sample will be shipped in a tube.", + "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", + "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." + ], + "examples": [ + { + "value": "B2" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 11, + "string_serialization": "{96 well plate pos}", + "alias": "rna_cont_well", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "required": false, + "recommended": true, + "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" + }, + "rna_container_id": { + "name": "rna_container_id", + "title": "RNA container label", + "comments": [ + "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." + ], + "examples": [ + { + "value": "Pond_MT_041618" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 9, + "string_serialization": "{text}", + "alias": "rna_container_id", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "required": false, + "recommended": true + }, + "rna_isolate_meth": { + "name": "rna_isolate_meth", + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "title": "RNA isolation method", + "examples": [ + { + "value": "phenol/chloroform extraction" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 16, + "string_serialization": "{text}", + "alias": "rna_isolate_meth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "required": false, + "recommended": true + }, + "rna_organisms": { + "name": "rna_organisms", + "description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", + "title": "RNA expected organisms", + "examples": [ + { + "value": "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 14, + "string_serialization": "{text}", + "alias": "rna_organisms", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "recommended": true + }, + "rna_project_contact": { + "name": "rna_project_contact", + "title": "RNA seq project contact", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "John Jones" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 18, + "string_serialization": "{text}", + "alias": "rna_project_contact", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "required": false, + "recommended": true + }, + "rna_samp_id": { + "name": "rna_samp_id", + "title": "RNA sample ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "187654" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 3, + "string_serialization": "{text}", + "alias": "rna_samp_id", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "required": false, + "recommended": true + }, + "rna_sample_format": { + "name": "rna_sample_format", + "description": "Solution in which the RNA sample has been suspended", + "title": "RNA sample format", + "examples": [ + { + "value": "Water" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 12, + "alias": "rna_sample_format", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "rna_sample_format_enum", + "required": false, + "recommended": true + }, + "rna_sample_name": { + "name": "rna_sample_name", + "description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "title": "RNA sample name", + "examples": [ + { + "value": "JGI_pond_041618" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 4, + "string_serialization": "{text}", + "alias": "rna_sample_name", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "required": false, + "recommended": true, + "minimum_value": 0, + "maximum_value": 2000 + }, + "rna_seq_project": { + "name": "rna_seq_project", + "title": "RNA seq project ID", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "1191234" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 1, + "string_serialization": "{text}", + "alias": "rna_seq_project", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "required": false, + "recommended": true + }, + "rna_seq_project_pi": { + "name": "rna_seq_project_pi", + "title": "RNA seq project PI", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "Jane Johnson" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 17, + "string_serialization": "{text}", + "alias": "rna_seq_project_pi", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "required": false, + "recommended": true + }, + "rna_seq_project_name": { + "name": "rna_seq_project_name", + "title": "RNA seq project name", + "comments": [ + "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." + ], + "examples": [ + { + "value": "JGI Pond metatranscriptomics" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 2, + "string_serialization": "{text}", + "alias": "rna_seq_project_name", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "required": false, + "recommended": true + }, + "rna_volume": { + "name": "rna_volume", + "title": "RNA volume in ul", + "comments": [ + "Units must be in uL. Enter the numerical part only. Value must 0-1000. Values <25 by special permission only." + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 6, + "string_serialization": "{float}", + "alias": "rna_volume", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "JGI-Metatranscriptomics", + "range": "string", + "required": false, + "recommended": true + }, + "collection_date_inc": { + "name": "collection_date_inc", + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:collection_date" + ], + "rank": 2, + "string_serialization": "{date, arbitrary precision}", + "alias": "collection_date_inc", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string", + "recommended": true + }, + "collection_time": { + "name": "collection_time", + "description": "The time of sampling, either as an instance (single point) or interval.", + "title": "collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:collection_date" + ], + "rank": 1, + "string_serialization": "{time, seconds optional}", + "alias": "collection_time", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string", + "recommended": true + }, + "collection_time_inc": { + "name": "collection_time_inc", + "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "title": "incubation collection time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:collection_date" + ], + "rank": 3, + "string_serialization": "{time, seconds optional}", + "alias": "collection_time_inc", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string", + "recommended": true + }, + "experimental_factor_other": { + "name": "experimental_factor_other", + "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", + "title": "experimental factor- other", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:experimental_factor|additional_info" + ], + "rank": 7, + "string_serialization": "{text}", + "alias": "experimental_factor_other", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string", + "recommended": true + }, + "filter_method": { + "name": "filter_method", + "description": "Type of filter used or how the sample was filtered", + "title": "filter method", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:filter_type" + ], + "rank": 6, + "string_serialization": "{text}", + "alias": "filter_method", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string", + "recommended": true + }, + "isotope_exposure": { + "name": "isotope_exposure", + "description": "List isotope exposure or addition applied to your sample.", + "title": "isotope exposure/addition", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:chem_administration" + ], + "rank": 16, + "string_serialization": "{termLabel} {[termID]}; {timestamp}", + "alias": "isotope_exposure", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string", + "recommended": true + }, + "micro_biomass_c_meth": { + "name": "micro_biomass_c_meth", + "description": "Reference or method used in determining microbial biomass", + "title": "microbial biomass carbon method", + "comments": [ + "required if \"microbial_biomass_c\" is provided" + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:micro_biomass_meth" + ], + "rank": 11, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "micro_biomass_c_meth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string", + "recommended": true + }, + "micro_biomass_n_meth": { + "name": "micro_biomass_n_meth", + "description": "Reference or method used in determining microbial biomass nitrogen", + "title": "microbial biomass nitrogen method", + "comments": [ + "required if \"microbial_biomass_n\" is provided" + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:micro_biomass_meth" + ], + "rank": 13, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "micro_biomass_n_meth", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string" + }, + "microbial_biomass_c": { + "name": "microbial_biomass_c", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "title": "microbial biomass carbon", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:microbial_biomass" + ], + "rank": 10, + "string_serialization": "{float} {unit}", + "alias": "microbial_biomass_c", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string" + }, + "microbial_biomass_n": { + "name": "microbial_biomass_n", + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "title": "microbial biomass nitrogen", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:microbial_biomass" + ], + "rank": 12, + "string_serialization": "{float} {unit}", + "alias": "microbial_biomass_n", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string" + }, + "non_microb_biomass": { + "name": "non_microb_biomass", + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", + "title": "non-microbial biomass", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:biomass|microbial_biomass" + ], + "rank": 8, + "string_serialization": "{text};{float} {unit}", + "alias": "non_microb_biomass", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string" + }, + "non_microb_biomass_method": { + "name": "non_microb_biomass_method", + "description": "Reference or method used in determining biomass", + "title": "non-microbial biomass method", + "comments": [ + "required if \"non-microbial biomass\" is provided" + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:microbial_biomass" + ], + "rank": 9, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "non_microb_biomass_method", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string" + }, + "org_nitro_method": { + "name": "org_nitro_method", + "description": "Method used for obtaining organic nitrogen", + "title": "organic nitrogen method", + "comments": [ + "required if \"org_nitro\" is provided" + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:org_nitro|tot_nitro_cont_meth" + ], + "rank": 14, + "string_serialization": "{PMID}|{DOI}|{URL}", + "alias": "org_nitro_method", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string" + }, + "other_treatment": { + "name": "other_treatment", + "description": "Other treatments applied to your samples that are not applicable to the provided fields", + "title": "other treatments", + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:additional_info" + ], + "rank": 15, + "string_serialization": "{text}", + "alias": "other_treatment", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string", + "recommended": true + }, + "start_date_inc": { + "name": "start_date_inc", + "description": "Date the incubation was started. Only relevant for incubation samples.", + "title": "incubation start date", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" + ], + "comments": [ + "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." + ], + "examples": [ + { + "value": "2021-04-15, 2021-04 and 2021 are all acceptable." + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:collection_date" + ], + "rank": 4, + "string_serialization": "{date, arbitrary precision}", + "alias": "start_date_inc", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string", + "recommended": true + }, + "start_time_inc": { + "name": "start_time_inc", + "description": "Time the incubation was started. Only relevant for incubation samples.", + "title": "incubation start time, GMT", + "notes": [ + "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" + ], + "comments": [ + "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" + ], + "examples": [ + { + "value": "13:33 or 13:33:55" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:collection_date" + ], + "rank": 5, + "string_serialization": "{time, seconds optional}", + "alias": "start_time_inc", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "MIxS Inspired", + "range": "string", + "recommended": true + }, + "project_id": { + "name": "project_id", + "description": "Proposal IDs or names associated with dataset", + "title": "project ID", + "from_schema": "https://microbiomedata/schema", + "rank": 1, + "string_serialization": "{text}", + "alias": "project_id", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "EMSL", + "range": "string", + "required": false, + "recommended": true + }, + "replicate_number": { + "name": "replicate_number", + "description": "If sending biological replicates, indicate the rep number here.", + "title": "replicate number", + "comments": [ + "This will guide staff in ensuring your samples are block & randomized correctly" + ], + "from_schema": "https://microbiomedata/schema", + "rank": 6, + "string_serialization": "{integer}", + "alias": "replicate_number", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "EMSL", + "range": "string", + "recommended": true + }, + "sample_shipped": { + "name": "sample_shipped", + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL", + "title": "sample shipped amount", + "from_schema": "https://microbiomedata/schema", + "rank": 3, + "string_serialization": "{float} {unit}", + "alias": "sample_shipped", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "EMSL", + "range": "string", + "required": false, + "recommended": true + }, + "sample_type": { + "name": "sample_type", + "description": "Type of sample being submitted", + "title": "sample type", + "comments": [ + "This can vary from 'environmental package' if the sample is an extraction." + ], + "examples": [ + { + "value": "water extracted soil" + } + ], + "from_schema": "https://microbiomedata/schema", + "rank": 2, + "alias": "sample_type", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "EMSL", + "range": "sample_type_enum", + "required": false, + "recommended": true + }, + "technical_reps": { + "name": "technical_reps", + "description": "If sending multiple technical replicates of the same sample, indicate how many replicates are being sent", + "title": "number technical replicate", + "from_schema": "https://microbiomedata/schema", + "rank": 5, + "string_serialization": "{integer}", + "alias": "technical_reps", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "EMSL", + "range": "string", + "recommended": true + }, + "analysis_type": { + "name": "analysis_type", + "description": "Select all the data types associated or available for this biosample", + "title": "analysis/data type", + "examples": [ + { + "value": "metagenomics; metabolomics; proteomics" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "MIxS:investigation_type" + ], + "rank": 3, + "multivalued": true, + "alias": "analysis_type", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "Sample ID", + "range": "analysis_type_enum", + "required": false, + "recommended": true + }, + "sample_link": { + "name": "sample_link", + "description": "JsonObj()", + "title": "sample linkage", + "from_schema": "https://microbiomedata/schema", + "rank": 5, + "string_serialization": "{text}:{text}", + "multivalued": true, + "alias": "sample_link", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "slot_group": "Sample ID", + "range": "string", + "required": false, + "recommended": true + }, + "zinc": { + "name": "zinc", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg (ppm)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of zinc in the sample", + "title": "zinc", + "examples": [ + { + "value": "2.5 mg/kg" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "zinc" + ], + "is_a": "attribute", + "multivalued": false, + "alias": "zinc", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "manganese": { + "name": "manganese", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg (ppm)" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of manganese in the sample", + "title": "manganese", + "examples": [ + { + "value": "24.7 mg/kg" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "manganese" + ], + "is_a": "attribute", + "multivalued": false, + "alias": "manganese", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "ammonium_nitrogen": { + "name": "ammonium_nitrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of ammonium nitrogen in the sample", + "title": "ammonium nitrogen", + "examples": [ + { + "value": "2.3 mg/kg" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "ammonium_nitrogen", + "NH4-N" + ], + "is_a": "attribute", + "multivalued": false, + "alias": "ammonium_nitrogen", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "nitrate_nitrogen": { + "name": "nitrate_nitrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrate nitrogen in the sample", + "title": "nitrate_nitrogen", + "comments": [ + "often below some specified limit of detection" + ], + "examples": [ + { + "value": "0.29 mg/kg" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "nitrate_nitrogen", + "NO3-N" + ], + "is_a": "attribute", + "multivalued": false, + "alias": "nitrate_nitrogen", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "nitrite_nitrogen": { + "name": "nitrite_nitrogen", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "mg/kg" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "Concentration of nitrite nitrogen in the sample", + "title": "nitrite_nitrogen", + "examples": [ + { + "value": "1.2 mg/kg" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "nitrite_nitrogen", + "NO2-N" + ], + "is_a": "attribute", + "multivalued": false, + "alias": "nitrite_nitrogen", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "lbc_thirty": { + "name": "lbc_thirty", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ppm CaCO3/pH" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "lime buffer capacity, determined after 30 minute incubation", + "title": "lime buffer capacity (at 30 minutes)", + "comments": [ + "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" + ], + "examples": [ + { + "value": "543 mg/kg" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0", + "https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF" + ], + "aliases": [ + "lbc_thirty", + "lbc30", + "lime buffer capacity (at 30 minutes)" + ], + "is_a": "attribute", + "multivalued": false, + "alias": "lbc_thirty", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "lbceq": { + "name": "lbceq", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "ppm CaCO3/pH" + }, + "occurrence": { + "tag": "occurrence", + "value": "1" + } + }, + "description": "lime buffer capacity, determined at equilibrium after 5 day incubation", + "title": "lime buffer capacity (after 5 day incubation)", + "comments": [ + "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" + ], + "examples": [ + { + "value": "1575 mg/kg" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://www.ornl.gov/content/bio-scales-0" + ], + "aliases": [ + "lbceq", + "lime buffer capacity (at 5-day equilibrium)" + ], + "is_a": "attribute", + "multivalued": false, + "alias": "lbceq", + "owner": "Biosample", + "domain_of": [ + "Biosample" + ], + "range": "QuantityValue" + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "Biosample", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "NamedThing", + "ImageValue" + ], + "range": "string" + } + } + }, + "Study": { + "name": "Study", + "description": "A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.", + "alt_descriptions": { + "embl.ena": { + "source": "embl.ena", + "description": "A study (project) groups together data submitted to the archive and controls its release date. A study accession is typically used when citing data submitted to ENA" + } + }, + "todos": [ + "determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor", + "project_name is redundant with name, so excluding it" + ], + "notes": [ + "sample GOLD link https://identifiers.org/gold:Gs0110115", + "sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?", + "sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757", + "GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers, but no longer for the Study.id" + ], + "in_subset": [ + "sample subset" + ], + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "proposal", + "research proposal", + "research study", + "investigation", + "project", + "umbrella project" + ], + "exact_mappings": [ + "SIO:001066", + "NCIT:C63536", + "OBI:0000066", + "ISA:Study" + ], + "close_mappings": [ + "NCIT:C41198", + "ISA:Investigation" + ], + "broad_mappings": [ + "prov:Activity" + ], + "is_a": "NamedThing", + "slots": [ + "id", + "alternative_identifiers", + "related_identifiers", + "emsl_proposal_identifier", + "emsl_proposal_doi", + "gold_study_identifiers", + "mgnify_project_identifiers", + "ecosystem", + "ecosystem_category", + "ecosystem_type", + "ecosystem_subtype", + "specific_ecosystem", + "principal_investigator", + "doi", + "title", + "alternative_titles", + "alternative_descriptions", + "alternative_names", + "abstract", + "objective", + "websites", + "publications", + "ess_dive_datasets", + "type", + "relevant_protocols", + "funding_sources", + "has_credit_associations", + "study_image" + ], + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:sty", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "doi": { + "name": "doi", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "DOI associated with the data in this study. This is required when data is already generated." + } + }, + "description": "The dataset citation for this study", + "domain_of": [ + "Study" + ] + }, + "name": { + "name": "name", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Provide a name for the study your samples will belong with." + } + }, + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Activity", + "NamedThing", + "PersonValue" + ] + }, + "websites": { + "name": "websites", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Link to the Principal Investigator's research lab webpage or the study webpage associated with this collection of samples. Multiple links can be provided." + } + }, + "domain_of": [ + "Study", + "PersonValue" + ] + }, + "description": { + "name": "description", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Provide a brief description of your study." + } + }, + "description": "A brief summary that details the study you're submitted to NMDC", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "NamedThing", + "ImageValue" + ] + }, + "notes": { + "name": "notes", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Add any additional notes or comments about this study." + } + } + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "NamedThing", + "MetaboliteQuantification" + ] + }, + "alternative_names": { + "name": "alternative_names", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Project, study, or sample set names the are also associated with this submission or other names / identifiers for this study." + } + }, + "domain_of": [ + "Study" + ] + }, + "related_identifiers": { + "name": "related_identifiers", + "description": "Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC", + "domain_of": [ + "Study" + ] + }, + "insdc_bioproject_identifiers": { + "name": "insdc_bioproject_identifiers", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Provide the NCBI BioProject Accession Number associated with the listed NCBI BioProject Title." + } + }, + "description": "Unique identifier for a bioproject submitted to INSDC that relates to the NMDC submitted study." + }, + "emsl_project_identifier": { + "name": "emsl_project_identifier", + "description": "The EMSL project ID that relates to the NMDC submitted study" + }, + "emsl_proposal_doi": { + "name": "emsl_proposal_doi", + "description": "The DOI for the EMSL awarded study that relates to the NMDC submitted study", + "domain_of": [ + "Study" + ] + } + }, + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "Study", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:sty", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "Study", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "NamedThing", + "MetaboliteQuantification" + ], + "range": "string" + }, + "related_identifiers": { + "name": "related_identifiers", + "description": "Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC", + "title": "Related Identifiers", + "from_schema": "https://microbiomedata/schema", + "alias": "related_identifiers", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "string" + }, + "emsl_proposal_identifier": { + "name": "emsl_proposal_identifier", + "description": "The proposal number assigned to the EMSL awarded study that relates to that which is represented in NMDC.", + "title": "EMSL Proposal Identifier", + "from_schema": "https://microbiomedata/schema", + "alias": "emsl_proposal_identifier", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "string" + }, + "emsl_proposal_doi": { + "name": "emsl_proposal_doi", + "description": "The DOI for the EMSL awarded study that relates to the NMDC submitted study", + "title": "EMSL Proposal DOI", + "from_schema": "https://microbiomedata/schema", + "alias": "emsl_proposal_doi", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "string" + }, + "gold_study_identifiers": { + "name": "gold_study_identifiers", + "description": "identifiers for corresponding project(s) in GOLD", + "title": "GOLD Study Identifiers", + "comments": [ + "uses the prefix GS (but possibly in a different case)" + ], + "examples": [ + { + "value": "https://identifiers.org/gold:Gs0110115" + } + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/studies" + ], + "is_a": "study_identifiers", + "mixins": [ + "gold_identifiers" + ], + "multivalued": true, + "alias": "gold_study_identifiers", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "uriorcurie", + "pattern": "^GOLD:Gs[0-9]+$" + }, + "mgnify_project_identifiers": { + "name": "mgnify_project_identifiers", + "description": "identifiers for corresponding project in MGnify", + "examples": [ + { + "value": "https://identifiers.org/mgnify.proj:MGYS00005757" + } + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "insdc_identifiers", + "alias": "mgnify_project_identifiers", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "string", + "pattern": "^mgnify.proj:[A-Z]+[0-9]+$" + }, + "ecosystem": { + "name": "ecosystem", + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "comments": [ + "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "alias": "ecosystem", + "owner": "Study", + "domain_of": [ + "Biosample", + "Study" + ], + "range": "string" + }, + "ecosystem_category": { + "name": "ecosystem_category", + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "comments": [ + "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "alias": "ecosystem_category", + "owner": "Study", + "domain_of": [ + "Biosample", + "Study" + ], + "range": "string" + }, + "ecosystem_type": { + "name": "ecosystem_type", + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "comments": [ + "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "alias": "ecosystem_type", + "owner": "Study", + "domain_of": [ + "Biosample", + "Study" + ], + "range": "string" + }, + "ecosystem_subtype": { + "name": "ecosystem_subtype", + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "comments": [ + "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "alias": "ecosystem_subtype", + "owner": "Study", + "domain_of": [ + "Biosample", + "Study" + ], + "range": "string" + }, + "specific_ecosystem": { + "name": "specific_ecosystem", + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "comments": [ + "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://gold.jgi.doe.gov/help" + ], + "is_a": "gold_path_field", + "alias": "specific_ecosystem", + "owner": "Study", + "domain_of": [ + "Biosample", + "Study" + ], + "range": "string" + }, + "principal_investigator": { + "name": "principal_investigator", + "description": "Principal Investigator who led the study and/or generated the dataset.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "PI" + ], + "is_a": "attribute", + "alias": "principal_investigator", + "owner": "Study", + "domain_of": [ + "Study", + "OmicsProcessing" + ], + "range": "PersonValue" + }, + "doi": { + "name": "doi", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "DOI associated with the data in this study. This is required when data is already generated." + } + }, + "description": "The dataset citation for this study", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "doi", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "AttributeValue" + }, + "title": { + "name": "title", + "description": "A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.", + "from_schema": "https://microbiomedata/schema", + "exact_mappings": [ + "dcterms:title" + ], + "multivalued": false, + "alias": "title", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "string" + }, + "alternative_titles": { + "name": "alternative_titles", + "description": "A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.", + "from_schema": "https://microbiomedata/schema", + "exact_mappings": [ + "dcterms:alternative" + ], + "multivalued": true, + "alias": "alternative_titles", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "string" + }, + "alternative_descriptions": { + "name": "alternative_descriptions", + "description": "A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_descriptions", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "string" + }, + "alternative_names": { + "name": "alternative_names", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Project, study, or sample set names the are also associated with this submission or other names / identifiers for this study." + } + }, + "description": "A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_names", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "string" + }, + "abstract": { + "name": "abstract", + "description": "The abstract of manuscript/grant associated with the entity; i.e., a summary of the resource.", + "from_schema": "https://microbiomedata/schema", + "exact_mappings": [ + "dcterms:abstract" + ], + "alias": "abstract", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "string" + }, + "objective": { + "name": "objective", + "description": "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "sio:000337" + ], + "multivalued": false, + "alias": "objective", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "string" + }, + "websites": { + "name": "websites", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Link to the Principal Investigator's research lab webpage or the study webpage associated with this collection of samples. Multiple links can be provided." + } + }, + "description": "A list of websites that are associated with the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "websites", + "owner": "Study", + "domain_of": [ + "Study", + "PersonValue" + ], + "range": "string" + }, + "publications": { + "name": "publications", + "description": "A list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "publications", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "string" + }, + "ess_dive_datasets": { + "name": "ess_dive_datasets", + "description": "List of ESS-DIVE dataset DOIs", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "ess_dive_datasets", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "string" + }, + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "examples": [ + { + "value": "nmdc:Biosample" + }, + { + "value": "nmdc:Study" + } + ], + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "Study", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "relevant_protocols": { + "name": "relevant_protocols", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "relevant_protocols", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "string" + }, + "funding_sources": { + "name": "funding_sources", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "funding_sources", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "string" + }, + "has_credit_associations": { + "name": "has_credit_associations", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Other researchers associated with this study." + } + }, + "description": "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study", + "notes": [ + "had just been \"inlined: true\"" + ], + "from_schema": "https://microbiomedata/schema", + "domain": "Study", + "slot_uri": "prov:qualifiedAssociation", + "multivalued": true, + "alias": "has_credit_associations", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "CreditAssociation", + "inlined_as_list": true + }, + "study_image": { + "name": "study_image", + "description": "Links a study to one or more images.", + "from_schema": "https://microbiomedata/schema", + "domain": "Study", + "multivalued": true, + "alias": "study_image", + "owner": "Study", + "domain_of": [ + "Study" + ], + "range": "ImageValue", + "inlined": true + }, + "name": { + "name": "name", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Provide a name for the study your samples will belong with." + } + }, + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "Study", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Provide a brief description of your study." + } + }, + "description": "A brief summary that details the study you're submitted to NMDC", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "Study", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "NamedThing", + "ImageValue" + ], + "range": "string" + } + } + }, + "BiosampleProcessing": { + "name": "BiosampleProcessing", + "description": "A process that takes one or more biosamples as inputs and generates one or as outputs. Examples of outputs include samples cultivated from another sample or data objects created by instruments runs.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "material processing" + ], + "broad_mappings": [ + "OBI:0000094" + ], + "is_a": "NamedThing", + "slots": [ + "has_input" + ], + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:bsmprc", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "has_input": { + "name": "has_input", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity" + ], + "range": "Biosample" + } + }, + "attributes": { + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_input", + "owner": "BiosampleProcessing", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity" + ], + "range": "Biosample" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "BiosampleProcessing", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:bsmprc", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "BiosampleProcessing", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "BiosampleProcessing", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "NamedThing", + "ImageValue" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "BiosampleProcessing", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "NamedThing", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "OmicsProcessing": { + "name": "OmicsProcessing", + "description": "The methods and processes used to generate omics data from a biosample or organism.", + "alt_descriptions": { + "embl.ena": { + "source": "embl.ena", + "description": "An experiment contains information about a sequencing experiment including library and instrument details." + } + }, + "comments": [ + "The ID prefix for objects coming from GOLD will be gold:Gp" + ], + "in_subset": [ + "sample subset" + ], + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "omics assay", + "sequencing project", + "experiment" + ], + "broad_mappings": [ + "OBI:0000070", + "ISA:Assay" + ], + "is_a": "BiosampleProcessing", + "slots": [ + "add_date", + "mod_date", + "has_input", + "has_output", + "instrument_name", + "ncbi_project_name", + "omics_type", + "part_of", + "principal_investigator", + "processing_institution", + "type", + "gold_sequencing_project_identifiers", + "insdc_experiment_identifiers", + "samp_vol_we_dna_ext", + "nucl_acid_ext", + "nucl_acid_amp", + "target_gene", + "target_subfragment", + "pcr_primers", + "pcr_cond", + "seq_meth", + "seq_quality_check", + "chimera_check" + ], + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:omprc", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "has_input": { + "name": "has_input", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity" + ], + "required": true + } + }, + "attributes": { + "add_date": { + "name": "add_date", + "description": "The date on which the information was added to the database.", + "from_schema": "https://microbiomedata/schema", + "alias": "add_date", + "owner": "OmicsProcessing", + "domain_of": [ + "Biosample", + "OmicsProcessing" + ], + "range": "string" + }, + "mod_date": { + "name": "mod_date", + "description": "The last date on which the database information was modified.", + "from_schema": "https://microbiomedata/schema", + "alias": "mod_date", + "owner": "OmicsProcessing", + "domain_of": [ + "Biosample", + "OmicsProcessing" + ], + "range": "string" + }, + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_input", + "owner": "OmicsProcessing", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity" + ], + "range": "Biosample", + "required": true + }, + "has_output": { + "name": "has_output", + "description": "An output biosample to a processing step", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "output" + ], + "domain": "NamedThing", + "multivalued": true, + "alias": "has_output", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity" + ], + "range": "NamedThing" + }, + "instrument_name": { + "name": "instrument_name", + "description": "The name of the instrument that was used for processing the sample.", + "from_schema": "https://microbiomedata/schema", + "alias": "instrument_name", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "string" + }, + "ncbi_project_name": { + "name": "ncbi_project_name", + "from_schema": "https://microbiomedata/schema", + "alias": "ncbi_project_name", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "string" + }, + "omics_type": { + "name": "omics_type", + "description": "The type of omics data", + "notes": [ + "was the range string at one point? the values in MongoDB don't look like NMDC classes" + ], + "examples": [ + { + "value": "metatranscriptome" + }, + { + "value": "metagenome" + } + ], + "from_schema": "https://microbiomedata/schema", + "alias": "omics_type", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "ControlledTermValue" + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "is part of" + ], + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "alias": "part_of", + "owner": "OmicsProcessing", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity" + ], + "range": "NamedThing" + }, + "principal_investigator": { + "name": "principal_investigator", + "description": "Principal Investigator who led the study and/or generated the dataset.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "PI" + ], + "is_a": "attribute", + "alias": "principal_investigator", + "owner": "OmicsProcessing", + "domain_of": [ + "Study", + "OmicsProcessing" + ], + "range": "PersonValue" + }, + "processing_institution": { + "name": "processing_institution", + "description": "The organization that processed the sample.", + "from_schema": "https://microbiomedata/schema", + "alias": "processing_institution", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "processing_institution_enum" + }, + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "examples": [ + { + "value": "nmdc:Biosample" + }, + { + "value": "nmdc:Study" + } + ], + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "OmicsProcessing", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "gold_sequencing_project_identifiers": { + "name": "gold_sequencing_project_identifiers", + "description": "identifiers for corresponding sequencing project in GOLD", + "examples": [ + { + "value": "https://identifiers.org/gold:Gp0108335" + } + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "omics_processing_identifiers", + "mixins": [ + "gold_identifiers" + ], + "multivalued": true, + "alias": "gold_sequencing_project_identifiers", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "uriorcurie", + "pattern": "^GOLD:Gp[0-9]+$" + }, + "insdc_experiment_identifiers": { + "name": "insdc_experiment_identifiers", + "from_schema": "https://microbiomedata/schema", + "is_a": "external_database_identifiers", + "mixins": [ + "insdc_identifiers" + ], + "multivalued": true, + "alias": "insdc_experiment_identifiers", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "uriorcurie", + "pattern": "^insdc.sra:(E|D|S)RX[0-9]{6,}$" + }, + "samp_vol_we_dna_ext": { + "name": "samp_vol_we_dna_ext", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "measurement value" + }, + "preferred_unit": { + "tag": "preferred_unit", + "value": "millliter, gram, milligram, square centimeter" + } + }, + "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001).", + "title": "sample volume or weight for DNA extraction", + "examples": [ + { + "value": "1500 milliliter" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sample volume or weight for DNA extraction" + ], + "is_a": "attribute", + "slot_uri": "mixs:0000111", + "multivalued": false, + "alias": "samp_vol_we_dna_ext", + "owner": "OmicsProcessing", + "domain_of": [ + "Biosample", + "OmicsProcessing" + ], + "range": "QuantityValue" + }, + "nucl_acid_ext": { + "name": "nucl_acid_ext", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID, DOI or URL" + } + }, + "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample", + "title": "nucleic acid extraction", + "examples": [ + { + "value": "https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "nucleic acid extraction" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000037", + "multivalued": false, + "alias": "nucl_acid_ext", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "TextValue" + }, + "nucl_acid_amp": { + "name": "nucl_acid_amp", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "PMID, DOI or URL" + } + }, + "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids", + "title": "nucleic acid amplification", + "examples": [ + { + "value": "https://phylogenomics.me/protocols/16s-pcr-protocol/" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "nucleic acid amplification" + ], + "is_a": "attribute", + "string_serialization": "{PMID}|{DOI}|{URL}", + "slot_uri": "mixs:0000038", + "multivalued": false, + "alias": "nucl_acid_amp", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "TextValue" + }, + "target_gene": { + "name": "target_gene", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gene name" + } + }, + "description": "Targeted gene or locus name for marker gene studies", + "title": "target gene", + "examples": [ + { + "value": "16S rRNA, 18S rRNA, nif, amoA, rpo" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "target gene" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000044", + "multivalued": false, + "alias": "target_gene", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "TextValue" + }, + "target_subfragment": { + "name": "target_subfragment", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "gene fragment name" + } + }, + "description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA", + "title": "target subfragment", + "examples": [ + { + "value": "V6, V9, ITS" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "target subfragment" + ], + "is_a": "attribute", + "string_serialization": "{text}", + "slot_uri": "mixs:0000045", + "multivalued": false, + "alias": "target_subfragment", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "TextValue" + }, + "pcr_primers": { + "name": "pcr_primers", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "FWD: forward primer sequence;REV:reverse primer sequence" + } + }, + "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters", + "title": "pcr primers", + "examples": [ + { + "value": "FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pcr primers" + ], + "is_a": "attribute", + "string_serialization": "FWD:{dna};REV:{dna}", + "slot_uri": "mixs:0000046", + "multivalued": false, + "alias": "pcr_primers", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "TextValue" + }, + "pcr_cond": { + "name": "pcr_cond", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles" + } + }, + "description": "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'", + "title": "pcr conditions", + "examples": [ + { + "value": "initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "pcr conditions" + ], + "is_a": "attribute", + "string_serialization": "initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles", + "slot_uri": "mixs:0000049", + "multivalued": false, + "alias": "pcr_cond", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "TextValue" + }, + "seq_meth": { + "name": "seq_meth", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "Text or OBI" + } + }, + "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).", + "title": "sequencing method", + "examples": [ + { + "value": "454 Genome Sequencer FLX [OBI:0000702]" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sequencing method" + ], + "is_a": "attribute", + "string_serialization": "{termLabel} {[termID]}|{text}", + "slot_uri": "mixs:0000050", + "multivalued": false, + "alias": "seq_meth", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "TextValue" + }, + "seq_quality_check": { + "name": "seq_quality_check", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "none or manually edited" + } + }, + "description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA", + "title": "sequence quality check", + "examples": [ + { + "value": "none" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "sequence quality check" + ], + "is_a": "attribute", + "string_serialization": "[none|manually edited]", + "slot_uri": "mixs:0000051", + "multivalued": false, + "alias": "seq_quality_check", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "TextValue" + }, + "chimera_check": { + "name": "chimera_check", + "annotations": { + "expected_value": { + "tag": "expected_value", + "value": "name and version of software, parameters used" + } + }, + "description": "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.", + "title": "chimera check software", + "examples": [ + { + "value": "uchime;v4.1;default parameters" + } + ], + "from_schema": "https://microbiomedata/schema", + "source": "http://w3id.org/mixs/terms", + "see_also": [ + "https://github.com/microbiomedata/nmdc-schema/blob/issue-291-mixs-submod/util/rebuild_mixs_yaml.py" + ], + "aliases": [ + "chimera check software" + ], + "is_a": "attribute", + "string_serialization": "{software};{version};{parameters}", + "slot_uri": "mixs:0000052", + "multivalued": false, + "alias": "chimera_check", + "owner": "OmicsProcessing", + "domain_of": [ + "OmicsProcessing" + ], + "range": "TextValue" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "OmicsProcessing", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:omprc", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "OmicsProcessing", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "OmicsProcessing", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "NamedThing", + "ImageValue" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "OmicsProcessing", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "NamedThing", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "CreditAssociation": { + "name": "CreditAssociation", + "description": "This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "study role", + "credit table", + "associated researchers" + ], + "slots": [ + "applies_to_person", + "applied_role", + "applied_roles", + "type" + ], + "attributes": { + "applies_to_person": { + "name": "applies_to_person", + "todos": [ + "prov:agent takes an Agent object. Is a person value an Agent? Also try to relate to principal investigator slot? could include OBI:0000103 principal investigator role... do we need to define the OBI prefix?" + ], + "from_schema": "https://microbiomedata/schema", + "domain": "CreditAssociation", + "slot_uri": "prov:agent", + "multivalued": false, + "alias": "applies_to_person", + "owner": "CreditAssociation", + "domain_of": [ + "CreditAssociation" + ], + "range": "PersonValue", + "required": true + }, + "applied_role": { + "name": "applied_role", + "deprecated": "A credit association may have multiple roles. So, use the applied roles slot.", + "from_schema": "https://microbiomedata/schema", + "domain": "CreditAssociation", + "slot_uri": "prov:hadRole", + "multivalued": false, + "alias": "applied_role", + "owner": "CreditAssociation", + "domain_of": [ + "CreditAssociation" + ], + "range": "credit enum", + "required": false + }, + "applied_roles": { + "name": "applied_roles", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Identify all CRediT roles associated with this contributor. CRediT Information: https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/" + } + }, + "from_schema": "https://microbiomedata/schema", + "domain": "CreditAssociation", + "multivalued": true, + "alias": "applied_roles", + "owner": "CreditAssociation", + "domain_of": [ + "CreditAssociation" + ], + "range": "credit enum", + "required": true + }, + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "examples": [ + { + "value": "nmdc:Biosample" + }, + { + "value": "nmdc:Study" + } + ], + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "CreditAssociation", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + } + }, + "class_uri": "prov:Association" + }, + "WorkflowExecutionActivity": { + "name": "WorkflowExecutionActivity", + "description": "Represents an instance of an execution of a particular workflow", + "alt_descriptions": { + "embl.ena": { + "source": "embl.ena", + "description": "An analysis contains secondary analysis results derived from sequence reads (e.g. a genome assembly)" + } + }, + "notes": [ + "MAM I don't think this is a reasonable override of the global range of Agent, but commenting that line out does not, on its own, fix the conversion to SQLite", + "inlining of was_associated_with values allows for collections (strings?) of WorkflowExecutionActivity id values" + ], + "comments": [ + "Each instance of this (and all other) activities is a distinct run with start and stop times, potentially with different inputs and outputs" + ], + "in_subset": [ + "workflow subset" + ], + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "analysis" + ], + "is_a": "Activity", + "slots": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "part_of", + "type" + ], + "slot_usage": { + "was_associated_with": { + "name": "was_associated_with", + "description": "the agent/entity associated with the generation of the file", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "Activity" + ], + "range": "WorkflowExecutionActivity", + "required": false, + "inlined": false + }, + "started_at_time": { + "name": "started_at_time", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "Activity" + ], + "required": true + }, + "ended_at_time": { + "name": "ended_at_time", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "Activity" + ], + "required": true + }, + "git_url": { + "name": "git_url", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity" + ], + "required": true + }, + "has_input": { + "name": "has_input", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity" + ], + "required": true + }, + "has_output": { + "name": "has_output", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity" + ], + "required": true + }, + "was_informed_by": { + "name": "was_informed_by", + "domain_of": [ + "Activity", + "Agent", + "WorkflowExecutionActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "Activity", + "Agent" + ], + "required": true + }, + "execution_resource": { + "name": "execution_resource", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity" + ], + "required": true + }, + "type": { + "name": "type", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ] + }, + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:wf", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "execution_resource": { + "name": "execution_resource", + "description": "Example: NERSC-Cori", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "execution_resource", + "owner": "WorkflowExecutionActivity", + "domain_of": [ + "WorkflowExecutionActivity" + ], + "range": "string", + "required": true + }, + "git_url": { + "name": "git_url", + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "git_url", + "owner": "WorkflowExecutionActivity", + "domain_of": [ + "WorkflowExecutionActivity" + ], + "range": "string", + "required": true + }, + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_input", + "owner": "WorkflowExecutionActivity", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity" + ], + "range": "NamedThing", + "required": true + }, + "has_output": { + "name": "has_output", + "description": "An output biosample to a processing step", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_output", + "owner": "WorkflowExecutionActivity", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity" + ], + "range": "NamedThing", + "required": true + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "is part of" + ], + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "alias": "part_of", + "owner": "WorkflowExecutionActivity", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity" + ], + "range": "NamedThing" + }, + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "WorkflowExecutionActivity", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "WorkflowExecutionActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:wf", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "WorkflowExecutionActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "started_at_time": { + "name": "started_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "started_at_time", + "owner": "WorkflowExecutionActivity", + "domain_of": [ + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "ended_at_time": { + "name": "ended_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "ended_at_time", + "owner": "WorkflowExecutionActivity", + "domain_of": [ + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "alias": "was_informed_by", + "owner": "WorkflowExecutionActivity", + "domain_of": [ + "Activity", + "Agent" + ], + "range": "Activity", + "required": true + }, + "was_associated_with": { + "name": "was_associated_with", + "description": "the agent/entity associated with the generation of the file", + "from_schema": "https://microbiomedata/schema", + "alias": "was_associated_with", + "owner": "WorkflowExecutionActivity", + "domain_of": [ + "Activity" + ], + "range": "WorkflowExecutionActivity", + "required": false, + "inlined": false + }, + "used": { + "name": "used", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:used" + ], + "domain": "Activity", + "alias": "used", + "owner": "WorkflowExecutionActivity", + "domain_of": [ + "Activity" + ], + "range": "string" + } + } + }, + "MetagenomeAssembly": { + "name": "MetagenomeAssembly", + "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", + "comments": [ + "instances of this class may use a de novo assembly strategy in most or all cases relevant to NMDC" + ], + "in_subset": [ + "workflow subset" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "WorkflowExecutionActivity", + "slots": [ + "type", + "asm_score", + "scaffolds", + "scaf_logsum", + "scaf_powsum", + "scaf_max", + "scaf_bp", + "scaf_n50", + "scaf_n90", + "scaf_l50", + "scaf_l90", + "scaf_n_gt50k", + "scaf_l_gt50k", + "scaf_pct_gt50k", + "contigs", + "contig_bp", + "ctg_n50", + "ctg_l50", + "ctg_n90", + "ctg_l90", + "ctg_logsum", + "ctg_powsum", + "ctg_max", + "gap_pct", + "gc_std", + "gc_avg", + "num_input_reads", + "num_aligned_reads", + "insdc_assembly_identifiers" + ], + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:wfmgas", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "MetagenomeAssembly", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "asm_score": { + "name": "asm_score", + "description": "A score for comparing metagenomic assembly quality from same sample.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "asm_score", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaffolds": { + "name": "scaffolds", + "description": "Total sequence count of all scaffolds.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaffolds", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_logsum": { + "name": "scaf_logsum", + "description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_logsum", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_powsum": { + "name": "scaf_powsum", + "description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_powsum", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_max": { + "name": "scaf_max", + "description": "Maximum scaffold length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_max", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_bp": { + "name": "scaf_bp", + "description": "Total size in bp of all scaffolds.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_bp", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_n50": { + "name": "scaf_n50", + "description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_n50", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_n90": { + "name": "scaf_n90", + "description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_n90", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_l50": { + "name": "scaf_l50", + "description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_l50", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_l90": { + "name": "scaf_l90", + "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_l90", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_n_gt50k": { + "name": "scaf_n_gt50k", + "description": "Total sequence count of scaffolds greater than 50 KB.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_n_gt50k", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_l_gt50k": { + "name": "scaf_l_gt50k", + "description": "Total size in bp of all scaffolds greater than 50 KB.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_l_gt50k", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_pct_gt50k": { + "name": "scaf_pct_gt50k", + "description": "Total sequence size percentage of scaffolds greater than 50 KB.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_pct_gt50k", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "contigs": { + "name": "contigs", + "description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "contigs", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "contig_bp": { + "name": "contig_bp", + "description": "Total size in bp of all contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "contig_bp", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "ctg_n50": { + "name": "ctg_n50", + "description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "ctg_n50", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "ctg_l50": { + "name": "ctg_l50", + "description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "ctg_l50", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "ctg_n90": { + "name": "ctg_n90", + "description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "ctg_n90", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "ctg_l90": { + "name": "ctg_l90", + "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "ctg_l90", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "ctg_logsum": { + "name": "ctg_logsum", + "description": "Maximum contig length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "ctg_logsum", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "ctg_powsum": { + "name": "ctg_powsum", + "description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "ctg_powsum", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "ctg_max": { + "name": "ctg_max", + "description": "Maximum contig length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "ctg_max", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "gap_pct": { + "name": "gap_pct", + "description": "The gap size percentage of all scaffolds.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "gap_pct", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "gc_std": { + "name": "gc_std", + "description": "Standard deviation of GC content of all contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "gc_std", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "gc_avg": { + "name": "gc_avg", + "description": "Average of GC content of all contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "gc_avg", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "num_input_reads": { + "name": "num_input_reads", + "description": "The sequence count number of input reads for assembly.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "num_input_reads", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "num_aligned_reads": { + "name": "num_aligned_reads", + "description": "The sequence count number of input reads aligned to assembled contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "num_aligned_reads", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "insdc_assembly_identifiers": { + "name": "insdc_assembly_identifiers", + "from_schema": "https://microbiomedata/schema", + "is_a": "assembly_identifiers", + "mixins": [ + "insdc_identifiers" + ], + "alias": "insdc_assembly_identifiers", + "owner": "MetagenomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "string", + "pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$" + }, + "execution_resource": { + "name": "execution_resource", + "description": "Example: NERSC-Cori", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "execution_resource", + "owner": "MetagenomeAssembly", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity" + ], + "range": "string", + "required": true + }, + "git_url": { + "name": "git_url", + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "git_url", + "owner": "MetagenomeAssembly", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity" + ], + "range": "string", + "required": true + }, + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_input", + "owner": "MetagenomeAssembly", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity" + ], + "range": "NamedThing", + "required": true + }, + "has_output": { + "name": "has_output", + "description": "An output biosample to a processing step", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_output", + "owner": "MetagenomeAssembly", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity" + ], + "range": "NamedThing", + "required": true + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "is part of" + ], + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "alias": "part_of", + "owner": "MetagenomeAssembly", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity" + ], + "range": "NamedThing" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "MetagenomeAssembly", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:wfmgas", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "MetagenomeAssembly", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "started_at_time": { + "name": "started_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "started_at_time", + "owner": "MetagenomeAssembly", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "ended_at_time": { + "name": "ended_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "ended_at_time", + "owner": "MetagenomeAssembly", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "alias": "was_informed_by", + "owner": "MetagenomeAssembly", + "domain_of": [ + "Activity", + "Agent", + "WorkflowExecutionActivity", + "Activity", + "Agent" + ], + "range": "Activity", + "required": true + }, + "was_associated_with": { + "name": "was_associated_with", + "description": "the agent/entity associated with the generation of the file", + "from_schema": "https://microbiomedata/schema", + "alias": "was_associated_with", + "owner": "MetagenomeAssembly", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity" + ], + "range": "WorkflowExecutionActivity", + "required": false, + "inlined": false + }, + "used": { + "name": "used", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:used" + ], + "domain": "Activity", + "alias": "used", + "owner": "MetagenomeAssembly", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity" + ], + "range": "string" + } + } + }, + "MetatranscriptomeAssembly": { + "name": "MetatranscriptomeAssembly", + "in_subset": [ + "workflow subset" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "WorkflowExecutionActivity", + "slots": [ + "asm_score", + "scaffolds", + "scaf_logsum", + "scaf_powsum", + "scaf_max", + "scaf_bp", + "scaf_n50", + "scaf_n90", + "scaf_l50", + "scaf_l90", + "scaf_n_gt50k", + "scaf_l_gt50k", + "scaf_pct_gt50k", + "contigs", + "contig_bp", + "ctg_n50", + "ctg_l50", + "ctg_n90", + "ctg_l90", + "ctg_logsum", + "ctg_powsum", + "ctg_max", + "gap_pct", + "gc_std", + "gc_avg", + "num_input_reads", + "num_aligned_reads", + "insdc_assembly_identifiers" + ], + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:wfmtas", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "asm_score": { + "name": "asm_score", + "description": "A score for comparing metagenomic assembly quality from same sample.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "asm_score", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaffolds": { + "name": "scaffolds", + "description": "Total sequence count of all scaffolds.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaffolds", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_logsum": { + "name": "scaf_logsum", + "description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_logsum", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_powsum": { + "name": "scaf_powsum", + "description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_powsum", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_max": { + "name": "scaf_max", + "description": "Maximum scaffold length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_max", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_bp": { + "name": "scaf_bp", + "description": "Total size in bp of all scaffolds.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_bp", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_n50": { + "name": "scaf_n50", + "description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_n50", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_n90": { + "name": "scaf_n90", + "description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_n90", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_l50": { + "name": "scaf_l50", + "description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_l50", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_l90": { + "name": "scaf_l90", + "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_l90", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_n_gt50k": { + "name": "scaf_n_gt50k", + "description": "Total sequence count of scaffolds greater than 50 KB.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_n_gt50k", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_l_gt50k": { + "name": "scaf_l_gt50k", + "description": "Total size in bp of all scaffolds greater than 50 KB.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_l_gt50k", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "scaf_pct_gt50k": { + "name": "scaf_pct_gt50k", + "description": "Total sequence size percentage of scaffolds greater than 50 KB.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "scaf_pct_gt50k", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "contigs": { + "name": "contigs", + "description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "contigs", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "contig_bp": { + "name": "contig_bp", + "description": "Total size in bp of all contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "contig_bp", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "ctg_n50": { + "name": "ctg_n50", + "description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "ctg_n50", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "ctg_l50": { + "name": "ctg_l50", + "description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "ctg_l50", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "ctg_n90": { + "name": "ctg_n90", + "description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "ctg_n90", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "ctg_l90": { + "name": "ctg_l90", + "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "ctg_l90", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "ctg_logsum": { + "name": "ctg_logsum", + "description": "Maximum contig length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "ctg_logsum", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "ctg_powsum": { + "name": "ctg_powsum", + "description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "ctg_powsum", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "ctg_max": { + "name": "ctg_max", + "description": "Maximum contig length.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "ctg_max", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "gap_pct": { + "name": "gap_pct", + "description": "The gap size percentage of all scaffolds.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "gap_pct", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "gc_std": { + "name": "gc_std", + "description": "Standard deviation of GC content of all contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "gc_std", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "gc_avg": { + "name": "gc_avg", + "description": "Average of GC content of all contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "gc_avg", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "num_input_reads": { + "name": "num_input_reads", + "description": "The sequence count number of input reads for assembly.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "num_input_reads", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "num_aligned_reads": { + "name": "num_aligned_reads", + "description": "The sequence count number of input reads aligned to assembled contigs.", + "from_schema": "https://microbiomedata/schema", + "is_a": "metagenome_assembly_parameter", + "alias": "num_aligned_reads", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "float" + }, + "insdc_assembly_identifiers": { + "name": "insdc_assembly_identifiers", + "from_schema": "https://microbiomedata/schema", + "is_a": "assembly_identifiers", + "mixins": [ + "insdc_identifiers" + ], + "alias": "insdc_assembly_identifiers", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "string", + "pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$" + }, + "execution_resource": { + "name": "execution_resource", + "description": "Example: NERSC-Cori", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "execution_resource", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly" + ], + "range": "string", + "required": true + }, + "git_url": { + "name": "git_url", + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "git_url", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly" + ], + "range": "string", + "required": true + }, + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_input", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly" + ], + "range": "NamedThing", + "required": true + }, + "has_output": { + "name": "has_output", + "description": "An output biosample to a processing step", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_output", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly" + ], + "range": "NamedThing", + "required": true + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "is part of" + ], + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "alias": "part_of", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly" + ], + "range": "NamedThing" + }, + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:wfmtas", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "started_at_time": { + "name": "started_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "started_at_time", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "ended_at_time": { + "name": "ended_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "ended_at_time", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "alias": "was_informed_by", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "Activity", + "Agent", + "WorkflowExecutionActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "Agent" + ], + "range": "Activity", + "required": true + }, + "was_associated_with": { + "name": "was_associated_with", + "description": "the agent/entity associated with the generation of the file", + "from_schema": "https://microbiomedata/schema", + "alias": "was_associated_with", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity" + ], + "range": "WorkflowExecutionActivity", + "required": false, + "inlined": false + }, + "used": { + "name": "used", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:used" + ], + "domain": "Activity", + "alias": "used", + "owner": "MetatranscriptomeAssembly", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity" + ], + "range": "string" + } + } + }, + "MetagenomeAnnotationActivity": { + "name": "MetagenomeAnnotationActivity", + "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", + "in_subset": [ + "workflow subset" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "WorkflowExecutionActivity", + "slots": [ + "type", + "gold_analysis_project_identifiers" + ], + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:wfmgan", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "MetagenomeAnnotationActivity", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "gold_analysis_project_identifiers": { + "name": "gold_analysis_project_identifiers", + "description": "identifiers for corresponding analysis project in GOLD", + "examples": [ + { + "value": "https://identifiers.org/gold:Ga0526289" + } + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "analysis_identifiers", + "mixins": [ + "gold_identifiers" + ], + "multivalued": true, + "alias": "gold_analysis_project_identifiers", + "owner": "MetagenomeAnnotationActivity", + "domain_of": [ + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity" + ], + "range": "uriorcurie", + "pattern": "^GOLD:Ga[0-9]+$" + }, + "execution_resource": { + "name": "execution_resource", + "description": "Example: NERSC-Cori", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "execution_resource", + "owner": "MetagenomeAnnotationActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "string", + "required": true + }, + "git_url": { + "name": "git_url", + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "git_url", + "owner": "MetagenomeAnnotationActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "string", + "required": true + }, + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_input", + "owner": "MetagenomeAnnotationActivity", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "NamedThing", + "required": true + }, + "has_output": { + "name": "has_output", + "description": "An output biosample to a processing step", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_output", + "owner": "MetagenomeAnnotationActivity", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "NamedThing", + "required": true + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "is part of" + ], + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "alias": "part_of", + "owner": "MetagenomeAnnotationActivity", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly" + ], + "range": "NamedThing" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "MetagenomeAnnotationActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:wfmgan", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "MetagenomeAnnotationActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "started_at_time": { + "name": "started_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "started_at_time", + "owner": "MetagenomeAnnotationActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "ended_at_time": { + "name": "ended_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "ended_at_time", + "owner": "MetagenomeAnnotationActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "alias": "was_informed_by", + "owner": "MetagenomeAnnotationActivity", + "domain_of": [ + "Activity", + "Agent", + "WorkflowExecutionActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "Agent" + ], + "range": "Activity", + "required": true + }, + "was_associated_with": { + "name": "was_associated_with", + "description": "the agent/entity associated with the generation of the file", + "from_schema": "https://microbiomedata/schema", + "alias": "was_associated_with", + "owner": "MetagenomeAnnotationActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity" + ], + "range": "WorkflowExecutionActivity", + "required": false, + "inlined": false + }, + "used": { + "name": "used", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:used" + ], + "domain": "Activity", + "alias": "used", + "owner": "MetagenomeAnnotationActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity" + ], + "range": "string" + } + } + }, + "MetatranscriptomeAnnotationActivity": { + "name": "MetatranscriptomeAnnotationActivity", + "in_subset": [ + "workflow subset" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "WorkflowExecutionActivity", + "slots": [ + "type", + "gold_analysis_project_identifiers" + ], + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:wfmtan", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "MetatranscriptomeAnnotationActivity", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "gold_analysis_project_identifiers": { + "name": "gold_analysis_project_identifiers", + "description": "identifiers for corresponding analysis project in GOLD", + "examples": [ + { + "value": "https://identifiers.org/gold:Ga0526289" + } + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "analysis_identifiers", + "mixins": [ + "gold_identifiers" + ], + "multivalued": true, + "alias": "gold_analysis_project_identifiers", + "owner": "MetatranscriptomeAnnotationActivity", + "domain_of": [ + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity" + ], + "range": "uriorcurie", + "pattern": "^GOLD:Ga[0-9]+$" + }, + "execution_resource": { + "name": "execution_resource", + "description": "Example: NERSC-Cori", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "execution_resource", + "owner": "MetatranscriptomeAnnotationActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity" + ], + "range": "string", + "required": true + }, + "git_url": { + "name": "git_url", + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "git_url", + "owner": "MetatranscriptomeAnnotationActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity" + ], + "range": "string", + "required": true + }, + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_input", + "owner": "MetatranscriptomeAnnotationActivity", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity" + ], + "range": "NamedThing", + "required": true + }, + "has_output": { + "name": "has_output", + "description": "An output biosample to a processing step", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_output", + "owner": "MetatranscriptomeAnnotationActivity", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity" + ], + "range": "NamedThing", + "required": true + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "is part of" + ], + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "alias": "part_of", + "owner": "MetatranscriptomeAnnotationActivity", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity" + ], + "range": "NamedThing" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "MetatranscriptomeAnnotationActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:wfmtan", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "MetatranscriptomeAnnotationActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "started_at_time": { + "name": "started_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "started_at_time", + "owner": "MetatranscriptomeAnnotationActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "ended_at_time": { + "name": "ended_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "ended_at_time", + "owner": "MetatranscriptomeAnnotationActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "alias": "was_informed_by", + "owner": "MetatranscriptomeAnnotationActivity", + "domain_of": [ + "Activity", + "Agent", + "WorkflowExecutionActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "Agent" + ], + "range": "Activity", + "required": true + }, + "was_associated_with": { + "name": "was_associated_with", + "description": "the agent/entity associated with the generation of the file", + "from_schema": "https://microbiomedata/schema", + "alias": "was_associated_with", + "owner": "MetatranscriptomeAnnotationActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity" + ], + "range": "WorkflowExecutionActivity", + "required": false, + "inlined": false + }, + "used": { + "name": "used", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:used" + ], + "domain": "Activity", + "alias": "used", + "owner": "MetatranscriptomeAnnotationActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity" + ], + "range": "string" + } + } + }, + "MetatranscriptomeActivity": { + "name": "MetatranscriptomeActivity", + "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", + "in_subset": [ + "workflow subset" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "WorkflowExecutionActivity", + "slots": [ + "type" + ], + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:wfmt", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "MetatranscriptomeActivity", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "execution_resource": { + "name": "execution_resource", + "description": "Example: NERSC-Cori", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "execution_resource", + "owner": "MetatranscriptomeActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity" + ], + "range": "string", + "required": true + }, + "git_url": { + "name": "git_url", + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "git_url", + "owner": "MetatranscriptomeActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity" + ], + "range": "string", + "required": true + }, + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_input", + "owner": "MetatranscriptomeActivity", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity" + ], + "range": "NamedThing", + "required": true + }, + "has_output": { + "name": "has_output", + "description": "An output biosample to a processing step", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_output", + "owner": "MetatranscriptomeActivity", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity" + ], + "range": "NamedThing", + "required": true + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "is part of" + ], + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "alias": "part_of", + "owner": "MetatranscriptomeActivity", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity" + ], + "range": "NamedThing" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "MetatranscriptomeActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:wfmt", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "MetatranscriptomeActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "started_at_time": { + "name": "started_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "started_at_time", + "owner": "MetatranscriptomeActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "ended_at_time": { + "name": "ended_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "ended_at_time", + "owner": "MetatranscriptomeActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "alias": "was_informed_by", + "owner": "MetatranscriptomeActivity", + "domain_of": [ + "Activity", + "Agent", + "WorkflowExecutionActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "Agent" + ], + "range": "Activity", + "required": true + }, + "was_associated_with": { + "name": "was_associated_with", + "description": "the agent/entity associated with the generation of the file", + "from_schema": "https://microbiomedata/schema", + "alias": "was_associated_with", + "owner": "MetatranscriptomeActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity" + ], + "range": "WorkflowExecutionActivity", + "required": false, + "inlined": false + }, + "used": { + "name": "used", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:used" + ], + "domain": "Activity", + "alias": "used", + "owner": "MetatranscriptomeActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity" + ], + "range": "string" + } + } + }, + "MagsAnalysisActivity": { + "name": "MagsAnalysisActivity", + "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", + "title": "Metagenome-Assembled Genome analysis activity", + "in_subset": [ + "workflow subset" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "WorkflowExecutionActivity", + "slots": [ + "type", + "input_contig_num", + "binned_contig_num", + "too_short_contig_num", + "low_depth_contig_num", + "unbinned_contig_num", + "mags_list" + ], + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:wfmag", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "input_contig_num": { + "name": "input_contig_num", + "from_schema": "https://microbiomedata/schema", + "alias": "input_contig_num", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "MagsAnalysisActivity" + ], + "range": "integer" + }, + "binned_contig_num": { + "name": "binned_contig_num", + "from_schema": "https://microbiomedata/schema", + "alias": "binned_contig_num", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "MagsAnalysisActivity" + ], + "range": "integer" + }, + "too_short_contig_num": { + "name": "too_short_contig_num", + "from_schema": "https://microbiomedata/schema", + "alias": "too_short_contig_num", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "MagsAnalysisActivity" + ], + "range": "integer" + }, + "low_depth_contig_num": { + "name": "low_depth_contig_num", + "from_schema": "https://microbiomedata/schema", + "alias": "low_depth_contig_num", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "MagsAnalysisActivity" + ], + "range": "integer" + }, + "unbinned_contig_num": { + "name": "unbinned_contig_num", + "from_schema": "https://microbiomedata/schema", + "alias": "unbinned_contig_num", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "MagsAnalysisActivity" + ], + "range": "integer" + }, + "mags_list": { + "name": "mags_list", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "mags_list", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "MagsAnalysisActivity" + ], + "range": "MagBin" + }, + "execution_resource": { + "name": "execution_resource", + "description": "Example: NERSC-Cori", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "execution_resource", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity" + ], + "range": "string", + "required": true + }, + "git_url": { + "name": "git_url", + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "git_url", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity" + ], + "range": "string", + "required": true + }, + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_input", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity" + ], + "range": "NamedThing", + "required": true + }, + "has_output": { + "name": "has_output", + "description": "An output biosample to a processing step", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_output", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity" + ], + "range": "NamedThing", + "required": true + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "is part of" + ], + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "alias": "part_of", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity" + ], + "range": "NamedThing" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:wfmag", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "started_at_time": { + "name": "started_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "started_at_time", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "ended_at_time": { + "name": "ended_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "ended_at_time", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "alias": "was_informed_by", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "Activity", + "Agent", + "WorkflowExecutionActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "Agent" + ], + "range": "Activity", + "required": true + }, + "was_associated_with": { + "name": "was_associated_with", + "description": "the agent/entity associated with the generation of the file", + "from_schema": "https://microbiomedata/schema", + "alias": "was_associated_with", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity" + ], + "range": "WorkflowExecutionActivity", + "required": false, + "inlined": false + }, + "used": { + "name": "used", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:used" + ], + "domain": "Activity", + "alias": "used", + "owner": "MagsAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity" + ], + "range": "string" + } + } + }, + "ReadQcAnalysisActivity": { + "name": "ReadQcAnalysisActivity", + "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", + "title": "Read quality control analysis activity", + "in_subset": [ + "workflow subset" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "WorkflowExecutionActivity", + "slots": [ + "type", + "input_read_count", + "input_base_count", + "output_read_count", + "output_base_count" + ], + "slot_usage": { + "input_read_bases": { + "name": "input_read_bases", + "description": "TODO", + "range": "float" + }, + "output_read_bases": { + "name": "output_read_bases", + "description": "TODO", + "range": "float" + }, + "has_input": { + "name": "has_input", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity" + ], + "inlined": false + }, + "has_output": { + "name": "has_output", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity" + ], + "inlined": false + }, + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:wfrqc", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "input_read_count": { + "name": "input_read_count", + "description": "The sequence count number of input reads for QC analysis.", + "from_schema": "https://microbiomedata/schema", + "is_a": "read_qc_analysis_statistic", + "alias": "input_read_count", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "ReadQcAnalysisActivity" + ], + "range": "float" + }, + "input_base_count": { + "name": "input_base_count", + "description": "The nucleotide base count number of input reads for QC analysis.", + "from_schema": "https://microbiomedata/schema", + "is_a": "read_qc_analysis_statistic", + "alias": "input_base_count", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "ReadQcAnalysisActivity" + ], + "range": "float" + }, + "output_read_count": { + "name": "output_read_count", + "description": "After QC analysis sequence count number.", + "from_schema": "https://microbiomedata/schema", + "is_a": "read_qc_analysis_statistic", + "alias": "output_read_count", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "ReadQcAnalysisActivity" + ], + "range": "float" + }, + "output_base_count": { + "name": "output_base_count", + "description": "After QC analysis nucleotide base count number.", + "from_schema": "https://microbiomedata/schema", + "is_a": "read_qc_analysis_statistic", + "alias": "output_base_count", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "ReadQcAnalysisActivity" + ], + "range": "float" + }, + "execution_resource": { + "name": "execution_resource", + "description": "Example: NERSC-Cori", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "execution_resource", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity" + ], + "range": "string", + "required": true + }, + "git_url": { + "name": "git_url", + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "git_url", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity" + ], + "range": "string", + "required": true + }, + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_input", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity" + ], + "range": "NamedThing", + "required": true, + "inlined": false + }, + "has_output": { + "name": "has_output", + "description": "An output biosample to a processing step", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_output", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity" + ], + "range": "NamedThing", + "required": true, + "inlined": false + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "is part of" + ], + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "alias": "part_of", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity" + ], + "range": "NamedThing" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:wfrqc", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "started_at_time": { + "name": "started_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "started_at_time", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "ended_at_time": { + "name": "ended_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "ended_at_time", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "alias": "was_informed_by", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "Activity", + "Agent", + "WorkflowExecutionActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "Agent" + ], + "range": "Activity", + "required": true + }, + "was_associated_with": { + "name": "was_associated_with", + "description": "the agent/entity associated with the generation of the file", + "from_schema": "https://microbiomedata/schema", + "alias": "was_associated_with", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity" + ], + "range": "WorkflowExecutionActivity", + "required": false, + "inlined": false + }, + "used": { + "name": "used", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:used" + ], + "domain": "Activity", + "alias": "used", + "owner": "ReadQcAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity" + ], + "range": "string" + } + } + }, + "ReadBasedTaxonomyAnalysisActivity": { + "name": "ReadBasedTaxonomyAnalysisActivity", + "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", + "title": "Read based analysis activity", + "in_subset": [ + "workflow subset" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "WorkflowExecutionActivity", + "slots": [ + "type" + ], + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:wfrbt", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "ReadBasedTaxonomyAnalysisActivity", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "execution_resource": { + "name": "execution_resource", + "description": "Example: NERSC-Cori", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "execution_resource", + "owner": "ReadBasedTaxonomyAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity" + ], + "range": "string", + "required": true + }, + "git_url": { + "name": "git_url", + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "git_url", + "owner": "ReadBasedTaxonomyAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity" + ], + "range": "string", + "required": true + }, + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_input", + "owner": "ReadBasedTaxonomyAnalysisActivity", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity" + ], + "range": "NamedThing", + "required": true + }, + "has_output": { + "name": "has_output", + "description": "An output biosample to a processing step", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_output", + "owner": "ReadBasedTaxonomyAnalysisActivity", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity" + ], + "range": "NamedThing", + "required": true + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "is part of" + ], + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "alias": "part_of", + "owner": "ReadBasedTaxonomyAnalysisActivity", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity" + ], + "range": "NamedThing" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "ReadBasedTaxonomyAnalysisActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:wfrbt", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "ReadBasedTaxonomyAnalysisActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "started_at_time": { + "name": "started_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "started_at_time", + "owner": "ReadBasedTaxonomyAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "ended_at_time": { + "name": "ended_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "ended_at_time", + "owner": "ReadBasedTaxonomyAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "alias": "was_informed_by", + "owner": "ReadBasedTaxonomyAnalysisActivity", + "domain_of": [ + "Activity", + "Agent", + "WorkflowExecutionActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "Agent" + ], + "range": "Activity", + "required": true + }, + "was_associated_with": { + "name": "was_associated_with", + "description": "the agent/entity associated with the generation of the file", + "from_schema": "https://microbiomedata/schema", + "alias": "was_associated_with", + "owner": "ReadBasedTaxonomyAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity" + ], + "range": "WorkflowExecutionActivity", + "required": false, + "inlined": false + }, + "used": { + "name": "used", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:used" + ], + "domain": "Activity", + "alias": "used", + "owner": "ReadBasedTaxonomyAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity" + ], + "range": "string" + } + } + }, + "MetabolomicsAnalysisActivity": { + "name": "MetabolomicsAnalysisActivity", + "in_subset": [ + "workflow subset" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "WorkflowExecutionActivity", + "slots": [ + "type" + ], + "slot_usage": { + "used": { + "name": "used", + "description": "The instrument used to collect the data used in the analysis", + "multivalued": false, + "domain_of": [ + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity" + ], + "range": "Instrument" + }, + "has_metabolite_quantifications": { + "name": "has_metabolite_quantifications", + "multivalued": true, + "range": "MetaboliteQuantification" + }, + "has_calibration": { + "name": "has_calibration", + "description": "TODO: Yuri to fill in" + }, + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:wfmb", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "MetabolomicsAnalysisActivity", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "execution_resource": { + "name": "execution_resource", + "description": "Example: NERSC-Cori", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "execution_resource", + "owner": "MetabolomicsAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity" + ], + "range": "string", + "required": true + }, + "git_url": { + "name": "git_url", + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "git_url", + "owner": "MetabolomicsAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity" + ], + "range": "string", + "required": true + }, + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_input", + "owner": "MetabolomicsAnalysisActivity", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity" + ], + "range": "NamedThing", + "required": true + }, + "has_output": { + "name": "has_output", + "description": "An output biosample to a processing step", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_output", + "owner": "MetabolomicsAnalysisActivity", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity" + ], + "range": "NamedThing", + "required": true + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "is part of" + ], + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "alias": "part_of", + "owner": "MetabolomicsAnalysisActivity", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity" + ], + "range": "NamedThing" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "MetabolomicsAnalysisActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:wfmb", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "MetabolomicsAnalysisActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "started_at_time": { + "name": "started_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "started_at_time", + "owner": "MetabolomicsAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "ended_at_time": { + "name": "ended_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "ended_at_time", + "owner": "MetabolomicsAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "alias": "was_informed_by", + "owner": "MetabolomicsAnalysisActivity", + "domain_of": [ + "Activity", + "Agent", + "WorkflowExecutionActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "Agent" + ], + "range": "Activity", + "required": true + }, + "was_associated_with": { + "name": "was_associated_with", + "description": "the agent/entity associated with the generation of the file", + "from_schema": "https://microbiomedata/schema", + "alias": "was_associated_with", + "owner": "MetabolomicsAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity" + ], + "range": "WorkflowExecutionActivity", + "required": false, + "inlined": false + }, + "used": { + "name": "used", + "description": "The instrument used to collect the data used in the analysis", + "from_schema": "https://microbiomedata/schema", + "domain": "Activity", + "multivalued": false, + "alias": "used", + "owner": "MetabolomicsAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity" + ], + "range": "Instrument" + } + } + }, + "MetaproteomicsAnalysisActivity": { + "name": "MetaproteomicsAnalysisActivity", + "in_subset": [ + "workflow subset" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "WorkflowExecutionActivity", + "slots": [ + "type" + ], + "slot_usage": { + "used": { + "name": "used", + "description": "The instrument used to collect the data used in the analysis", + "multivalued": false, + "domain_of": [ + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity" + ], + "range": "Instrument" + }, + "has_peptide_quantifications": { + "name": "has_peptide_quantifications", + "multivalued": true, + "range": "PeptideQuantification" + }, + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:wfmp", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "MetaproteomicsAnalysisActivity", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "execution_resource": { + "name": "execution_resource", + "description": "Example: NERSC-Cori", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "execution_resource", + "owner": "MetaproteomicsAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity" + ], + "range": "string", + "required": true + }, + "git_url": { + "name": "git_url", + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "git_url", + "owner": "MetaproteomicsAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity" + ], + "range": "string", + "required": true + }, + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_input", + "owner": "MetaproteomicsAnalysisActivity", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity" + ], + "range": "NamedThing", + "required": true + }, + "has_output": { + "name": "has_output", + "description": "An output biosample to a processing step", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_output", + "owner": "MetaproteomicsAnalysisActivity", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity" + ], + "range": "NamedThing", + "required": true + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "is part of" + ], + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "alias": "part_of", + "owner": "MetaproteomicsAnalysisActivity", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity" + ], + "range": "NamedThing" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "MetaproteomicsAnalysisActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:wfmp", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "MetaproteomicsAnalysisActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "started_at_time": { + "name": "started_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "started_at_time", + "owner": "MetaproteomicsAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "ended_at_time": { + "name": "ended_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "ended_at_time", + "owner": "MetaproteomicsAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "alias": "was_informed_by", + "owner": "MetaproteomicsAnalysisActivity", + "domain_of": [ + "Activity", + "Agent", + "WorkflowExecutionActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity", + "Agent" + ], + "range": "Activity", + "required": true + }, + "was_associated_with": { + "name": "was_associated_with", + "description": "the agent/entity associated with the generation of the file", + "from_schema": "https://microbiomedata/schema", + "alias": "was_associated_with", + "owner": "MetaproteomicsAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity" + ], + "range": "WorkflowExecutionActivity", + "required": false, + "inlined": false + }, + "used": { + "name": "used", + "description": "The instrument used to collect the data used in the analysis", + "from_schema": "https://microbiomedata/schema", + "domain": "Activity", + "multivalued": false, + "alias": "used", + "owner": "MetaproteomicsAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity" + ], + "range": "Instrument" + } + } + }, + "NomAnalysisActivity": { + "name": "NomAnalysisActivity", + "in_subset": [ + "workflow subset" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "WorkflowExecutionActivity", + "slots": [ + "type" + ], + "slot_usage": { + "used": { + "name": "used", + "description": "The instrument used to collect the data used in the analysis", + "multivalued": false, + "domain_of": [ + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "Activity" + ], + "range": "Instrument" + }, + "has_calibration": { + "name": "has_calibration", + "description": "A reference to a file that holds calibration information.", + "range": "string" + }, + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:wfnom", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "NomAnalysisActivity", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin", + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + }, + "execution_resource": { + "name": "execution_resource", + "description": "Example: NERSC-Cori", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "execution_resource", + "owner": "NomAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity" + ], + "range": "string", + "required": true + }, + "git_url": { + "name": "git_url", + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "git_url", + "owner": "NomAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity" + ], + "range": "string", + "required": true + }, + "has_input": { + "name": "has_input", + "description": "An input to a process.", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_input", + "owner": "NomAnalysisActivity", + "domain_of": [ + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity" + ], + "range": "NamedThing", + "required": true + }, + "has_output": { + "name": "has_output", + "description": "An output biosample to a processing step", + "from_schema": "https://microbiomedata/schema", + "domain": "NamedThing", + "multivalued": true, + "alias": "has_output", + "owner": "NomAnalysisActivity", + "domain_of": [ + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity" + ], + "range": "NamedThing", + "required": true + }, + "part_of": { + "name": "part_of", + "description": "Links a resource to another resource that either logically or physically includes it.", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "is part of" + ], + "domain": "NamedThing", + "slot_uri": "dcterms:isPartOf", + "multivalued": true, + "alias": "part_of", + "owner": "NomAnalysisActivity", + "domain_of": [ + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "Biosample", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity" + ], + "range": "NamedThing" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "NomAnalysisActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:wfnom", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "NomAnalysisActivity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "started_at_time": { + "name": "started_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "started_at_time", + "owner": "NomAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "ended_at_time": { + "name": "ended_at_time", + "from_schema": "https://microbiomedata/schema", + "alias": "ended_at_time", + "owner": "NomAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "Activity" + ], + "range": "datetime", + "required": true, + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "alias": "was_informed_by", + "owner": "NomAnalysisActivity", + "domain_of": [ + "Activity", + "Agent", + "WorkflowExecutionActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity", + "Agent", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "Activity", + "Agent" + ], + "range": "Activity", + "required": true + }, + "was_associated_with": { + "name": "was_associated_with", + "description": "the agent/entity associated with the generation of the file", + "from_schema": "https://microbiomedata/schema", + "alias": "was_associated_with", + "owner": "NomAnalysisActivity", + "domain_of": [ + "Activity", + "WorkflowExecutionActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "Activity", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "Activity" + ], + "range": "WorkflowExecutionActivity", + "required": false, + "inlined": false + }, + "used": { + "name": "used", + "description": "The instrument used to collect the data used in the analysis", + "from_schema": "https://microbiomedata/schema", + "domain": "Activity", + "multivalued": false, + "alias": "used", + "owner": "NomAnalysisActivity", + "domain_of": [ + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "Activity" + ], + "range": "Instrument" + } + } + }, + "Activity": { + "name": "Activity", + "description": "a provence-generating activity", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:Activity" + ], + "slots": [ + "id", + "name", + "started_at_time", + "ended_at_time", + "was_informed_by", + "was_associated_with", + "used" + ], + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing" + ], + "pattern": "^nmdc:act", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:act-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false, + "todos": [ + "remove the static pattern once the minter can generate ids that satisfy this structured_pattern and gen-linkml can expand the structured_pattern" + ] + } + } + }, + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "Activity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing" + ], + "range": "string", + "pattern": "^nmdc:act", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:act-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false, + "todos": [ + "remove the static pattern once the minter can generate ids that satisfy this structured_pattern and gen-linkml can expand the structured_pattern" + ] + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "Activity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "started_at_time": { + "name": "started_at_time", + "notes": [ + "The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/ It may not be complete, but it is good enough for now." + ], + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:startedAtTime" + ], + "alias": "started_at_time", + "owner": "Activity", + "domain_of": [ + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity" + ], + "range": "datetime", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "ended_at_time": { + "name": "ended_at_time", + "notes": [ + "The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/ It may not be complete, but it is good enough for now." + ], + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:endedAtTime" + ], + "alias": "ended_at_time", + "owner": "Activity", + "domain_of": [ + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity" + ], + "range": "datetime", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasInformedBy" + ], + "alias": "was_informed_by", + "owner": "Activity", + "domain_of": [ + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "Agent" + ], + "range": "Activity" + }, + "was_associated_with": { + "name": "was_associated_with", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasAssociatedWith" + ], + "alias": "was_associated_with", + "owner": "Activity", + "domain_of": [ + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity" + ], + "range": "Agent" + }, + "used": { + "name": "used", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:used" + ], + "domain": "Activity", + "alias": "used", + "owner": "Activity", + "domain_of": [ + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity" + ], + "range": "string" + } + } + }, + "Agent": { + "name": "Agent", + "description": "a provence-generating agent", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:Agent" + ], + "slots": [ + "acted_on_behalf_of", + "was_informed_by" + ], + "attributes": { + "acted_on_behalf_of": { + "name": "acted_on_behalf_of", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:actedOnBehalfOf" + ], + "alias": "acted_on_behalf_of", + "owner": "Agent", + "domain_of": [ + "Agent" + ], + "range": "Agent" + }, + "was_informed_by": { + "name": "was_informed_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasInformedBy" + ], + "alias": "was_informed_by", + "owner": "Agent", + "domain_of": [ + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "Agent" + ], + "range": "Activity" + } + } + }, + "NamedThing": { + "name": "NamedThing", + "description": "a databased entity or concept/class", + "from_schema": "https://microbiomedata/schema", + "abstract": true, + "slots": [ + "id", + "name", + "description", + "alternative_identifiers" + ], + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "notes": [ + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", + "minting authority shoulders should probably be enumerated and checked in the pattern" + ], + "examples": [ + { + "value": "nmdc:mgmag-00-x012.1_7_c1", + "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" + } + ], + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "NamedThing", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing" + ], + "range": "string" + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "NamedThing", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "NamedThing", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "NamedThing", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "MaterialEntity": { + "name": "MaterialEntity", + "title": "Material Entity", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "Material", + "Physical entity" + ], + "is_a": "NamedThing", + "abstract": true, + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "notes": [ + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", + "minting authority shoulders should probably be enumerated and checked in the pattern" + ], + "examples": [ + { + "value": "nmdc:mgmag-00-x012.1_7_c1", + "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" + } + ], + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "MaterialEntity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing" + ], + "range": "string" + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "MaterialEntity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "MaterialEntity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "MaterialEntity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "AnalyticalSample": { + "name": "AnalyticalSample", + "title": "Analytical Sample", + "from_schema": "https://microbiomedata/schema", + "is_a": "MaterialEntity", + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity" + ], + "pattern": "^nmdc:ansm", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:ansm-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "AnalyticalSample", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity" + ], + "range": "string", + "pattern": "^nmdc:ansm", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:ansm-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "AnalyticalSample", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "PersonValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "AnalyticalSample", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "ImageValue" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "AnalyticalSample", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "Site": { + "name": "Site", + "title": "Site", + "comments": [ + "BCO sample collection site ?" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "MaterialEntity", + "abstract": true, + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample" + ], + "pattern": "^nmdc:site", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:site-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "Site", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample" + ], + "range": "string", + "pattern": "^nmdc:site", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:site-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "Site", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "PersonValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "Site", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "ImageValue" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "Site", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "PlannedProcess": { + "name": "PlannedProcess", + "title": "Planned Process", + "from_schema": "https://microbiomedata/schema", + "is_a": "NamedThing", + "abstract": true, + "slots": [ + "has_inputs", + "has_outputs", + "participating_agent" + ], + "attributes": { + "has_inputs": { + "name": "has_inputs", + "from_schema": "https://microbiomedata/schema", + "domain": "PlannedProcess", + "multivalued": true, + "alias": "has_inputs", + "owner": "PlannedProcess", + "domain_of": [ + "CollectingBiosamplesFromSite", + "PlannedProcess" + ], + "range": "NamedThing" + }, + "has_outputs": { + "name": "has_outputs", + "from_schema": "https://microbiomedata/schema", + "domain": "PlannedProcess", + "multivalued": true, + "alias": "has_outputs", + "owner": "PlannedProcess", + "domain_of": [ + "CollectingBiosamplesFromSite", + "PlannedProcess" + ], + "range": "NamedThing" + }, + "participating_agent": { + "name": "participating_agent", + "from_schema": "https://microbiomedata/schema", + "domain": "PlannedProcess", + "alias": "participating_agent", + "owner": "PlannedProcess", + "domain_of": [ + "CollectingBiosamplesFromSite", + "PlannedProcess" + ], + "range": "Agent" + }, + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "notes": [ + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", + "minting authority shoulders should probably be enumerated and checked in the pattern" + ], + "examples": [ + { + "value": "nmdc:mgmag-00-x012.1_7_c1", + "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" + } + ], + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "PlannedProcess", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site" + ], + "range": "string" + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "PlannedProcess", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PersonValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "PlannedProcess", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "ImageValue" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "PlannedProcess", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "MetaboliteQuantification" + ], + "range": "string" + } + }, + "class_uri": "OBI:0000011" + }, + "OntologyClass": { + "name": "OntologyClass", + "notes": [ + "The identifiers for terms from external ontologies can't have their ids constrained to the nmdc namespace" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "NamedThing", + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "notes": [ + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", + "minting authority shoulders should probably be enumerated and checked in the pattern" + ], + "examples": [ + { + "value": "nmdc:mgmag-00-x012.1_7_c1", + "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" + } + ], + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "OntologyClass", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess" + ], + "range": "string" + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "OntologyClass", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "PersonValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "OntologyClass", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "ImageValue" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "OntologyClass", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "EnvironmentalMaterialTerm": { + "name": "EnvironmentalMaterialTerm", + "from_schema": "https://microbiomedata/schema", + "is_a": "OntologyClass", + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "notes": [ + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", + "minting authority shoulders should probably be enumerated and checked in the pattern" + ], + "examples": [ + { + "value": "nmdc:mgmag-00-x012.1_7_c1", + "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" + } + ], + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "EnvironmentalMaterialTerm", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass" + ], + "range": "string" + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "EnvironmentalMaterialTerm", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "PersonValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "EnvironmentalMaterialTerm", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "ImageValue" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "EnvironmentalMaterialTerm", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "AttributeValue": { + "name": "AttributeValue", + "description": "The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value", + "from_schema": "https://microbiomedata/schema", + "slots": [ + "has_raw_value", + "was_generated_by" + ], + "slot_usage": { + "type": { + "name": "type", + "description": "An optional string that specified the type of object.", + "required": false + } + }, + "attributes": { + "has_raw_value": { + "name": "has_raw_value", + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "from_schema": "https://microbiomedata/schema", + "domain": "AttributeValue", + "multivalued": false, + "alias": "has_raw_value", + "owner": "AttributeValue", + "domain_of": [ + "AttributeValue" + ], + "range": "string", + "required": false + }, + "was_generated_by": { + "name": "was_generated_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasGeneratedBy" + ], + "alias": "was_generated_by", + "owner": "AttributeValue", + "domain_of": [ + "DataObject", + "AttributeValue", + "FunctionalAnnotation" + ], + "range": "Activity" + } + } + }, + "QuantityValue": { + "name": "QuantityValue", + "description": "A simple quantity, e.g. 2cm", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "schema:QuantityValue" + ], + "is_a": "AttributeValue", + "slots": [ + "has_unit", + "has_numeric_value", + "has_minimum_numeric_value", + "has_maximum_numeric_value" + ], + "slot_usage": { + "has_raw_value": { + "name": "has_raw_value", + "description": "Unnormalized atomic string representation, should in syntax {number} {unit}", + "domain_of": [ + "AttributeValue" + ] + }, + "has_unit": { + "name": "has_unit", + "description": "The unit of the quantity", + "domain_of": [ + "QuantityValue" + ] + }, + "has_numeric_value": { + "name": "has_numeric_value", + "description": "The number part of the quantity", + "domain_of": [ + "QuantityValue", + "IntegerValue" + ], + "range": "double" + } + }, + "attributes": { + "has_unit": { + "name": "has_unit", + "description": "The unit of the quantity", + "from_schema": "https://microbiomedata/schema", + "alias": "has_unit", + "owner": "QuantityValue", + "domain_of": [ + "QuantityValue" + ], + "range": "unit" + }, + "has_numeric_value": { + "name": "has_numeric_value", + "description": "The number part of the quantity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "has_numeric_value", + "owner": "QuantityValue", + "domain_of": [ + "QuantityValue", + "IntegerValue" + ], + "range": "double" + }, + "has_minimum_numeric_value": { + "name": "has_minimum_numeric_value", + "description": "The minimum value part, expressed as number, of the quantity value when the value covers a range.", + "from_schema": "https://microbiomedata/schema", + "is_a": "has_numeric_value", + "alias": "has_minimum_numeric_value", + "owner": "QuantityValue", + "domain_of": [ + "QuantityValue" + ], + "range": "float" + }, + "has_maximum_numeric_value": { + "name": "has_maximum_numeric_value", + "description": "The maximum value part, expressed as number, of the quantity value when the value covers a range.", + "from_schema": "https://microbiomedata/schema", + "is_a": "has_numeric_value", + "alias": "has_maximum_numeric_value", + "owner": "QuantityValue", + "domain_of": [ + "QuantityValue" + ], + "range": "float" + }, + "has_raw_value": { + "name": "has_raw_value", + "description": "Unnormalized atomic string representation, should in syntax {number} {unit}", + "from_schema": "https://microbiomedata/schema", + "domain": "AttributeValue", + "multivalued": false, + "alias": "has_raw_value", + "owner": "QuantityValue", + "domain_of": [ + "AttributeValue" + ], + "range": "string", + "required": false + }, + "was_generated_by": { + "name": "was_generated_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasGeneratedBy" + ], + "alias": "was_generated_by", + "owner": "QuantityValue", + "domain_of": [ + "DataObject", + "AttributeValue", + "FunctionalAnnotation", + "DataObject", + "AttributeValue", + "FunctionalAnnotation" + ], + "range": "Activity" + } + } + }, + "ImageValue": { + "name": "ImageValue", + "description": "An attribute value representing an image.", + "from_schema": "https://microbiomedata/schema", + "is_a": "AttributeValue", + "slots": [ + "url", + "description", + "display_order" + ], + "attributes": { + "url": { + "name": "url", + "notes": [ + "See issue 207 - this clashes with the mixs field" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "url", + "owner": "ImageValue", + "domain_of": [ + "DataObject", + "ImageValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "ImageValue", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "ImageValue" + ], + "range": "string" + }, + "display_order": { + "name": "display_order", + "description": "When rendering information, this attribute to specify the order in which the information should be rendered.", + "from_schema": "https://microbiomedata/schema", + "is_a": "attribute", + "alias": "display_order", + "owner": "ImageValue", + "domain_of": [ + "ImageValue" + ], + "range": "string" + }, + "has_raw_value": { + "name": "has_raw_value", + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "from_schema": "https://microbiomedata/schema", + "domain": "AttributeValue", + "multivalued": false, + "alias": "has_raw_value", + "owner": "ImageValue", + "domain_of": [ + "AttributeValue", + "AttributeValue", + "QuantityValue" + ], + "range": "string", + "required": false + }, + "was_generated_by": { + "name": "was_generated_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasGeneratedBy" + ], + "alias": "was_generated_by", + "owner": "ImageValue", + "domain_of": [ + "DataObject", + "AttributeValue", + "FunctionalAnnotation", + "DataObject", + "AttributeValue", + "QuantityValue", + "FunctionalAnnotation" + ], + "range": "Activity" + } + } + }, + "PersonValue": { + "name": "PersonValue", + "description": "An attribute value representing a person", + "todos": [ + "add additional fields e.g for institution", + "deprecate \"has_raw_value\" in favor of \"name\"" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "AttributeValue", + "slots": [ + "orcid", + "profile_image_url", + "email", + "name", + "websites" + ], + "slot_usage": { + "orcid": { + "name": "orcid", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Open Researcher and Contributor ID for this person. See https://orcid.org" + } + }, + "domain_of": [ + "PersonValue" + ] + }, + "email": { + "name": "email", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Email address for this person." + } + }, + "domain_of": [ + "PersonValue" + ] + }, + "has_raw_value": { + "name": "has_raw_value", + "description": "The full name of the Investigator in format FIRST LAST.", + "notes": [ + "May eventually be deprecated in favor of \"name\"." + ], + "domain_of": [ + "AttributeValue", + "QuantityValue", + "ImageValue" + ] + }, + "name": { + "name": "name", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "First name, middle initial, and last name of this person." + } + }, + "description": "The full name of the Investigator. It should follow the format FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "PersonValue" + ] + } + }, + "attributes": { + "orcid": { + "name": "orcid", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Open Researcher and Contributor ID for this person. See https://orcid.org" + } + }, + "description": "The ORCID of a person.", + "from_schema": "https://microbiomedata/schema", + "domain": "PersonValue", + "alias": "orcid", + "owner": "PersonValue", + "domain_of": [ + "PersonValue" + ], + "range": "string" + }, + "profile_image_url": { + "name": "profile_image_url", + "description": "A url that points to an image of a person.", + "from_schema": "https://microbiomedata/schema", + "domain": "PersonValue", + "alias": "profile_image_url", + "owner": "PersonValue", + "domain_of": [ + "PersonValue" + ], + "range": "string" + }, + "email": { + "name": "email", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "Email address for this person." + } + }, + "description": "An email address for an entity such as a person. This should be the primarly email address used.", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "schema:email", + "alias": "email", + "owner": "PersonValue", + "domain_of": [ + "PersonValue" + ], + "range": "string" + }, + "name": { + "name": "name", + "annotations": { + "display_hint": { + "tag": "display_hint", + "value": "First name, middle initial, and last name of this person." + } + }, + "description": "The full name of the Investigator. It should follow the format FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "PersonValue", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "PersonValue" + ], + "range": "string" + }, + "websites": { + "name": "websites", + "description": "A list of websites that are associated with the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "websites", + "owner": "PersonValue", + "domain_of": [ + "Study", + "PersonValue" + ], + "range": "string" + }, + "has_raw_value": { + "name": "has_raw_value", + "description": "The full name of the Investigator in format FIRST LAST.", + "notes": [ + "May eventually be deprecated in favor of \"name\"." + ], + "from_schema": "https://microbiomedata/schema", + "domain": "AttributeValue", + "multivalued": false, + "alias": "has_raw_value", + "owner": "PersonValue", + "domain_of": [ + "AttributeValue", + "QuantityValue", + "ImageValue" + ], + "range": "string", + "required": false + }, + "was_generated_by": { + "name": "was_generated_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasGeneratedBy" + ], + "alias": "was_generated_by", + "owner": "PersonValue", + "domain_of": [ + "DataObject", + "AttributeValue", + "FunctionalAnnotation", + "DataObject", + "AttributeValue", + "QuantityValue", + "ImageValue", + "FunctionalAnnotation" + ], + "range": "Activity" + } + } + }, + "Person": { + "name": "Person", + "description": "represents a person, such as a researcher", + "notes": [ + "not yet in use" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "NamedThing", + "slot_usage": { + "id": { + "name": "id", + "description": "Should be an ORCID. Specify in CURIE format. E.g ORCID:0000-1111-...", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm" + ] + } + }, + "attributes": { + "id": { + "name": "id", + "description": "Should be an ORCID. Specify in CURIE format. E.g ORCID:0000-1111-...", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "Person", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm" + ], + "range": "string" + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "Person", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "PersonValue" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "Person", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "ImageValue" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "Person", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "MagBin": { + "name": "MagBin", + "from_schema": "https://microbiomedata/schema", + "slots": [ + "type" + ], + "attributes": { + "bin_name": { + "name": "bin_name", + "from_schema": "https://microbiomedata/schema/core", + "alias": "bin_name", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "string" + }, + "number_of_contig": { + "name": "number_of_contig", + "from_schema": "https://microbiomedata/schema/core", + "alias": "number_of_contig", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "integer" + }, + "completeness": { + "name": "completeness", + "from_schema": "https://microbiomedata/schema/core", + "alias": "completeness", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "float" + }, + "contamination": { + "name": "contamination", + "from_schema": "https://microbiomedata/schema/core", + "alias": "contamination", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "float" + }, + "gene_count": { + "name": "gene_count", + "from_schema": "https://microbiomedata/schema/core", + "alias": "gene_count", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "integer" + }, + "bin_quality": { + "name": "bin_quality", + "from_schema": "https://microbiomedata/schema/core", + "alias": "bin_quality", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "string" + }, + "num_16s": { + "name": "num_16s", + "from_schema": "https://microbiomedata/schema/core", + "alias": "num_16s", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "integer" + }, + "num_5s": { + "name": "num_5s", + "from_schema": "https://microbiomedata/schema/core", + "alias": "num_5s", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "integer" + }, + "num_23s": { + "name": "num_23s", + "from_schema": "https://microbiomedata/schema/core", + "alias": "num_23s", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "integer" + }, + "num_t_rna": { + "name": "num_t_rna", + "from_schema": "https://microbiomedata/schema/core", + "alias": "num_t_rna", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "integer" + }, + "gtdbtk_domain": { + "name": "gtdbtk_domain", + "from_schema": "https://microbiomedata/schema/core", + "alias": "gtdbtk_domain", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "string", + "required": false + }, + "gtdbtk_phylum": { + "name": "gtdbtk_phylum", + "from_schema": "https://microbiomedata/schema/core", + "alias": "gtdbtk_phylum", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "string", + "required": false + }, + "gtdbtk_class": { + "name": "gtdbtk_class", + "from_schema": "https://microbiomedata/schema/core", + "alias": "gtdbtk_class", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "string", + "required": false + }, + "gtdbtk_order": { + "name": "gtdbtk_order", + "from_schema": "https://microbiomedata/schema/core", + "alias": "gtdbtk_order", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "string", + "required": false + }, + "gtdbtk_family": { + "name": "gtdbtk_family", + "from_schema": "https://microbiomedata/schema/core", + "alias": "gtdbtk_family", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "string", + "required": false + }, + "gtdbtk_genus": { + "name": "gtdbtk_genus", + "from_schema": "https://microbiomedata/schema/core", + "alias": "gtdbtk_genus", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "string", + "required": false + }, + "gtdbtk_species": { + "name": "gtdbtk_species", + "from_schema": "https://microbiomedata/schema/core", + "alias": "gtdbtk_species", + "owner": "MagBin", + "domain_of": [ + "MagBin" + ], + "range": "string", + "required": false + }, + "type": { + "name": "type", + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "deprecated": "Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30", + "examples": [ + { + "value": "nmdc:Biosample" + }, + { + "value": "nmdc:Study" + } + ], + "from_schema": "https://microbiomedata/schema", + "alias": "type", + "owner": "MagBin", + "domain_of": [ + "DataObject", + "Biosample", + "Study", + "OmicsProcessing", + "CreditAssociation", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "MagBin" + ], + "range": "string" + } + } + }, + "Instrument": { + "name": "Instrument", + "description": "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI].", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "device" + ], + "exact_mappings": [ + "OBI:0000485" + ], + "is_a": "NamedThing", + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person" + ], + "pattern": "^nmdc:inst", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "Instrument", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person" + ], + "range": "string", + "pattern": "^nmdc:inst", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "Instrument", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "PersonValue", + "Person" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "Instrument", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "ImageValue", + "Person" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "Instrument", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "MetaboliteQuantification": { + "name": "MetaboliteQuantification", + "description": "This is used to link a metabolomics analysis workflow to a specific metabolite", + "from_schema": "https://microbiomedata/schema", + "slots": [ + "alternative_identifiers" + ], + "slot_usage": { + "metabolite_quantified": { + "name": "metabolite_quantified", + "description": "the specific metabolite identifier", + "range": "ChemicalEntity" + }, + "highest_similarity_score": { + "name": "highest_similarity_score", + "description": "TODO: Yuri to fill in", + "range": "float" + } + }, + "attributes": { + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "MetaboliteQuantification", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "PeptideQuantification": { + "name": "PeptideQuantification", + "description": "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information", + "from_schema": "https://microbiomedata/schema", + "slot_usage": { + "peptide_sequence": { + "name": "peptide_sequence", + "range": "string" + }, + "best_protein": { + "name": "best_protein", + "description": "the specific protein identifier most correctly associated with the peptide sequence", + "range": "GeneProduct" + }, + "all_proteins": { + "name": "all_proteins", + "description": "the list of protein identifiers that are associated with the peptide sequence", + "multivalued": true, + "range": "GeneProduct" + }, + "min_q_value": { + "name": "min_q_value", + "description": "smallest Q-Value associated with the peptide sequence as provided by MSGFPlus tool", + "see_also": [ + "OBI:0001442" + ], + "range": "float" + }, + "peptide_spectral_count": { + "name": "peptide_spectral_count", + "description": "sum of filter passing MS2 spectra associated with the peptide sequence within a given LC-MS/MS data file", + "range": "integer" + }, + "peptide_sum_masic_abundance": { + "name": "peptide_sum_masic_abundance", + "description": "combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the peptide sequence from a given LC-MS/MS data file using the MASIC tool", + "range": "integer" + } + } + }, + "ProteinQuantification": { + "name": "ProteinQuantification", + "description": "This is used to link a metaproteomics analysis workflow to a specific protein", + "from_schema": "https://microbiomedata/schema", + "slot_usage": { + "best_protein": { + "name": "best_protein", + "description": "the specific protein identifier most correctly grouped to its associated peptide sequences", + "range": "GeneProduct" + }, + "all_proteins": { + "name": "all_proteins", + "description": "the grouped list of protein identifiers associated with the peptide sequences that were grouped to a best protein", + "multivalued": true, + "range": "GeneProduct" + }, + "peptide_sequence_count": { + "name": "peptide_sequence_count", + "description": "count of peptide sequences grouped to the best_protein", + "range": "integer" + }, + "protein_spectral_count": { + "name": "protein_spectral_count", + "description": "sum of filter passing MS2 spectra associated with the best protein within a given LC-MS/MS data file", + "range": "integer" + }, + "protein_sum_masic_abundance": { + "name": "protein_sum_masic_abundance", + "description": "combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the best protein from a given LC-MS/MS data file using the MASIC tool", + "range": "integer" + } + } + }, + "ChemicalEntity": { + "name": "ChemicalEntity", + "id_prefixes": [ + "CAS", + "CHEBI", + "CHEMBL.COMPOUND", + "DRUGBANK", + "HMDB", + "KEGG.COMPOUND", + "MESH", + "PUBCHEM.COMPOUND" + ], + "description": "An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states", + "comments": [ + "As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode to this class." + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html" + ], + "aliases": [ + "metabolite", + "chemical substance", + "chemical compound", + "chemical" + ], + "exact_mappings": [ + "biolink:ChemicalSubstance" + ], + "is_a": "OntologyClass", + "slot_usage": { + "inchi": { + "name": "inchi", + "multivalued": false, + "key": false, + "range": "string" + }, + "inchi_key": { + "name": "inchi_key", + "multivalued": false, + "key": false, + "range": "string" + }, + "smiles": { + "name": "smiles", + "description": "A string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol.", + "multivalued": true, + "range": "string" + }, + "chemical_formula": { + "name": "chemical_formula", + "description": "A generic grouping for miolecular formulae and empirican formulae", + "multivalued": false, + "key": false, + "range": "string" + } + }, + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "notes": [ + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", + "minting authority shoulders should probably be enumerated and checked in the pattern" + ], + "examples": [ + { + "value": "nmdc:mgmag-00-x012.1_7_c1", + "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" + } + ], + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "ChemicalEntity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument" + ], + "range": "string" + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "ChemicalEntity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "PersonValue", + "Person", + "Instrument" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "ChemicalEntity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "ImageValue", + "Person", + "Instrument" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "ChemicalEntity", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "MetaboliteQuantification" + ], + "range": "string" + } + } + }, + "GeneProduct": { + "name": "GeneProduct", + "id_prefixes": [ + "PR", + "UniProtKB", + "gtpo" + ], + "description": "A molecule encoded by a gene that has an evolved function", + "notes": [ + "we may include a more general gene product class in future to allow for ncRNA annotation" + ], + "from_schema": "https://microbiomedata/schema", + "exact_mappings": [ + "biolink:GeneProduct" + ], + "is_a": "NamedThing", + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "notes": [ + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", + "minting authority shoulders should probably be enumerated and checked in the pattern" + ], + "examples": [ + { + "value": "nmdc:mgmag-00-x012.1_7_c1", + "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" + } + ], + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "GeneProduct", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "ChemicalEntity" + ], + "range": "string" + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "GeneProduct", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "PersonValue", + "Person", + "Instrument", + "ChemicalEntity" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "GeneProduct", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "ImageValue", + "Person", + "Instrument", + "ChemicalEntity" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "GeneProduct", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "MetaboliteQuantification", + "ChemicalEntity" + ], + "range": "string" + } + } + }, + "TextValue": { + "name": "TextValue", + "description": "A basic string value", + "from_schema": "https://microbiomedata/schema", + "is_a": "AttributeValue", + "slots": [ + "language" + ], + "attributes": { + "language": { + "name": "language", + "description": "Should use ISO 639-1 code e.g. \"en\", \"fr\"", + "from_schema": "https://microbiomedata/schema", + "alias": "language", + "owner": "TextValue", + "domain_of": [ + "TextValue" + ], + "range": "language code" + }, + "has_raw_value": { + "name": "has_raw_value", + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "from_schema": "https://microbiomedata/schema", + "domain": "AttributeValue", + "multivalued": false, + "alias": "has_raw_value", + "owner": "TextValue", + "domain_of": [ + "AttributeValue", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue" + ], + "range": "string", + "required": false + }, + "was_generated_by": { + "name": "was_generated_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasGeneratedBy" + ], + "alias": "was_generated_by", + "owner": "TextValue", + "domain_of": [ + "DataObject", + "AttributeValue", + "FunctionalAnnotation", + "DataObject", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "FunctionalAnnotation" + ], + "range": "Activity" + } + } + }, + "UrlValue": { + "name": "UrlValue", + "description": "A value that is a string that conforms to URL syntax", + "from_schema": "https://microbiomedata/schema", + "is_a": "AttributeValue", + "attributes": { + "has_raw_value": { + "name": "has_raw_value", + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "from_schema": "https://microbiomedata/schema", + "domain": "AttributeValue", + "multivalued": false, + "alias": "has_raw_value", + "owner": "UrlValue", + "domain_of": [ + "AttributeValue", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue" + ], + "range": "string", + "required": false + }, + "was_generated_by": { + "name": "was_generated_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasGeneratedBy" + ], + "alias": "was_generated_by", + "owner": "UrlValue", + "domain_of": [ + "DataObject", + "AttributeValue", + "FunctionalAnnotation", + "DataObject", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "FunctionalAnnotation" + ], + "range": "Activity" + } + } + }, + "TimestampValue": { + "name": "TimestampValue", + "description": "A value that is a timestamp. The range should be ISO-8601", + "notes": [ + "removed the following slots: year, month, day" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "AttributeValue", + "attributes": { + "has_raw_value": { + "name": "has_raw_value", + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "from_schema": "https://microbiomedata/schema", + "domain": "AttributeValue", + "multivalued": false, + "alias": "has_raw_value", + "owner": "TimestampValue", + "domain_of": [ + "AttributeValue", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue" + ], + "range": "string", + "required": false + }, + "was_generated_by": { + "name": "was_generated_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasGeneratedBy" + ], + "alias": "was_generated_by", + "owner": "TimestampValue", + "domain_of": [ + "DataObject", + "AttributeValue", + "FunctionalAnnotation", + "DataObject", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "FunctionalAnnotation" + ], + "range": "Activity" + } + } + }, + "IntegerValue": { + "name": "IntegerValue", + "description": "A value that is an integer", + "from_schema": "https://microbiomedata/schema", + "is_a": "AttributeValue", + "slots": [ + "has_numeric_value" + ], + "attributes": { + "has_numeric_value": { + "name": "has_numeric_value", + "description": "Links a quantity value to a number", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "qud:quantityValue", + "schema:value" + ], + "multivalued": false, + "alias": "has_numeric_value", + "owner": "IntegerValue", + "domain_of": [ + "QuantityValue", + "IntegerValue" + ], + "range": "float" + }, + "has_raw_value": { + "name": "has_raw_value", + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "from_schema": "https://microbiomedata/schema", + "domain": "AttributeValue", + "multivalued": false, + "alias": "has_raw_value", + "owner": "IntegerValue", + "domain_of": [ + "AttributeValue", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue" + ], + "range": "string", + "required": false + }, + "was_generated_by": { + "name": "was_generated_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasGeneratedBy" + ], + "alias": "was_generated_by", + "owner": "IntegerValue", + "domain_of": [ + "DataObject", + "AttributeValue", + "FunctionalAnnotation", + "DataObject", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue", + "FunctionalAnnotation" + ], + "range": "Activity" + } + } + }, + "BooleanValue": { + "name": "BooleanValue", + "description": "A value that is a boolean", + "from_schema": "https://microbiomedata/schema", + "is_a": "AttributeValue", + "slots": [ + "has_boolean_value" + ], + "attributes": { + "has_boolean_value": { + "name": "has_boolean_value", + "description": "Links a quantity value to a boolean", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "has_boolean_value", + "owner": "BooleanValue", + "domain_of": [ + "BooleanValue" + ], + "range": "boolean" + }, + "has_raw_value": { + "name": "has_raw_value", + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "from_schema": "https://microbiomedata/schema", + "domain": "AttributeValue", + "multivalued": false, + "alias": "has_raw_value", + "owner": "BooleanValue", + "domain_of": [ + "AttributeValue", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue", + "IntegerValue" + ], + "range": "string", + "required": false + }, + "was_generated_by": { + "name": "was_generated_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasGeneratedBy" + ], + "alias": "was_generated_by", + "owner": "BooleanValue", + "domain_of": [ + "DataObject", + "AttributeValue", + "FunctionalAnnotation", + "DataObject", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue", + "IntegerValue", + "FunctionalAnnotation" + ], + "range": "Activity" + } + } + }, + "ControlledTermValue": { + "name": "ControlledTermValue", + "description": "A controlled term or class from an ontology", + "todos": [ + "add fields for ontology, branch" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "AttributeValue", + "slots": [ + "term" + ], + "attributes": { + "term": { + "name": "term", + "description": "pointer to an ontology class", + "notes": [ + "removed 'slot_uri: rdf:type'" + ], + "from_schema": "https://microbiomedata/schema", + "domain": "ControlledTermValue", + "alias": "term", + "owner": "ControlledTermValue", + "domain_of": [ + "ControlledTermValue" + ], + "range": "OntologyClass", + "inlined": true + }, + "has_raw_value": { + "name": "has_raw_value", + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "from_schema": "https://microbiomedata/schema", + "domain": "AttributeValue", + "multivalued": false, + "alias": "has_raw_value", + "owner": "ControlledTermValue", + "domain_of": [ + "AttributeValue", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue", + "IntegerValue", + "BooleanValue" + ], + "range": "string", + "required": false + }, + "was_generated_by": { + "name": "was_generated_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasGeneratedBy" + ], + "alias": "was_generated_by", + "owner": "ControlledTermValue", + "domain_of": [ + "DataObject", + "AttributeValue", + "FunctionalAnnotation", + "DataObject", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue", + "IntegerValue", + "BooleanValue", + "FunctionalAnnotation" + ], + "range": "Activity" + } + } + }, + "ControlledIdentifiedTermValue": { + "name": "ControlledIdentifiedTermValue", + "description": "A controlled term or class from an ontology, requiring the presence of term with an id", + "notes": [ + "To be used for slots like env_broad_scale" + ], + "from_schema": "https://microbiomedata/schema", + "is_a": "ControlledTermValue", + "slot_usage": { + "term": { + "name": "term", + "domain_of": [ + "ControlledTermValue" + ], + "required": true + } + }, + "attributes": { + "term": { + "name": "term", + "description": "pointer to an ontology class", + "from_schema": "https://microbiomedata/schema", + "domain": "ControlledTermValue", + "alias": "term", + "owner": "ControlledIdentifiedTermValue", + "domain_of": [ + "ControlledTermValue" + ], + "range": "OntologyClass", + "required": true, + "inlined": true + }, + "has_raw_value": { + "name": "has_raw_value", + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "from_schema": "https://microbiomedata/schema", + "domain": "AttributeValue", + "multivalued": false, + "alias": "has_raw_value", + "owner": "ControlledIdentifiedTermValue", + "domain_of": [ + "AttributeValue", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue", + "IntegerValue", + "BooleanValue", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue", + "IntegerValue", + "BooleanValue", + "ControlledTermValue" + ], + "range": "string", + "required": false + }, + "was_generated_by": { + "name": "was_generated_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasGeneratedBy" + ], + "alias": "was_generated_by", + "owner": "ControlledIdentifiedTermValue", + "domain_of": [ + "DataObject", + "AttributeValue", + "FunctionalAnnotation", + "DataObject", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue", + "IntegerValue", + "BooleanValue", + "FunctionalAnnotation", + "DataObject", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue", + "IntegerValue", + "BooleanValue", + "ControlledTermValue", + "FunctionalAnnotation" + ], + "range": "Activity" + } + } + }, + "GeolocationValue": { + "name": "GeolocationValue", + "description": "A normalized value for a location on the earth's surface", + "notes": [ + "what did 'to_str: {latitude} {longitude}' mean?" + ], + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "schema:GeoCoordinates" + ], + "is_a": "AttributeValue", + "slots": [ + "latitude", + "longitude" + ], + "slot_usage": { + "has_raw_value": { + "name": "has_raw_value", + "description": "The raw value for a geolocation should follow {lat} {long}", + "domain_of": [ + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue", + "IntegerValue", + "BooleanValue", + "ControlledTermValue", + "ControlledIdentifiedTermValue" + ] + } + }, + "attributes": { + "latitude": { + "name": "latitude", + "description": "latitude", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "schema:latitude" + ], + "domain": "GeolocationValue", + "slot_uri": "wgs84:lat", + "alias": "latitude", + "owner": "GeolocationValue", + "domain_of": [ + "GeolocationValue" + ], + "range": "decimal degree" + }, + "longitude": { + "name": "longitude", + "description": "longitude", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "schema:longitude" + ], + "domain": "GeolocationValue", + "slot_uri": "wgs84:long", + "alias": "longitude", + "owner": "GeolocationValue", + "domain_of": [ + "GeolocationValue" + ], + "range": "decimal degree" + }, + "has_raw_value": { + "name": "has_raw_value", + "description": "The raw value for a geolocation should follow {lat} {long}", + "from_schema": "https://microbiomedata/schema", + "domain": "AttributeValue", + "multivalued": false, + "alias": "has_raw_value", + "owner": "GeolocationValue", + "domain_of": [ + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue", + "IntegerValue", + "BooleanValue", + "ControlledTermValue", + "ControlledIdentifiedTermValue" + ], + "range": "string", + "required": false + }, + "was_generated_by": { + "name": "was_generated_by", + "from_schema": "https://microbiomedata/schema", + "mappings": [ + "prov:wasGeneratedBy" + ], + "alias": "was_generated_by", + "owner": "GeolocationValue", + "domain_of": [ + "DataObject", + "AttributeValue", + "FunctionalAnnotation", + "DataObject", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue", + "IntegerValue", + "BooleanValue", + "ControlledTermValue", + "ControlledIdentifiedTermValue", + "FunctionalAnnotation" + ], + "range": "Activity" + } + } + }, + "DissolvingActivity": { + "name": "DissolvingActivity", + "title": "Dissolving activity", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "dissolution-activity" + ], + "slots": [ + "dissolution_aided_by", + "dissolution_reagent", + "dissolution_volume", + "dissolved_in", + "material_input", + "material_output" + ], + "slot_usage": { + "material_input": { + "name": "material_input", + "examples": [ + { + "value": "somextract:6" + } + ], + "domain_of": [ + "DissolvingActivity", + "ReactionActivity" + ], + "range": "MaterialSample" + }, + "material_output": { + "name": "material_output", + "examples": [ + { + "value": "somextract:7" + } + ], + "domain_of": [ + "DissolvingActivity", + "MaterialSamplingActivity", + "ReactionActivity" + ], + "range": "MaterialSample" + } + }, + "attributes": { + "dissolution_aided_by": { + "name": "dissolution_aided_by", + "title": "dissolution aided by", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "shaker" + ], + "alias": "dissolution_aided_by", + "owner": "DissolvingActivity", + "domain_of": [ + "DissolvingActivity" + ], + "range": "LabDevice", + "inlined": true + }, + "dissolution_reagent": { + "name": "dissolution_reagent", + "title": "dissolution reagent", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "solvent" + ], + "alias": "dissolution_reagent", + "owner": "DissolvingActivity", + "domain_of": [ + "DissolvingActivity" + ], + "range": "SolventEnum" + }, + "dissolution_volume": { + "name": "dissolution_volume", + "title": "dissolution volume", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "volume" + ], + "alias": "dissolution_volume", + "owner": "DissolvingActivity", + "domain_of": [ + "DissolvingActivity" + ], + "range": "QuantityValue", + "inlined": true + }, + "dissolved_in": { + "name": "dissolved_in", + "title": "dissolved in", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "container" + ], + "alias": "dissolved_in", + "owner": "DissolvingActivity", + "domain_of": [ + "DissolvingActivity" + ], + "range": "MaterialContainer", + "inlined": true + }, + "material_input": { + "name": "material_input", + "title": "material input", + "examples": [ + { + "value": "somextract:6" + } + ], + "from_schema": "https://microbiomedata/schema", + "alias": "material_input", + "owner": "DissolvingActivity", + "domain_of": [ + "DissolvingActivity", + "ReactionActivity" + ], + "range": "MaterialSample" + }, + "material_output": { + "name": "material_output", + "title": "material output", + "examples": [ + { + "value": "somextract:7" + } + ], + "from_schema": "https://microbiomedata/schema", + "alias": "material_output", + "owner": "DissolvingActivity", + "domain_of": [ + "DissolvingActivity", + "MaterialSamplingActivity", + "ReactionActivity" + ], + "range": "MaterialSample" + } + }, + "class_uri": "CHMO:0002773" + }, + "LabDevice": { + "name": "LabDevice", + "title": "Lab device", + "from_schema": "https://microbiomedata/schema", + "slots": [ + "device_type", + "activity_speed", + "activity_temperature", + "activity_time" + ], + "attributes": { + "device_type": { + "name": "device_type", + "title": "device type", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "shaker type" + ], + "alias": "device_type", + "owner": "LabDevice", + "domain_of": [ + "LabDevice" + ], + "range": "DeviceTypeEnum" + }, + "activity_speed": { + "name": "activity_speed", + "title": "activity speed", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "shake_speed" + ], + "alias": "activity_speed", + "owner": "LabDevice", + "domain_of": [ + "LabDevice" + ], + "range": "QuantityValue", + "inlined": true + }, + "activity_temperature": { + "name": "activity_temperature", + "todos": [ + "constrain units" + ], + "from_schema": "https://microbiomedata/schema", + "alias": "activity_temperature", + "owner": "LabDevice", + "domain_of": [ + "LabDevice" + ], + "range": "QuantityValue", + "inlined": true + }, + "activity_time": { + "name": "activity_time", + "title": "activity time", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "shake_time" + ], + "alias": "activity_time", + "owner": "LabDevice", + "domain_of": [ + "LabDevice" + ], + "range": "QuantityValue", + "inlined": true + } + } + }, + "MaterialContainer": { + "name": "MaterialContainer", + "title": "Material container", + "from_schema": "https://microbiomedata/schema", + "slots": [ + "container_size", + "container_type" + ], + "attributes": { + "container_size": { + "name": "container_size", + "title": "container size", + "from_schema": "https://microbiomedata/schema", + "alias": "container_size", + "owner": "MaterialContainer", + "domain_of": [ + "MaterialContainer" + ], + "range": "QuantityValue", + "inlined": true + }, + "container_type": { + "name": "container_type", + "title": "container type", + "from_schema": "https://microbiomedata/schema", + "alias": "container_type", + "owner": "MaterialContainer", + "domain_of": [ + "MaterialContainer" + ], + "range": "ContainerTypeEnum" + } + } + }, + "MaterialSample": { + "name": "MaterialSample", + "title": "Material sample", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "Material entity" + ], + "is_a": "NamedThing", + "slot_usage": { + "id": { + "name": "id", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct" + ], + "pattern": "^nmdc:matsm", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:matsm-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + } + }, + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "MaterialSample", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct" + ], + "range": "string", + "pattern": "^nmdc:matsm", + "structured_pattern": { + "syntax": "{id_nmdc_prefix}:matsm-{id_shoulder}-{id_blade}{id_version}{id_locus}", + "interpolated": true, + "partial_match": false + } + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "MaterialSample", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "PersonValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "MaterialSample", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "ImageValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "MaterialSample", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "MetaboliteQuantification", + "ChemicalEntity", + "GeneProduct" + ], + "range": "string" + } + } + }, + "MaterialSamplingActivity": { + "name": "MaterialSamplingActivity", + "title": "Material sampling activity", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "weighing-activity" + ], + "slots": [ + "amount_collected", + "collected_into", + "biosample_input", + "material_output", + "sampling_method" ], "slot_usage": { - "id": { - "name": "id", - "description": "An NMDC assigned unique identifier for a biosample submitted to NMDC.", - "required": true, - "pattern": "^nmdc:", - "structured_pattern": { - "syntax": "{id_nmdc_prefix}:{id_typecode_biosample}-{id_shoulder}-{id_blade}{id_version}{id_locus}", - "interpolated": true, - "partial_match": false - } + "amount_collected": { + "name": "amount_collected", + "aliases": [ + "weighing-activity.weight" + ], + "domain_of": [ + "MaterialSamplingActivity" + ] }, - "gold_biosample_identifiers": { - "name": "gold_biosample_identifiers", - "annotations": { - "display_hint": { - "tag": "display_hint", - "value": "Provide the GOLD biosample IDs associated with this biosample." + "collected_into": { + "name": "collected_into", + "aliases": [ + "weighing-activity.contanier" + ], + "domain_of": [ + "MaterialSamplingActivity" + ], + "range": "MaterialContainer", + "inlined": true + }, + "biosample_input": { + "name": "biosample_input", + "examples": [ + { + "value": "soil:1" } - }, - "description": "Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample", - "comments": [ - "This is the ID provided by GOLD that starts with 'GB'" + ], + "aliases": [ + "weighing-activity.source_material" + ], + "domain_of": [ + "MaterialSamplingActivity" ] }, - "alternative_identifiers": { - "name": "alternative_identifiers", - "description": "Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC", - "required": false + "material_output": { + "name": "material_output", + "examples": [ + { + "value": "somextract:6" + } + ], + "aliases": [ + "weighing-activity.id" + ], + "domain_of": [ + "DissolvingActivity", + "MaterialSamplingActivity", + "ReactionActivity" + ], + "range": "MaterialSample" }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "required": false + "sampling_method": { + "name": "sampling_method", + "domain_of": [ + "MaterialSamplingActivity" + ] + } + }, + "attributes": { + "amount_collected": { + "name": "amount_collected", + "title": "amount collected", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "weighing-activity.weight" + ], + "alias": "amount_collected", + "owner": "MaterialSamplingActivity", + "domain_of": [ + "MaterialSamplingActivity" + ], + "range": "QuantityValue", + "inlined": true }, - "env_broad_scale": { - "name": "env_broad_scale", + "collected_into": { + "name": "collected_into", + "title": "collected into", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "weighing-activity.contanier" + ], + "alias": "collected_into", + "owner": "MaterialSamplingActivity", + "domain_of": [ + "MaterialSamplingActivity" + ], + "range": "MaterialContainer", + "inlined": true + }, + "biosample_input": { + "name": "biosample_input", + "title": "biosample input", + "examples": [ + { + "value": "soil:1" + } + ], + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "weighing-activity.source_material" + ], + "alias": "biosample_input", + "owner": "MaterialSamplingActivity", + "domain_of": [ + "MaterialSamplingActivity" + ], + "range": "Biosample" + }, + "material_output": { + "name": "material_output", + "title": "material output", + "examples": [ + { + "value": "somextract:6" + } + ], + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "weighing-activity.id" + ], + "alias": "material_output", + "owner": "MaterialSamplingActivity", + "domain_of": [ + "DissolvingActivity", + "MaterialSamplingActivity", + "ReactionActivity" + ], + "range": "MaterialSample" + }, + "sampling_method": { + "name": "sampling_method", + "title": "sampling method", + "from_schema": "https://microbiomedata/schema", + "alias": "sampling_method", + "owner": "MaterialSamplingActivity", + "domain_of": [ + "MaterialSamplingActivity" + ], + "range": "SamplingMethodEnum" + } + }, + "class_uri": "OBI:0000744" + }, + "ReactionActivity": { + "name": "ReactionActivity", + "title": "Reaction activity", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "reaction-activity" + ], + "slots": [ + "material_input", + "material_output", + "reaction_aided_by", + "reaction_temperature", + "reaction_time" + ], + "slot_usage": { + "material_input": { + "name": "material_input", + "domain_of": [ + "DissolvingActivity", + "ReactionActivity" + ], + "range": "MaterialSample" + }, + "material_output": { + "name": "material_output", + "domain_of": [ + "DissolvingActivity", + "MaterialSamplingActivity", + "ReactionActivity" + ], + "range": "MaterialSample" + }, + "reaction_time": { + "name": "reaction_time", + "todos": [ + "constrain units", + "align with activity_time" + ], + "domain_of": [ + "ReactionActivity" + ], + "range": "QuantityValue", + "inlined": true + } + }, + "attributes": { + "material_input": { + "name": "material_input", + "title": "material input", + "from_schema": "https://microbiomedata/schema", + "alias": "material_input", + "owner": "ReactionActivity", + "domain_of": [ + "DissolvingActivity", + "ReactionActivity" + ], + "range": "MaterialSample" + }, + "material_output": { + "name": "material_output", + "title": "material output", + "from_schema": "https://microbiomedata/schema", + "alias": "material_output", + "owner": "ReactionActivity", + "domain_of": [ + "DissolvingActivity", + "MaterialSamplingActivity", + "ReactionActivity" + ], + "range": "MaterialSample" + }, + "reaction_aided_by": { + "name": "reaction_aided_by", + "title": "reaction aided by", + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "shaker" + ], + "alias": "reaction_aided_by", + "owner": "ReactionActivity", + "domain_of": [ + "ReactionActivity" + ], + "range": "LabDevice", + "inlined": true + }, + "reaction_temperature": { + "name": "reaction_temperature", + "from_schema": "https://microbiomedata/schema", + "alias": "reaction_temperature", + "owner": "ReactionActivity", + "domain_of": [ + "ReactionActivity" + ], + "range": "string" + }, + "reaction_time": { + "name": "reaction_time", + "todos": [ + "constrain units", + "align with activity_time" + ], + "from_schema": "https://microbiomedata/schema", + "alias": "reaction_time", + "owner": "ReactionActivity", + "domain_of": [ + "ReactionActivity" + ], + "range": "QuantityValue", + "inlined": true + } + } + }, + "GenomeFeature": { + "name": "GenomeFeature", + "description": "A feature localized to an interval along a genome", + "comments": [ + "corresponds to an entry in GFF3" + ], + "from_schema": "https://microbiomedata/schema", + "see_also": [ + "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md" + ], + "slot_usage": { + "seqid": { + "name": "seqid", + "description": "The ID of the landmark used to establish the coordinate system for the current feature.", + "range": "string", "required": true }, - "env_local_scale": { - "name": "env_local_scale", + "type": { + "name": "type", + "description": "A type from the sequence ontology", + "range": "OntologyClass" + }, + "start": { + "name": "start", + "description": "The start of the feature in positive 1-based integer coordinates", + "close_mappings": [ + "biolink:start_interbase_coordinate" + ], + "is_a": "gff_coordinate", "required": true }, - "env_medium": { - "name": "env_medium", + "end": { + "name": "end", + "description": "The end of the feature in positive 1-based integer coordinates", + "comments": [ + "- \"constraint: end > start\" - \"For features that cross the origin of a circular feature, end = the position of the end + the length of the landmark feature.\"" + ], + "close_mappings": [ + "biolink:end_interbase_coordinate" + ], + "is_a": "gff_coordinate", "required": true }, - "sample_link": { - "name": "sample_link", - "description": "JsonObj()", - "required": false + "strand": { + "name": "strand", + "description": "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).", + "exact_mappings": [ + "biolink:strand" + ] }, - "part_of": { - "name": "part_of", - "required": true + "phase": { + "name": "phase", + "description": "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2.", + "exact_mappings": [ + "biolink:phase" + ], + "range": "integer", + "minimum_value": 0, + "maximum_value": 0 }, - "extreme_event": { - "name": "extreme_event", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date, string" - } - }, + "encodes": { + "name": "encodes", + "description": "The gene product encoded by this feature. Typically this is used for a CDS feature or gene feature which will encode a protein. It can also be used by a nc transcript ot gene feature that encoded a ncRNA", + "range": "GeneProduct", + "required": false + }, + "feature_type": { + "name": "feature_type", + "description": "TODO: Yuri to write" + } + } + }, + "FunctionalAnnotationTerm": { + "name": "FunctionalAnnotationTerm", + "description": "Abstract grouping class for any term/descriptor that can be applied to a functional unit of a genome (protein, ncRNA, complex).", + "todos": [ + "decide if this should be used for product naming" + ], + "from_schema": "https://microbiomedata/schema", + "aliases": [ + "function", + "FunctionalAnnotation" + ], + "is_a": "OntologyClass", + "abstract": true, + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "notes": [ + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", + "minting authority shoulders should probably be enumerated and checked in the pattern" + ], "examples": [ { - "value": "1980-05-18, volcanic eruption" + "value": "nmdc:mgmag-00-x012.1_7_c1", + "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" } ], + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "FunctionalAnnotationTerm", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample" + ], + "range": "string" + }, + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "FunctionalAnnotationTerm", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "PersonValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "FunctionalAnnotationTerm", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "ImageValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "FunctionalAnnotationTerm", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "MetaboliteQuantification", + "ChemicalEntity", + "GeneProduct", + "MaterialSample" + ], "range": "string" } } }, - "Study": { - "name": "Study", + "Pathway": { + "name": "Pathway", "id_prefixes": [ - "GOLD", - "insdc.srs", - "mgnify" - ], - "description": "A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.", - "alt_descriptions": { - "embl.ena": { - "source": "embl.ena", - "description": "A study (project) groups together data submitted to the archive and controls its release date. A study accession is typically used when citing data submitted to ENA" - } - }, - "todos": [ - "determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor", - "project_name is redundant with name, so excluding it" - ], - "notes": [ - "sample GOLD link https://identifiers.org/gold:Gs0110115", - "sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?", - "sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757" - ], - "in_subset": [ - "sample subset" + "KEGG_PATHWAY", + "COG" ], + "description": "A pathway is a sequence of steps/reactions carried out by an organism or community of organisms", "from_schema": "https://microbiomedata/schema", "aliases": [ - "proposal", - "research proposal", - "research study", - "investigation", - "project", - "umbrella project" + "biological process", + "metabolic pathway", + "signaling pathway" ], "exact_mappings": [ - "SIO:001066", - "NCIT:C63536", - "OBI:0000066", - "ISA:Study" - ], - "close_mappings": [ - "NCIT:C41198", - "ISA:Investigation" - ], - "broad_mappings": [ - "prov:Activity" - ], - "is_a": "NamedThing", - "slots": [ - "id", - "alternative_identifiers", - "related_identifiers", - "emsl_proposal_identifier", - "emsl_proposal_doi", - "gold_study_identifiers", - "mgnify_project_identifiers", - "ecosystem", - "ecosystem_category", - "ecosystem_type", - "ecosystem_subtype", - "specific_ecosystem", - "principal_investigator", - "doi", - "title", - "alternative_titles", - "alternative_descriptions", - "alternative_names", - "abstract", - "objective", - "websites", - "publications", - "ess_dive_datasets", - "type", - "relevant_protocols", - "funding_sources", - "has_credit_associations", - "study_image" + "biolink:Pathway" ], + "is_a": "FunctionalAnnotationTerm", "slot_usage": { - "id": { - "name": "id", - "description": "An NMDC assigned unique identifier for a sample submitted to NMDC.", - "structured_pattern": { - "syntax": "{id_nmdc_prefix}:{id_typecode_study}-{id_shoulder}-{id_blade}{id_version}{id_locus}", - "interpolated": true, - "partial_match": false - } - }, - "doi": { - "name": "doi", - "annotations": { - "display_hint": { - "tag": "display_hint", - "value": "DOI associated with the data in this study. This is required when data is already generated." + "has_part": { + "name": "has_part", + "description": "A pathway can be broken down to a series of reaction step", + "multivalued": true, + "range": "Reaction" + } + }, + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "notes": [ + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", + "minting authority shoulders should probably be enumerated and checked in the pattern" + ], + "examples": [ + { + "value": "nmdc:mgmag-00-x012.1_7_c1", + "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" } - }, - "description": "The dataset citation for this study" + ], + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "Pathway", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FunctionalAnnotationTerm" + ], + "range": "string" }, "name": { "name": "name", - "annotations": { - "display_hint": { - "tag": "display_hint", - "value": "Provide a name for the study your samples will belong with." - } - } - }, - "websites": { - "name": "websites", - "annotations": { - "display_hint": { - "tag": "display_hint", - "value": "Link to the Principal Investigator's research lab webpage or the study webpage associated with this collection of samples. Multiple links can be provided." - } - } + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "Pathway", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "PersonValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "PersonValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FunctionalAnnotationTerm" + ], + "range": "string" }, "description": { "name": "description", - "annotations": { - "display_hint": { - "tag": "display_hint", - "value": "Provide a brief description of your study." - } - }, - "description": "A brief summary that details the study you're submitted to NMDC" - }, - "notes": { - "name": "notes", - "annotations": { - "display_hint": { - "tag": "display_hint", - "value": "Add any additional notes or comments about this study." - } - } + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "Pathway", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "ImageValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "ImageValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FunctionalAnnotationTerm" + ], + "range": "string" }, "alternative_identifiers": { "name": "alternative_identifiers", - "description": "Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC" + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "Pathway", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "MetaboliteQuantification", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "MetaboliteQuantification", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FunctionalAnnotationTerm" + ], + "range": "string" + } + } + }, + "Reaction": { + "name": "Reaction", + "id_prefixes": [ + "KEGG.REACTION", + "RHEA", + "MetaCyc", + "EC", + "GO", + "MetaNetX", + "SEED", + "RetroRules" + ], + "description": "An individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters", + "from_schema": "https://microbiomedata/schema", + "exact_mappings": [ + "biolink:MolecularActivity" + ], + "is_a": "FunctionalAnnotationTerm", + "slot_usage": { + "left_participants": { + "name": "left_participants", + "is_a": "has_participants", + "multivalued": true, + "range": "ReactionParticipant" }, - "alternative_names": { - "name": "alternative_names", - "annotations": { - "display_hint": { - "tag": "display_hint", - "value": "Project, study, or sample set names the are also associated with this submission or other names / identifiers for this study." - } - } + "right_participants": { + "name": "right_participants", + "is_a": "has_participants", + "multivalued": true, + "range": "ReactionParticipant" }, - "related_identifiers": { - "name": "related_identifiers", - "description": "Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC" + "direction": { + "name": "direction", + "description": "One of l->r, r->l, bidirectional, neutral" }, - "insdc_bioproject_identifiers": { - "name": "insdc_bioproject_identifiers", - "annotations": { - "display_hint": { - "tag": "display_hint", - "value": "Provide the NCBI BioProject Accession Number associated with the listed NCBI BioProject Title." + "smarts_string": { + "name": "smarts_string", + "range": "string" + }, + "is_diastereoselective": { + "name": "is_diastereoselective", + "range": "boolean" + }, + "is_stereo": { + "name": "is_stereo", + "range": "boolean" + }, + "is_balanced": { + "name": "is_balanced", + "range": "boolean" + }, + "is_transport": { + "name": "is_transport", + "range": "boolean" + }, + "is_fully_characterized": { + "name": "is_fully_characterized", + "description": "False if includes R-groups", + "range": "boolean" + } + }, + "attributes": { + "id": { + "name": "id", + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "notes": [ + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", + "minting authority shoulders should probably be enumerated and checked in the pattern" + ], + "examples": [ + { + "value": "nmdc:mgmag-00-x012.1_7_c1", + "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" } - }, - "description": "Unique identifier for a bioproject submitted to INSDC that relates to the NMDC submitted study." + ], + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "Reaction", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FunctionalAnnotationTerm", + "Pathway" + ], + "range": "string" }, - "emsl_project_identifier": { - "name": "emsl_project_identifier", - "description": "The EMSL project ID that relates to the NMDC submitted study" + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "Reaction", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "PersonValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "PersonValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FunctionalAnnotationTerm", + "Pathway" + ], + "range": "string" }, - "emsl_proposal_doi": { - "name": "emsl_proposal_doi", - "description": "The DOI for the EMSL awarded study that relates to the NMDC submitted study" + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "Reaction", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "ImageValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "ImageValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FunctionalAnnotationTerm", + "Pathway" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "Reaction", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "MetaboliteQuantification", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "MetaboliteQuantification", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FunctionalAnnotationTerm", + "Pathway" + ], + "range": "string" } } }, - "BiosampleProcessing": { - "name": "BiosampleProcessing", - "description": "A process that takes one or more biosamples as inputs and generates one or as outputs. Examples of outputs include samples cultivated from another sample or data objects created by instruments runs.", + "ReactionParticipant": { + "name": "ReactionParticipant", + "description": "Instances of this link a reaction to a chemical entity participant", "from_schema": "https://microbiomedata/schema", - "aliases": [ - "material processing" - ], - "broad_mappings": [ - "OBI:0000094" - ], - "is_a": "NamedThing", - "slots": [ - "has_input" - ], "slot_usage": { - "id": { - "name": "id", - "structured_pattern": { - "syntax": "{id_nmdc_prefix}:{id_typecode_biosample_processing}-{id_shoulder}-{id_blade}{id_version}{id_locus}", - "interpolated": true, - "partial_match": false - } + "chemical": { + "name": "chemical", + "range": "ChemicalEntity" }, - "has_input": { - "name": "has_input", - "range": "Biosample" + "stoichiometry": { + "name": "stoichiometry", + "range": "integer" } } }, - "OmicsProcessing": { - "name": "OmicsProcessing", - "description": "The methods and processes used to generate omics data from a biosample or organism.", - "alt_descriptions": { - "embl.ena": { - "source": "embl.ena", - "description": "An experiment contains information about a sequencing experiment including library and instrument details." - } - }, - "comments": [ - "The ID prefix for objects coming from GOLD will be gold:Gp" + "OrthologyGroup": { + "name": "OrthologyGroup", + "id_prefixes": [ + "CATH", + "EGGNOG", + "KEGG.ORTHOLOGY", + "PANTHER.FAMILY", + "PFAM", + "SUPFAM", + "TIGRFAM" ], - "in_subset": [ - "sample subset" + "description": "A set of genes or gene products in which all members are orthologous", + "notes": [ + "KEGG.ORTHOLOGY prefix is used for KO numbers" ], "from_schema": "https://microbiomedata/schema", - "aliases": [ - "omics assay", - "sequencing project", - "experiment" - ], - "broad_mappings": [ - "OBI:0000070", - "ISA:Assay" - ], - "is_a": "BiosampleProcessing", - "slots": [ - "add_date", - "mod_date", - "has_input", - "has_output", - "instrument_name", - "ncbi_project_name", - "omics_type", - "part_of", - "principal_investigator", - "processing_institution", - "type", - "gold_sequencing_project_identifiers", - "insdc_experiment_identifiers", - "samp_vol_we_dna_ext", - "nucl_acid_ext", - "nucl_acid_amp", - "target_gene", - "target_subfragment", - "pcr_primers", - "pcr_cond", - "seq_meth", - "seq_quality_check", - "chimera_check" + "exact_mappings": [ + "biolink:GeneFamily" ], - "slot_usage": { + "is_a": "FunctionalAnnotationTerm", + "attributes": { "id": { "name": "id", - "structured_pattern": { - "syntax": "{id_nmdc_prefix}:{id_typecode_omics_processing}-{id_shoulder}-{id_blade}{id_version}{id_locus}", - "interpolated": true, - "partial_match": false - } + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "notes": [ + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", + "minting authority shoulders should probably be enumerated and checked in the pattern" + ], + "examples": [ + { + "value": "nmdc:mgmag-00-x012.1_7_c1", + "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" + } + ], + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "identifier": true, + "alias": "id", + "owner": "OrthologyGroup", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FunctionalAnnotationTerm", + "Pathway", + "Reaction" + ], + "range": "string" }, - "has_input": { - "name": "has_input", - "required": true + "name": { + "name": "name", + "description": "A human readable label for an entity", + "from_schema": "https://microbiomedata/schema", + "multivalued": false, + "alias": "name", + "owner": "OrthologyGroup", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "PersonValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "PersonValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "WorkflowExecutionActivity", + "MetagenomeAssembly", + "MetatranscriptomeAssembly", + "MetagenomeAnnotationActivity", + "MetatranscriptomeAnnotationActivity", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetabolomicsAnalysisActivity", + "MetaproteomicsAnalysisActivity", + "NomAnalysisActivity", + "Activity", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "PersonValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FunctionalAnnotationTerm", + "Pathway", + "Reaction" + ], + "range": "string" + }, + "description": { + "name": "description", + "description": "a human-readable description of a thing", + "from_schema": "https://microbiomedata/schema", + "slot_uri": "dcterms:description", + "multivalued": false, + "alias": "description", + "owner": "OrthologyGroup", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "ImageValue", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "ImageValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "ImageValue", + "Person", + "Instrument", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FunctionalAnnotationTerm", + "Pathway", + "Reaction" + ], + "range": "string" + }, + "alternative_identifiers": { + "name": "alternative_identifiers", + "description": "A list of alternative identifiers for the entity.", + "from_schema": "https://microbiomedata/schema", + "multivalued": true, + "alias": "alternative_identifiers", + "owner": "OrthologyGroup", + "domain_of": [ + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "MetaboliteQuantification", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "MetaboliteQuantification", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FieldResearchSite", + "CollectingBiosamplesFromSite", + "DataObject", + "Biosample", + "Study", + "BiosampleProcessing", + "OmicsProcessing", + "NamedThing", + "MaterialEntity", + "AnalyticalSample", + "Site", + "PlannedProcess", + "OntologyClass", + "EnvironmentalMaterialTerm", + "Person", + "Instrument", + "MetaboliteQuantification", + "ChemicalEntity", + "GeneProduct", + "MaterialSample", + "FunctionalAnnotationTerm", + "Pathway", + "Reaction" + ], + "range": "string" } } }, - "CreditAssociation": { - "name": "CreditAssociation", - "description": "This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0", + "FunctionalAnnotation": { + "name": "FunctionalAnnotation", + "description": "An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods", + "notes": [ + "move id slot usage patterns to has_function slot usage?" + ], "from_schema": "https://microbiomedata/schema", - "aliases": [ - "study role", - "credit table", - "associated researchers" + "see_also": [ + "https://img.jgi.doe.gov/docs/functional-annotation.pdf", + "https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl" + ], + "narrow_mappings": [ + "biolink:GeneToGoTermAssociation" ], "slots": [ - "applies_to_person", - "applied_role", - "applied_roles", - "type" + "was_generated_by", + "subject", + "has_function" ], - "class_uri": "prov:Association" + "slot_usage": { + "has_function": { + "name": "has_function", + "notes": [ + "this slot had been called id", + "Still missing patterns for COG and RetroRules.", + "These patterns aren't tied to the listed prefixes. A discussion about that possibility had been started, including the question of whether these lists are intended to be open examples or closed" + ], + "domain_of": [ + "FunctionalAnnotation" + ], + "pattern": "^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$" + }, + "type": { + "name": "type", + "description": "TODO", + "range": "OntologyClass" + }, + "was_generated_by": { + "name": "was_generated_by", + "description": "provenance for the annotation.", + "notes": [ + "Note to be consistent with the rest of the NMDC schema we use the PROV annotation model, rather than GPAD" + ], + "domain_of": [ + "DataObject", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue", + "IntegerValue", + "BooleanValue", + "ControlledTermValue", + "ControlledIdentifiedTermValue", + "GeolocationValue", + "FunctionalAnnotation" + ], + "range": "MetagenomeAnnotationActivity" + } + }, + "attributes": { + "was_generated_by": { + "name": "was_generated_by", + "description": "provenance for the annotation.", + "notes": [ + "Note to be consistent with the rest of the NMDC schema we use the PROV annotation model, rather than GPAD" + ], + "from_schema": "https://microbiomedata/schema", + "alias": "was_generated_by", + "owner": "FunctionalAnnotation", + "domain_of": [ + "DataObject", + "AttributeValue", + "QuantityValue", + "ImageValue", + "PersonValue", + "TextValue", + "UrlValue", + "TimestampValue", + "IntegerValue", + "BooleanValue", + "ControlledTermValue", + "ControlledIdentifiedTermValue", + "GeolocationValue", + "FunctionalAnnotation" + ], + "range": "MetagenomeAnnotationActivity" + }, + "subject": { + "name": "subject", + "from_schema": "https://microbiomedata/schema", + "alias": "subject", + "owner": "FunctionalAnnotation", + "domain_of": [ + "FunctionalAnnotation" + ], + "range": "GeneProduct" + }, + "has_function": { + "name": "has_function", + "notes": [ + "this slot had been called id", + "Still missing patterns for COG and RetroRules.", + "These patterns aren't tied to the listed prefixes. A discussion about that possibility had been started, including the question of whether these lists are intended to be open examples or closed" + ], + "from_schema": "https://microbiomedata/schema", + "alias": "has_function", + "owner": "FunctionalAnnotation", + "domain_of": [ + "FunctionalAnnotation" + ], + "range": "string", + "pattern": "^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$" + } + } } }, "source_file": "src/schema/nmdc.yaml", @@ -1975,10 +49279,6 @@ "setting_key": "id_nmdc_prefix", "setting_value": "^(nmdc)" }, - "id_typecode": { - "setting_key": "id_typecode", - "setting_value": "([a-z]{1,6})" - }, "id_shoulder": { "setting_key": "id_shoulder", "setting_value": "([0-9][a-z]{0,6}[0-9])" @@ -1994,22 +49294,6 @@ "id_locus": { "setting_key": "id_locus", "setting_value": "(_[A-Za-z0-9_\\.-]+)?$" - }, - "id_typecode_biosample": { - "setting_key": "id_typecode_biosample", - "setting_value": "bsm" - }, - "id_typecode_study": { - "setting_key": "id_typecode_study", - "setting_value": "sty" - }, - "id_typecode_biosample_processing": { - "setting_key": "id_typecode_biosample_processing", - "setting_value": "bsmprc" - }, - "id_typecode_omics_processing": { - "setting_key": "id_typecode_omics_processing", - "setting_value": "omprc" } }, "@type": "SchemaDefinition" diff --git a/jsonld-context/nmdc.context.jsonld b/jsonld-context/nmdc.context.jsonld index 6f27471b7c..941af6aa44 100644 --- a/jsonld-context/nmdc.context.jsonld +++ b/jsonld-context/nmdc.context.jsonld @@ -1,5 +1,9 @@ { - "_comments": "Auto generated from nmdc.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-12-22T13:46:54\n Schema: NMDC\n metamodel version: 1.7.0\n model version: 7.0.0\n \n id: https://microbiomedata/schema\n description: Schema for National Microbiome Data Collaborative (NMDC).\nThis schema is organized into distinct modules:\n\n * a set of core types for representing data values\n * the mixs schema (auto-translated from mixs excel)\n * annotation schema\n * the NMDC schema itself\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", + "comments": { + "description": "Auto generated by LinkML jsonld context generator", + "generation_date": "2023-01-20T13:16:29", + "source": "nmdc.yaml" + }, "@context": { "CAS": "http://identifiers.org/cas/", "CATH": "http://identifiers.org/cath/", @@ -101,6 +105,7 @@ "acted_on_behalf_of": { "@type": "@id" }, + "id": "@id", "activity_set": { "@type": "@id" }, @@ -333,7 +338,6 @@ "meaning": "@id" } }, - "id": "@id", "biosample_identifiers": { "@type": "@id" }, diff --git a/jsonschema/nmdc.schema.json b/jsonschema/nmdc.schema.json index 25ae6de4fc..71442f7add 100644 --- a/jsonschema/nmdc.schema.json +++ b/jsonschema/nmdc.schema.json @@ -1 +1,5573 @@ -{"$defs": {"Activity": {"additionalProperties": false, "description": "a provence-generating activity", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"$ref": "#/$defs/Agent"}, "was_informed_by": {"type": "string"}}, "required": ["id"], "title": "Activity", "type": "object"}, "Agent": {"additionalProperties": false, "description": "a provence-generating agent", "properties": {"acted_on_behalf_of": {"$ref": "#/$defs/Agent"}, "was_informed_by": {"type": "string"}}, "title": "Agent", "type": "object"}, "AnalysisTypeEnum": {"description": "", "enum": ["metabolomics", "metagenomics", "metaproteomics", "metatranscriptomics", "natural organic matter"], "title": "AnalysisTypeEnum", "type": "string"}, "AnalyticalSample": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "AnalyticalSample", "type": "object"}, "ArchStrucEnum": {"description": "", "enum": ["building", "shed", "home"], "title": "ArchStrucEnum", "type": "string"}, "AttributeValue": {"additionalProperties": false, "description": "The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "AttributeValue", "type": "object"}, "BiolStatEnum": {"description": "", "enum": ["wild", "natural", "semi-natural", "inbred line", "breeder's line", "hybrid", "clonal selection", "mutant"], "title": "BiolStatEnum", "type": "string"}, "Biosample": {"additionalProperties": false, "description": "Biological source material which can be characterized by an experiment.", "properties": {"add_date": {"description": "The date on which the information was added to the database.", "type": "string"}, "agrochem_addition": {"$ref": "#/$defs/QuantityValue", "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications"}, "air_temp_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens"}, "al_sat": {"$ref": "#/$defs/QuantityValue", "description": "Aluminum saturation (esp. For tropical soils)"}, "al_sat_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining Al saturation"}, "alkalinity": {"$ref": "#/$defs/QuantityValue", "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate"}, "alkalinity_method": {"$ref": "#/$defs/TextValue", "description": "Method used for alkalinity measurement"}, "alkyl_diethers": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of alkyl diethers"}, "alt": {"$ref": "#/$defs/QuantityValue", "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air"}, "alternative_identifiers": {"description": "Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC", "items": {"type": "string"}, "type": "array"}, "aminopept_act": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of aminopeptidase activity"}, "ammonium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of ammonium in the sample"}, "ammonium_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of ammonium nitrogen in the sample"}, "analysis_type": {"description": "Select all the data types associated or available for this biosample", "items": {"$ref": "#/$defs/AnalysisTypeEnum"}, "type": "array"}, "annual_precpt": {"$ref": "#/$defs/QuantityValue", "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps."}, "annual_temp": {"$ref": "#/$defs/QuantityValue", "description": "Mean annual temperature"}, "bacteria_carb_prod": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of bacterial carbon production"}, "biosample_categories": {"items": {"$ref": "#/$defs/BiosampleCategoryEnum"}, "type": "array"}, "biotic_regm": {"$ref": "#/$defs/TextValue", "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi."}, "biotic_relationship": {"$ref": "#/$defs/TextValue", "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object"}, "bishomohopanol": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of bishomohopanol"}, "bromide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of bromide"}, "calcium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of calcium in the sample"}, "carb_nitro_ratio": {"$ref": "#/$defs/QuantityValue", "description": "Ratio of amount or concentrations of carbon to nitrogen"}, "chem_administration": {"$ref": "#/$defs/ControlledTermValue", "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi"}, "chloride": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of chloride in the sample"}, "chlorophyll": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of chlorophyll"}, "climate_environment": {"$ref": "#/$defs/TextValue", "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates"}, "collected_from": {"description": "The Site from which a Biosample was collected", "type": "string"}, "collection_date": {"$ref": "#/$defs/TimestampValue", "description": "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant"}, "collection_date_inc": {"description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", "type": "string"}, "collection_time": {"description": "The time of sampling, either as an instance (single point) or interval.", "type": "string"}, "collection_time_inc": {"description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", "type": "string"}, "community": {"type": "string"}, "crop_rotation": {"$ref": "#/$defs/TextValue", "description": "Whether or not crop is rotated, and if yes, rotation schedule"}, "cur_land_use": {"$ref": "#/$defs/TextValue", "description": "Present state of sample site"}, "cur_vegetation": {"$ref": "#/$defs/TextValue", "description": "Vegetation classification from one or more standard classification systems, or agricultural crop"}, "cur_vegetation_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in vegetation classification"}, "density": {"$ref": "#/$defs/QuantityValue", "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)"}, "depth": {"$ref": "#/$defs/QuantityValue", "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "diss_carb_dioxide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample"}, "diss_hydrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved hydrogen"}, "diss_inorg_carb": {"$ref": "#/$defs/QuantityValue", "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter"}, "diss_inorg_phosp": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved inorganic phosphorus in the sample"}, "diss_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid"}, "diss_org_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2"}, "diss_oxygen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved oxygen"}, "dna_absorb1": {"description": "260/280 measurement of DNA sample purity", "type": "string"}, "dna_absorb2": {"description": "260/230 measurement of DNA sample purity", "type": "string"}, "dna_collect_site": {"description": "Provide information on the site your DNA sample was collected from", "type": "string"}, "dna_concentration": {"maximum": 2000, "minimum": 0, "type": "string"}, "dna_cont_type": {"$ref": "#/$defs/DnaContTypeEnum", "description": "Tube or plate (96-well)"}, "dna_cont_well": {"type": "string"}, "dna_container_id": {"type": "string"}, "dna_dnase": {"$ref": "#/$defs/DnaDnaseEnum"}, "dna_isolate_meth": {"description": "Describe the method/protocol/kit used to extract DNA/RNA.", "type": "string"}, "dna_organisms": {"description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", "type": "string"}, "dna_project_contact": {"type": "string"}, "dna_samp_id": {"type": "string"}, "dna_sample_format": {"$ref": "#/$defs/DnaSampleFormatEnum", "description": "Solution in which the DNA sample has been suspended"}, "dna_sample_name": {"description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", "type": "string"}, "dna_seq_project": {"type": "string"}, "dna_seq_project_name": {"type": "string"}, "dna_seq_project_pi": {"type": "string"}, "dna_volume": {"maximum": 1000, "minimum": 0, "type": "string"}, "dnase_rna": {"$ref": "#/$defs/DnaseRnaEnum"}, "drainage_class": {"$ref": "#/$defs/TextValue", "description": "Drainage classification from a standard system such as the USDA system"}, "ecosystem": {"description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", "type": "string"}, "ecosystem_category": {"description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", "type": "string"}, "ecosystem_subtype": {"description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", "type": "string"}, "ecosystem_type": {"description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", "type": "string"}, "elev": {"$ref": "#/$defs/QuantityValue", "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit."}, "emsl_biosample_identifiers": {"description": "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.", "items": {"type": "string"}, "type": "array"}, "env_broad_scale": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS"}, "env_local_scale": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS."}, "env_medium": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top)."}, "env_package": {"$ref": "#/$defs/TextValue", "description": "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported", "pattern": "[air|built environment|host\\-associated|human\\-associated|human\\-skin|human\\-oral|human\\-gut|human\\-vaginal|hydrocarbon resources\\-cores|hydrocarbon resources\\-fluids\\/swabs|microbial mat\\/biofilm|misc environment|plant\\-associated|sediment|soil|wastewater\\/sludge|water]"}, "experimental_factor": {"$ref": "#/$defs/ControlledTermValue", "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI"}, "experimental_factor_other": {"description": "Other details about your sample that you feel can't be accurately represented in the available columns.", "type": "string"}, "extreme_event": {"description": "Unusual physical events that may have affected microbial populations", "type": "string"}, "fao_class": {"$ref": "#/$defs/TextValue", "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups"}, "filter_method": {"description": "Type of filter used or how the sample was filtered", "type": "string"}, "fire": {"$ref": "#/$defs/TimestampValue", "description": "Historical and/or physical evidence of fire"}, "flooding": {"$ref": "#/$defs/TimestampValue", "description": "Historical and/or physical evidence of flooding"}, "gaseous_environment": {"$ref": "#/$defs/QuantityValue", "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens"}, "geo_loc_name": {"$ref": "#/$defs/TextValue", "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)"}, "glucosidase_act": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of glucosidase activity"}, "gold_biosample_identifiers": {"description": "Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample", "items": {"type": "string"}, "pattern": "^GOLD:Gb[0-9]+$", "type": "array"}, "growth_facil": {"$ref": "#/$defs/ControlledTermValue", "description": "Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research"}, "habitat": {"type": "string"}, "heavy_metals": {"$ref": "#/$defs/QuantityValue", "description": "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field."}, "heavy_metals_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining heavy metals"}, "host_name": {"type": "string"}, "humidity_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens"}, "id": {"description": "An NMDC assigned unique identifier for a biosample submitted to NMDC.", "pattern": "^nmdc:", "type": "string"}, "igsn_biosample_identifiers": {"description": "A list of identifiers for the biosample from the IGSN database.", "items": {"type": "string"}, "type": "array"}, "img_identifiers": {"description": "A list of identifiers that relate the biosample to records in the IMG database.", "items": {"type": "string"}, "type": "array"}, "insdc_biosample_identifiers": {"description": "identifiers for corresponding sample in INSDC", "items": {"type": "string"}, "pattern": "^biosample:SAM[NED]([A-Z])?[0-9]+$", "type": "array"}, "isotope_exposure": {"description": "List isotope exposure or addition applied to your sample.", "type": "string"}, "lat_lon": {"$ref": "#/$defs/GeolocationValue", "description": "This is currently a required field but it's not clear if this should be required for human hosts"}, "lbc_thirty": {"$ref": "#/$defs/QuantityValue", "description": "lime buffer capacity, determined after 30 minute incubation"}, "lbceq": {"$ref": "#/$defs/QuantityValue", "description": "lime buffer capacity, determined at equilibrium after 5 day incubation"}, "light_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality."}, "link_addit_analys": {"$ref": "#/$defs/TextValue", "description": "Link to additional analysis results performed on the sample"}, "link_class_info": {"$ref": "#/$defs/TextValue", "description": "Link to digitized soil maps or other soil classification information"}, "link_climate_info": {"$ref": "#/$defs/TextValue", "description": "Link to climate resource"}, "local_class": {"$ref": "#/$defs/TextValue", "description": "Soil classification based on local soil classification system"}, "local_class_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining the local soil classification"}, "location": {"type": "string"}, "magnesium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of magnesium in the sample"}, "manganese": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of manganese in the sample"}, "mean_frict_vel": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of mean friction velocity"}, "mean_peak_frict_vel": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of mean peak friction velocity"}, "micro_biomass_c_meth": {"description": "Reference or method used in determining microbial biomass", "type": "string"}, "micro_biomass_n_meth": {"description": "Reference or method used in determining microbial biomass nitrogen", "type": "string"}, "microbial_biomass_c": {"description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", "type": "string"}, "microbial_biomass_n": {"description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", "type": "string"}, "misc_param": {"$ref": "#/$defs/QuantityValue", "description": "Any other measurement performed or parameter collected, that is not listed here"}, "mod_date": {"description": "The last date on which the database information was modified.", "type": "string"}, "n_alkanes": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of n-alkanes; can include multiple n-alkanes"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "ncbi_taxonomy_name": {"type": "string"}, "nitrate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrate in the sample"}, "nitrate_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrate nitrogen in the sample"}, "nitrite": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrite in the sample"}, "nitrite_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrite nitrogen in the sample"}, "non_microb_biomass": {"description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", "type": "string"}, "non_microb_biomass_method": {"description": "Reference or method used in determining biomass", "type": "string"}, "org_matter": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of organic matter"}, "org_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of organic nitrogen"}, "org_nitro_method": {"description": "Method used for obtaining organic nitrogen", "type": "string"}, "organism_count": {"$ref": "#/$defs/QuantityValue", "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)"}, "other_treatment": {"description": "Other treatments applied to your samples that are not applicable to the provided fields", "type": "string"}, "oxy_stat_samp": {"$ref": "#/$defs/TextValue", "description": "Oxygenation status of sample"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "part_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of particulate organic carbon"}, "perturbation": {"$ref": "#/$defs/TextValue", "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types"}, "petroleum_hydrocarb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of petroleum hydrocarbon"}, "ph": {"$ref": "#/$defs/QuantityValue", "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid"}, "ph_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining ph"}, "phaeopigments": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phaeopigments; can include multiple phaeopigments"}, "phosphate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phosphate"}, "phosplipid_fatt_acid": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phospholipid fatty acids; can include multiple values"}, "pool_dna_extracts": {"$ref": "#/$defs/TextValue", "description": "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given"}, "potassium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of potassium in the sample"}, "pressure": {"$ref": "#/$defs/QuantityValue", "description": "Pressure to which the sample is subject to, in atmospheres"}, "profile_position": {"$ref": "#/$defs/TextValue", "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas"}, "project_id": {"description": "Proposal IDs or names associated with dataset", "type": "string"}, "proport_woa_temperature": {"type": "string"}, "proposal_dna": {"type": "string"}, "proposal_rna": {"type": "string"}, "redox_potential": {"$ref": "#/$defs/QuantityValue", "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential"}, "rel_to_oxygen": {"$ref": "#/$defs/TextValue", "description": "Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments"}, "replicate_number": {"description": "If sending biological replicates, indicate the rep number here.", "type": "string"}, "rna_absorb1": {"description": "260/280 measurement of RNA sample purity", "type": "string"}, "rna_absorb2": {"description": "260/230 measurement of RNA sample purity", "type": "string"}, "rna_collect_site": {"description": "Provide information on the site your RNA sample was collected from", "type": "string"}, "rna_concentration": {"maximum": 1000, "minimum": 0, "type": "string"}, "rna_cont_type": {"$ref": "#/$defs/RnaContTypeEnum", "description": "Tube or plate (96-well)"}, "rna_cont_well": {"type": "string"}, "rna_container_id": {"type": "string"}, "rna_isolate_meth": {"description": "Describe the method/protocol/kit used to extract DNA/RNA.", "type": "string"}, "rna_organisms": {"description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", "type": "string"}, "rna_project_contact": {"type": "string"}, "rna_samp_id": {"type": "string"}, "rna_sample_format": {"$ref": "#/$defs/RnaSampleFormatEnum", "description": "Solution in which the RNA sample has been suspended"}, "rna_sample_name": {"description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", "maximum": 2000, "minimum": 0, "type": "string"}, "rna_seq_project": {"type": "string"}, "rna_seq_project_name": {"type": "string"}, "rna_seq_project_pi": {"type": "string"}, "rna_volume": {"type": "string"}, "salinity": {"$ref": "#/$defs/QuantityValue", "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater."}, "salinity_category": {"description": "Categorcial description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline", "type": "string"}, "salinity_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining salinity"}, "samp_collec_method": {"description": "The method employed for collecting the sample.", "type": "string"}, "samp_mat_process": {"$ref": "#/$defs/ControlledTermValue", "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed."}, "samp_name": {"description": "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.", "type": "string"}, "samp_size": {"$ref": "#/$defs/QuantityValue", "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected."}, "samp_store_dur": {"$ref": "#/$defs/TextValue", "description": "Duration for which the sample was stored"}, "samp_store_loc": {"$ref": "#/$defs/TextValue", "description": "Location at which sample was stored, usually name of a specific freezer/room"}, "samp_store_temp": {"$ref": "#/$defs/QuantityValue", "description": "Temperature at which sample was stored, e.g. -80 degree Celsius"}, "samp_vol_we_dna_ext": {"$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)."}, "sample_collection_site": {"type": "string"}, "sample_link": {"description": "JsonObj()", "items": {"type": "string"}, "type": "array"}, "sample_shipped": {"description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL", "type": "string"}, "sample_type": {"$ref": "#/$defs/SampleTypeEnum", "description": "Type of sample being submitted"}, "season_precpt": {"$ref": "#/$defs/QuantityValue", "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps."}, "season_temp": {"$ref": "#/$defs/QuantityValue", "description": "Mean seasonal temperature"}, "sieving": {"$ref": "#/$defs/QuantityValue", "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved"}, "size_frac_low": {"$ref": "#/$defs/QuantityValue", "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample"}, "size_frac_up": {"$ref": "#/$defs/QuantityValue", "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample"}, "slope_aspect": {"$ref": "#/$defs/QuantityValue", "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration."}, "slope_gradient": {"$ref": "#/$defs/QuantityValue", "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer"}, "sodium": {"$ref": "#/$defs/QuantityValue", "description": "Sodium concentration in the sample"}, "soil_type": {"$ref": "#/$defs/TextValue", "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes."}, "soil_type_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining soil series name or other lower-level classification"}, "soluble_iron_micromol": {"type": "string"}, "source_mat_id": {"$ref": "#/$defs/TextValue", "description": "A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2)."}, "specific_ecosystem": {"description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", "type": "string"}, "start_date_inc": {"description": "Date the incubation was started. Only relevant for incubation samples.", "type": "string"}, "start_time_inc": {"description": "Time the incubation was started. Only relevant for incubation samples.", "type": "string"}, "store_cond": {"$ref": "#/$defs/TextValue", "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)."}, "subsurface_depth": {"$ref": "#/$defs/QuantityValue"}, "sulfate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of sulfate in the sample"}, "sulfide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of sulfide in the sample"}, "technical_reps": {"description": "If sending multiple technical replicates of the same sample, indicate how many replicates are being sent", "type": "string"}, "temp": {"$ref": "#/$defs/QuantityValue", "description": "Temperature of the sample at the time of sampling."}, "tidal_stage": {"$ref": "#/$defs/TextValue", "description": "Stage of tide"}, "tillage": {"$ref": "#/$defs/TextValue", "description": "Note method(s) used for tilling"}, "tot_carb": {"$ref": "#/$defs/QuantityValue", "description": "Total carbon content"}, "tot_depth_water_col": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of total depth of water column"}, "tot_diss_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen"}, "tot_nitro_cont_meth": {"description": "Reference or method used in determining the total nitrogen", "type": "string"}, "tot_nitro_content": {"$ref": "#/$defs/QuantityValue", "description": "Total nitrogen content of the sample"}, "tot_org_c_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining total organic carbon"}, "tot_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content"}, "tot_phosp": {"$ref": "#/$defs/QuantityValue", "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "water_cont_soil_meth": {"description": "Reference or method used in determining the water content of soil", "type": "string"}, "water_content": {"$ref": "#/$defs/QuantityValue", "description": "Water content measurement"}, "watering_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens"}, "zinc": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of zinc in the sample"}}, "required": ["part_of", "id", "env_broad_scale", "env_local_scale", "env_medium"], "title": "Biosample", "type": "object"}, "BiosampleCategoryEnum": {"description": "Funding-based, sample location-based, or experimental method-based defined categories", "enum": ["LTER", "SIP", "SFA", "FICUS", "NEON"], "title": "BiosampleCategoryEnum", "type": "string"}, "BiosampleProcessing": {"additionalProperties": false, "description": "A process that takes one or more biosamples as inputs and generates one or as outputs. Examples of outputs include samples cultivated from another sample or data objects created by instruments runs.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "BiosampleProcessing", "type": "object"}, "BioticRelationshipEnum": {"description": "", "enum": ["free living", "parasite", "commensal", "symbiont"], "title": "BioticRelationshipEnum", "type": "string"}, "BooleanValue": {"additionalProperties": false, "description": "A value that is a boolean", "properties": {"has_boolean_value": {"description": "Links a quantity value to a boolean", "type": "boolean"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "BooleanValue", "type": "object"}, "BuildDocsEnum": {"description": "", "enum": ["building information model", "commissioning report", "complaint logs", "contract administration", "cost estimate", "janitorial schedules or logs", "maintenance plans", "schedule", "sections", "shop drawings", "submittals", "ventilation system", "windows"], "title": "BuildDocsEnum", "type": "string"}, "BuildOccupTypeEnum": {"description": "", "enum": ["office", "market", "restaurant", "residence", "school", "residential", "commercial", "low rise", "high rise", "wood framed", "health care", "airport", "sports complex"], "title": "BuildOccupTypeEnum", "type": "string"}, "BuildingSettingEnum": {"description": "", "enum": ["urban", "suburban", "exurban", "rural"], "title": "BuildingSettingEnum", "type": "string"}, "CeilCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "CeilCondEnum", "type": "string"}, "CeilFinishMatEnum": {"description": "", "enum": ["drywall", "mineral fibre", "tiles", "PVC", "plasterboard", "metal", "fiberglass", "stucco", "mineral wool/calcium silicate", "wood"], "title": "CeilFinishMatEnum", "type": "string"}, "CeilTextureEnum": {"description": "", "enum": ["crows feet", "crows-foot stomp", "double skip", "hawk and trowel", "knockdown", "popcorn", "orange peel", "rosebud stomp", "Santa-Fe texture", "skip trowel", "smooth", "stomp knockdown", "swirl"], "title": "CeilTextureEnum", "type": "string"}, "CeilTypeEnum": {"description": "", "enum": ["cathedral", "dropped", "concave", "barrel-shaped", "coffered", "cove", "stretched"], "title": "CeilTypeEnum", "type": "string"}, "ChemicalEntity": {"additionalProperties": false, "description": "An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "ChemicalEntity", "type": "object"}, "CollectingBiosamplesFromSite": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_inputs": {"items": {"type": "string"}, "type": "array"}, "has_outputs": {"items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "participating_agent": {"$ref": "#/$defs/Agent"}}, "required": ["has_inputs", "has_outputs", "id"], "title": "CollectingBiosamplesFromSite", "type": "object"}, "ContainerTypeEnum": {"description": "", "enum": ["screw_top_conical"], "title": "ContainerTypeEnum", "type": "string"}, "ControlledIdentifiedTermValue": {"additionalProperties": false, "description": "A controlled term or class from an ontology, requiring the presence of term with an id", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "term": {"$ref": "#/$defs/OntologyClass", "description": "pointer to an ontology class"}, "was_generated_by": {"type": "string"}}, "required": ["term"], "title": "ControlledIdentifiedTermValue", "type": "object"}, "ControlledTermValue": {"additionalProperties": false, "description": "A controlled term or class from an ontology", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "term": {"$ref": "#/$defs/OntologyClass", "description": "pointer to an ontology class"}, "was_generated_by": {"type": "string"}}, "title": "ControlledTermValue", "type": "object"}, "CreditAssociation": {"additionalProperties": false, "description": "This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0", "properties": {"applied_role": {"$ref": "#/$defs/CreditEnum"}, "applied_roles": {"items": {"$ref": "#/$defs/CreditEnum"}, "type": "array"}, "applies_to_person": {"$ref": "#/$defs/PersonValue"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "required": ["applies_to_person", "applied_roles"], "title": "CreditAssociation", "type": "object"}, "CreditEnum": {"description": "", "enum": ["Conceptualization", "Data curation", "Formal Analysis", "Funding acquisition", "Investigation", "Methodology", "Project administration", "Resources", "Software", "Supervision", "Validation", "Visualization", "Writing original draft", "Writing review and editing", "Principal Investigator", "Submitter"], "title": "CreditEnum", "type": "string"}, "CurLandUseEnum": {"description": "", "enum": ["cities", "farmstead", "industrial areas", "roads/railroads", "rock", "sand", "gravel", "mudflats", "salt flats", "badlands", "permanent snow or ice", "saline seeps", "mines/quarries", "oil waste areas", "small grains", "row crops", "vegetable crops", "horticultural plants (e.g. tulips)", "marshlands (grass,sedges,rushes)", "tundra (mosses,lichens)", "rangeland", "pastureland (grasslands used for livestock grazing)", "hayland", "meadows (grasses,alfalfa,fescue,bromegrass,timothy)", "shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)", "successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)", "shrub crops (blueberries,nursery ornamentals,filberts)", "vine crops (grapes)", "conifers (e.g. pine,spruce,fir,cypress)", "hardwoods (e.g. oak,hickory,elm,aspen)", "intermixed hardwood and conifers", "tropical (e.g. mangrove,palms)", "rainforest (evergreen forest receiving greater than 406 cm annual rainfall)", "swamp (permanent or semi-permanent water body dominated by woody plants)", "crop trees (nuts,fruit,christmas trees,nursery trees)"], "title": "CurLandUseEnum", "type": "string"}, "DataObject": {"additionalProperties": false, "description": "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "compression_type": {"description": "If provided, specifies the compression type", "type": "string"}, "data_object_type": {"$ref": "#/$defs/FileTypeEnum", "description": "The type of file represented by the data object."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "file_size_bytes": {"description": "Size of the file in bytes", "type": "integer"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "md5_checksum": {"description": "MD5 checksum of file (pre-compressed)", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "url": {"type": "string"}, "was_generated_by": {"type": "string"}}, "required": ["id", "name", "description"], "title": "DataObject", "type": "object"}, "Database": {"additionalProperties": false, "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest", "properties": {"activity_set": {"description": "This property links a database object to the set of workflow activities.", "items": {"$ref": "#/$defs/WorkflowExecutionActivity"}, "type": "array"}, "biosample_set": {"description": "This property links a database object to the set of samples within it.", "items": {"$ref": "#/$defs/Biosample"}, "type": "array"}, "collecting_biosamples_from_site_set": {"items": {"$ref": "#/$defs/CollectingBiosamplesFromSite"}, "type": "array"}, "data_object_set": {"description": "This property links a database object to the set of data objects within it.", "items": {"$ref": "#/$defs/DataObject"}, "type": "array"}, "dissolving_activity_set": {"items": {"$ref": "#/$defs/DissolvingActivity"}, "type": "array"}, "field_research_site_set": {"items": {"$ref": "#/$defs/FieldResearchSite"}, "type": "array"}, "functional_annotation_set": {"description": "This property links a database object to the set of all functional annotations", "items": {"$ref": "#/$defs/FunctionalAnnotation"}, "type": "array"}, "genome_feature_set": {"description": "This property links a database object to the set of all features", "items": {"$ref": "#/$defs/GenomeFeature"}, "type": "array"}, "mags_activity_set": {"description": "This property links a database object to the set of MAGs analysis activities.", "items": {"$ref": "#/$defs/MagsAnalysisActivity"}, "type": "array"}, "material_sample_set": {"items": {"$ref": "#/$defs/MaterialSample"}, "type": "array"}, "material_sampling_activity_set": {"items": {"$ref": "#/$defs/MaterialSamplingActivity"}, "type": "array"}, "metabolomics_analysis_activity_set": {"description": "This property links a database object to the set of metabolomics analysis activities.", "items": {"$ref": "#/$defs/MetabolomicsAnalysisActivity"}, "type": "array"}, "metagenome_annotation_activity_set": {"description": "This property links a database object to the set of metagenome annotation activities.", "items": {"$ref": "#/$defs/MetagenomeAnnotationActivity"}, "type": "array"}, "metagenome_assembly_set": {"description": "This property links a database object to the set of metagenome assembly activities.", "items": {"$ref": "#/$defs/MetagenomeAssembly"}, "type": "array"}, "metaproteomics_analysis_activity_set": {"description": "This property links a database object to the set of metaproteomics analysis activities.", "items": {"$ref": "#/$defs/MetaproteomicsAnalysisActivity"}, "type": "array"}, "metatranscriptome_activity_set": {"description": "TODO", "items": {"$ref": "#/$defs/MetatranscriptomeActivity"}, "type": "array"}, "nom_analysis_activity_set": {"description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", "items": {"$ref": "#/$defs/NomAnalysisActivity"}, "type": "array"}, "omics_processing_set": {"description": "This property links a database object to the set of omics processings within it.", "items": {"$ref": "#/$defs/OmicsProcessing"}, "type": "array"}, "reaction_activity_set": {"items": {"$ref": "#/$defs/ReactionActivity"}, "type": "array"}, "read_based_taxonomy_analysis_activity_set": {"description": "This property links a database object to the set of read based analysis activities.", "items": {"$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity"}, "type": "array"}, "read_qc_analysis_activity_set": {"description": "This property links a database object to the set of read QC analysis activities.", "items": {"$ref": "#/$defs/ReadQcAnalysisActivity"}, "type": "array"}, "study_set": {"description": "This property links a database object to the set of studies within it.", "items": {"$ref": "#/$defs/Study"}, "type": "array"}}, "title": "Database", "type": "object"}, "DeposEnvEnum": {"description": "", "enum": ["Continental - Alluvial", "Continental - Aeolian", "Continental - Fluvial", "Continental - Lacustrine", "Transitional - Deltaic", "Transitional - Tidal", "Transitional - Lagoonal", "Transitional - Beach", "Transitional - Lake", "Marine - Shallow", "Marine - Deep", "Marine - Reef", "Other - Evaporite", "Other - Glacial", "Other - Volcanic", "other"], "title": "DeposEnvEnum", "type": "string"}, "DeviceTypeEnum": {"description": "", "enum": ["orbital_shaker", "thermomixer"], "title": "DeviceTypeEnum", "type": "string"}, "DissolvingActivity": {"additionalProperties": false, "description": "", "properties": {"dissolution_aided_by": {"$ref": "#/$defs/LabDevice"}, "dissolution_reagent": {"$ref": "#/$defs/SolventEnum"}, "dissolution_volume": {"$ref": "#/$defs/QuantityValue"}, "dissolved_in": {"$ref": "#/$defs/MaterialContainer"}, "material_input": {"type": "string"}, "material_output": {"type": "string"}}, "title": "DissolvingActivity", "type": "object"}, "DnaContTypeEnum": {"description": "", "enum": ["plate", "tube"], "title": "DnaContTypeEnum", "type": "string"}, "DnaDnaseEnum": {"description": "", "enum": ["no", "yes"], "title": "DnaDnaseEnum", "type": "string"}, "DnaSampleFormatEnum": {"description": "", "enum": ["10 mM Tris-HCl", "DNAStable", "Ethanol", "Low EDTA TE", "MDA reaction buffer", "PBS", "Pellet", "RNAStable", "TE", "Water", "Gentegra-DNA", "Gentegra-RNA"], "title": "DnaSampleFormatEnum", "type": "string"}, "DnaseRnaEnum": {"description": "", "enum": ["no", "yes"], "title": "DnaseRnaEnum", "type": "string"}, "DoorCompTypeEnum": {"description": "", "enum": ["metal covered", "revolving", "sliding", "telescopic"], "title": "DoorCompTypeEnum", "type": "string"}, "DoorCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "DoorCondEnum", "type": "string"}, "DoorDirectEnum": {"description": "", "enum": ["inward", "outward", "sideways"], "title": "DoorDirectEnum", "type": "string"}, "DoorLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "DoorLocEnum", "type": "string"}, "DoorMatEnum": {"description": "", "enum": ["aluminum", "cellular PVC", "engineered plastic", "fiberboard", "fiberglass", "metal", "thermoplastic alloy", "vinyl", "wood", "wood/plastic composite"], "title": "DoorMatEnum", "type": "string"}, "DoorMoveEnum": {"description": "", "enum": ["collapsible", "folding", "revolving", "rolling shutter", "sliding", "swinging"], "title": "DoorMoveEnum", "type": "string"}, "DoorTypeEnum": {"description": "", "enum": ["composite", "metal", "wooden"], "title": "DoorTypeEnum", "type": "string"}, "DoorTypeMetalEnum": {"description": "", "enum": ["collapsible", "corrugated steel", "hollow", "rolling shutters", "steel plate"], "title": "DoorTypeMetalEnum", "type": "string"}, "DoorTypeWoodEnum": {"description": "", "enum": ["bettened and ledged", "battened", "ledged and braced", "ledged and framed", "ledged, braced and frame", "framed and paneled", "glashed or sash", "flush", "louvered", "wire gauged"], "title": "DoorTypeWoodEnum", "type": "string"}, "DrainageClassEnum": {"description": "", "enum": ["very poorly", "poorly", "somewhat poorly", "moderately well", "well", "excessively drained"], "title": "DrainageClassEnum", "type": "string"}, "DrawingsEnum": {"description": "", "enum": ["operation", "as built", "construction", "bid", "design", "building navigation map", "diagram", "sketch"], "title": "DrawingsEnum", "type": "string"}, "EnvironmentalMaterialTerm": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "EnvironmentalMaterialTerm", "type": "object"}, "ExtWallOrientEnum": {"description": "", "enum": ["north", "south", "east", "west", "northeast", "southeast", "southwest", "northwest"], "title": "ExtWallOrientEnum", "type": "string"}, "ExtWindowOrientEnum": {"description": "", "enum": ["north", "south", "east", "west", "northeast", "southeast", "southwest", "northwest"], "title": "ExtWindowOrientEnum", "type": "string"}, "FaoClassEnum": {"description": "", "enum": ["Acrisols", "Andosols", "Arenosols", "Cambisols", "Chernozems", "Ferralsols", "Fluvisols", "Gleysols", "Greyzems", "Gypsisols", "Histosols", "Kastanozems", "Lithosols", "Luvisols", "Nitosols", "Phaeozems", "Planosols", "Podzols", "Podzoluvisols", "Rankers", "Regosols", "Rendzinas", "Solonchaks", "Solonetz", "Vertisols", "Yermosols"], "title": "FaoClassEnum", "type": "string"}, "FieldResearchSite": {"additionalProperties": false, "description": "A site, outside of a laboratory, from which biosamples may be collected.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "FieldResearchSite", "type": "object"}, "FileTypeEnum": {"description": "", "enum": ["Metagenome Raw Reads", "FT ICR-MS Analysis Results", "GC-MS Metabolomics Results", "Metaproteomics Workflow Statistics", "Protein Report", "Peptide Report", "Unfiltered Metaproteomics Results", "Read Count and RPKM", "QC non-rRNA R2", "QC non-rRNA R1", "Metagenome Bins", "CheckM Statistics", "GOTTCHA2 Krona Plot", "GOTTCHA2 Classification Report", "GOTTCHA2 Report Full", "Kraken2 Krona Plot", "Centrifuge Krona Plot", "Centrifuge output report file", "Kraken2 Classification Report", "Kraken2 Taxonomic Classification", "Centrifuge Classification Report", "Centrifuge Taxonomic Classification", "Structural Annotation GFF", "Functional Annotation GFF", "Annotation Amino Acid FASTA", "Annotation Enzyme Commission", "Annotation KEGG Orthology", "Assembly Coverage BAM", "Assembly AGP", "Assembly Scaffolds", "Assembly Contigs", "Assembly Coverage Stats", "Filtered Sequencing Reads", "QC Statistics", "TIGRFam Annotation GFF", "CRT Annotation GFF", "Genmark Annotation GFF", "Prodigal Annotation GFF", "TRNA Annotation GFF", "Misc Annotation GFF", "RFAM Annotation GFF", "TMRNA Annotation GFF", "KO_EC Annotation GFF", "Product Names", "Gene Phylogeny tsv", "Crisprt Terms", "Clusters of Orthologous Groups (COG) Annotation GFF", "CATH FunFams (Functional Families) Annotation GFF", "SUPERFam Annotation GFF", "SMART Annotation GFF", "Pfam Annotation GFF", "Direct Infusion FT ICR-MS Raw Data"], "title": "FileTypeEnum", "type": "string"}, "FilterTypeEnum": {"description": "", "enum": ["particulate air filter", "chemical air filter", "low-MERV pleated media", "HEPA", "electrostatic", "gas-phase or ultraviolet air treatments"], "title": "FilterTypeEnum", "type": "string"}, "FloorCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "FloorCondEnum", "type": "string"}, "FloorFinishMatEnum": {"description": "", "enum": ["tile", "wood strip or parquet", "carpet", "rug", "laminate wood", "lineoleum", "vinyl composition tile", "sheet vinyl", "stone", "bamboo", "cork", "terrazo", "concrete", "none", "sealed", "clear finish", "paint", "none or unfinished"], "title": "FloorFinishMatEnum", "type": "string"}, "FloorStrucEnum": {"description": "", "enum": ["balcony", "floating floor", "glass floor", "raised floor", "sprung floor", "wood-framed", "concrete"], "title": "FloorStrucEnum", "type": "string"}, "FloorWaterMoldEnum": {"description": "", "enum": ["mold odor", "wet floor", "water stains", "wall discoloration", "floor discoloration", "ceiling discoloration", "peeling paint or wallpaper", "bulging walls", "condensation"], "title": "FloorWaterMoldEnum", "type": "string"}, "FreqCleanEnum": {"description": "", "enum": ["Daily", "Weekly", "Monthly", "Quarterly", "Annually", "other"], "title": "FreqCleanEnum", "type": "string"}, "FunctionalAnnotation": {"additionalProperties": false, "description": "An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods", "properties": {"has_function": {"pattern": "^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$", "type": "string"}, "subject": {"type": "string"}, "was_generated_by": {"description": "provenance for the annotation.", "type": "string"}}, "title": "FunctionalAnnotation", "type": "object"}, "FurnitureEnum": {"description": "", "enum": ["cabinet", "chair", "desks"], "title": "FurnitureEnum", "type": "string"}, "GenderRestroomEnum": {"description": "", "enum": ["all gender", "female", "gender neurtral", "male", "male and female", "unisex"], "title": "GenderRestroomEnum", "type": "string"}, "GeneProduct": {"additionalProperties": false, "description": "A molecule encoded by a gene that has an evolved function", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "GeneProduct", "type": "object"}, "GenomeFeature": {"additionalProperties": false, "description": "A feature localized to an interval along a genome", "title": "GenomeFeature", "type": "object"}, "GeolocationValue": {"additionalProperties": false, "description": "A normalized value for a location on the earth's surface", "properties": {"has_raw_value": {"description": "The raw value for a geolocation should follow {lat} {long}", "type": "string"}, "latitude": {"description": "latitude", "type": "number"}, "longitude": {"description": "longitude", "type": "number"}, "was_generated_by": {"type": "string"}}, "title": "GeolocationValue", "type": "object"}, "GrowthHabitEnum": {"description": "", "enum": ["erect", "semi-erect", "spreading", "prostrate"], "title": "GrowthHabitEnum", "type": "string"}, "HandidnessEnum": {"description": "", "enum": ["ambidexterity", "left handedness", "mixed-handedness", "right handedness"], "title": "HandidnessEnum", "type": "string"}, "HcProducedEnum": {"description": "", "enum": ["Oil", "Gas-Condensate", "Gas", "Bitumen", "Coalbed Methane", "other"], "title": "HcProducedEnum", "type": "string"}, "HcrEnum": {"description": "", "enum": ["Oil Reservoir", "Gas Reservoir", "Oil Sand", "Coalbed", "Shale", "Tight Oil Reservoir", "Tight Gas Reservoir", "other"], "title": "HcrEnum", "type": "string"}, "HcrGeolAgeEnum": {"description": "", "enum": ["Archean", "Cambrian", "Carboniferous", "Cenozoic", "Cretaceous", "Devonian", "Jurassic", "Mesozoic", "Neogene", "Ordovician", "Paleogene", "Paleozoic", "Permian", "Precambrian", "Proterozoic", "Silurian", "Triassic", "other"], "title": "HcrGeolAgeEnum", "type": "string"}, "HeatCoolTypeEnum": {"description": "", "enum": ["radiant system", "heat pump", "forced air system", "steam forced heat", "wood stove"], "title": "HeatCoolTypeEnum", "type": "string"}, "HeatDelivLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "HeatDelivLocEnum", "type": "string"}, "HorizonEnum": {"description": "", "enum": ["O horizon", "A horizon", "E horizon", "B horizon", "C horizon", "R layer", "Permafrost"], "title": "HorizonEnum", "type": "string"}, "HostSexEnum": {"description": "", "enum": ["female", "hermaphrodite", "male", "neuter"], "title": "HostSexEnum", "type": "string"}, "ImageValue": {"additionalProperties": false, "description": "An attribute value representing an image.", "properties": {"description": {"description": "a human-readable description of a thing", "type": "string"}, "display_order": {"description": "When rendering information, this attribute to specify the order in which the information should be rendered.", "type": "string"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "url": {"type": "string"}, "was_generated_by": {"type": "string"}}, "title": "ImageValue", "type": "object"}, "IndoorSpaceEnum": {"description": "", "enum": ["bedroom", "office", "bathroom", "foyer", "kitchen", "locker room", "hallway", "elevator"], "title": "IndoorSpaceEnum", "type": "string"}, "IndoorSurfEnum": {"description": "", "enum": ["cabinet", "ceiling", "counter top", "door", "shelving", "vent cover", "window", "wall"], "title": "IndoorSurfEnum", "type": "string"}, "Instrument": {"additionalProperties": false, "description": "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI].", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Instrument", "type": "object"}, "IntWallCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "IntWallCondEnum", "type": "string"}, "IntegerValue": {"additionalProperties": false, "description": "A value that is an integer", "properties": {"has_numeric_value": {"description": "Links a quantity value to a number", "type": "number"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "IntegerValue", "type": "object"}, "LabDevice": {"additionalProperties": false, "description": "", "properties": {"activity_speed": {"$ref": "#/$defs/QuantityValue"}, "activity_temperature": {"$ref": "#/$defs/QuantityValue"}, "activity_time": {"$ref": "#/$defs/QuantityValue"}, "device_type": {"$ref": "#/$defs/DeviceTypeEnum"}}, "title": "LabDevice", "type": "object"}, "LightTypeEnum": {"description": "", "enum": ["natural light", "electric light", "desk lamp", "flourescent lights", "none"], "title": "LightTypeEnum", "type": "string"}, "LithologyEnum": {"description": "", "enum": ["Basement", "Chalk", "Chert", "Coal", "Conglomerate", "Diatomite", "Dolomite", "Limestone", "Sandstone", "Shale", "Siltstone", "Volcanic", "other"], "title": "LithologyEnum", "type": "string"}, "MagBin": {"additionalProperties": false, "description": "", "properties": {"bin_name": {"type": "string"}, "bin_quality": {"type": "string"}, "completeness": {"type": "number"}, "contamination": {"type": "number"}, "gene_count": {"type": "integer"}, "gtdbtk_class": {"type": "string"}, "gtdbtk_domain": {"type": "string"}, "gtdbtk_family": {"type": "string"}, "gtdbtk_genus": {"type": "string"}, "gtdbtk_order": {"type": "string"}, "gtdbtk_phylum": {"type": "string"}, "gtdbtk_species": {"type": "string"}, "num_16s": {"type": "integer"}, "num_23s": {"type": "integer"}, "num_5s": {"type": "integer"}, "num_t_rna": {"type": "integer"}, "number_of_contig": {"type": "integer"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "title": "MagBin", "type": "object"}, "MagsAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", "properties": {"binned_contig_num": {"type": "integer"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "input_contig_num": {"type": "integer"}, "low_depth_contig_num": {"type": "integer"}, "mags_list": {"items": {"$ref": "#/$defs/MagBin"}, "type": "array"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "too_short_contig_num": {"type": "integer"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "unbinned_contig_num": {"type": "integer"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MagsAnalysisActivity", "type": "object"}, "MaterialContainer": {"additionalProperties": false, "description": "", "properties": {"container_size": {"$ref": "#/$defs/QuantityValue"}, "container_type": {"$ref": "#/$defs/ContainerTypeEnum"}}, "title": "MaterialContainer", "type": "object"}, "MaterialEntity": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "MaterialEntity", "type": "object"}, "MaterialSample": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "MaterialSample", "type": "object"}, "MaterialSamplingActivity": {"additionalProperties": false, "description": "", "properties": {"amount_collected": {"$ref": "#/$defs/QuantityValue"}, "biosample_input": {"type": "string"}, "collected_into": {"$ref": "#/$defs/MaterialContainer"}, "material_output": {"type": "string"}, "sampling_method": {"$ref": "#/$defs/SamplingMethodEnum"}}, "title": "MaterialSamplingActivity", "type": "object"}, "MechStrucEnum": {"description": "", "enum": ["subway", "coach", "carriage", "elevator", "escalator", "boat", "train", "car", "bus"], "title": "MechStrucEnum", "type": "string"}, "MetaboliteQuantification": {"additionalProperties": false, "description": "This is used to link a metabolomics analysis workflow to a specific metabolite", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "MetaboliteQuantification", "type": "object"}, "MetabolomicsAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetabolomicsAnalysisActivity", "type": "object"}, "MetagenomeAnnotationActivity": {"additionalProperties": false, "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "gold_analysis_project_identifiers": {"description": "identifiers for corresponding analysis project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Ga[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetagenomeAnnotationActivity", "type": "object"}, "MetagenomeAssembly": {"additionalProperties": false, "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", "properties": {"asm_score": {"description": "A score for comparing metagenomic assembly quality from same sample.", "type": "number"}, "contig_bp": {"description": "Total size in bp of all contigs.", "type": "number"}, "contigs": {"description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "ctg_l50": {"description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", "type": "number"}, "ctg_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", "type": "number"}, "ctg_logsum": {"description": "Maximum contig length.", "type": "number"}, "ctg_max": {"description": "Maximum contig length.", "type": "number"}, "ctg_n50": {"description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", "type": "number"}, "ctg_n90": {"description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", "type": "number"}, "ctg_powsum": {"description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "gap_pct": {"description": "The gap size percentage of all scaffolds.", "type": "number"}, "gc_avg": {"description": "Average of GC content of all contigs.", "type": "number"}, "gc_std": {"description": "Standard deviation of GC content of all contigs.", "type": "number"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_assembly_identifiers": {"pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "num_aligned_reads": {"description": "The sequence count number of input reads aligned to assembled contigs.", "type": "number"}, "num_input_reads": {"description": "The sequence count number of input reads for assembly.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "scaf_bp": {"description": "Total size in bp of all scaffolds.", "type": "number"}, "scaf_l50": {"description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", "type": "number"}, "scaf_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", "type": "number"}, "scaf_l_gt50k": {"description": "Total size in bp of all scaffolds greater than 50 KB.", "type": "number"}, "scaf_logsum": {"description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "scaf_max": {"description": "Maximum scaffold length.", "type": "number"}, "scaf_n50": {"description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", "type": "number"}, "scaf_n90": {"description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", "type": "number"}, "scaf_n_gt50k": {"description": "Total sequence count of scaffolds greater than 50 KB.", "type": "number"}, "scaf_pct_gt50k": {"description": "Total sequence size percentage of scaffolds greater than 50 KB.", "type": "number"}, "scaf_powsum": {"description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "scaffolds": {"description": "Total sequence count of all scaffolds.", "type": "number"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetagenomeAssembly", "type": "object"}, "MetaproteomicsAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetaproteomicsAnalysisActivity", "type": "object"}, "MetatranscriptomeActivity": {"additionalProperties": false, "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeActivity", "type": "object"}, "MetatranscriptomeAnnotationActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "gold_analysis_project_identifiers": {"description": "identifiers for corresponding analysis project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Ga[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeAnnotationActivity", "type": "object"}, "MetatranscriptomeAssembly": {"additionalProperties": false, "description": "", "properties": {"asm_score": {"description": "A score for comparing metagenomic assembly quality from same sample.", "type": "number"}, "contig_bp": {"description": "Total size in bp of all contigs.", "type": "number"}, "contigs": {"description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "ctg_l50": {"description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", "type": "number"}, "ctg_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", "type": "number"}, "ctg_logsum": {"description": "Maximum contig length.", "type": "number"}, "ctg_max": {"description": "Maximum contig length.", "type": "number"}, "ctg_n50": {"description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", "type": "number"}, "ctg_n90": {"description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", "type": "number"}, "ctg_powsum": {"description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "gap_pct": {"description": "The gap size percentage of all scaffolds.", "type": "number"}, "gc_avg": {"description": "Average of GC content of all contigs.", "type": "number"}, "gc_std": {"description": "Standard deviation of GC content of all contigs.", "type": "number"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_assembly_identifiers": {"pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "num_aligned_reads": {"description": "The sequence count number of input reads aligned to assembled contigs.", "type": "number"}, "num_input_reads": {"description": "The sequence count number of input reads for assembly.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "scaf_bp": {"description": "Total size in bp of all scaffolds.", "type": "number"}, "scaf_l50": {"description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", "type": "number"}, "scaf_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", "type": "number"}, "scaf_l_gt50k": {"description": "Total size in bp of all scaffolds greater than 50 KB.", "type": "number"}, "scaf_logsum": {"description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "scaf_max": {"description": "Maximum scaffold length.", "type": "number"}, "scaf_n50": {"description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", "type": "number"}, "scaf_n90": {"description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", "type": "number"}, "scaf_n_gt50k": {"description": "Total sequence count of scaffolds greater than 50 KB.", "type": "number"}, "scaf_pct_gt50k": {"description": "Total sequence size percentage of scaffolds greater than 50 KB.", "type": "number"}, "scaf_powsum": {"description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "scaffolds": {"description": "Total sequence count of all scaffolds.", "type": "number"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeAssembly", "type": "object"}, "NomAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "NomAnalysisActivity", "type": "object"}, "OccupDocumentEnum": {"description": "", "enum": ["automated count", "estimate", "manual count", "videos"], "title": "OccupDocumentEnum", "type": "string"}, "OmicsProcessing": {"additionalProperties": false, "description": "The methods and processes used to generate omics data from a biosample or organism.", "properties": {"add_date": {"description": "The date on which the information was added to the database.", "type": "string"}, "alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "chimera_check": {"$ref": "#/$defs/TextValue", "description": "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "gold_sequencing_project_identifiers": {"description": "identifiers for corresponding sequencing project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Gp[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_experiment_identifiers": {"items": {"type": "string"}, "pattern": "^insdc.sra:(E|D|S)RX[0-9]{6,}$", "type": "array"}, "instrument_name": {"description": "The name of the instrument that was used for processing the sample.", "type": "string"}, "mod_date": {"description": "The last date on which the database information was modified.", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "ncbi_project_name": {"type": "string"}, "nucl_acid_amp": {"$ref": "#/$defs/TextValue", "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids"}, "nucl_acid_ext": {"$ref": "#/$defs/TextValue", "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample"}, "omics_type": {"$ref": "#/$defs/ControlledTermValue", "description": "The type of omics data"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "pcr_cond": {"$ref": "#/$defs/TextValue", "description": "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'"}, "pcr_primers": {"$ref": "#/$defs/TextValue", "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters"}, "principal_investigator": {"$ref": "#/$defs/PersonValue", "description": "Principal Investigator who led the study and/or generated the dataset."}, "processing_institution": {"$ref": "#/$defs/ProcessingInstitutionEnum", "description": "The organization that processed the sample."}, "samp_vol_we_dna_ext": {"$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)."}, "seq_meth": {"$ref": "#/$defs/TextValue", "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)."}, "seq_quality_check": {"$ref": "#/$defs/TextValue", "description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA"}, "target_gene": {"$ref": "#/$defs/TextValue", "description": "Targeted gene or locus name for marker gene studies"}, "target_subfragment": {"$ref": "#/$defs/TextValue", "description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "required": ["has_input"], "title": "OmicsProcessing", "type": "object"}, "OntologyClass": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "OntologyClass", "type": "object"}, "OrganismCountEnum": {"description": "", "enum": ["ATP", "MPN", "other"], "title": "OrganismCountEnum", "type": "string"}, "OrthologyGroup": {"additionalProperties": false, "description": "A set of genes or gene products in which all members are orthologous", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "OrthologyGroup", "type": "object"}, "OxyStatSampEnum": {"description": "", "enum": ["aerobic", "anaerobic", "other"], "title": "OxyStatSampEnum", "type": "string"}, "Pathway": {"additionalProperties": false, "description": "A pathway is a sequence of steps/reactions carried out by an organism or community of organisms", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Pathway", "type": "object"}, "PeptideQuantification": {"additionalProperties": false, "description": "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information", "title": "PeptideQuantification", "type": "object"}, "Person": {"additionalProperties": false, "description": "represents a person, such as a researcher", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "Should be an ORCID. Specify in CURIE format. E.g ORCID:0000-1111-...", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Person", "type": "object"}, "PersonValue": {"additionalProperties": false, "description": "An attribute value representing a person", "properties": {"email": {"description": "An email address for an entity such as a person. This should be the primarly email address used.", "type": "string"}, "has_raw_value": {"description": "The full name of the Investigator in format FIRST LAST.", "type": "string"}, "name": {"description": "The full name of the Investigator. It should follow the format FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.", "type": "string"}, "orcid": {"description": "The ORCID of a person.", "type": "string"}, "profile_image_url": {"description": "A url that points to an image of a person.", "type": "string"}, "was_generated_by": {"type": "string"}, "websites": {"description": "A list of websites that are associated with the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "PersonValue", "type": "object"}, "PlannedProcess": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_inputs": {"items": {"type": "string"}, "type": "array"}, "has_outputs": {"items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "participating_agent": {"$ref": "#/$defs/Agent"}}, "required": ["id"], "title": "PlannedProcess", "type": "object"}, "PlantGrowthMedEnum": {"description": "", "enum": ["other artificial liquid medium", "other artificial solid medium", "peat moss", "perlite", "pumice", "sand", "soil", "vermiculite", "water"], "title": "PlantGrowthMedEnum", "type": "string"}, "PlantSexEnum": {"description": "", "enum": ["Androdioecious", "Androecious", "Androgynous", "Androgynomonoecious", "Andromonoecious", "Bisexual", "Dichogamous", "Diclinous", "Dioecious", "Gynodioecious", "Gynoecious", "Gynomonoecious", "Hermaphroditic", "Imperfect", "Monoclinous", "Monoecious", "Perfect", "Polygamodioecious", "Polygamomonoecious", "Polygamous", "Protandrous", "Protogynous", "Subandroecious", "Subdioecious", "Subgynoecious", "Synoecious", "Trimonoecious", "Trioecious", "Unisexual"], "title": "PlantSexEnum", "type": "string"}, "ProcessingInstitutionEnum": {"description": "", "enum": ["UCSD", "JGI", "EMSL"], "title": "ProcessingInstitutionEnum", "type": "string"}, "ProfilePositionEnum": {"description": "", "enum": ["summit", "shoulder", "backslope", "footslope", "toeslope"], "title": "ProfilePositionEnum", "type": "string"}, "ProteinQuantification": {"additionalProperties": false, "description": "This is used to link a metaproteomics analysis workflow to a specific protein", "title": "ProteinQuantification", "type": "object"}, "QuadPosEnum": {"description": "", "enum": ["North side", "West side", "South side", "East side"], "title": "QuadPosEnum", "type": "string"}, "QuantityValue": {"additionalProperties": false, "description": "A simple quantity, e.g. 2cm", "properties": {"has_maximum_numeric_value": {"description": "The maximum value part, expressed as number, of the quantity value when the value covers a range.", "type": "number"}, "has_minimum_numeric_value": {"description": "The minimum value part, expressed as number, of the quantity value when the value covers a range.", "type": "number"}, "has_numeric_value": {"description": "The number part of the quantity", "type": "number"}, "has_raw_value": {"description": "Unnormalized atomic string representation, should in syntax {number} {unit}", "type": "string"}, "has_unit": {"description": "The unit of the quantity", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "QuantityValue", "type": "object"}, "Reaction": {"additionalProperties": false, "description": "An individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Reaction", "type": "object"}, "ReactionActivity": {"additionalProperties": false, "description": "", "properties": {"material_input": {"type": "string"}, "material_output": {"type": "string"}, "reaction_aided_by": {"$ref": "#/$defs/LabDevice"}, "reaction_temperature": {"type": "string"}, "reaction_time": {"$ref": "#/$defs/QuantityValue"}}, "title": "ReactionActivity", "type": "object"}, "ReactionParticipant": {"additionalProperties": false, "description": "Instances of this link a reaction to a chemical entity participant", "title": "ReactionParticipant", "type": "object"}, "ReadBasedTaxonomyAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "ReadBasedTaxonomyAnalysisActivity", "type": "object"}, "ReadQcAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "input_base_count": {"description": "The nucleotide base count number of input reads for QC analysis.", "type": "number"}, "input_read_count": {"description": "The sequence count number of input reads for QC analysis.", "type": "number"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "output_base_count": {"description": "After QC analysis nucleotide base count number.", "type": "number"}, "output_read_count": {"description": "After QC analysis sequence count number.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "ReadQcAnalysisActivity", "type": "object"}, "RelSampLocEnum": {"description": "", "enum": ["edge of car", "center of car", "under a seat"], "title": "RelSampLocEnum", "type": "string"}, "RelToOxygenEnum": {"description": "", "enum": ["aerobe", "anaerobe", "facultative", "microaerophilic", "microanaerobe", "obligate aerobe", "obligate anaerobe"], "title": "RelToOxygenEnum", "type": "string"}, "RnaContTypeEnum": {"description": "", "enum": ["plate", "tube"], "title": "RnaContTypeEnum", "type": "string"}, "RnaSampleFormatEnum": {"description": "", "enum": ["10 mM Tris-HCl", "DNAStable", "Ethanol", "Low EDTA TE", "MDA reaction buffer", "PBS", "Pellet", "RNAStable", "TE", "Water", "Gentegra-DNA", "Gentegra-RNA"], "title": "RnaSampleFormatEnum", "type": "string"}, "RoomCondtEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture", "visible signs of mold/mildew"], "title": "RoomCondtEnum", "type": "string"}, "RoomConnectedEnum": {"description": "", "enum": ["attic", "bathroom", "closet", "conference room", "elevator", "examining room", "hallway", "kitchen", "mail room", "office", "stairwell"], "title": "RoomConnectedEnum", "type": "string"}, "RoomLocEnum": {"description": "", "enum": ["corner room", "interior room", "exterior wall"], "title": "RoomLocEnum", "type": "string"}, "RoomSampPosEnum": {"description": "", "enum": ["north corner", "south corner", "west corner", "east corner", "northeast corner", "northwest corner", "southeast corner", "southwest corner", "center"], "title": "RoomSampPosEnum", "type": "string"}, "RoomTypeEnum": {"description": "", "enum": ["attic", "bathroom", "closet", "conference room", "elevator", "examining room", "hallway", "kitchen", "mail room", "private office", "open office", "stairwell", ",restroom", "lobby", "vestibule", "mechanical or electrical room", "data center", "laboratory_wet", "laboratory_dry", "gymnasium", "natatorium", "auditorium", "lockers", "cafe", "warehouse"], "title": "RoomTypeEnum", "type": "string"}, "SampCaptStatusEnum": {"description": "", "enum": ["active surveillance in response to an outbreak", "active surveillance not initiated by an outbreak", "farm sample", "market sample", "other"], "title": "SampCaptStatusEnum", "type": "string"}, "SampCollectPointEnum": {"description": "", "enum": ["well", "test well", "drilling rig", "wellhead", "separator", "storage tank", "other"], "title": "SampCollectPointEnum", "type": "string"}, "SampDisStageEnum": {"description": "", "enum": ["dissemination", "growth and reproduction", "infection", "inoculation", "penetration", "other"], "title": "SampDisStageEnum", "type": "string"}, "SampFloorEnum": {"description": "", "enum": ["1st floor", "2nd floor", "basement", "lobby"], "title": "SampFloorEnum", "type": "string"}, "SampMdEnum": {"description": "", "enum": ["DF", "RT", "KB", "MSL", "other"], "title": "SampMdEnum", "type": "string"}, "SampSubtypeEnum": {"description": "", "enum": ["oil phase", "water phase", "biofilm", "not applicable", "other"], "title": "SampSubtypeEnum", "type": "string"}, "SampWeatherEnum": {"description": "", "enum": ["clear sky", "cloudy", "foggy", "hail", "rain", "snow", "sleet", "sunny", "windy"], "title": "SampWeatherEnum", "type": "string"}, "SampleTypeEnum": {"description": "", "enum": ["soil", "water_extract_soil"], "title": "SampleTypeEnum", "type": "string"}, "SamplingMethodEnum": {"description": "", "enum": ["weighing"], "title": "SamplingMethodEnum", "type": "string"}, "SeasonUseEnum": {"description": "", "enum": ["Spring", "Summer", "Fall", "Winter"], "title": "SeasonUseEnum", "type": "string"}, "SedimentTypeEnum": {"description": "", "enum": ["biogenous", "cosmogenous", "hydrogenous", "lithogenous"], "title": "SedimentTypeEnum", "type": "string"}, "ShadingDeviceCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "ShadingDeviceCondEnum", "type": "string"}, "ShadingDeviceTypeEnum": {"description": "", "enum": ["bahama shutters", "exterior roll blind", "gambrel awning", "hood awning", "porchroller awning", "sarasota shutters", "slatted aluminum", "solid aluminum awning", "sun screen", "tree", "trellis", "venetian awning"], "title": "ShadingDeviceTypeEnum", "type": "string"}, "Site": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Site", "type": "object"}, "SoilHorizonEnum": {"description": "", "enum": ["O horizon", "A horizon", "E horizon", "B horizon", "C horizon", "R layer", "Permafrost"], "title": "SoilHorizonEnum", "type": "string"}, "SolventEnum": {"description": "", "enum": ["deionized_water", "methanol", "chloroform"], "title": "SolventEnum", "type": "string"}, "SpecificEnum": {"description": "", "enum": ["operation", "as built", "construction", "bid", "design", "photos"], "title": "SpecificEnum", "type": "string"}, "SrDepEnvEnum": {"description": "", "enum": ["Lacustine", "Fluvioldeltaic", "Fluviomarine", "Marine", "other"], "title": "SrDepEnvEnum", "type": "string"}, "SrGeolAgeEnum": {"description": "", "enum": ["Archean", "Cambrian", "Carboniferous", "Cenozoic", "Cretaceous", "Devonian", "Jurassic", "Mesozoic", "Neogene", "Ordovician", "Paleogene", "Paleozoic", "Permian", "Precambrian", "Proterozoic", "Silurian", "Triassic", "other"], "title": "SrGeolAgeEnum", "type": "string"}, "SrKerogTypeEnum": {"description": "", "enum": ["Type I", "Type II", "Type III", "Type IV", "other"], "title": "SrKerogTypeEnum", "type": "string"}, "SrLithologyEnum": {"description": "", "enum": ["Clastic", "Carbonate", "Coal", "Biosilicieous", "other"], "title": "SrLithologyEnum", "type": "string"}, "Study": {"additionalProperties": false, "description": "A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.", "properties": {"abstract": {"description": "The abstract of manuscript/grant associated with the entity; i.e., a summary of the resource.", "type": "string"}, "alternative_descriptions": {"description": "A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.", "items": {"type": "string"}, "type": "array"}, "alternative_identifiers": {"description": "Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC", "items": {"type": "string"}, "type": "array"}, "alternative_names": {"description": "A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.", "items": {"type": "string"}, "type": "array"}, "alternative_titles": {"description": "A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "A brief summary that details the study you're submitted to NMDC", "type": "string"}, "doi": {"$ref": "#/$defs/AttributeValue", "description": "The dataset citation for this study"}, "ecosystem": {"description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", "type": "string"}, "ecosystem_category": {"description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", "type": "string"}, "ecosystem_subtype": {"description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", "type": "string"}, "ecosystem_type": {"description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", "type": "string"}, "emsl_proposal_doi": {"description": "The DOI for the EMSL awarded study that relates to the NMDC submitted study", "type": "string"}, "emsl_proposal_identifier": {"description": "The proposal number assigned to the EMSL awarded study that relates to that which is represented in NMDC.", "type": "string"}, "ess_dive_datasets": {"description": "List of ESS-DIVE dataset DOIs", "items": {"type": "string"}, "type": "array"}, "funding_sources": {"items": {"type": "string"}, "type": "array"}, "gold_study_identifiers": {"description": "identifiers for corresponding project(s) in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Gs[0-9]+$", "type": "array"}, "has_credit_associations": {"description": "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study", "items": {"$ref": "#/$defs/CreditAssociation"}, "type": "array"}, "id": {"description": "An NMDC assigned unique identifier for a sample submitted to NMDC.", "type": "string"}, "mgnify_project_identifiers": {"description": "identifiers for corresponding project in MGnify", "pattern": "^mgnify.proj:[A-Z]+[0-9]+$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "objective": {"description": "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.", "type": "string"}, "principal_investigator": {"$ref": "#/$defs/PersonValue", "description": "Principal Investigator who led the study and/or generated the dataset."}, "publications": {"description": "A list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.", "items": {"type": "string"}, "type": "array"}, "related_identifiers": {"description": "Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC", "type": "string"}, "relevant_protocols": {"items": {"type": "string"}, "type": "array"}, "specific_ecosystem": {"description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", "type": "string"}, "study_image": {"description": "Links a study to one or more images.", "items": {"$ref": "#/$defs/ImageValue"}, "type": "array"}, "title": {"description": "A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "websites": {"description": "A list of websites that are associated with the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "Study", "type": "object"}, "SubstructureTypeEnum": {"description": "", "enum": ["crawlspace", "slab on grade", "basement"], "title": "SubstructureTypeEnum", "type": "string"}, "SurfAirContEnum": {"description": "", "enum": ["dust", "organic matter", "particulate matter", "volatile organic compounds", "biological contaminants", "radon", "nutrients", "biocides"], "title": "SurfAirContEnum", "type": "string"}, "SurfMaterialEnum": {"description": "", "enum": ["adobe", "carpet", "cinder blocks", "concrete", "hay bales", "glass", "metal", "paint", "plastic", "stainless steel", "stone", "stucco", "tile", "vinyl", "wood"], "title": "SurfMaterialEnum", "type": "string"}, "TextValue": {"additionalProperties": false, "description": "A basic string value", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "language": {"description": "Should use ISO 639-1 code e.g. \"en\", \"fr\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "TextValue", "type": "object"}, "TidalStageEnum": {"description": "", "enum": ["low tide", "ebb tide", "flood tide", "high tide"], "title": "TidalStageEnum", "type": "string"}, "TillageEnum": {"description": "", "enum": ["drill", "cutting disc", "ridge till", "strip tillage", "zonal tillage", "chisel", "tined", "mouldboard", "disc plough"], "title": "TillageEnum", "type": "string"}, "TimestampValue": {"additionalProperties": false, "description": "A value that is a timestamp. The range should be ISO-8601", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "TimestampValue", "type": "object"}, "TrainLineEnum": {"description": "", "enum": ["red", "green", "orange"], "title": "TrainLineEnum", "type": "string"}, "TrainStatLocEnum": {"description": "", "enum": ["south station above ground", "south station underground", "south station amtrak", "forest hills", "riverside"], "title": "TrainStatLocEnum", "type": "string"}, "TrainStopLocEnum": {"description": "", "enum": ["end", "mid", "downtown"], "title": "TrainStopLocEnum", "type": "string"}, "UrlValue": {"additionalProperties": false, "description": "A value that is a string that conforms to URL syntax", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "UrlValue", "type": "object"}, "VisMediaEnum": {"description": "", "enum": ["photos", "videos", "commonly of the building", "site context (adjacent buildings, vegetation, terrain, streets)", "interiors", "equipment", "3D scans"], "title": "VisMediaEnum", "type": "string"}, "WallConstTypeEnum": {"description": "", "enum": ["frame construction", "joisted masonry", "light noncombustible", "masonry noncombustible", "modified fire resistive", "fire resistive"], "title": "WallConstTypeEnum", "type": "string"}, "WallFinishMatEnum": {"description": "", "enum": ["plaster", "gypsum plaster", "veneer plaster", "gypsum board", "tile", "terrazzo", "stone facing", "acoustical treatment", "wood", "metal", "masonry"], "title": "WallFinishMatEnum", "type": "string"}, "WallLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "WallLocEnum", "type": "string"}, "WallSurfTreatmentEnum": {"description": "", "enum": ["painted", "wall paper", "no treatment", "paneling", "stucco", "fabric"], "title": "WallSurfTreatmentEnum", "type": "string"}, "WallTextureEnum": {"description": "", "enum": ["crows feet", "crows-foot stomp", "double skip", "hawk and trowel", "knockdown", "popcorn", "orange peel", "rosebud stomp", "Santa-Fe texture", "skip trowel", "smooth", "stomp knockdown", "swirl"], "title": "WallTextureEnum", "type": "string"}, "WaterFeatTypeEnum": {"description": "", "enum": ["fountain", "pool", "standing feature", "stream", "waterfall"], "title": "WaterFeatTypeEnum", "type": "string"}, "WeekdayEnum": {"description": "", "enum": ["Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday", "Sunday"], "title": "WeekdayEnum", "type": "string"}, "WindowCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "WindowCondEnum", "type": "string"}, "WindowCoverEnum": {"description": "", "enum": ["blinds", "curtains", "none"], "title": "WindowCoverEnum", "type": "string"}, "WindowHorizPosEnum": {"description": "", "enum": ["left", "middle", "right"], "title": "WindowHorizPosEnum", "type": "string"}, "WindowLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "WindowLocEnum", "type": "string"}, "WindowMatEnum": {"description": "", "enum": ["clad", "fiberglass", "metal", "vinyl", "wood"], "title": "WindowMatEnum", "type": "string"}, "WindowTypeEnum": {"description": "", "enum": ["single-hung sash window", "horizontal sash window", "fixed window"], "title": "WindowTypeEnum", "type": "string"}, "WindowVertPosEnum": {"description": "", "enum": ["bottom", "middle", "top", "low", "high"], "title": "WindowVertPosEnum", "type": "string"}, "WorkflowExecutionActivity": {"additionalProperties": false, "description": "Represents an instance of an execution of a particular workflow", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"description": "the agent/entity associated with the generation of the file", "type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "WorkflowExecutionActivity", "type": "object"}}, "$id": "https://microbiomedata/schema", "$schema": "http://json-schema.org/draft-07/schema#", "additionalProperties": false, "metamodel_version": "1.7.0", "properties": {"activity_set": {"description": "This property links a database object to the set of workflow activities.", "items": {"$ref": "#/$defs/WorkflowExecutionActivity"}, "type": "array"}, "biosample_set": {"description": "This property links a database object to the set of samples within it.", "items": {"$ref": "#/$defs/Biosample"}, "type": "array"}, "collecting_biosamples_from_site_set": {"items": {"$ref": "#/$defs/CollectingBiosamplesFromSite"}, "type": "array"}, "data_object_set": {"description": "This property links a database object to the set of data objects within it.", "items": {"$ref": "#/$defs/DataObject"}, "type": "array"}, "dissolving_activity_set": {"items": {"$ref": "#/$defs/DissolvingActivity"}, "type": "array"}, "field_research_site_set": {"items": {"$ref": "#/$defs/FieldResearchSite"}, "type": "array"}, "functional_annotation_set": {"description": "This property links a database object to the set of all functional annotations", "items": {"$ref": "#/$defs/FunctionalAnnotation"}, "type": "array"}, "genome_feature_set": {"description": "This property links a database object to the set of all features", "items": {"$ref": "#/$defs/GenomeFeature"}, "type": "array"}, "mags_activity_set": {"description": "This property links a database object to the set of MAGs analysis activities.", "items": {"$ref": "#/$defs/MagsAnalysisActivity"}, "type": "array"}, "material_sample_set": {"items": {"$ref": "#/$defs/MaterialSample"}, "type": "array"}, "material_sampling_activity_set": {"items": {"$ref": "#/$defs/MaterialSamplingActivity"}, "type": "array"}, "metabolomics_analysis_activity_set": {"description": "This property links a database object to the set of metabolomics analysis activities.", "items": {"$ref": "#/$defs/MetabolomicsAnalysisActivity"}, "type": "array"}, "metagenome_annotation_activity_set": {"description": "This property links a database object to the set of metagenome annotation activities.", "items": {"$ref": "#/$defs/MetagenomeAnnotationActivity"}, "type": "array"}, "metagenome_assembly_set": {"description": "This property links a database object to the set of metagenome assembly activities.", "items": {"$ref": "#/$defs/MetagenomeAssembly"}, "type": "array"}, "metaproteomics_analysis_activity_set": {"description": "This property links a database object to the set of metaproteomics analysis activities.", "items": {"$ref": "#/$defs/MetaproteomicsAnalysisActivity"}, "type": "array"}, "metatranscriptome_activity_set": {"description": "TODO", "items": {"$ref": "#/$defs/MetatranscriptomeActivity"}, "type": "array"}, "nom_analysis_activity_set": {"description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", "items": {"$ref": "#/$defs/NomAnalysisActivity"}, "type": "array"}, "omics_processing_set": {"description": "This property links a database object to the set of omics processings within it.", "items": {"$ref": "#/$defs/OmicsProcessing"}, "type": "array"}, "reaction_activity_set": {"items": {"$ref": "#/$defs/ReactionActivity"}, "type": "array"}, "read_based_taxonomy_analysis_activity_set": {"description": "This property links a database object to the set of read based analysis activities.", "items": {"$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity"}, "type": "array"}, "read_qc_analysis_activity_set": {"description": "This property links a database object to the set of read QC analysis activities.", "items": {"$ref": "#/$defs/ReadQcAnalysisActivity"}, "type": "array"}, "study_set": {"description": "This property links a database object to the set of studies within it.", "items": {"$ref": "#/$defs/Study"}, "type": "array"}}, "title": "NMDC", "type": "object", "version": "7.0.0"} +{ + "$defs": { + "Activity": { + "additionalProperties": false, + "description": "a provence-generating activity", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):act-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "$ref": "#/$defs/Agent" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "Activity", + "type": "object" + }, + "Agent": { + "additionalProperties": false, + "description": "a provence-generating agent", + "properties": { + "acted_on_behalf_of": { + "$ref": "#/$defs/Agent" + }, + "was_informed_by": { + "type": "string" + } + }, + "title": "Agent", + "type": "object" + }, + "AnalysisTypeEnum": { + "description": "", + "enum": [ + "metabolomics", + "metagenomics", + "metaproteomics", + "metatranscriptomics", + "natural organic matter" + ], + "title": "AnalysisTypeEnum", + "type": "string" + }, + "AnalyticalSample": { + "additionalProperties": false, + "description": "", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):ansm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "AnalyticalSample", + "type": "object" + }, + "ArchStrucEnum": { + "description": "", + "enum": [ + "building", + "shed", + "home" + ], + "title": "ArchStrucEnum", + "type": "string" + }, + "AttributeValue": { + "additionalProperties": false, + "description": "The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value", + "properties": { + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "AttributeValue", + "type": "object" + }, + "BiolStatEnum": { + "description": "", + "enum": [ + "wild", + "natural", + "semi-natural", + "inbred line", + "breeder's line", + "hybrid", + "clonal selection", + "mutant" + ], + "title": "BiolStatEnum", + "type": "string" + }, + "Biosample": { + "additionalProperties": false, + "description": "Biological source material which can be characterized by an experiment.", + "properties": { + "add_date": { + "description": "The date on which the information was added to the database.", + "type": "string" + }, + "agrochem_addition": { + "$ref": "#/$defs/QuantityValue", + "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications" + }, + "air_temp_regm": { + "$ref": "#/$defs/QuantityValue", + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens" + }, + "al_sat": { + "$ref": "#/$defs/QuantityValue", + "description": "Aluminum saturation (esp. For tropical soils)" + }, + "al_sat_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in determining Al saturation" + }, + "alkalinity": { + "$ref": "#/$defs/QuantityValue", + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate" + }, + "alkalinity_method": { + "$ref": "#/$defs/TextValue", + "description": "Method used for alkalinity measurement" + }, + "alkyl_diethers": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of alkyl diethers" + }, + "alt": { + "$ref": "#/$defs/QuantityValue", + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air" + }, + "alternative_identifiers": { + "description": "Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC", + "items": { + "type": "string" + }, + "type": "array" + }, + "aminopept_act": { + "$ref": "#/$defs/QuantityValue", + "description": "Measurement of aminopeptidase activity" + }, + "ammonium": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of ammonium in the sample" + }, + "ammonium_nitrogen": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of ammonium nitrogen in the sample" + }, + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "annual_precpt": { + "$ref": "#/$defs/QuantityValue", + "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps." + }, + "annual_temp": { + "$ref": "#/$defs/QuantityValue", + "description": "Mean annual temperature" + }, + "bacteria_carb_prod": { + "$ref": "#/$defs/QuantityValue", + "description": "Measurement of bacterial carbon production" + }, + "biosample_categories": { + "items": { + "$ref": "#/$defs/BiosampleCategoryEnum" + }, + "type": "array" + }, + "biotic_regm": { + "$ref": "#/$defs/TextValue", + "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi." + }, + "biotic_relationship": { + "$ref": "#/$defs/TextValue", + "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object" + }, + "bishomohopanol": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of bishomohopanol" + }, + "bromide": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of bromide" + }, + "calcium": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of calcium in the sample" + }, + "carb_nitro_ratio": { + "$ref": "#/$defs/QuantityValue", + "description": "Ratio of amount or concentrations of carbon to nitrogen" + }, + "chem_administration": { + "$ref": "#/$defs/ControlledTermValue", + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi" + }, + "chloride": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of chloride in the sample" + }, + "chlorophyll": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of chlorophyll" + }, + "climate_environment": { + "$ref": "#/$defs/TextValue", + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates" + }, + "collected_from": { + "description": "The Site from which a Biosample was collected", + "type": "string" + }, + "collection_date": { + "$ref": "#/$defs/TimestampValue", + "description": "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant" + }, + "collection_date_inc": { + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "type": "string" + }, + "collection_time": { + "description": "The time of sampling, either as an instance (single point) or interval.", + "type": "string" + }, + "collection_time_inc": { + "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "type": "string" + }, + "community": { + "type": "string" + }, + "crop_rotation": { + "$ref": "#/$defs/TextValue", + "description": "Whether or not crop is rotated, and if yes, rotation schedule" + }, + "cur_land_use": { + "$ref": "#/$defs/TextValue", + "description": "Present state of sample site" + }, + "cur_vegetation": { + "$ref": "#/$defs/TextValue", + "description": "Vegetation classification from one or more standard classification systems, or agricultural crop" + }, + "cur_vegetation_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in vegetation classification" + }, + "density": { + "$ref": "#/$defs/QuantityValue", + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)" + }, + "depth": { + "$ref": "#/$defs/QuantityValue", + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples." + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "diss_carb_dioxide": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample" + }, + "diss_hydrogen": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of dissolved hydrogen" + }, + "diss_inorg_carb": { + "$ref": "#/$defs/QuantityValue", + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter" + }, + "diss_inorg_phosp": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of dissolved inorganic phosphorus in the sample" + }, + "diss_org_carb": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid" + }, + "diss_org_nitro": { + "$ref": "#/$defs/QuantityValue", + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2" + }, + "diss_oxygen": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of dissolved oxygen" + }, + "dna_absorb1": { + "description": "260/280 measurement of DNA sample purity", + "type": "string" + }, + "dna_absorb2": { + "description": "260/230 measurement of DNA sample purity", + "type": "string" + }, + "dna_collect_site": { + "description": "Provide information on the site your DNA sample was collected from", + "type": "string" + }, + "dna_concentration": { + "maximum": 2000, + "minimum": 0, + "type": "string" + }, + "dna_cont_type": { + "$ref": "#/$defs/DnaContTypeEnum", + "description": "Tube or plate (96-well)" + }, + "dna_cont_well": { + "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$", + "type": "string" + }, + "dna_container_id": { + "type": "string" + }, + "dna_dnase": { + "$ref": "#/$defs/DnaDnaseEnum" + }, + "dna_isolate_meth": { + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "type": "string" + }, + "dna_organisms": { + "description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", + "type": "string" + }, + "dna_project_contact": { + "type": "string" + }, + "dna_samp_id": { + "type": "string" + }, + "dna_sample_format": { + "$ref": "#/$defs/DnaSampleFormatEnum", + "description": "Solution in which the DNA sample has been suspended" + }, + "dna_sample_name": { + "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "type": "string" + }, + "dna_seq_project": { + "type": "string" + }, + "dna_seq_project_name": { + "type": "string" + }, + "dna_seq_project_pi": { + "type": "string" + }, + "dna_volume": { + "maximum": 1000, + "minimum": 0, + "type": "string" + }, + "dnase_rna": { + "$ref": "#/$defs/DnaseRnaEnum" + }, + "drainage_class": { + "$ref": "#/$defs/TextValue", + "description": "Drainage classification from a standard system such as the USDA system" + }, + "ecosystem": { + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "type": "string" + }, + "ecosystem_category": { + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "type": "string" + }, + "ecosystem_subtype": { + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "type": "string" + }, + "ecosystem_type": { + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "type": "string" + }, + "elev": { + "$ref": "#/$defs/QuantityValue", + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit." + }, + "emsl_biosample_identifiers": { + "description": "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.", + "items": { + "type": "string" + }, + "type": "array" + }, + "env_broad_scale": { + "$ref": "#/$defs/ControlledIdentifiedTermValue", + "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS" + }, + "env_local_scale": { + "$ref": "#/$defs/ControlledIdentifiedTermValue", + "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS." + }, + "env_medium": { + "$ref": "#/$defs/ControlledIdentifiedTermValue", + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top)." + }, + "env_package": { + "$ref": "#/$defs/TextValue", + "description": "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported", + "pattern": "[air|built environment|host\\-associated|human\\-associated|human\\-skin|human\\-oral|human\\-gut|human\\-vaginal|hydrocarbon resources\\-cores|hydrocarbon resources\\-fluids\\/swabs|microbial mat\\/biofilm|misc environment|plant\\-associated|sediment|soil|wastewater\\/sludge|water]" + }, + "experimental_factor": { + "$ref": "#/$defs/ControlledTermValue", + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI" + }, + "experimental_factor_other": { + "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", + "type": "string" + }, + "extreme_event": { + "description": "Unusual physical events that may have affected microbial populations", + "type": "string" + }, + "fao_class": { + "$ref": "#/$defs/TextValue", + "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups" + }, + "filter_method": { + "description": "Type of filter used or how the sample was filtered", + "type": "string" + }, + "fire": { + "$ref": "#/$defs/TimestampValue", + "description": "Historical and/or physical evidence of fire" + }, + "flooding": { + "$ref": "#/$defs/TimestampValue", + "description": "Historical and/or physical evidence of flooding" + }, + "gaseous_environment": { + "$ref": "#/$defs/QuantityValue", + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens" + }, + "geo_loc_name": { + "$ref": "#/$defs/TextValue", + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)" + }, + "glucosidase_act": { + "$ref": "#/$defs/QuantityValue", + "description": "Measurement of glucosidase activity" + }, + "gold_biosample_identifiers": { + "description": "Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample", + "items": { + "type": "string" + }, + "pattern": "^GOLD:Gb[0-9]+$", + "type": "array" + }, + "growth_facil": { + "$ref": "#/$defs/ControlledTermValue", + "description": "Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research" + }, + "habitat": { + "type": "string" + }, + "heavy_metals": { + "$ref": "#/$defs/QuantityValue", + "description": "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field." + }, + "heavy_metals_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in determining heavy metals" + }, + "host_name": { + "type": "string" + }, + "humidity_regm": { + "$ref": "#/$defs/QuantityValue", + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens" + }, + "id": { + "description": "An NMDC assigned unique identifier for a biosample submitted to NMDC.", + "pattern": "^(nmdc):bsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "igsn_biosample_identifiers": { + "description": "A list of identifiers for the biosample from the IGSN database.", + "items": { + "type": "string" + }, + "type": "array" + }, + "img_identifiers": { + "description": "A list of identifiers that relate the biosample to records in the IMG database.", + "items": { + "type": "string" + }, + "type": "array" + }, + "insdc_biosample_identifiers": { + "description": "identifiers for corresponding sample in INSDC", + "items": { + "type": "string" + }, + "pattern": "^biosample:SAM[NED]([A-Z])?[0-9]+$", + "type": "array" + }, + "isotope_exposure": { + "description": "List isotope exposure or addition applied to your sample.", + "type": "string" + }, + "lat_lon": { + "$ref": "#/$defs/GeolocationValue", + "description": "This is currently a required field but it's not clear if this should be required for human hosts" + }, + "lbc_thirty": { + "$ref": "#/$defs/QuantityValue", + "description": "lime buffer capacity, determined after 30 minute incubation" + }, + "lbceq": { + "$ref": "#/$defs/QuantityValue", + "description": "lime buffer capacity, determined at equilibrium after 5 day incubation" + }, + "light_regm": { + "$ref": "#/$defs/QuantityValue", + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality." + }, + "link_addit_analys": { + "$ref": "#/$defs/TextValue", + "description": "Link to additional analysis results performed on the sample" + }, + "link_class_info": { + "$ref": "#/$defs/TextValue", + "description": "Link to digitized soil maps or other soil classification information" + }, + "link_climate_info": { + "$ref": "#/$defs/TextValue", + "description": "Link to climate resource" + }, + "local_class": { + "$ref": "#/$defs/TextValue", + "description": "Soil classification based on local soil classification system" + }, + "local_class_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in determining the local soil classification" + }, + "location": { + "type": "string" + }, + "magnesium": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of magnesium in the sample" + }, + "manganese": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of manganese in the sample" + }, + "mean_frict_vel": { + "$ref": "#/$defs/QuantityValue", + "description": "Measurement of mean friction velocity" + }, + "mean_peak_frict_vel": { + "$ref": "#/$defs/QuantityValue", + "description": "Measurement of mean peak friction velocity" + }, + "micro_biomass_c_meth": { + "description": "Reference or method used in determining microbial biomass", + "type": "string" + }, + "micro_biomass_n_meth": { + "description": "Reference or method used in determining microbial biomass nitrogen", + "type": "string" + }, + "microbial_biomass_c": { + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "type": "string" + }, + "microbial_biomass_n": { + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "type": "string" + }, + "misc_param": { + "$ref": "#/$defs/QuantityValue", + "description": "Any other measurement performed or parameter collected, that is not listed here" + }, + "mod_date": { + "description": "The last date on which the database information was modified.", + "type": "string" + }, + "n_alkanes": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of n-alkanes; can include multiple n-alkanes" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "ncbi_taxonomy_name": { + "type": "string" + }, + "nitrate": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of nitrate in the sample" + }, + "nitrate_nitrogen": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of nitrate nitrogen in the sample" + }, + "nitrite": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of nitrite in the sample" + }, + "nitrite_nitrogen": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of nitrite nitrogen in the sample" + }, + "non_microb_biomass": { + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", + "type": "string" + }, + "non_microb_biomass_method": { + "description": "Reference or method used in determining biomass", + "type": "string" + }, + "org_matter": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of organic matter" + }, + "org_nitro": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of organic nitrogen" + }, + "org_nitro_method": { + "description": "Method used for obtaining organic nitrogen", + "type": "string" + }, + "organism_count": { + "$ref": "#/$defs/QuantityValue", + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)" + }, + "other_treatment": { + "description": "Other treatments applied to your samples that are not applicable to the provided fields", + "type": "string" + }, + "oxy_stat_samp": { + "$ref": "#/$defs/TextValue", + "description": "Oxygenation status of sample" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "part_org_carb": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of particulate organic carbon" + }, + "perturbation": { + "$ref": "#/$defs/TextValue", + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types" + }, + "petroleum_hydrocarb": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of petroleum hydrocarbon" + }, + "ph": { + "$ref": "#/$defs/QuantityValue", + "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid" + }, + "ph_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in determining ph" + }, + "phaeopigments": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of phaeopigments; can include multiple phaeopigments" + }, + "phosphate": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of phosphate" + }, + "phosplipid_fatt_acid": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of phospholipid fatty acids; can include multiple values" + }, + "pool_dna_extracts": { + "$ref": "#/$defs/TextValue", + "description": "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given" + }, + "potassium": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of potassium in the sample" + }, + "pressure": { + "$ref": "#/$defs/QuantityValue", + "description": "Pressure to which the sample is subject to, in atmospheres" + }, + "profile_position": { + "$ref": "#/$defs/TextValue", + "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas" + }, + "project_id": { + "description": "Proposal IDs or names associated with dataset", + "type": "string" + }, + "proport_woa_temperature": { + "type": "string" + }, + "proposal_dna": { + "type": "string" + }, + "proposal_rna": { + "type": "string" + }, + "redox_potential": { + "$ref": "#/$defs/QuantityValue", + "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential" + }, + "rel_to_oxygen": { + "$ref": "#/$defs/TextValue", + "description": "Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments" + }, + "replicate_number": { + "description": "If sending biological replicates, indicate the rep number here.", + "type": "string" + }, + "rna_absorb1": { + "description": "260/280 measurement of RNA sample purity", + "type": "string" + }, + "rna_absorb2": { + "description": "260/230 measurement of RNA sample purity", + "type": "string" + }, + "rna_collect_site": { + "description": "Provide information on the site your RNA sample was collected from", + "type": "string" + }, + "rna_concentration": { + "maximum": 1000, + "minimum": 0, + "type": "string" + }, + "rna_cont_type": { + "$ref": "#/$defs/RnaContTypeEnum", + "description": "Tube or plate (96-well)" + }, + "rna_cont_well": { + "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$", + "type": "string" + }, + "rna_container_id": { + "type": "string" + }, + "rna_isolate_meth": { + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "type": "string" + }, + "rna_organisms": { + "description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", + "type": "string" + }, + "rna_project_contact": { + "type": "string" + }, + "rna_samp_id": { + "type": "string" + }, + "rna_sample_format": { + "$ref": "#/$defs/RnaSampleFormatEnum", + "description": "Solution in which the RNA sample has been suspended" + }, + "rna_sample_name": { + "description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "maximum": 2000, + "minimum": 0, + "type": "string" + }, + "rna_seq_project": { + "type": "string" + }, + "rna_seq_project_name": { + "type": "string" + }, + "rna_seq_project_pi": { + "type": "string" + }, + "rna_volume": { + "type": "string" + }, + "salinity": { + "$ref": "#/$defs/QuantityValue", + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater." + }, + "salinity_category": { + "description": "Categorcial description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline", + "type": "string" + }, + "salinity_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in determining salinity" + }, + "samp_collec_method": { + "description": "The method employed for collecting the sample.", + "type": "string" + }, + "samp_mat_process": { + "$ref": "#/$defs/ControlledTermValue", + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed." + }, + "samp_name": { + "description": "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.", + "type": "string" + }, + "samp_size": { + "$ref": "#/$defs/QuantityValue", + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected." + }, + "samp_store_dur": { + "$ref": "#/$defs/TextValue", + "description": "Duration for which the sample was stored" + }, + "samp_store_loc": { + "$ref": "#/$defs/TextValue", + "description": "Location at which sample was stored, usually name of a specific freezer/room" + }, + "samp_store_temp": { + "$ref": "#/$defs/QuantityValue", + "description": "Temperature at which sample was stored, e.g. -80 degree Celsius" + }, + "samp_vol_we_dna_ext": { + "$ref": "#/$defs/QuantityValue", + "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)." + }, + "sample_collection_site": { + "type": "string" + }, + "sample_link": { + "description": "JsonObj()", + "items": { + "type": "string" + }, + "type": "array" + }, + "sample_shipped": { + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL", + "type": "string" + }, + "sample_type": { + "$ref": "#/$defs/SampleTypeEnum", + "description": "Type of sample being submitted" + }, + "season_precpt": { + "$ref": "#/$defs/QuantityValue", + "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps." + }, + "season_temp": { + "$ref": "#/$defs/QuantityValue", + "description": "Mean seasonal temperature" + }, + "sieving": { + "$ref": "#/$defs/QuantityValue", + "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved" + }, + "size_frac_low": { + "$ref": "#/$defs/QuantityValue", + "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample" + }, + "size_frac_up": { + "$ref": "#/$defs/QuantityValue", + "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample" + }, + "slope_aspect": { + "$ref": "#/$defs/QuantityValue", + "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration." + }, + "slope_gradient": { + "$ref": "#/$defs/QuantityValue", + "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer" + }, + "sodium": { + "$ref": "#/$defs/QuantityValue", + "description": "Sodium concentration in the sample" + }, + "soil_type": { + "$ref": "#/$defs/TextValue", + "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes." + }, + "soil_type_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in determining soil series name or other lower-level classification" + }, + "soluble_iron_micromol": { + "type": "string" + }, + "source_mat_id": { + "$ref": "#/$defs/TextValue", + "description": "A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2)." + }, + "specific_ecosystem": { + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "type": "string" + }, + "start_date_inc": { + "description": "Date the incubation was started. Only relevant for incubation samples.", + "type": "string" + }, + "start_time_inc": { + "description": "Time the incubation was started. Only relevant for incubation samples.", + "type": "string" + }, + "store_cond": { + "$ref": "#/$defs/TextValue", + "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)." + }, + "subsurface_depth": { + "$ref": "#/$defs/QuantityValue" + }, + "sulfate": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of sulfate in the sample" + }, + "sulfide": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of sulfide in the sample" + }, + "technical_reps": { + "description": "If sending multiple technical replicates of the same sample, indicate how many replicates are being sent", + "type": "string" + }, + "temp": { + "$ref": "#/$defs/QuantityValue", + "description": "Temperature of the sample at the time of sampling." + }, + "tidal_stage": { + "$ref": "#/$defs/TextValue", + "description": "Stage of tide" + }, + "tillage": { + "$ref": "#/$defs/TextValue", + "description": "Note method(s) used for tilling" + }, + "tot_carb": { + "$ref": "#/$defs/QuantityValue", + "description": "Total carbon content" + }, + "tot_depth_water_col": { + "$ref": "#/$defs/QuantityValue", + "description": "Measurement of total depth of water column" + }, + "tot_diss_nitro": { + "$ref": "#/$defs/QuantityValue", + "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen" + }, + "tot_nitro_cont_meth": { + "description": "Reference or method used in determining the total nitrogen", + "type": "string" + }, + "tot_nitro_content": { + "$ref": "#/$defs/QuantityValue", + "description": "Total nitrogen content of the sample" + }, + "tot_org_c_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in determining total organic carbon" + }, + "tot_org_carb": { + "$ref": "#/$defs/QuantityValue", + "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content" + }, + "tot_phosp": { + "$ref": "#/$defs/QuantityValue", + "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "water_cont_soil_meth": { + "description": "Reference or method used in determining the water content of soil", + "type": "string" + }, + "water_content": { + "$ref": "#/$defs/QuantityValue", + "description": "Water content measurement" + }, + "watering_regm": { + "$ref": "#/$defs/QuantityValue", + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens" + }, + "zinc": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of zinc in the sample" + } + }, + "required": [ + "part_of", + "id", + "env_broad_scale", + "env_local_scale", + "env_medium" + ], + "title": "Biosample", + "type": "object" + }, + "BiosampleCategoryEnum": { + "description": "Funding-based, sample location-based, or experimental method-based defined categories", + "enum": [ + "LTER", + "SIP", + "SFA", + "FICUS", + "NEON" + ], + "title": "BiosampleCategoryEnum", + "type": "string" + }, + "BiosampleProcessing": { + "additionalProperties": false, + "description": "A process that takes one or more biosamples as inputs and generates one or as outputs. Examples of outputs include samples cultivated from another sample or data objects created by instruments runs.", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):bsmprc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "BiosampleProcessing", + "type": "object" + }, + "BioticRelationshipEnum": { + "description": "", + "enum": [ + "free living", + "parasite", + "commensal", + "symbiont" + ], + "title": "BioticRelationshipEnum", + "type": "string" + }, + "BooleanValue": { + "additionalProperties": false, + "description": "A value that is a boolean", + "properties": { + "has_boolean_value": { + "description": "Links a quantity value to a boolean", + "type": "boolean" + }, + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "BooleanValue", + "type": "object" + }, + "BuildDocsEnum": { + "description": "", + "enum": [ + "building information model", + "commissioning report", + "complaint logs", + "contract administration", + "cost estimate", + "janitorial schedules or logs", + "maintenance plans", + "schedule", + "sections", + "shop drawings", + "submittals", + "ventilation system", + "windows" + ], + "title": "BuildDocsEnum", + "type": "string" + }, + "BuildOccupTypeEnum": { + "description": "", + "enum": [ + "office", + "market", + "restaurant", + "residence", + "school", + "residential", + "commercial", + "low rise", + "high rise", + "wood framed", + "health care", + "airport", + "sports complex" + ], + "title": "BuildOccupTypeEnum", + "type": "string" + }, + "BuildingSettingEnum": { + "description": "", + "enum": [ + "urban", + "suburban", + "exurban", + "rural" + ], + "title": "BuildingSettingEnum", + "type": "string" + }, + "CeilCondEnum": { + "description": "", + "enum": [ + "new", + "visible wear", + "needs repair", + "damaged", + "rupture" + ], + "title": "CeilCondEnum", + "type": "string" + }, + "CeilFinishMatEnum": { + "description": "", + "enum": [ + "drywall", + "mineral fibre", + "tiles", + "PVC", + "plasterboard", + "metal", + "fiberglass", + "stucco", + "mineral wool/calcium silicate", + "wood" + ], + "title": "CeilFinishMatEnum", + "type": "string" + }, + "CeilTextureEnum": { + "description": "", + "enum": [ + "crows feet", + "crows-foot stomp", + "double skip", + "hawk and trowel", + "knockdown", + "popcorn", + "orange peel", + "rosebud stomp", + "Santa-Fe texture", + "skip trowel", + "smooth", + "stomp knockdown", + "swirl" + ], + "title": "CeilTextureEnum", + "type": "string" + }, + "CeilTypeEnum": { + "description": "", + "enum": [ + "cathedral", + "dropped", + "concave", + "barrel-shaped", + "coffered", + "cove", + "stretched" + ], + "title": "CeilTypeEnum", + "type": "string" + }, + "ChemicalEntity": { + "additionalProperties": false, + "description": "An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "ChemicalEntity", + "type": "object" + }, + "CollectingBiosamplesFromSite": { + "additionalProperties": false, + "description": "", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "has_inputs": { + "items": { + "type": "string" + }, + "type": "array" + }, + "has_outputs": { + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):clsite-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "participating_agent": { + "$ref": "#/$defs/Agent" + } + }, + "required": [ + "has_inputs", + "has_outputs", + "id" + ], + "title": "CollectingBiosamplesFromSite", + "type": "object" + }, + "ContainerTypeEnum": { + "description": "", + "enum": [ + "screw_top_conical" + ], + "title": "ContainerTypeEnum", + "type": "string" + }, + "ControlledIdentifiedTermValue": { + "additionalProperties": false, + "description": "A controlled term or class from an ontology, requiring the presence of term with an id", + "properties": { + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "term": { + "$ref": "#/$defs/OntologyClass", + "description": "pointer to an ontology class" + }, + "was_generated_by": { + "type": "string" + } + }, + "required": [ + "term" + ], + "title": "ControlledIdentifiedTermValue", + "type": "object" + }, + "ControlledTermValue": { + "additionalProperties": false, + "description": "A controlled term or class from an ontology", + "properties": { + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "term": { + "$ref": "#/$defs/OntologyClass", + "description": "pointer to an ontology class" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "ControlledTermValue", + "type": "object" + }, + "CreditAssociation": { + "additionalProperties": false, + "description": "This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0", + "properties": { + "applied_role": { + "$ref": "#/$defs/CreditEnum" + }, + "applied_roles": { + "items": { + "$ref": "#/$defs/CreditEnum" + }, + "type": "array" + }, + "applies_to_person": { + "$ref": "#/$defs/PersonValue" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + } + }, + "required": [ + "applies_to_person", + "applied_roles" + ], + "title": "CreditAssociation", + "type": "object" + }, + "CreditEnum": { + "description": "", + "enum": [ + "Conceptualization", + "Data curation", + "Formal Analysis", + "Funding acquisition", + "Investigation", + "Methodology", + "Project administration", + "Resources", + "Software", + "Supervision", + "Validation", + "Visualization", + "Writing original draft", + "Writing review and editing", + "Principal Investigator", + "Submitter" + ], + "title": "CreditEnum", + "type": "string" + }, + "CurLandUseEnum": { + "description": "", + "enum": [ + "cities", + "farmstead", + "industrial areas", + "roads/railroads", + "rock", + "sand", + "gravel", + "mudflats", + "salt flats", + "badlands", + "permanent snow or ice", + "saline seeps", + "mines/quarries", + "oil waste areas", + "small grains", + "row crops", + "vegetable crops", + "horticultural plants (e.g. tulips)", + "marshlands (grass,sedges,rushes)", + "tundra (mosses,lichens)", + "rangeland", + "pastureland (grasslands used for livestock grazing)", + "hayland", + "meadows (grasses,alfalfa,fescue,bromegrass,timothy)", + "shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)", + "successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)", + "shrub crops (blueberries,nursery ornamentals,filberts)", + "vine crops (grapes)", + "conifers (e.g. pine,spruce,fir,cypress)", + "hardwoods (e.g. oak,hickory,elm,aspen)", + "intermixed hardwood and conifers", + "tropical (e.g. mangrove,palms)", + "rainforest (evergreen forest receiving greater than 406 cm annual rainfall)", + "swamp (permanent or semi-permanent water body dominated by woody plants)", + "crop trees (nuts,fruit,christmas trees,nursery trees)" + ], + "title": "CurLandUseEnum", + "type": "string" + }, + "DataObject": { + "additionalProperties": false, + "description": "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "compression_type": { + "description": "If provided, specifies the compression type", + "type": "string" + }, + "data_object_type": { + "$ref": "#/$defs/FileTypeEnum", + "description": "The type of file represented by the data object." + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "file_size_bytes": { + "description": "Size of the file in bytes", + "type": "integer" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "md5_checksum": { + "description": "MD5 checksum of file (pre-compressed)", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "url": { + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "required": [ + "name", + "description" + ], + "title": "DataObject", + "type": "object" + }, + "Database": { + "additionalProperties": false, + "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest", + "properties": { + "activity_set": { + "description": "This property links a database object to the set of workflow activities.", + "items": { + "$ref": "#/$defs/WorkflowExecutionActivity" + }, + "type": "array" + }, + "biosample_set": { + "description": "This property links a database object to the set of samples within it.", + "items": { + "$ref": "#/$defs/Biosample" + }, + "type": "array" + }, + "collecting_biosamples_from_site_set": { + "items": { + "$ref": "#/$defs/CollectingBiosamplesFromSite" + }, + "type": "array" + }, + "data_object_set": { + "description": "This property links a database object to the set of data objects within it.", + "items": { + "$ref": "#/$defs/DataObject" + }, + "type": "array" + }, + "dissolving_activity_set": { + "items": { + "$ref": "#/$defs/DissolvingActivity" + }, + "type": "array" + }, + "field_research_site_set": { + "items": { + "$ref": "#/$defs/FieldResearchSite" + }, + "type": "array" + }, + "functional_annotation_set": { + "description": "This property links a database object to the set of all functional annotations", + "items": { + "$ref": "#/$defs/FunctionalAnnotation" + }, + "type": "array" + }, + "genome_feature_set": { + "description": "This property links a database object to the set of all features", + "items": { + "$ref": "#/$defs/GenomeFeature" + }, + "type": "array" + }, + "mags_activity_set": { + "description": "This property links a database object to the set of MAGs analysis activities.", + "items": { + "$ref": "#/$defs/MagsAnalysisActivity" + }, + "type": "array" + }, + "material_sample_set": { + "items": { + "$ref": "#/$defs/MaterialSample" + }, + "type": "array" + }, + "material_sampling_activity_set": { + "items": { + "$ref": "#/$defs/MaterialSamplingActivity" + }, + "type": "array" + }, + "metabolomics_analysis_activity_set": { + "description": "This property links a database object to the set of metabolomics analysis activities.", + "items": { + "$ref": "#/$defs/MetabolomicsAnalysisActivity" + }, + "type": "array" + }, + "metagenome_annotation_activity_set": { + "description": "This property links a database object to the set of metagenome annotation activities.", + "items": { + "$ref": "#/$defs/MetagenomeAnnotationActivity" + }, + "type": "array" + }, + "metagenome_assembly_set": { + "description": "This property links a database object to the set of metagenome assembly activities.", + "items": { + "$ref": "#/$defs/MetagenomeAssembly" + }, + "type": "array" + }, + "metaproteomics_analysis_activity_set": { + "description": "This property links a database object to the set of metaproteomics analysis activities.", + "items": { + "$ref": "#/$defs/MetaproteomicsAnalysisActivity" + }, + "type": "array" + }, + "metatranscriptome_activity_set": { + "description": "TODO", + "items": { + "$ref": "#/$defs/MetatranscriptomeActivity" + }, + "type": "array" + }, + "nom_analysis_activity_set": { + "description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", + "items": { + "$ref": "#/$defs/NomAnalysisActivity" + }, + "type": "array" + }, + "omics_processing_set": { + "description": "This property links a database object to the set of omics processings within it.", + "items": { + "$ref": "#/$defs/OmicsProcessing" + }, + "type": "array" + }, + "reaction_activity_set": { + "items": { + "$ref": "#/$defs/ReactionActivity" + }, + "type": "array" + }, + "read_based_taxonomy_analysis_activity_set": { + "description": "This property links a database object to the set of read based analysis activities.", + "items": { + "$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity" + }, + "type": "array" + }, + "read_qc_analysis_activity_set": { + "description": "This property links a database object to the set of read QC analysis activities.", + "items": { + "$ref": "#/$defs/ReadQcAnalysisActivity" + }, + "type": "array" + }, + "study_set": { + "description": "This property links a database object to the set of studies within it.", + "items": { + "$ref": "#/$defs/Study" + }, + "type": "array" + } + }, + "title": "Database", + "type": "object" + }, + "DeposEnvEnum": { + "description": "", + "enum": [ + "Continental - Alluvial", + "Continental - Aeolian", + "Continental - Fluvial", + "Continental - Lacustrine", + "Transitional - Deltaic", + "Transitional - Tidal", + "Transitional - Lagoonal", + "Transitional - Beach", + "Transitional - Lake", + "Marine - Shallow", + "Marine - Deep", + "Marine - Reef", + "Other - Evaporite", + "Other - Glacial", + "Other - Volcanic", + "other" + ], + "title": "DeposEnvEnum", + "type": "string" + }, + "DeviceTypeEnum": { + "description": "", + "enum": [ + "orbital_shaker", + "thermomixer" + ], + "title": "DeviceTypeEnum", + "type": "string" + }, + "DissolvingActivity": { + "additionalProperties": false, + "description": "", + "properties": { + "dissolution_aided_by": { + "$ref": "#/$defs/LabDevice" + }, + "dissolution_reagent": { + "$ref": "#/$defs/SolventEnum" + }, + "dissolution_volume": { + "$ref": "#/$defs/QuantityValue" + }, + "dissolved_in": { + "$ref": "#/$defs/MaterialContainer" + }, + "material_input": { + "type": "string" + }, + "material_output": { + "type": "string" + } + }, + "title": "DissolvingActivity", + "type": "object" + }, + "DnaContTypeEnum": { + "description": "", + "enum": [ + "plate", + "tube" + ], + "title": "DnaContTypeEnum", + "type": "string" + }, + "DnaDnaseEnum": { + "description": "", + "enum": [ + "no", + "yes" + ], + "title": "DnaDnaseEnum", + "type": "string" + }, + "DnaSampleFormatEnum": { + "description": "", + "enum": [ + "10 mM Tris-HCl", + "DNAStable", + "Ethanol", + "Low EDTA TE", + "MDA reaction buffer", + "PBS", + "Pellet", + "RNAStable", + "TE", + "Water", + "Gentegra-DNA", + "Gentegra-RNA" + ], + "title": "DnaSampleFormatEnum", + "type": "string" + }, + "DnaseRnaEnum": { + "description": "", + "enum": [ + "no", + "yes" + ], + "title": "DnaseRnaEnum", + "type": "string" + }, + "DoorCompTypeEnum": { + "description": "", + "enum": [ + "metal covered", + "revolving", + "sliding", + "telescopic" + ], + "title": "DoorCompTypeEnum", + "type": "string" + }, + "DoorCondEnum": { + "description": "", + "enum": [ + "damaged", + "needs repair", + "new", + "rupture", + "visible wear" + ], + "title": "DoorCondEnum", + "type": "string" + }, + "DoorDirectEnum": { + "description": "", + "enum": [ + "inward", + "outward", + "sideways" + ], + "title": "DoorDirectEnum", + "type": "string" + }, + "DoorLocEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west" + ], + "title": "DoorLocEnum", + "type": "string" + }, + "DoorMatEnum": { + "description": "", + "enum": [ + "aluminum", + "cellular PVC", + "engineered plastic", + "fiberboard", + "fiberglass", + "metal", + "thermoplastic alloy", + "vinyl", + "wood", + "wood/plastic composite" + ], + "title": "DoorMatEnum", + "type": "string" + }, + "DoorMoveEnum": { + "description": "", + "enum": [ + "collapsible", + "folding", + "revolving", + "rolling shutter", + "sliding", + "swinging" + ], + "title": "DoorMoveEnum", + "type": "string" + }, + "DoorTypeEnum": { + "description": "", + "enum": [ + "composite", + "metal", + "wooden" + ], + "title": "DoorTypeEnum", + "type": "string" + }, + "DoorTypeMetalEnum": { + "description": "", + "enum": [ + "collapsible", + "corrugated steel", + "hollow", + "rolling shutters", + "steel plate" + ], + "title": "DoorTypeMetalEnum", + "type": "string" + }, + "DoorTypeWoodEnum": { + "description": "", + "enum": [ + "bettened and ledged", + "battened", + "ledged and braced", + "ledged and framed", + "ledged, braced and frame", + "framed and paneled", + "glashed or sash", + "flush", + "louvered", + "wire gauged" + ], + "title": "DoorTypeWoodEnum", + "type": "string" + }, + "DrainageClassEnum": { + "description": "", + "enum": [ + "very poorly", + "poorly", + "somewhat poorly", + "moderately well", + "well", + "excessively drained" + ], + "title": "DrainageClassEnum", + "type": "string" + }, + "DrawingsEnum": { + "description": "", + "enum": [ + "operation", + "as built", + "construction", + "bid", + "design", + "building navigation map", + "diagram", + "sketch" + ], + "title": "DrawingsEnum", + "type": "string" + }, + "EnvironmentalMaterialTerm": { + "additionalProperties": false, + "description": "", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "EnvironmentalMaterialTerm", + "type": "object" + }, + "ExtWallOrientEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west", + "northeast", + "southeast", + "southwest", + "northwest" + ], + "title": "ExtWallOrientEnum", + "type": "string" + }, + "ExtWindowOrientEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west", + "northeast", + "southeast", + "southwest", + "northwest" + ], + "title": "ExtWindowOrientEnum", + "type": "string" + }, + "FaoClassEnum": { + "description": "", + "enum": [ + "Acrisols", + "Andosols", + "Arenosols", + "Cambisols", + "Chernozems", + "Ferralsols", + "Fluvisols", + "Gleysols", + "Greyzems", + "Gypsisols", + "Histosols", + "Kastanozems", + "Lithosols", + "Luvisols", + "Nitosols", + "Phaeozems", + "Planosols", + "Podzols", + "Podzoluvisols", + "Rankers", + "Regosols", + "Rendzinas", + "Solonchaks", + "Solonetz", + "Vertisols", + "Yermosols" + ], + "title": "FaoClassEnum", + "type": "string" + }, + "FieldResearchSite": { + "additionalProperties": false, + "description": "A site, outside of a laboratory, from which biosamples may be collected.", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):frsite-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "FieldResearchSite", + "type": "object" + }, + "FileTypeEnum": { + "description": "", + "enum": [ + "Metagenome Raw Reads", + "FT ICR-MS Analysis Results", + "GC-MS Metabolomics Results", + "Metaproteomics Workflow Statistics", + "Protein Report", + "Peptide Report", + "Unfiltered Metaproteomics Results", + "Read Count and RPKM", + "QC non-rRNA R2", + "QC non-rRNA R1", + "Metagenome Bins", + "CheckM Statistics", + "GOTTCHA2 Krona Plot", + "GOTTCHA2 Classification Report", + "GOTTCHA2 Report Full", + "Kraken2 Krona Plot", + "Centrifuge Krona Plot", + "Centrifuge output report file", + "Kraken2 Classification Report", + "Kraken2 Taxonomic Classification", + "Centrifuge Classification Report", + "Centrifuge Taxonomic Classification", + "Structural Annotation GFF", + "Functional Annotation GFF", + "Annotation Amino Acid FASTA", + "Annotation Enzyme Commission", + "Annotation KEGG Orthology", + "Assembly Coverage BAM", + "Assembly AGP", + "Assembly Scaffolds", + "Assembly Contigs", + "Assembly Coverage Stats", + "Filtered Sequencing Reads", + "QC Statistics", + "TIGRFam Annotation GFF", + "CRT Annotation GFF", + "Genmark Annotation GFF", + "Prodigal Annotation GFF", + "TRNA Annotation GFF", + "Misc Annotation GFF", + "RFAM Annotation GFF", + "TMRNA Annotation GFF", + "KO_EC Annotation GFF", + "Product Names", + "Gene Phylogeny tsv", + "Crisprt Terms", + "Clusters of Orthologous Groups (COG) Annotation GFF", + "CATH FunFams (Functional Families) Annotation GFF", + "SUPERFam Annotation GFF", + "SMART Annotation GFF", + "Pfam Annotation GFF", + "Direct Infusion FT ICR-MS Raw Data" + ], + "title": "FileTypeEnum", + "type": "string" + }, + "FilterTypeEnum": { + "description": "", + "enum": [ + "particulate air filter", + "chemical air filter", + "low-MERV pleated media", + "HEPA", + "electrostatic", + "gas-phase or ultraviolet air treatments" + ], + "title": "FilterTypeEnum", + "type": "string" + }, + "FloorCondEnum": { + "description": "", + "enum": [ + "new", + "visible wear", + "needs repair", + "damaged", + "rupture" + ], + "title": "FloorCondEnum", + "type": "string" + }, + "FloorFinishMatEnum": { + "description": "", + "enum": [ + "tile", + "wood strip or parquet", + "carpet", + "rug", + "laminate wood", + "lineoleum", + "vinyl composition tile", + "sheet vinyl", + "stone", + "bamboo", + "cork", + "terrazo", + "concrete", + "none", + "sealed", + "clear finish", + "paint", + "none or unfinished" + ], + "title": "FloorFinishMatEnum", + "type": "string" + }, + "FloorStrucEnum": { + "description": "", + "enum": [ + "balcony", + "floating floor", + "glass floor", + "raised floor", + "sprung floor", + "wood-framed", + "concrete" + ], + "title": "FloorStrucEnum", + "type": "string" + }, + "FloorWaterMoldEnum": { + "description": "", + "enum": [ + "mold odor", + "wet floor", + "water stains", + "wall discoloration", + "floor discoloration", + "ceiling discoloration", + "peeling paint or wallpaper", + "bulging walls", + "condensation" + ], + "title": "FloorWaterMoldEnum", + "type": "string" + }, + "FreqCleanEnum": { + "description": "", + "enum": [ + "Daily", + "Weekly", + "Monthly", + "Quarterly", + "Annually", + "other" + ], + "title": "FreqCleanEnum", + "type": "string" + }, + "FunctionalAnnotation": { + "additionalProperties": false, + "description": "An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods", + "properties": { + "has_function": { + "pattern": "^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$", + "type": "string" + }, + "subject": { + "type": "string" + }, + "was_generated_by": { + "description": "provenance for the annotation.", + "type": "string" + } + }, + "title": "FunctionalAnnotation", + "type": "object" + }, + "FurnitureEnum": { + "description": "", + "enum": [ + "cabinet", + "chair", + "desks" + ], + "title": "FurnitureEnum", + "type": "string" + }, + "GenderRestroomEnum": { + "description": "", + "enum": [ + "all gender", + "female", + "gender neurtral", + "male", + "male and female", + "unisex" + ], + "title": "GenderRestroomEnum", + "type": "string" + }, + "GeneProduct": { + "additionalProperties": false, + "description": "A molecule encoded by a gene that has an evolved function", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "GeneProduct", + "type": "object" + }, + "GenomeFeature": { + "additionalProperties": false, + "description": "A feature localized to an interval along a genome", + "title": "GenomeFeature", + "type": "object" + }, + "GeolocationValue": { + "additionalProperties": false, + "description": "A normalized value for a location on the earth's surface", + "properties": { + "has_raw_value": { + "description": "The raw value for a geolocation should follow {lat} {long}", + "type": "string" + }, + "latitude": { + "description": "latitude", + "type": "number" + }, + "longitude": { + "description": "longitude", + "type": "number" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "GeolocationValue", + "type": "object" + }, + "GrowthHabitEnum": { + "description": "", + "enum": [ + "erect", + "semi-erect", + "spreading", + "prostrate" + ], + "title": "GrowthHabitEnum", + "type": "string" + }, + "HandidnessEnum": { + "description": "", + "enum": [ + "ambidexterity", + "left handedness", + "mixed-handedness", + "right handedness" + ], + "title": "HandidnessEnum", + "type": "string" + }, + "HcProducedEnum": { + "description": "", + "enum": [ + "Oil", + "Gas-Condensate", + "Gas", + "Bitumen", + "Coalbed Methane", + "other" + ], + "title": "HcProducedEnum", + "type": "string" + }, + "HcrEnum": { + "description": "", + "enum": [ + "Oil Reservoir", + "Gas Reservoir", + "Oil Sand", + "Coalbed", + "Shale", + "Tight Oil Reservoir", + "Tight Gas Reservoir", + "other" + ], + "title": "HcrEnum", + "type": "string" + }, + "HcrGeolAgeEnum": { + "description": "", + "enum": [ + "Archean", + "Cambrian", + "Carboniferous", + "Cenozoic", + "Cretaceous", + "Devonian", + "Jurassic", + "Mesozoic", + "Neogene", + "Ordovician", + "Paleogene", + "Paleozoic", + "Permian", + "Precambrian", + "Proterozoic", + "Silurian", + "Triassic", + "other" + ], + "title": "HcrGeolAgeEnum", + "type": "string" + }, + "HeatCoolTypeEnum": { + "description": "", + "enum": [ + "radiant system", + "heat pump", + "forced air system", + "steam forced heat", + "wood stove" + ], + "title": "HeatCoolTypeEnum", + "type": "string" + }, + "HeatDelivLocEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west" + ], + "title": "HeatDelivLocEnum", + "type": "string" + }, + "HorizonEnum": { + "description": "", + "enum": [ + "O horizon", + "A horizon", + "E horizon", + "B horizon", + "C horizon", + "R layer", + "Permafrost" + ], + "title": "HorizonEnum", + "type": "string" + }, + "HostSexEnum": { + "description": "", + "enum": [ + "female", + "hermaphrodite", + "male", + "neuter" + ], + "title": "HostSexEnum", + "type": "string" + }, + "ImageValue": { + "additionalProperties": false, + "description": "An attribute value representing an image.", + "properties": { + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "display_order": { + "description": "When rendering information, this attribute to specify the order in which the information should be rendered.", + "type": "string" + }, + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "url": { + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "ImageValue", + "type": "object" + }, + "IndoorSpaceEnum": { + "description": "", + "enum": [ + "bedroom", + "office", + "bathroom", + "foyer", + "kitchen", + "locker room", + "hallway", + "elevator" + ], + "title": "IndoorSpaceEnum", + "type": "string" + }, + "IndoorSurfEnum": { + "description": "", + "enum": [ + "cabinet", + "ceiling", + "counter top", + "door", + "shelving", + "vent cover", + "window", + "wall" + ], + "title": "IndoorSurfEnum", + "type": "string" + }, + "Instrument": { + "additionalProperties": false, + "description": "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI].", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):inst-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "Instrument", + "type": "object" + }, + "IntWallCondEnum": { + "description": "", + "enum": [ + "new", + "visible wear", + "needs repair", + "damaged", + "rupture" + ], + "title": "IntWallCondEnum", + "type": "string" + }, + "IntegerValue": { + "additionalProperties": false, + "description": "A value that is an integer", + "properties": { + "has_numeric_value": { + "description": "Links a quantity value to a number", + "type": "number" + }, + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "IntegerValue", + "type": "object" + }, + "LabDevice": { + "additionalProperties": false, + "description": "", + "properties": { + "activity_speed": { + "$ref": "#/$defs/QuantityValue" + }, + "activity_temperature": { + "$ref": "#/$defs/QuantityValue" + }, + "activity_time": { + "$ref": "#/$defs/QuantityValue" + }, + "device_type": { + "$ref": "#/$defs/DeviceTypeEnum" + } + }, + "title": "LabDevice", + "type": "object" + }, + "LightTypeEnum": { + "description": "", + "enum": [ + "natural light", + "electric light", + "desk lamp", + "flourescent lights", + "none" + ], + "title": "LightTypeEnum", + "type": "string" + }, + "LithologyEnum": { + "description": "", + "enum": [ + "Basement", + "Chalk", + "Chert", + "Coal", + "Conglomerate", + "Diatomite", + "Dolomite", + "Limestone", + "Sandstone", + "Shale", + "Siltstone", + "Volcanic", + "other" + ], + "title": "LithologyEnum", + "type": "string" + }, + "MagBin": { + "additionalProperties": false, + "description": "", + "properties": { + "bin_name": { + "type": "string" + }, + "bin_quality": { + "type": "string" + }, + "completeness": { + "type": "number" + }, + "contamination": { + "type": "number" + }, + "gene_count": { + "type": "integer" + }, + "gtdbtk_class": { + "type": "string" + }, + "gtdbtk_domain": { + "type": "string" + }, + "gtdbtk_family": { + "type": "string" + }, + "gtdbtk_genus": { + "type": "string" + }, + "gtdbtk_order": { + "type": "string" + }, + "gtdbtk_phylum": { + "type": "string" + }, + "gtdbtk_species": { + "type": "string" + }, + "num_16s": { + "type": "integer" + }, + "num_23s": { + "type": "integer" + }, + "num_5s": { + "type": "integer" + }, + "num_t_rna": { + "type": "integer" + }, + "number_of_contig": { + "type": "integer" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + } + }, + "title": "MagBin", + "type": "object" + }, + "MagsAnalysisActivity": { + "additionalProperties": false, + "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", + "properties": { + "binned_contig_num": { + "type": "integer" + }, + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmag-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "input_contig_num": { + "type": "integer" + }, + "low_depth_contig_num": { + "type": "integer" + }, + "mags_list": { + "items": { + "$ref": "#/$defs/MagBin" + }, + "type": "array" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "too_short_contig_num": { + "type": "integer" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "unbinned_contig_num": { + "type": "integer" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MagsAnalysisActivity", + "type": "object" + }, + "MaterialContainer": { + "additionalProperties": false, + "description": "", + "properties": { + "container_size": { + "$ref": "#/$defs/QuantityValue" + }, + "container_type": { + "$ref": "#/$defs/ContainerTypeEnum" + } + }, + "title": "MaterialContainer", + "type": "object" + }, + "MaterialSample": { + "additionalProperties": false, + "description": "", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):matsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "title": "MaterialSample", + "type": "object" + }, + "MaterialSamplingActivity": { + "additionalProperties": false, + "description": "", + "properties": { + "amount_collected": { + "$ref": "#/$defs/QuantityValue" + }, + "biosample_input": { + "type": "string" + }, + "collected_into": { + "$ref": "#/$defs/MaterialContainer" + }, + "material_output": { + "type": "string" + }, + "sampling_method": { + "$ref": "#/$defs/SamplingMethodEnum" + } + }, + "title": "MaterialSamplingActivity", + "type": "object" + }, + "MechStrucEnum": { + "description": "", + "enum": [ + "subway", + "coach", + "carriage", + "elevator", + "escalator", + "boat", + "train", + "car", + "bus" + ], + "title": "MechStrucEnum", + "type": "string" + }, + "MetaboliteQuantification": { + "additionalProperties": false, + "description": "This is used to link a metabolomics analysis workflow to a specific metabolite", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "title": "MetaboliteQuantification", + "type": "object" + }, + "MetabolomicsAnalysisActivity": { + "additionalProperties": false, + "description": "", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmb-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "description": "The instrument used to collect the data used in the analysis", + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MetabolomicsAnalysisActivity", + "type": "object" + }, + "MetagenomeAnnotationActivity": { + "additionalProperties": false, + "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "gold_analysis_project_identifiers": { + "description": "identifiers for corresponding analysis project in GOLD", + "items": { + "type": "string" + }, + "pattern": "^GOLD:Ga[0-9]+$", + "type": "array" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmgan-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MetagenomeAnnotationActivity", + "type": "object" + }, + "MetagenomeAssembly": { + "additionalProperties": false, + "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", + "properties": { + "asm_score": { + "description": "A score for comparing metagenomic assembly quality from same sample.", + "type": "number" + }, + "contig_bp": { + "description": "Total size in bp of all contigs.", + "type": "number" + }, + "contigs": { + "description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", + "type": "number" + }, + "ctg_l50": { + "description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", + "type": "number" + }, + "ctg_l90": { + "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", + "type": "number" + }, + "ctg_logsum": { + "description": "Maximum contig length.", + "type": "number" + }, + "ctg_max": { + "description": "Maximum contig length.", + "type": "number" + }, + "ctg_n50": { + "description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", + "type": "number" + }, + "ctg_n90": { + "description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", + "type": "number" + }, + "ctg_powsum": { + "description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", + "type": "number" + }, + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "gap_pct": { + "description": "The gap size percentage of all scaffolds.", + "type": "number" + }, + "gc_avg": { + "description": "Average of GC content of all contigs.", + "type": "number" + }, + "gc_std": { + "description": "Standard deviation of GC content of all contigs.", + "type": "number" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmgas-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "insdc_assembly_identifiers": { + "pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "num_aligned_reads": { + "description": "The sequence count number of input reads aligned to assembled contigs.", + "type": "number" + }, + "num_input_reads": { + "description": "The sequence count number of input reads for assembly.", + "type": "number" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "scaf_bp": { + "description": "Total size in bp of all scaffolds.", + "type": "number" + }, + "scaf_l50": { + "description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", + "type": "number" + }, + "scaf_l90": { + "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", + "type": "number" + }, + "scaf_l_gt50k": { + "description": "Total size in bp of all scaffolds greater than 50 KB.", + "type": "number" + }, + "scaf_logsum": { + "description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", + "type": "number" + }, + "scaf_max": { + "description": "Maximum scaffold length.", + "type": "number" + }, + "scaf_n50": { + "description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", + "type": "number" + }, + "scaf_n90": { + "description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", + "type": "number" + }, + "scaf_n_gt50k": { + "description": "Total sequence count of scaffolds greater than 50 KB.", + "type": "number" + }, + "scaf_pct_gt50k": { + "description": "Total sequence size percentage of scaffolds greater than 50 KB.", + "type": "number" + }, + "scaf_powsum": { + "description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", + "type": "number" + }, + "scaffolds": { + "description": "Total sequence count of all scaffolds.", + "type": "number" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MetagenomeAssembly", + "type": "object" + }, + "MetaproteomicsAnalysisActivity": { + "additionalProperties": false, + "description": "", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmp-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "description": "The instrument used to collect the data used in the analysis", + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MetaproteomicsAnalysisActivity", + "type": "object" + }, + "MetatranscriptomeActivity": { + "additionalProperties": false, + "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmt-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MetatranscriptomeActivity", + "type": "object" + }, + "MetatranscriptomeAnnotationActivity": { + "additionalProperties": false, + "description": "", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "gold_analysis_project_identifiers": { + "description": "identifiers for corresponding analysis project in GOLD", + "items": { + "type": "string" + }, + "pattern": "^GOLD:Ga[0-9]+$", + "type": "array" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmtan-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "id", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MetatranscriptomeAnnotationActivity", + "type": "object" + }, + "MetatranscriptomeAssembly": { + "additionalProperties": false, + "description": "", + "properties": { + "asm_score": { + "description": "A score for comparing metagenomic assembly quality from same sample.", + "type": "number" + }, + "contig_bp": { + "description": "Total size in bp of all contigs.", + "type": "number" + }, + "contigs": { + "description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", + "type": "number" + }, + "ctg_l50": { + "description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", + "type": "number" + }, + "ctg_l90": { + "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", + "type": "number" + }, + "ctg_logsum": { + "description": "Maximum contig length.", + "type": "number" + }, + "ctg_max": { + "description": "Maximum contig length.", + "type": "number" + }, + "ctg_n50": { + "description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", + "type": "number" + }, + "ctg_n90": { + "description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", + "type": "number" + }, + "ctg_powsum": { + "description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", + "type": "number" + }, + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "gap_pct": { + "description": "The gap size percentage of all scaffolds.", + "type": "number" + }, + "gc_avg": { + "description": "Average of GC content of all contigs.", + "type": "number" + }, + "gc_std": { + "description": "Standard deviation of GC content of all contigs.", + "type": "number" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmtas-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "insdc_assembly_identifiers": { + "pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "num_aligned_reads": { + "description": "The sequence count number of input reads aligned to assembled contigs.", + "type": "number" + }, + "num_input_reads": { + "description": "The sequence count number of input reads for assembly.", + "type": "number" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "scaf_bp": { + "description": "Total size in bp of all scaffolds.", + "type": "number" + }, + "scaf_l50": { + "description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", + "type": "number" + }, + "scaf_l90": { + "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", + "type": "number" + }, + "scaf_l_gt50k": { + "description": "Total size in bp of all scaffolds greater than 50 KB.", + "type": "number" + }, + "scaf_logsum": { + "description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", + "type": "number" + }, + "scaf_max": { + "description": "Maximum scaffold length.", + "type": "number" + }, + "scaf_n50": { + "description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", + "type": "number" + }, + "scaf_n90": { + "description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", + "type": "number" + }, + "scaf_n_gt50k": { + "description": "Total sequence count of scaffolds greater than 50 KB.", + "type": "number" + }, + "scaf_pct_gt50k": { + "description": "Total sequence size percentage of scaffolds greater than 50 KB.", + "type": "number" + }, + "scaf_powsum": { + "description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", + "type": "number" + }, + "scaffolds": { + "description": "Total sequence count of all scaffolds.", + "type": "number" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "id", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MetatranscriptomeAssembly", + "type": "object" + }, + "NomAnalysisActivity": { + "additionalProperties": false, + "description": "", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfnom-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "description": "The instrument used to collect the data used in the analysis", + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "NomAnalysisActivity", + "type": "object" + }, + "OccupDocumentEnum": { + "description": "", + "enum": [ + "automated count", + "estimate", + "manual count", + "videos" + ], + "title": "OccupDocumentEnum", + "type": "string" + }, + "OmicsProcessing": { + "additionalProperties": false, + "description": "The methods and processes used to generate omics data from a biosample or organism.", + "properties": { + "add_date": { + "description": "The date on which the information was added to the database.", + "type": "string" + }, + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "chimera_check": { + "$ref": "#/$defs/TextValue", + "description": "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences." + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "gold_sequencing_project_identifiers": { + "description": "identifiers for corresponding sequencing project in GOLD", + "items": { + "type": "string" + }, + "pattern": "^GOLD:Gp[0-9]+$", + "type": "array" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):omprc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "insdc_experiment_identifiers": { + "items": { + "type": "string" + }, + "pattern": "^insdc.sra:(E|D|S)RX[0-9]{6,}$", + "type": "array" + }, + "instrument_name": { + "description": "The name of the instrument that was used for processing the sample.", + "type": "string" + }, + "mod_date": { + "description": "The last date on which the database information was modified.", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "ncbi_project_name": { + "type": "string" + }, + "nucl_acid_amp": { + "$ref": "#/$defs/TextValue", + "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids" + }, + "nucl_acid_ext": { + "$ref": "#/$defs/TextValue", + "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample" + }, + "omics_type": { + "$ref": "#/$defs/ControlledTermValue", + "description": "The type of omics data" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "pcr_cond": { + "$ref": "#/$defs/TextValue", + "description": "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'" + }, + "pcr_primers": { + "$ref": "#/$defs/TextValue", + "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters" + }, + "principal_investigator": { + "$ref": "#/$defs/PersonValue", + "description": "Principal Investigator who led the study and/or generated the dataset." + }, + "processing_institution": { + "$ref": "#/$defs/ProcessingInstitutionEnum", + "description": "The organization that processed the sample." + }, + "samp_vol_we_dna_ext": { + "$ref": "#/$defs/QuantityValue", + "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)." + }, + "seq_meth": { + "$ref": "#/$defs/TextValue", + "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)." + }, + "seq_quality_check": { + "$ref": "#/$defs/TextValue", + "description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA" + }, + "target_gene": { + "$ref": "#/$defs/TextValue", + "description": "Targeted gene or locus name for marker gene studies" + }, + "target_subfragment": { + "$ref": "#/$defs/TextValue", + "description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + } + }, + "required": [ + "has_input" + ], + "title": "OmicsProcessing", + "type": "object" + }, + "OntologyClass": { + "additionalProperties": false, + "description": "", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "OntologyClass", + "type": "object" + }, + "OrganismCountEnum": { + "description": "", + "enum": [ + "ATP", + "MPN", + "other" + ], + "title": "OrganismCountEnum", + "type": "string" + }, + "OrthologyGroup": { + "additionalProperties": false, + "description": "A set of genes or gene products in which all members are orthologous", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "OrthologyGroup", + "type": "object" + }, + "OxyStatSampEnum": { + "description": "", + "enum": [ + "aerobic", + "anaerobic", + "other" + ], + "title": "OxyStatSampEnum", + "type": "string" + }, + "Pathway": { + "additionalProperties": false, + "description": "A pathway is a sequence of steps/reactions carried out by an organism or community of organisms", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "Pathway", + "type": "object" + }, + "PeptideQuantification": { + "additionalProperties": false, + "description": "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information", + "title": "PeptideQuantification", + "type": "object" + }, + "Person": { + "additionalProperties": false, + "description": "represents a person, such as a researcher", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "Should be an ORCID. Specify in CURIE format. E.g ORCID:0000-1111-...", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "Person", + "type": "object" + }, + "PersonValue": { + "additionalProperties": false, + "description": "An attribute value representing a person", + "properties": { + "email": { + "description": "An email address for an entity such as a person. This should be the primarly email address used.", + "type": "string" + }, + "has_raw_value": { + "description": "The full name of the Investigator in format FIRST LAST.", + "type": "string" + }, + "name": { + "description": "The full name of the Investigator. It should follow the format FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.", + "type": "string" + }, + "orcid": { + "description": "The ORCID of a person.", + "type": "string" + }, + "profile_image_url": { + "description": "A url that points to an image of a person.", + "type": "string" + }, + "was_generated_by": { + "type": "string" + }, + "websites": { + "description": "A list of websites that are associated with the entity.", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "title": "PersonValue", + "type": "object" + }, + "PlantGrowthMedEnum": { + "description": "", + "enum": [ + "other artificial liquid medium", + "other artificial solid medium", + "peat moss", + "perlite", + "pumice", + "sand", + "soil", + "vermiculite", + "water" + ], + "title": "PlantGrowthMedEnum", + "type": "string" + }, + "PlantSexEnum": { + "description": "", + "enum": [ + "Androdioecious", + "Androecious", + "Androgynous", + "Androgynomonoecious", + "Andromonoecious", + "Bisexual", + "Dichogamous", + "Diclinous", + "Dioecious", + "Gynodioecious", + "Gynoecious", + "Gynomonoecious", + "Hermaphroditic", + "Imperfect", + "Monoclinous", + "Monoecious", + "Perfect", + "Polygamodioecious", + "Polygamomonoecious", + "Polygamous", + "Protandrous", + "Protogynous", + "Subandroecious", + "Subdioecious", + "Subgynoecious", + "Synoecious", + "Trimonoecious", + "Trioecious", + "Unisexual" + ], + "title": "PlantSexEnum", + "type": "string" + }, + "ProcessingInstitutionEnum": { + "description": "", + "enum": [ + "UCSD", + "JGI", + "EMSL" + ], + "title": "ProcessingInstitutionEnum", + "type": "string" + }, + "ProfilePositionEnum": { + "description": "", + "enum": [ + "summit", + "shoulder", + "backslope", + "footslope", + "toeslope" + ], + "title": "ProfilePositionEnum", + "type": "string" + }, + "ProteinQuantification": { + "additionalProperties": false, + "description": "This is used to link a metaproteomics analysis workflow to a specific protein", + "title": "ProteinQuantification", + "type": "object" + }, + "QuadPosEnum": { + "description": "", + "enum": [ + "North side", + "West side", + "South side", + "East side" + ], + "title": "QuadPosEnum", + "type": "string" + }, + "QuantityValue": { + "additionalProperties": false, + "description": "A simple quantity, e.g. 2cm", + "properties": { + "has_maximum_numeric_value": { + "description": "The maximum value part, expressed as number, of the quantity value when the value covers a range.", + "type": "number" + }, + "has_minimum_numeric_value": { + "description": "The minimum value part, expressed as number, of the quantity value when the value covers a range.", + "type": "number" + }, + "has_numeric_value": { + "description": "The number part of the quantity", + "type": "number" + }, + "has_raw_value": { + "description": "Unnormalized atomic string representation, should in syntax {number} {unit}", + "type": "string" + }, + "has_unit": { + "description": "The unit of the quantity", + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "QuantityValue", + "type": "object" + }, + "Reaction": { + "additionalProperties": false, + "description": "An individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "Reaction", + "type": "object" + }, + "ReactionActivity": { + "additionalProperties": false, + "description": "", + "properties": { + "material_input": { + "type": "string" + }, + "material_output": { + "type": "string" + }, + "reaction_aided_by": { + "$ref": "#/$defs/LabDevice" + }, + "reaction_temperature": { + "type": "string" + }, + "reaction_time": { + "$ref": "#/$defs/QuantityValue" + } + }, + "title": "ReactionActivity", + "type": "object" + }, + "ReactionParticipant": { + "additionalProperties": false, + "description": "Instances of this link a reaction to a chemical entity participant", + "title": "ReactionParticipant", + "type": "object" + }, + "ReadBasedTaxonomyAnalysisActivity": { + "additionalProperties": false, + "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfrbt-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "ReadBasedTaxonomyAnalysisActivity", + "type": "object" + }, + "ReadQcAnalysisActivity": { + "additionalProperties": false, + "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfrqc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "input_base_count": { + "description": "The nucleotide base count number of input reads for QC analysis.", + "type": "number" + }, + "input_read_count": { + "description": "The sequence count number of input reads for QC analysis.", + "type": "number" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "output_base_count": { + "description": "After QC analysis nucleotide base count number.", + "type": "number" + }, + "output_read_count": { + "description": "After QC analysis sequence count number.", + "type": "number" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "ReadQcAnalysisActivity", + "type": "object" + }, + "RelSampLocEnum": { + "description": "", + "enum": [ + "edge of car", + "center of car", + "under a seat" + ], + "title": "RelSampLocEnum", + "type": "string" + }, + "RelToOxygenEnum": { + "description": "", + "enum": [ + "aerobe", + "anaerobe", + "facultative", + "microaerophilic", + "microanaerobe", + "obligate aerobe", + "obligate anaerobe" + ], + "title": "RelToOxygenEnum", + "type": "string" + }, + "RnaContTypeEnum": { + "description": "", + "enum": [ + "plate", + "tube" + ], + "title": "RnaContTypeEnum", + "type": "string" + }, + "RnaSampleFormatEnum": { + "description": "", + "enum": [ + "10 mM Tris-HCl", + "DNAStable", + "Ethanol", + "Low EDTA TE", + "MDA reaction buffer", + "PBS", + "Pellet", + "RNAStable", + "TE", + "Water", + "Gentegra-DNA", + "Gentegra-RNA" + ], + "title": "RnaSampleFormatEnum", + "type": "string" + }, + "RoomCondtEnum": { + "description": "", + "enum": [ + "new", + "visible wear", + "needs repair", + "damaged", + "rupture", + "visible signs of mold/mildew" + ], + "title": "RoomCondtEnum", + "type": "string" + }, + "RoomConnectedEnum": { + "description": "", + "enum": [ + "attic", + "bathroom", + "closet", + "conference room", + "elevator", + "examining room", + "hallway", + "kitchen", + "mail room", + "office", + "stairwell" + ], + "title": "RoomConnectedEnum", + "type": "string" + }, + "RoomLocEnum": { + "description": "", + "enum": [ + "corner room", + "interior room", + "exterior wall" + ], + "title": "RoomLocEnum", + "type": "string" + }, + "RoomSampPosEnum": { + "description": "", + "enum": [ + "north corner", + "south corner", + "west corner", + "east corner", + "northeast corner", + "northwest corner", + "southeast corner", + "southwest corner", + "center" + ], + "title": "RoomSampPosEnum", + "type": "string" + }, + "RoomTypeEnum": { + "description": "", + "enum": [ + "attic", + "bathroom", + "closet", + "conference room", + "elevator", + "examining room", + "hallway", + "kitchen", + "mail room", + "private office", + "open office", + "stairwell", + ",restroom", + "lobby", + "vestibule", + "mechanical or electrical room", + "data center", + "laboratory_wet", + "laboratory_dry", + "gymnasium", + "natatorium", + "auditorium", + "lockers", + "cafe", + "warehouse" + ], + "title": "RoomTypeEnum", + "type": "string" + }, + "SampCaptStatusEnum": { + "description": "", + "enum": [ + "active surveillance in response to an outbreak", + "active surveillance not initiated by an outbreak", + "farm sample", + "market sample", + "other" + ], + "title": "SampCaptStatusEnum", + "type": "string" + }, + "SampCollectPointEnum": { + "description": "", + "enum": [ + "well", + "test well", + "drilling rig", + "wellhead", + "separator", + "storage tank", + "other" + ], + "title": "SampCollectPointEnum", + "type": "string" + }, + "SampDisStageEnum": { + "description": "", + "enum": [ + "dissemination", + "growth and reproduction", + "infection", + "inoculation", + "penetration", + "other" + ], + "title": "SampDisStageEnum", + "type": "string" + }, + "SampFloorEnum": { + "description": "", + "enum": [ + "1st floor", + "2nd floor", + "basement", + "lobby" + ], + "title": "SampFloorEnum", + "type": "string" + }, + "SampMdEnum": { + "description": "", + "enum": [ + "DF", + "RT", + "KB", + "MSL", + "other" + ], + "title": "SampMdEnum", + "type": "string" + }, + "SampSubtypeEnum": { + "description": "", + "enum": [ + "oil phase", + "water phase", + "biofilm", + "not applicable", + "other" + ], + "title": "SampSubtypeEnum", + "type": "string" + }, + "SampWeatherEnum": { + "description": "", + "enum": [ + "clear sky", + "cloudy", + "foggy", + "hail", + "rain", + "snow", + "sleet", + "sunny", + "windy" + ], + "title": "SampWeatherEnum", + "type": "string" + }, + "SampleTypeEnum": { + "description": "", + "enum": [ + "soil", + "water_extract_soil" + ], + "title": "SampleTypeEnum", + "type": "string" + }, + "SamplingMethodEnum": { + "description": "", + "enum": [ + "weighing" + ], + "title": "SamplingMethodEnum", + "type": "string" + }, + "SeasonUseEnum": { + "description": "", + "enum": [ + "Spring", + "Summer", + "Fall", + "Winter" + ], + "title": "SeasonUseEnum", + "type": "string" + }, + "SedimentTypeEnum": { + "description": "", + "enum": [ + "biogenous", + "cosmogenous", + "hydrogenous", + "lithogenous" + ], + "title": "SedimentTypeEnum", + "type": "string" + }, + "ShadingDeviceCondEnum": { + "description": "", + "enum": [ + "damaged", + "needs repair", + "new", + "rupture", + "visible wear" + ], + "title": "ShadingDeviceCondEnum", + "type": "string" + }, + "ShadingDeviceTypeEnum": { + "description": "", + "enum": [ + "bahama shutters", + "exterior roll blind", + "gambrel awning", + "hood awning", + "porchroller awning", + "sarasota shutters", + "slatted aluminum", + "solid aluminum awning", + "sun screen", + "tree", + "trellis", + "venetian awning" + ], + "title": "ShadingDeviceTypeEnum", + "type": "string" + }, + "SoilHorizonEnum": { + "description": "", + "enum": [ + "O horizon", + "A horizon", + "E horizon", + "B horizon", + "C horizon", + "R layer", + "Permafrost" + ], + "title": "SoilHorizonEnum", + "type": "string" + }, + "SolventEnum": { + "description": "", + "enum": [ + "deionized_water", + "methanol", + "chloroform" + ], + "title": "SolventEnum", + "type": "string" + }, + "SpecificEnum": { + "description": "", + "enum": [ + "operation", + "as built", + "construction", + "bid", + "design", + "photos" + ], + "title": "SpecificEnum", + "type": "string" + }, + "SrDepEnvEnum": { + "description": "", + "enum": [ + "Lacustine", + "Fluvioldeltaic", + "Fluviomarine", + "Marine", + "other" + ], + "title": "SrDepEnvEnum", + "type": "string" + }, + "SrGeolAgeEnum": { + "description": "", + "enum": [ + "Archean", + "Cambrian", + "Carboniferous", + "Cenozoic", + "Cretaceous", + "Devonian", + "Jurassic", + "Mesozoic", + "Neogene", + "Ordovician", + "Paleogene", + "Paleozoic", + "Permian", + "Precambrian", + "Proterozoic", + "Silurian", + "Triassic", + "other" + ], + "title": "SrGeolAgeEnum", + "type": "string" + }, + "SrKerogTypeEnum": { + "description": "", + "enum": [ + "Type I", + "Type II", + "Type III", + "Type IV", + "other" + ], + "title": "SrKerogTypeEnum", + "type": "string" + }, + "SrLithologyEnum": { + "description": "", + "enum": [ + "Clastic", + "Carbonate", + "Coal", + "Biosilicieous", + "other" + ], + "title": "SrLithologyEnum", + "type": "string" + }, + "Study": { + "additionalProperties": false, + "description": "A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.", + "properties": { + "abstract": { + "description": "The abstract of manuscript/grant associated with the entity; i.e., a summary of the resource.", + "type": "string" + }, + "alternative_descriptions": { + "description": "A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.", + "items": { + "type": "string" + }, + "type": "array" + }, + "alternative_identifiers": { + "description": "Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC", + "items": { + "type": "string" + }, + "type": "array" + }, + "alternative_names": { + "description": "A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.", + "items": { + "type": "string" + }, + "type": "array" + }, + "alternative_titles": { + "description": "A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "A brief summary that details the study you're submitted to NMDC", + "type": "string" + }, + "doi": { + "$ref": "#/$defs/AttributeValue", + "description": "The dataset citation for this study" + }, + "ecosystem": { + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "type": "string" + }, + "ecosystem_category": { + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "type": "string" + }, + "ecosystem_subtype": { + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "type": "string" + }, + "ecosystem_type": { + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "type": "string" + }, + "emsl_proposal_doi": { + "description": "The DOI for the EMSL awarded study that relates to the NMDC submitted study", + "type": "string" + }, + "emsl_proposal_identifier": { + "description": "The proposal number assigned to the EMSL awarded study that relates to that which is represented in NMDC.", + "type": "string" + }, + "ess_dive_datasets": { + "description": "List of ESS-DIVE dataset DOIs", + "items": { + "type": "string" + }, + "type": "array" + }, + "funding_sources": { + "items": { + "type": "string" + }, + "type": "array" + }, + "gold_study_identifiers": { + "description": "identifiers for corresponding project(s) in GOLD", + "items": { + "type": "string" + }, + "pattern": "^GOLD:Gs[0-9]+$", + "type": "array" + }, + "has_credit_associations": { + "description": "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study", + "items": { + "$ref": "#/$defs/CreditAssociation" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):sty-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "mgnify_project_identifiers": { + "description": "identifiers for corresponding project in MGnify", + "pattern": "^mgnify.proj:[A-Z]+[0-9]+$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "objective": { + "description": "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.", + "type": "string" + }, + "principal_investigator": { + "$ref": "#/$defs/PersonValue", + "description": "Principal Investigator who led the study and/or generated the dataset." + }, + "publications": { + "description": "A list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.", + "items": { + "type": "string" + }, + "type": "array" + }, + "related_identifiers": { + "description": "Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC", + "type": "string" + }, + "relevant_protocols": { + "items": { + "type": "string" + }, + "type": "array" + }, + "specific_ecosystem": { + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "type": "string" + }, + "study_image": { + "description": "Links a study to one or more images.", + "items": { + "$ref": "#/$defs/ImageValue" + }, + "type": "array" + }, + "title": { + "description": "A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "websites": { + "description": "A list of websites that are associated with the entity.", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "title": "Study", + "type": "object" + }, + "SubstructureTypeEnum": { + "description": "", + "enum": [ + "crawlspace", + "slab on grade", + "basement" + ], + "title": "SubstructureTypeEnum", + "type": "string" + }, + "SurfAirContEnum": { + "description": "", + "enum": [ + "dust", + "organic matter", + "particulate matter", + "volatile organic compounds", + "biological contaminants", + "radon", + "nutrients", + "biocides" + ], + "title": "SurfAirContEnum", + "type": "string" + }, + "SurfMaterialEnum": { + "description": "", + "enum": [ + "adobe", + "carpet", + "cinder blocks", + "concrete", + "hay bales", + "glass", + "metal", + "paint", + "plastic", + "stainless steel", + "stone", + "stucco", + "tile", + "vinyl", + "wood" + ], + "title": "SurfMaterialEnum", + "type": "string" + }, + "TextValue": { + "additionalProperties": false, + "description": "A basic string value", + "properties": { + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "language": { + "description": "Should use ISO 639-1 code e.g. \"en\", \"fr\"", + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "TextValue", + "type": "object" + }, + "TidalStageEnum": { + "description": "", + "enum": [ + "low tide", + "ebb tide", + "flood tide", + "high tide" + ], + "title": "TidalStageEnum", + "type": "string" + }, + "TillageEnum": { + "description": "", + "enum": [ + "drill", + "cutting disc", + "ridge till", + "strip tillage", + "zonal tillage", + "chisel", + "tined", + "mouldboard", + "disc plough" + ], + "title": "TillageEnum", + "type": "string" + }, + "TimestampValue": { + "additionalProperties": false, + "description": "A value that is a timestamp. The range should be ISO-8601", + "properties": { + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "TimestampValue", + "type": "object" + }, + "TrainLineEnum": { + "description": "", + "enum": [ + "red", + "green", + "orange" + ], + "title": "TrainLineEnum", + "type": "string" + }, + "TrainStatLocEnum": { + "description": "", + "enum": [ + "south station above ground", + "south station underground", + "south station amtrak", + "forest hills", + "riverside" + ], + "title": "TrainStatLocEnum", + "type": "string" + }, + "TrainStopLocEnum": { + "description": "", + "enum": [ + "end", + "mid", + "downtown" + ], + "title": "TrainStopLocEnum", + "type": "string" + }, + "UrlValue": { + "additionalProperties": false, + "description": "A value that is a string that conforms to URL syntax", + "properties": { + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "UrlValue", + "type": "object" + }, + "VisMediaEnum": { + "description": "", + "enum": [ + "photos", + "videos", + "commonly of the building", + "site context (adjacent buildings, vegetation, terrain, streets)", + "interiors", + "equipment", + "3D scans" + ], + "title": "VisMediaEnum", + "type": "string" + }, + "WallConstTypeEnum": { + "description": "", + "enum": [ + "frame construction", + "joisted masonry", + "light noncombustible", + "masonry noncombustible", + "modified fire resistive", + "fire resistive" + ], + "title": "WallConstTypeEnum", + "type": "string" + }, + "WallFinishMatEnum": { + "description": "", + "enum": [ + "plaster", + "gypsum plaster", + "veneer plaster", + "gypsum board", + "tile", + "terrazzo", + "stone facing", + "acoustical treatment", + "wood", + "metal", + "masonry" + ], + "title": "WallFinishMatEnum", + "type": "string" + }, + "WallLocEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west" + ], + "title": "WallLocEnum", + "type": "string" + }, + "WallSurfTreatmentEnum": { + "description": "", + "enum": [ + "painted", + "wall paper", + "no treatment", + "paneling", + "stucco", + "fabric" + ], + "title": "WallSurfTreatmentEnum", + "type": "string" + }, + "WallTextureEnum": { + "description": "", + "enum": [ + "crows feet", + "crows-foot stomp", + "double skip", + "hawk and trowel", + "knockdown", + "popcorn", + "orange peel", + "rosebud stomp", + "Santa-Fe texture", + "skip trowel", + "smooth", + "stomp knockdown", + "swirl" + ], + "title": "WallTextureEnum", + "type": "string" + }, + "WaterFeatTypeEnum": { + "description": "", + "enum": [ + "fountain", + "pool", + "standing feature", + "stream", + "waterfall" + ], + "title": "WaterFeatTypeEnum", + "type": "string" + }, + "WeekdayEnum": { + "description": "", + "enum": [ + "Monday", + "Tuesday", + "Wednesday", + "Thursday", + "Friday", + "Saturday", + "Sunday" + ], + "title": "WeekdayEnum", + "type": "string" + }, + "WindowCondEnum": { + "description": "", + "enum": [ + "damaged", + "needs repair", + "new", + "rupture", + "visible wear" + ], + "title": "WindowCondEnum", + "type": "string" + }, + "WindowCoverEnum": { + "description": "", + "enum": [ + "blinds", + "curtains", + "none" + ], + "title": "WindowCoverEnum", + "type": "string" + }, + "WindowHorizPosEnum": { + "description": "", + "enum": [ + "left", + "middle", + "right" + ], + "title": "WindowHorizPosEnum", + "type": "string" + }, + "WindowLocEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west" + ], + "title": "WindowLocEnum", + "type": "string" + }, + "WindowMatEnum": { + "description": "", + "enum": [ + "clad", + "fiberglass", + "metal", + "vinyl", + "wood" + ], + "title": "WindowMatEnum", + "type": "string" + }, + "WindowTypeEnum": { + "description": "", + "enum": [ + "single-hung sash window", + "horizontal sash window", + "fixed window" + ], + "title": "WindowTypeEnum", + "type": "string" + }, + "WindowVertPosEnum": { + "description": "", + "enum": [ + "bottom", + "middle", + "top", + "low", + "high" + ], + "title": "WindowVertPosEnum", + "type": "string" + }, + "WorkflowExecutionActivity": { + "additionalProperties": false, + "description": "Represents an instance of an execution of a particular workflow", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wf-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "WorkflowExecutionActivity", + "type": "object" + } + }, + "$id": "https://microbiomedata/schema", + "$schema": "http://json-schema.org/draft-07/schema#", + "additionalProperties": false, + "metamodel_version": "1.7.0", + "properties": { + "activity_set": { + "description": "This property links a database object to the set of workflow activities.", + "items": { + "$ref": "#/$defs/WorkflowExecutionActivity" + }, + "type": "array" + }, + "biosample_set": { + "description": "This property links a database object to the set of samples within it.", + "items": { + "$ref": "#/$defs/Biosample" + }, + "type": "array" + }, + "collecting_biosamples_from_site_set": { + "items": { + "$ref": "#/$defs/CollectingBiosamplesFromSite" + }, + "type": "array" + }, + "data_object_set": { + "description": "This property links a database object to the set of data objects within it.", + "items": { + "$ref": "#/$defs/DataObject" + }, + "type": "array" + }, + "dissolving_activity_set": { + "items": { + "$ref": "#/$defs/DissolvingActivity" + }, + "type": "array" + }, + "field_research_site_set": { + "items": { + "$ref": "#/$defs/FieldResearchSite" + }, + "type": "array" + }, + "functional_annotation_set": { + "description": "This property links a database object to the set of all functional annotations", + "items": { + "$ref": "#/$defs/FunctionalAnnotation" + }, + "type": "array" + }, + "genome_feature_set": { + "description": "This property links a database object to the set of all features", + "items": { + "$ref": "#/$defs/GenomeFeature" + }, + "type": "array" + }, + "mags_activity_set": { + "description": "This property links a database object to the set of MAGs analysis activities.", + "items": { + "$ref": "#/$defs/MagsAnalysisActivity" + }, + "type": "array" + }, + "material_sample_set": { + "items": { + "$ref": "#/$defs/MaterialSample" + }, + "type": "array" + }, + "material_sampling_activity_set": { + "items": { + "$ref": "#/$defs/MaterialSamplingActivity" + }, + "type": "array" + }, + "metabolomics_analysis_activity_set": { + "description": "This property links a database object to the set of metabolomics analysis activities.", + "items": { + "$ref": "#/$defs/MetabolomicsAnalysisActivity" + }, + "type": "array" + }, + "metagenome_annotation_activity_set": { + "description": "This property links a database object to the set of metagenome annotation activities.", + "items": { + "$ref": "#/$defs/MetagenomeAnnotationActivity" + }, + "type": "array" + }, + "metagenome_assembly_set": { + "description": "This property links a database object to the set of metagenome assembly activities.", + "items": { + "$ref": "#/$defs/MetagenomeAssembly" + }, + "type": "array" + }, + "metaproteomics_analysis_activity_set": { + "description": "This property links a database object to the set of metaproteomics analysis activities.", + "items": { + "$ref": "#/$defs/MetaproteomicsAnalysisActivity" + }, + "type": "array" + }, + "metatranscriptome_activity_set": { + "description": "TODO", + "items": { + "$ref": "#/$defs/MetatranscriptomeActivity" + }, + "type": "array" + }, + "nom_analysis_activity_set": { + "description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", + "items": { + "$ref": "#/$defs/NomAnalysisActivity" + }, + "type": "array" + }, + "omics_processing_set": { + "description": "This property links a database object to the set of omics processings within it.", + "items": { + "$ref": "#/$defs/OmicsProcessing" + }, + "type": "array" + }, + "reaction_activity_set": { + "items": { + "$ref": "#/$defs/ReactionActivity" + }, + "type": "array" + }, + "read_based_taxonomy_analysis_activity_set": { + "description": "This property links a database object to the set of read based analysis activities.", + "items": { + "$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity" + }, + "type": "array" + }, + "read_qc_analysis_activity_set": { + "description": "This property links a database object to the set of read QC analysis activities.", + "items": { + "$ref": "#/$defs/ReadQcAnalysisActivity" + }, + "type": "array" + }, + "study_set": { + "description": "This property links a database object to the set of studies within it.", + "items": { + "$ref": "#/$defs/Study" + }, + "type": "array" + } + }, + "title": "NMDC", + "type": "object", + "version": "7.0.0" +} diff --git a/nmdc_schema/annotation.py b/nmdc_schema/annotation.py index 0070d5857c..1d35f0330d 100644 --- a/nmdc_schema/annotation.py +++ b/nmdc_schema/annotation.py @@ -1,5 +1,5 @@ # Auto generated from annotation.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:22 +# Generation date: 2023-01-20T13:16:52 # Schema: NMDC-Annotation # # id: https://microbiomedata/schema/annotation @@ -394,15 +394,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -458,11 +449,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -2681,6 +2667,14 @@ class slots: slots.FunctionalAnnotation_was_generated_by = Slot(uri=NMDC.was_generated_by, name="FunctionalAnnotation_was_generated_by", curie=NMDC.curie('was_generated_by'), model_uri=NMDC.FunctionalAnnotation_was_generated_by, domain=FunctionalAnnotation, range=Optional[Union[str, MetagenomeAnnotationActivityId]], mappings = [PROV.wasGeneratedBy]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -2708,6 +2702,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -2765,6 +2763,10 @@ class slots: slots.GeolocationValue_has_raw_value = Slot(uri=NMDC.has_raw_value, name="GeolocationValue_has_raw_value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) + slots.WorkflowExecutionActivity_was_associated_with = Slot(uri=NMDC.was_associated_with, name="WorkflowExecutionActivity_was_associated_with", curie=NMDC.curie('was_associated_with'), model_uri=NMDC.WorkflowExecutionActivity_was_associated_with, domain=WorkflowExecutionActivity, range=Optional[Union[str, WorkflowExecutionActivityId]], mappings = [PROV.wasAssociatedWith]) @@ -2794,6 +2796,34 @@ class slots: slots.WorkflowExecutionActivity_type = Slot(uri=NMDC.type, name="WorkflowExecutionActivity_type", curie=NMDC.curie('type'), model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) +slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], + pattern=re.compile(r'^nmdc:wf')) + +slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmgas')) + +slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmtas')) + +slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmgan')) + +slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmtan')) + +slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], + pattern=re.compile(r'^nmdc:wfmt')) + +slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmag')) + slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -2806,6 +2836,14 @@ class slots: slots.ReadQcAnalysisActivity_has_output = Slot(uri=NMDC.has_output, name="ReadQcAnalysisActivity_has_output", curie=NMDC.curie('has_output'), model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) +slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrqc')) + +slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrbt')) + slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2815,14 +2853,26 @@ class slots: slots.MetabolomicsAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="MetabolomicsAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) +slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmb')) + slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.MetaproteomicsAnalysisActivity_has_peptide_quantifications = Slot(uri=NMDC.has_peptide_quantifications, name="MetaproteomicsAnalysisActivity_has_peptide_quantifications", curie=NMDC.curie('has_peptide_quantifications'), model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, PeptideQuantification], List[Union[dict, PeptideQuantification]]]]) +slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmp')) + slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.NomAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="NomAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) + +slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfnom')) diff --git a/nmdc_schema/basic_slots.py b/nmdc_schema/basic_slots.py index 233a2877f5..3caaf63148 100644 --- a/nmdc_schema/basic_slots.py +++ b/nmdc_schema/basic_slots.py @@ -1,5 +1,5 @@ # Auto generated from basic_slots.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:03 +# Generation date: 2023-01-20T13:16:40 # Schema: NMDC-Basic-Slots # # id: https://microbiomedata/schema/basic_slots @@ -188,15 +188,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -252,11 +243,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -1236,6 +1222,14 @@ class slots: slots.magBin__gtdbtk_species = Slot(uri=NMDC.gtdbtk_species, name="magBin__gtdbtk_species", curie=NMDC.curie('gtdbtk_species'), model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1263,6 +1257,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1319,3 +1317,7 @@ class slots: slots.GeolocationValue_has_raw_value = Slot(uri=NMDC.has_raw_value, name="GeolocationValue_has_raw_value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) + +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) diff --git a/nmdc_schema/bioscales.py b/nmdc_schema/bioscales.py index 0fe7ef5672..c096d0d0dc 100644 --- a/nmdc_schema/bioscales.py +++ b/nmdc_schema/bioscales.py @@ -1,5 +1,5 @@ # Auto generated from bioscales.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:46:59 +# Generation date: 2023-01-20T13:17:05 # Schema: NMDC-Bioscales # # id: https://microbiomedata/schema/bioscales @@ -189,15 +189,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -253,11 +244,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -1258,6 +1244,14 @@ class slots: slots.magBin__gtdbtk_species = Slot(uri=NMDC.gtdbtk_species, name="magBin__gtdbtk_species", curie=NMDC.curie('gtdbtk_species'), model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1285,6 +1279,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1341,3 +1339,7 @@ class slots: slots.GeolocationValue_has_raw_value = Slot(uri=NMDC.has_raw_value, name="GeolocationValue_has_raw_value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) + +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) diff --git a/nmdc_schema/core.py b/nmdc_schema/core.py index 8532137de5..b93015a04e 100644 --- a/nmdc_schema/core.py +++ b/nmdc_schema/core.py @@ -1,5 +1,5 @@ # Auto generated from core.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:24 +# Generation date: 2023-01-20T13:17:14 # Schema: NMDC-Core # # id: https://microbiomedata/schema/core @@ -189,15 +189,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -253,11 +244,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -1237,6 +1223,14 @@ class slots: slots.magBin__gtdbtk_species = Slot(uri=NMDC.gtdbtk_species, name="magBin__gtdbtk_species", curie=NMDC.curie('gtdbtk_species'), model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1264,6 +1258,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1320,3 +1318,7 @@ class slots: slots.GeolocationValue_has_raw_value = Slot(uri=NMDC.has_raw_value, name="GeolocationValue_has_raw_value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) + +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) diff --git a/nmdc_schema/external_identifiers.py b/nmdc_schema/external_identifiers.py index 891ee5f3a9..1215e5e6da 100644 --- a/nmdc_schema/external_identifiers.py +++ b/nmdc_schema/external_identifiers.py @@ -1,5 +1,5 @@ # Auto generated from external_identifiers.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:26 +# Generation date: 2023-01-20T13:16:54 # Schema: external_identifiers # # id: https://microbiomedata/schema/external_identifiers @@ -195,15 +195,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -259,11 +250,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -1321,6 +1307,14 @@ class slots: slots.magBin__gtdbtk_species = Slot(uri=NMDC.gtdbtk_species, name="magBin__gtdbtk_species", curie=NMDC.curie('gtdbtk_species'), model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1348,6 +1342,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1404,3 +1402,7 @@ class slots: slots.GeolocationValue_has_raw_value = Slot(uri=NMDC.has_raw_value, name="GeolocationValue_has_raw_value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) + +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) diff --git a/nmdc_schema/mixs.py b/nmdc_schema/mixs.py index 66a2bd2633..8fcb469f11 100644 --- a/nmdc_schema/mixs.py +++ b/nmdc_schema/mixs.py @@ -1,5 +1,5 @@ # Auto generated from mixs.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:18 +# Generation date: 2023-01-20T13:16:58 # Schema: mixs-schema # # id: https://microbiomedata/schema/mixs @@ -186,15 +186,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -250,11 +241,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -4676,6 +4662,14 @@ class slots: slots.magBin__gtdbtk_species = Slot(uri=NMDC.gtdbtk_species, name="magBin__gtdbtk_species", curie=NMDC.curie('gtdbtk_species'), model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -4703,6 +4697,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -4759,3 +4757,7 @@ class slots: slots.GeolocationValue_has_raw_value = Slot(uri=NMDC.has_raw_value, name="GeolocationValue_has_raw_value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) + +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) diff --git a/nmdc_schema/mixs_legacy.py b/nmdc_schema/mixs_legacy.py deleted file mode 100644 index f9f56e2fa9..0000000000 --- a/nmdc_schema/mixs_legacy.py +++ /dev/null @@ -1,3311 +0,0 @@ -# Auto generated from mixs_legacy.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-05-06T11:21:59 -# Schema: mixs-schema -# -# id: https://microbiomedata/schema/mixs -# description: -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import Boolean, Datetime, Double, Float, Integer, String -from linkml_runtime.utils.metamodelcore import Bool, XSDDateTime - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CAS = CurieNamespace('CAS', 'http://identifiers.org/cas/') -CHEBI = CurieNamespace('CHEBI', 'http://purl.obolibrary.org/obo/CHEBI_') -CHEMBL_COMPOUND = CurieNamespace('CHEMBL_COMPOUND', 'http://identifiers.org/chembl.compound/') -DRUGBANK = CurieNamespace('DRUGBANK', 'http://identifiers.org/drugbank/') -HMDB = CurieNamespace('HMDB', 'http://identifiers.org/hmdb/') -KEGG_COMPOUND = CurieNamespace('KEGG_COMPOUND', 'http://identifiers.org/kegg.compound/') -MESH = CurieNamespace('MESH', 'http://identifiers.org/mesh/') -OBI = CurieNamespace('OBI', 'http://purl.obolibrary.org/obo/OBI_') -PR = CurieNamespace('PR', 'http://purl.obolibrary.org/obo/PR_') -PUBCHEM_COMPOUND = CurieNamespace('PUBCHEM_COMPOUND', 'http://identifiers.org/pubchem.compound/') -UNIPROTKB = CurieNamespace('UniProtKB', 'http://example.org/UNKNOWN/UniProtKB/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -DCTERMS = CurieNamespace('dcterms', 'http://purl.org/dc/terms/') -GTPO = CurieNamespace('gtpo', 'http://example.org/UNKNOWN/gtpo/') -MIXS = CurieNamespace('mixs', 'https://w3id.org/gensc/') -NMDC = CurieNamespace('nmdc', 'https://microbiomedata/meta/') -PROV = CurieNamespace('prov', 'http://www.w3.org/ns/prov#') -QUD = CurieNamespace('qud', 'http://qudt.org/1.1/schema/qudt#') -RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#') -SCHEMA = CurieNamespace('schema', 'http://schema.org/') -SIO = CurieNamespace('sio', 'http://semanticscience.org/resource/SIO_') -SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#') -WGS = CurieNamespace('wgs', 'http://www.w3.org/2003/01/geo/wgs84_pos') -XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#') -DEFAULT_ = CurieNamespace('', 'https://microbiomedata/schema/mixs/') - - -# Types -class Bytes(int): - """ An integer value that corresponds to a size in bytes """ - type_class_uri = XSD.int - type_class_curie = "xsd:int" - type_name = "bytes" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/Bytes") - - -class DecimalDegree(float): - """ A decimal degree expresses latitude or longitude as decimal fractions. """ - type_class_uri = XSD.decimal - type_class_curie = "xsd:decimal" - type_name = "decimal degree" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/DecimalDegree") - - -class LanguageCode(str): - """ A language code conforming to ISO_639-1 """ - type_class_uri = XSD.language - type_class_curie = "xsd:language" - type_name = "language code" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/LanguageCode") - - -class Unit(str): - type_class_uri = XSD.string - type_class_curie = "xsd:string" - type_name = "unit" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/Unit") - - -# Class references -class NamedThingId(extended_str): - pass - - -class OntologyClassId(NamedThingId): - pass - - -class EnvironmentalMaterialTermId(OntologyClassId): - pass - - -class PersonId(NamedThingId): - pass - - -class InstrumentId(NamedThingId): - pass - - -class ChemicalEntityId(OntologyClassId): - pass - - -class GeneProductId(NamedThingId): - pass - - -class ActivityId(extended_str): - pass - - -@dataclass -class NamedThing(YAMLRoot): - """ - a databased entity or concept/class - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.NamedThing - class_class_curie: ClassVar[str] = "nmdc:NamedThing" - class_name: ClassVar[str] = "named thing" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/NamedThing") - - id: Union[str, NamedThingId] = None - name: Optional[str] = None - description: Optional[str] = None - alternative_identifiers: Optional[Union[str, List[str]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedThingId): - self.id = NamedThingId(self.id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.alternative_identifiers, list): - self.alternative_identifiers = [self.alternative_identifiers] if self.alternative_identifiers is not None else [] - self.alternative_identifiers = [v if isinstance(v, str) else str(v) for v in self.alternative_identifiers] - - super().__post_init__(**kwargs) - - -@dataclass -class OntologyClass(NamedThing): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.OntologyClass - class_class_curie: ClassVar[str] = "nmdc:OntologyClass" - class_name: ClassVar[str] = "ontology class" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/OntologyClass") - - id: Union[str, OntologyClassId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OntologyClassId): - self.id = OntologyClassId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class EnvironmentalMaterialTerm(OntologyClass): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.EnvironmentalMaterialTerm - class_class_curie: ClassVar[str] = "nmdc:EnvironmentalMaterialTerm" - class_name: ClassVar[str] = "environmental material term" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/EnvironmentalMaterialTerm") - - id: Union[str, EnvironmentalMaterialTermId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentalMaterialTermId): - self.id = EnvironmentalMaterialTermId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class AttributeValue(YAMLRoot): - """ - The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and - the structured value - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.AttributeValue - class_class_curie: ClassVar[str] = "nmdc:AttributeValue" - class_name: ClassVar[str] = "attribute value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/AttributeValue") - - has_raw_value: Optional[str] = None - was_generated_by: Optional[Union[str, ActivityId]] = None - type: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - if self.was_generated_by is not None and not isinstance(self.was_generated_by, ActivityId): - self.was_generated_by = ActivityId(self.was_generated_by) - - if self.type is not None and not isinstance(self.type, str): - self.type = str(self.type) - - super().__post_init__(**kwargs) - - -@dataclass -class QuantityValue(AttributeValue): - """ - A simple quantity, e.g. 2cm - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.QuantityValue - class_class_curie: ClassVar[str] = "nmdc:QuantityValue" - class_name: ClassVar[str] = "quantity value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/QuantityValue") - - has_unit: Optional[str] = None - has_numeric_value: Optional[float] = None - has_minimum_numeric_value: Optional[float] = None - has_maximum_numeric_value: Optional[float] = None - has_raw_value: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_unit is not None and not isinstance(self.has_unit, str): - self.has_unit = str(self.has_unit) - - if self.has_numeric_value is not None and not isinstance(self.has_numeric_value, float): - self.has_numeric_value = float(self.has_numeric_value) - - if self.has_minimum_numeric_value is not None and not isinstance(self.has_minimum_numeric_value, float): - self.has_minimum_numeric_value = float(self.has_minimum_numeric_value) - - if self.has_maximum_numeric_value is not None and not isinstance(self.has_maximum_numeric_value, float): - self.has_maximum_numeric_value = float(self.has_maximum_numeric_value) - - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - super().__post_init__(**kwargs) - - -@dataclass -class ImageValue(AttributeValue): - """ - An attribute value representing an image. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ImageValue - class_class_curie: ClassVar[str] = "nmdc:ImageValue" - class_name: ClassVar[str] = "image value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ImageValue") - - url: Optional[str] = None - description: Optional[str] = None - display_order: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.url is not None and not isinstance(self.url, str): - self.url = str(self.url) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if self.display_order is not None and not isinstance(self.display_order, str): - self.display_order = str(self.display_order) - - super().__post_init__(**kwargs) - - -@dataclass -class PersonValue(AttributeValue): - """ - An attribute value representing a person - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.PersonValue - class_class_curie: ClassVar[str] = "nmdc:PersonValue" - class_name: ClassVar[str] = "person value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/PersonValue") - - orcid: Optional[str] = None - profile_image_url: Optional[str] = None - email: Optional[str] = None - name: Optional[str] = None - websites: Optional[Union[str, List[str]]] = empty_list() - has_raw_value: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.orcid is not None and not isinstance(self.orcid, str): - self.orcid = str(self.orcid) - - if self.profile_image_url is not None and not isinstance(self.profile_image_url, str): - self.profile_image_url = str(self.profile_image_url) - - if self.email is not None and not isinstance(self.email, str): - self.email = str(self.email) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if not isinstance(self.websites, list): - self.websites = [self.websites] if self.websites is not None else [] - self.websites = [v if isinstance(v, str) else str(v) for v in self.websites] - - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - super().__post_init__(**kwargs) - - -@dataclass -class Person(NamedThing): - """ - represents a person, such as a researcher - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Person - class_class_curie: ClassVar[str] = "nmdc:Person" - class_name: ClassVar[str] = "person" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Person") - - id: Union[str, PersonId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PersonId): - self.id = PersonId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class MAGBin(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.MAGBin - class_class_curie: ClassVar[str] = "nmdc:MAGBin" - class_name: ClassVar[str] = "MAG bin" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/MAGBin") - - type: Optional[str] = None - bin_name: Optional[str] = None - number_of_contig: Optional[int] = None - completeness: Optional[float] = None - contamination: Optional[float] = None - gene_count: Optional[int] = None - bin_quality: Optional[str] = None - num_16s: Optional[int] = None - num_5s: Optional[int] = None - num_23s: Optional[int] = None - num_tRNA: Optional[int] = None - gtdbtk_domain: Optional[str] = None - gtdbtk_phylum: Optional[str] = None - gtdbtk_class: Optional[str] = None - gtdbtk_order: Optional[str] = None - gtdbtk_family: Optional[str] = None - gtdbtk_genus: Optional[str] = None - gtdbtk_species: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.type is not None and not isinstance(self.type, str): - self.type = str(self.type) - - if self.bin_name is not None and not isinstance(self.bin_name, str): - self.bin_name = str(self.bin_name) - - if self.number_of_contig is not None and not isinstance(self.number_of_contig, int): - self.number_of_contig = int(self.number_of_contig) - - if self.completeness is not None and not isinstance(self.completeness, float): - self.completeness = float(self.completeness) - - if self.contamination is not None and not isinstance(self.contamination, float): - self.contamination = float(self.contamination) - - if self.gene_count is not None and not isinstance(self.gene_count, int): - self.gene_count = int(self.gene_count) - - if self.bin_quality is not None and not isinstance(self.bin_quality, str): - self.bin_quality = str(self.bin_quality) - - if self.num_16s is not None and not isinstance(self.num_16s, int): - self.num_16s = int(self.num_16s) - - if self.num_5s is not None and not isinstance(self.num_5s, int): - self.num_5s = int(self.num_5s) - - if self.num_23s is not None and not isinstance(self.num_23s, int): - self.num_23s = int(self.num_23s) - - if self.num_tRNA is not None and not isinstance(self.num_tRNA, int): - self.num_tRNA = int(self.num_tRNA) - - if self.gtdbtk_domain is not None and not isinstance(self.gtdbtk_domain, str): - self.gtdbtk_domain = str(self.gtdbtk_domain) - - if self.gtdbtk_phylum is not None and not isinstance(self.gtdbtk_phylum, str): - self.gtdbtk_phylum = str(self.gtdbtk_phylum) - - if self.gtdbtk_class is not None and not isinstance(self.gtdbtk_class, str): - self.gtdbtk_class = str(self.gtdbtk_class) - - if self.gtdbtk_order is not None and not isinstance(self.gtdbtk_order, str): - self.gtdbtk_order = str(self.gtdbtk_order) - - if self.gtdbtk_family is not None and not isinstance(self.gtdbtk_family, str): - self.gtdbtk_family = str(self.gtdbtk_family) - - if self.gtdbtk_genus is not None and not isinstance(self.gtdbtk_genus, str): - self.gtdbtk_genus = str(self.gtdbtk_genus) - - if self.gtdbtk_species is not None and not isinstance(self.gtdbtk_species, str): - self.gtdbtk_species = str(self.gtdbtk_species) - - super().__post_init__(**kwargs) - - -@dataclass -class Instrument(NamedThing): - """ - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI]. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Instrument - class_class_curie: ClassVar[str] = "nmdc:Instrument" - class_name: ClassVar[str] = "instrument" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Instrument") - - id: Union[str, InstrumentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, InstrumentId): - self.id = InstrumentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class MetaboliteQuantification(YAMLRoot): - """ - This is used to link a metabolomics analysis workflow to a specific metabolite - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.MetaboliteQuantification - class_class_curie: ClassVar[str] = "nmdc:MetaboliteQuantification" - class_name: ClassVar[str] = "metabolite quantification" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/MetaboliteQuantification") - - alternative_identifiers: Optional[Union[str, List[str]]] = empty_list() - metabolite_quantified: Optional[Union[str, ChemicalEntityId]] = None - highest_similarity_score: Optional[float] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.alternative_identifiers, list): - self.alternative_identifiers = [self.alternative_identifiers] if self.alternative_identifiers is not None else [] - self.alternative_identifiers = [v if isinstance(v, str) else str(v) for v in self.alternative_identifiers] - - if self.metabolite_quantified is not None and not isinstance(self.metabolite_quantified, ChemicalEntityId): - self.metabolite_quantified = ChemicalEntityId(self.metabolite_quantified) - - if self.highest_similarity_score is not None and not isinstance(self.highest_similarity_score, float): - self.highest_similarity_score = float(self.highest_similarity_score) - - super().__post_init__(**kwargs) - - -@dataclass -class PeptideQuantification(YAMLRoot): - """ - This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.PeptideQuantification - class_class_curie: ClassVar[str] = "nmdc:PeptideQuantification" - class_name: ClassVar[str] = "peptide quantification" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/PeptideQuantification") - - peptide_sequence: Optional[str] = None - best_protein: Optional[Union[str, GeneProductId]] = None - all_proteins: Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]] = empty_list() - min_q_value: Optional[float] = None - peptide_spectral_count: Optional[int] = None - peptide_sum_masic_abundance: Optional[int] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.peptide_sequence is not None and not isinstance(self.peptide_sequence, str): - self.peptide_sequence = str(self.peptide_sequence) - - if self.best_protein is not None and not isinstance(self.best_protein, GeneProductId): - self.best_protein = GeneProductId(self.best_protein) - - if not isinstance(self.all_proteins, list): - self.all_proteins = [self.all_proteins] if self.all_proteins is not None else [] - self.all_proteins = [v if isinstance(v, GeneProductId) else GeneProductId(v) for v in self.all_proteins] - - if self.min_q_value is not None and not isinstance(self.min_q_value, float): - self.min_q_value = float(self.min_q_value) - - if self.peptide_spectral_count is not None and not isinstance(self.peptide_spectral_count, int): - self.peptide_spectral_count = int(self.peptide_spectral_count) - - if self.peptide_sum_masic_abundance is not None and not isinstance(self.peptide_sum_masic_abundance, int): - self.peptide_sum_masic_abundance = int(self.peptide_sum_masic_abundance) - - super().__post_init__(**kwargs) - - -@dataclass -class ProteinQuantification(YAMLRoot): - """ - This is used to link a metaproteomics analysis workflow to a specific protein - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ProteinQuantification - class_class_curie: ClassVar[str] = "nmdc:ProteinQuantification" - class_name: ClassVar[str] = "protein quantification" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ProteinQuantification") - - best_protein: Optional[Union[str, GeneProductId]] = None - all_proteins: Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]] = empty_list() - peptide_sequence_count: Optional[int] = None - protein_spectral_count: Optional[int] = None - protein_sum_masic_abundance: Optional[int] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.best_protein is not None and not isinstance(self.best_protein, GeneProductId): - self.best_protein = GeneProductId(self.best_protein) - - if not isinstance(self.all_proteins, list): - self.all_proteins = [self.all_proteins] if self.all_proteins is not None else [] - self.all_proteins = [v if isinstance(v, GeneProductId) else GeneProductId(v) for v in self.all_proteins] - - if self.peptide_sequence_count is not None and not isinstance(self.peptide_sequence_count, int): - self.peptide_sequence_count = int(self.peptide_sequence_count) - - if self.protein_spectral_count is not None and not isinstance(self.protein_spectral_count, int): - self.protein_spectral_count = int(self.protein_spectral_count) - - if self.protein_sum_masic_abundance is not None and not isinstance(self.protein_sum_masic_abundance, int): - self.protein_sum_masic_abundance = int(self.protein_sum_masic_abundance) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalEntity(OntologyClass): - """ - An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, - drugs. There may be different terms for distinct acid-base forms, protonation states - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ChemicalEntity - class_class_curie: ClassVar[str] = "nmdc:ChemicalEntity" - class_name: ClassVar[str] = "chemical entity" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ChemicalEntity") - - id: Union[str, ChemicalEntityId] = None - inchi: Optional[str] = None - inchi_key: Optional[str] = None - smiles: Optional[Union[str, List[str]]] = empty_list() - chemical_formula: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalEntityId): - self.id = ChemicalEntityId(self.id) - - if self.inchi is not None and not isinstance(self.inchi, str): - self.inchi = str(self.inchi) - - if self.inchi_key is not None and not isinstance(self.inchi_key, str): - self.inchi_key = str(self.inchi_key) - - if not isinstance(self.smiles, list): - self.smiles = [self.smiles] if self.smiles is not None else [] - self.smiles = [v if isinstance(v, str) else str(v) for v in self.smiles] - - if self.chemical_formula is not None and not isinstance(self.chemical_formula, str): - self.chemical_formula = str(self.chemical_formula) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneProduct(NamedThing): - """ - A molecule encoded by a gene that has an evolved function - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.GeneProduct - class_class_curie: ClassVar[str] = "nmdc:GeneProduct" - class_name: ClassVar[str] = "gene product" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/GeneProduct") - - id: Union[str, GeneProductId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneProductId): - self.id = GeneProductId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class TextValue(AttributeValue): - """ - A basic string value - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.TextValue - class_class_curie: ClassVar[str] = "nmdc:TextValue" - class_name: ClassVar[str] = "text value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/TextValue") - - language: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.language is not None and not isinstance(self.language, str): - self.language = str(self.language) - - super().__post_init__(**kwargs) - - -class UrlValue(AttributeValue): - """ - A value that is a string that conforms to URL syntax - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.UrlValue - class_class_curie: ClassVar[str] = "nmdc:UrlValue" - class_name: ClassVar[str] = "url value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/UrlValue") - - -class TimestampValue(AttributeValue): - """ - A value that is a timestamp. The range should be ISO-8601 - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.TimestampValue - class_class_curie: ClassVar[str] = "nmdc:TimestampValue" - class_name: ClassVar[str] = "timestamp value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/TimestampValue") - - -@dataclass -class IntegerValue(AttributeValue): - """ - A value that is an integer - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.IntegerValue - class_class_curie: ClassVar[str] = "nmdc:IntegerValue" - class_name: ClassVar[str] = "integer value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/IntegerValue") - - has_numeric_value: Optional[float] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_numeric_value is not None and not isinstance(self.has_numeric_value, float): - self.has_numeric_value = float(self.has_numeric_value) - - super().__post_init__(**kwargs) - - -@dataclass -class BooleanValue(AttributeValue): - """ - A value that is a boolean - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.BooleanValue - class_class_curie: ClassVar[str] = "nmdc:BooleanValue" - class_name: ClassVar[str] = "boolean value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/BooleanValue") - - has_boolean_value: Optional[Union[bool, Bool]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_boolean_value is not None and not isinstance(self.has_boolean_value, Bool): - self.has_boolean_value = Bool(self.has_boolean_value) - - super().__post_init__(**kwargs) - - -@dataclass -class ControlledTermValue(AttributeValue): - """ - A controlled term or class from an ontology - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ControlledTermValue - class_class_curie: ClassVar[str] = "nmdc:ControlledTermValue" - class_name: ClassVar[str] = "controlled term value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ControlledTermValue") - - term: Optional[Union[dict, OntologyClass]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.term is not None and not isinstance(self.term, OntologyClass): - self.term = OntologyClass(**as_dict(self.term)) - - super().__post_init__(**kwargs) - - -@dataclass -class GeolocationValue(AttributeValue): - """ - A normalized value for a location on the earth's surface - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.GeolocationValue - class_class_curie: ClassVar[str] = "nmdc:GeolocationValue" - class_name: ClassVar[str] = "geolocation value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/GeolocationValue") - - latitude: Optional[float] = None - longitude: Optional[float] = None - has_raw_value: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.latitude is not None and not isinstance(self.latitude, float): - self.latitude = float(self.latitude) - - if self.longitude is not None and not isinstance(self.longitude, float): - self.longitude = float(self.longitude) - - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - super().__post_init__(**kwargs) - - -@dataclass -class Activity(YAMLRoot): - """ - a provence-generating activity - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Activity - class_class_curie: ClassVar[str] = "nmdc:Activity" - class_name: ClassVar[str] = "activity" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Activity") - - id: Union[str, ActivityId] = None - name: Optional[str] = None - started_at_time: Optional[Union[str, XSDDateTime]] = None - ended_at_time: Optional[Union[str, XSDDateTime]] = None - was_informed_by: Optional[Union[str, ActivityId]] = None - was_associated_with: Optional[Union[dict, "Agent"]] = None - used: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ActivityId): - self.id = ActivityId(self.id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.started_at_time is not None and not isinstance(self.started_at_time, XSDDateTime): - self.started_at_time = XSDDateTime(self.started_at_time) - - if self.ended_at_time is not None and not isinstance(self.ended_at_time, XSDDateTime): - self.ended_at_time = XSDDateTime(self.ended_at_time) - - if self.was_informed_by is not None and not isinstance(self.was_informed_by, ActivityId): - self.was_informed_by = ActivityId(self.was_informed_by) - - if self.was_associated_with is not None and not isinstance(self.was_associated_with, Agent): - self.was_associated_with = Agent(**as_dict(self.was_associated_with)) - - if self.used is not None and not isinstance(self.used, str): - self.used = str(self.used) - - super().__post_init__(**kwargs) - - -@dataclass -class Agent(YAMLRoot): - """ - a provence-generating agent - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Agent - class_class_curie: ClassVar[str] = "nmdc:Agent" - class_name: ClassVar[str] = "agent" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Agent") - - acted_on_behalf_of: Optional[Union[dict, "Agent"]] = None - was_informed_by: Optional[Union[str, ActivityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.acted_on_behalf_of is not None and not isinstance(self.acted_on_behalf_of, Agent): - self.acted_on_behalf_of = Agent(**as_dict(self.acted_on_behalf_of)) - - if self.was_informed_by is not None and not isinstance(self.was_informed_by, ActivityId): - self.was_informed_by = ActivityId(self.was_informed_by) - - super().__post_init__(**kwargs) - - -# Enumerations - - -# Slots -class slots: - pass - -slots.submitted_to_insdc = Slot(uri=DEFAULT_.submitted_to_insdc, name="submitted_to_insdc", curie=DEFAULT_.curie('submitted_to_insdc'), - model_uri=DEFAULT_.submitted_to_insdc, domain=None, range=Optional[Union[dict, BooleanValue]], mappings = [MIXS.submitted_to_insdc], - pattern=re.compile(r'[true|false]')) - -slots.investigation_type = Slot(uri=DEFAULT_.investigation_type, name="investigation_type", curie=DEFAULT_.curie('investigation_type'), - model_uri=DEFAULT_.investigation_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.investigation_type], - pattern=re.compile(r'[eukaryote|bacteria_archaea|plasmid|virus|organelle|metagenome|metatranscriptome|mimarks\-survey|mimarks\-specimen|misag|mimag|miuvig]')) - -slots.project_name = Slot(uri=DEFAULT_.project_name, name="project_name", curie=DEFAULT_.curie('project_name'), - model_uri=DEFAULT_.project_name, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.project_name]) - -slots.experimental_factor = Slot(uri=DEFAULT_.experimental_factor, name="experimental_factor", curie=DEFAULT_.curie('experimental_factor'), - model_uri=DEFAULT_.experimental_factor, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.experimental_factor]) - -slots.lat_lon = Slot(uri=DEFAULT_.lat_lon, name="lat_lon", curie=DEFAULT_.curie('lat_lon'), - model_uri=DEFAULT_.lat_lon, domain=None, range=Optional[Union[dict, GeolocationValue]], mappings = [MIXS.lat_lon], - pattern=re.compile(r'\d+[.\d+] \d+[.\d+]')) - -slots.depth = Slot(uri=DEFAULT_.depth, name="depth", curie=DEFAULT_.curie('depth'), - model_uri=DEFAULT_.depth, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.depth]) - -slots.alt = Slot(uri=DEFAULT_.alt, name="alt", curie=DEFAULT_.curie('alt'), - model_uri=DEFAULT_.alt, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.alt], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.elev = Slot(uri=DEFAULT_.elev, name="elev", curie=DEFAULT_.curie('elev'), - model_uri=DEFAULT_.elev, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.elev], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.geo_loc_name = Slot(uri=DEFAULT_.geo_loc_name, name="geo_loc_name", curie=DEFAULT_.curie('geo_loc_name'), - model_uri=DEFAULT_.geo_loc_name, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.geo_loc_name]) - -slots.collection_date = Slot(uri=DEFAULT_.collection_date, name="collection_date", curie=DEFAULT_.curie('collection_date'), - model_uri=DEFAULT_.collection_date, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.collection_date]) - -slots.env_broad_scale = Slot(uri=DEFAULT_.env_broad_scale, name="env_broad_scale", curie=DEFAULT_.curie('env_broad_scale'), - model_uri=DEFAULT_.env_broad_scale, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.env_broad_scale], - pattern=re.compile(r'.* \S+:\S+')) - -slots.env_local_scale = Slot(uri=DEFAULT_.env_local_scale, name="env_local_scale", curie=DEFAULT_.curie('env_local_scale'), - model_uri=DEFAULT_.env_local_scale, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.env_local_scale], - pattern=re.compile(r'.* \S+:\S+')) - -slots.env_medium = Slot(uri=DEFAULT_.env_medium, name="env_medium", curie=DEFAULT_.curie('env_medium'), - model_uri=DEFAULT_.env_medium, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.env_medium], - pattern=re.compile(r'.* \S+:\S+')) - -slots.env_package = Slot(uri=DEFAULT_.env_package, name="env_package", curie=DEFAULT_.curie('env_package'), - model_uri=DEFAULT_.env_package, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.env_package], - pattern=re.compile(r'[air|built environment|host\-associated|human\-associated|human\-skin|human\-oral|human\-gut|human\-vaginal|hydrocarbon resources\-cores|hydrocarbon resources\-fluids\/swabs|microbial mat\/biofilm|misc environment|plant\-associated|sediment|soil|wastewater\/sludge|water]')) - -slots.subspecf_gen_lin = Slot(uri=DEFAULT_.subspecf_gen_lin, name="subspecf_gen_lin", curie=DEFAULT_.curie('subspecf_gen_lin'), - model_uri=DEFAULT_.subspecf_gen_lin, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.subspecf_gen_lin]) - -slots.ploidy = Slot(uri=DEFAULT_.ploidy, name="ploidy", curie=DEFAULT_.curie('ploidy'), - model_uri=DEFAULT_.ploidy, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.ploidy], - pattern=re.compile(r'.* \S+:\S+')) - -slots.num_replicons = Slot(uri=DEFAULT_.num_replicons, name="num_replicons", curie=DEFAULT_.curie('num_replicons'), - model_uri=DEFAULT_.num_replicons, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.num_replicons]) - -slots.extrachrom_elements = Slot(uri=DEFAULT_.extrachrom_elements, name="extrachrom_elements", curie=DEFAULT_.curie('extrachrom_elements'), - model_uri=DEFAULT_.extrachrom_elements, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.extrachrom_elements]) - -slots.estimated_size = Slot(uri=DEFAULT_.estimated_size, name="estimated_size", curie=DEFAULT_.curie('estimated_size'), - model_uri=DEFAULT_.estimated_size, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.estimated_size]) - -slots.ref_biomaterial = Slot(uri=DEFAULT_.ref_biomaterial, name="ref_biomaterial", curie=DEFAULT_.curie('ref_biomaterial'), - model_uri=DEFAULT_.ref_biomaterial, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ref_biomaterial]) - -slots.source_mat_id = Slot(uri=DEFAULT_.source_mat_id, name="source_mat_id", curie=DEFAULT_.curie('source_mat_id'), - model_uri=DEFAULT_.source_mat_id, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.source_mat_id]) - -slots.pathogenicity = Slot(uri=DEFAULT_.pathogenicity, name="pathogenicity", curie=DEFAULT_.curie('pathogenicity'), - model_uri=DEFAULT_.pathogenicity, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pathogenicity]) - -slots.biotic_relationship = Slot(uri=DEFAULT_.biotic_relationship, name="biotic_relationship", curie=DEFAULT_.curie('biotic_relationship'), - model_uri=DEFAULT_.biotic_relationship, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.biotic_relationship], - pattern=re.compile(r'[free living|parasitism|commensalism|symbiotic|mutualism]')) - -slots.specific_host = Slot(uri=DEFAULT_.specific_host, name="specific_host", curie=DEFAULT_.curie('specific_host'), - model_uri=DEFAULT_.specific_host, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.specific_host]) - -slots.host_spec_range = Slot(uri=DEFAULT_.host_spec_range, name="host_spec_range", curie=DEFAULT_.curie('host_spec_range'), - model_uri=DEFAULT_.host_spec_range, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_spec_range]) - -slots.health_disease_stat = Slot(uri=DEFAULT_.health_disease_stat, name="health_disease_stat", curie=DEFAULT_.curie('health_disease_stat'), - model_uri=DEFAULT_.health_disease_stat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.health_disease_stat], - pattern=re.compile(r'[healthy|diseased|dead|disease\-free|undetermined|recovering|resolving|pre\-existing condition|pathological|life threatening|congenital]')) - -slots.trophic_level = Slot(uri=DEFAULT_.trophic_level, name="trophic_level", curie=DEFAULT_.curie('trophic_level'), - model_uri=DEFAULT_.trophic_level, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.trophic_level], - pattern=re.compile(r'[autotroph|carboxydotroph|chemoautotroph|chemoheterotroph|chemolithoautotroph|chemolithotroph|chemoorganoheterotroph|chemoorganotroph|chemosynthetic|chemotroph|copiotroph|diazotroph|facultative|autotroph|heterotroph|lithoautotroph|lithoheterotroph|lithotroph|methanotroph|methylotroph|mixotroph|obligate|chemoautolithotroph|oligotroph|organoheterotroph|organotroph|photoautotroph|photoheterotroph|photolithoautotroph|photolithotroph|photosynthetic|phototroph]')) - -slots.propagation = Slot(uri=DEFAULT_.propagation, name="propagation", curie=DEFAULT_.curie('propagation'), - model_uri=DEFAULT_.propagation, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.propagation]) - -slots.encoded_traits = Slot(uri=DEFAULT_.encoded_traits, name="encoded_traits", curie=DEFAULT_.curie('encoded_traits'), - model_uri=DEFAULT_.encoded_traits, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.encoded_traits]) - -slots.rel_to_oxygen = Slot(uri=DEFAULT_.rel_to_oxygen, name="rel_to_oxygen", curie=DEFAULT_.curie('rel_to_oxygen'), - model_uri=DEFAULT_.rel_to_oxygen, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.rel_to_oxygen], - pattern=re.compile(r'[aerobe|anaerobe|facultative|microaerophilic|microanaerobe|obligate aerobe|obligate anaerobe]')) - -slots.isol_growth_condt = Slot(uri=DEFAULT_.isol_growth_condt, name="isol_growth_condt", curie=DEFAULT_.curie('isol_growth_condt'), - model_uri=DEFAULT_.isol_growth_condt, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.isol_growth_condt]) - -slots.samp_collect_device = Slot(uri=DEFAULT_.samp_collect_device, name="samp_collect_device", curie=DEFAULT_.curie('samp_collect_device'), - model_uri=DEFAULT_.samp_collect_device, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_collect_device]) - -slots.samp_mat_process = Slot(uri=DEFAULT_.samp_mat_process, name="samp_mat_process", curie=DEFAULT_.curie('samp_mat_process'), - model_uri=DEFAULT_.samp_mat_process, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.samp_mat_process]) - -slots.size_frac = Slot(uri=DEFAULT_.size_frac, name="size_frac", curie=DEFAULT_.curie('size_frac'), - model_uri=DEFAULT_.size_frac, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.size_frac], - pattern=re.compile(r'\d+[.\d+]\-\d+[.\d+] \S+')) - -slots.samp_size = Slot(uri=DEFAULT_.samp_size, name="samp_size", curie=DEFAULT_.curie('samp_size'), - model_uri=DEFAULT_.samp_size, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_size], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.source_uvig = Slot(uri=DEFAULT_.source_uvig, name="source_uvig", curie=DEFAULT_.curie('source_uvig'), - model_uri=DEFAULT_.source_uvig, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.source_uvig], - pattern=re.compile(r'[metagenome (not viral targeted)|viral fraction metagenome (virome)|sequence\-targeted metagenome|metatranscriptome (not viral targeted)|viral fraction RNA metagenome (RNA virome)|sequence\-targeted RNA metagenome|microbial single amplified genome (SAG)|viral single amplified genome (vSAG)|isolate microbial genome|other]')) - -slots.virus_enrich_appr = Slot(uri=DEFAULT_.virus_enrich_appr, name="virus_enrich_appr", curie=DEFAULT_.curie('virus_enrich_appr'), - model_uri=DEFAULT_.virus_enrich_appr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.virus_enrich_appr], - pattern=re.compile(r'[filtration|ultrafiltration|centrifugation|ultracentrifugation|PEG Precipitation|FeCl Precipitation|CsCl density gradient|DNAse|RNAse|targeted sequence capture|other|none]')) - -slots.nucl_acid_ext = Slot(uri=DEFAULT_.nucl_acid_ext, name="nucl_acid_ext", curie=DEFAULT_.curie('nucl_acid_ext'), - model_uri=DEFAULT_.nucl_acid_ext, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.nucl_acid_ext]) - -slots.nucl_acid_amp = Slot(uri=DEFAULT_.nucl_acid_amp, name="nucl_acid_amp", curie=DEFAULT_.curie('nucl_acid_amp'), - model_uri=DEFAULT_.nucl_acid_amp, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.nucl_acid_amp]) - -slots.lib_size = Slot(uri=DEFAULT_.lib_size, name="lib_size", curie=DEFAULT_.curie('lib_size'), - model_uri=DEFAULT_.lib_size, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.lib_size]) - -slots.lib_reads_seqd = Slot(uri=DEFAULT_.lib_reads_seqd, name="lib_reads_seqd", curie=DEFAULT_.curie('lib_reads_seqd'), - model_uri=DEFAULT_.lib_reads_seqd, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.lib_reads_seqd]) - -slots.lib_layout = Slot(uri=DEFAULT_.lib_layout, name="lib_layout", curie=DEFAULT_.curie('lib_layout'), - model_uri=DEFAULT_.lib_layout, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.lib_layout], - pattern=re.compile(r'[paired|single|vector|other]')) - -slots.lib_vector = Slot(uri=DEFAULT_.lib_vector, name="lib_vector", curie=DEFAULT_.curie('lib_vector'), - model_uri=DEFAULT_.lib_vector, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.lib_vector]) - -slots.lib_screen = Slot(uri=DEFAULT_.lib_screen, name="lib_screen", curie=DEFAULT_.curie('lib_screen'), - model_uri=DEFAULT_.lib_screen, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.lib_screen]) - -slots.target_gene = Slot(uri=DEFAULT_.target_gene, name="target_gene", curie=DEFAULT_.curie('target_gene'), - model_uri=DEFAULT_.target_gene, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.target_gene]) - -slots.target_subfragment = Slot(uri=DEFAULT_.target_subfragment, name="target_subfragment", curie=DEFAULT_.curie('target_subfragment'), - model_uri=DEFAULT_.target_subfragment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.target_subfragment]) - -slots.pcr_primers = Slot(uri=DEFAULT_.pcr_primers, name="pcr_primers", curie=DEFAULT_.curie('pcr_primers'), - model_uri=DEFAULT_.pcr_primers, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pcr_primers]) - -slots.mid = Slot(uri=DEFAULT_.mid, name="mid", curie=DEFAULT_.curie('mid'), - model_uri=DEFAULT_.mid, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.mid]) - -slots.adapters = Slot(uri=DEFAULT_.adapters, name="adapters", curie=DEFAULT_.curie('adapters'), - model_uri=DEFAULT_.adapters, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.adapters]) - -slots.pcr_cond = Slot(uri=DEFAULT_.pcr_cond, name="pcr_cond", curie=DEFAULT_.curie('pcr_cond'), - model_uri=DEFAULT_.pcr_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pcr_cond], - pattern=re.compile(r'initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles')) - -slots.seq_meth = Slot(uri=DEFAULT_.seq_meth, name="seq_meth", curie=DEFAULT_.curie('seq_meth'), - model_uri=DEFAULT_.seq_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.seq_meth], - pattern=re.compile(r'[MinION|GridION|PromethION|454 GS|454 GS 20|454 GS FLX|454 GS FLX+|454 GS FLX Titanium|454 GS Junior|Illumina Genome Analyzer|Illumina Genome Analyzer II|Illumina Genome Analyzer IIx|Illumina HiSeq 4000|Illumina HiSeq 3000|Illumina HiSeq 2500|Illumina HiSeq 2000|Illumina HiSeq 1500|Illumina HiSeq 1000|Illumina HiScanSQ|Illumina MiSeq|Illumina HiSeq X Five|Illumina HiSeq X Ten|Illumina NextSeq 500|Illumina NextSeq 550|AB SOLiD System|AB SOLiD System 2.0|AB SOLiD System 3.0|AB SOLiD 3 Plus System|AB SOLiD 4 System|AB SOLiD 4hq System|AB SOLiD PI System|AB 5500 Genetic Analyzer|AB 5500xl Genetic Analyzer|AB 5500xl\-W Genetic Analysis System|Ion Torrent PGM|Ion Torrent Proton|Ion Torrent S5|Ion Torrent S5 XL|PacBio RS|PacBio RS II|Sequel|AB 3730xL Genetic Analyzer|AB 3730 Genetic Analyzer|AB 3500xL Genetic Analyzer|AB 3500 Genetic Analyzer|AB 3130xL Genetic Analyzer|AB 3130 Genetic Analyzer|AB 310 Genetic Analyzer|BGISEQ\-500]')) - -slots.seq_quality_check = Slot(uri=DEFAULT_.seq_quality_check, name="seq_quality_check", curie=DEFAULT_.curie('seq_quality_check'), - model_uri=DEFAULT_.seq_quality_check, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.seq_quality_check], - pattern=re.compile(r'[none|manually edited]')) - -slots.chimera_check = Slot(uri=DEFAULT_.chimera_check, name="chimera_check", curie=DEFAULT_.curie('chimera_check'), - model_uri=DEFAULT_.chimera_check, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.chimera_check]) - -slots.tax_ident = Slot(uri=DEFAULT_.tax_ident, name="tax_ident", curie=DEFAULT_.curie('tax_ident'), - model_uri=DEFAULT_.tax_ident, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tax_ident], - pattern=re.compile(r'[16S rRNA gene|multi\-marker approach|other]')) - -slots.assembly_qual = Slot(uri=DEFAULT_.assembly_qual, name="assembly_qual", curie=DEFAULT_.curie('assembly_qual'), - model_uri=DEFAULT_.assembly_qual, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.assembly_qual], - pattern=re.compile(r'[Finished genome|High\-quality draft genome|Medium\-quality draft genome|Low\-quality draft genome|Genome fragment(s)]')) - -slots.assembly_name = Slot(uri=DEFAULT_.assembly_name, name="assembly_name", curie=DEFAULT_.curie('assembly_name'), - model_uri=DEFAULT_.assembly_name, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.assembly_name]) - -slots.assembly_software = Slot(uri=DEFAULT_.assembly_software, name="assembly_software", curie=DEFAULT_.curie('assembly_software'), - model_uri=DEFAULT_.assembly_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.assembly_software]) - -slots.annot = Slot(uri=DEFAULT_.annot, name="annot", curie=DEFAULT_.curie('annot'), - model_uri=DEFAULT_.annot, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.annot]) - -slots.number_contig = Slot(uri=DEFAULT_.number_contig, name="number_contig", curie=DEFAULT_.curie('number_contig'), - model_uri=DEFAULT_.number_contig, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.number_contig]) - -slots.feat_pred = Slot(uri=DEFAULT_.feat_pred, name="feat_pred", curie=DEFAULT_.curie('feat_pred'), - model_uri=DEFAULT_.feat_pred, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.feat_pred]) - -slots.ref_db = Slot(uri=DEFAULT_.ref_db, name="ref_db", curie=DEFAULT_.curie('ref_db'), - model_uri=DEFAULT_.ref_db, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ref_db]) - -slots.sim_search_meth = Slot(uri=DEFAULT_.sim_search_meth, name="sim_search_meth", curie=DEFAULT_.curie('sim_search_meth'), - model_uri=DEFAULT_.sim_search_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sim_search_meth]) - -slots.tax_class = Slot(uri=DEFAULT_.tax_class, name="tax_class", curie=DEFAULT_.curie('tax_class'), - model_uri=DEFAULT_.tax_class, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tax_class]) - -slots._16s_recover = Slot(uri=DEFAULT_._16s_recover, name="_16s_recover", curie=DEFAULT_.curie('_16s_recover'), - model_uri=DEFAULT_._16s_recover, domain=None, range=Optional[Union[dict, BooleanValue]], mappings = [MIXS._16s_recover], - pattern=re.compile(r'[true|false]')) - -slots._16s_recover_software = Slot(uri=DEFAULT_._16s_recover_software, name="_16s_recover_software", curie=DEFAULT_.curie('_16s_recover_software'), - model_uri=DEFAULT_._16s_recover_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS._16s_recover_software]) - -slots.trnas = Slot(uri=DEFAULT_.trnas, name="trnas", curie=DEFAULT_.curie('trnas'), - model_uri=DEFAULT_.trnas, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.trnas]) - -slots.trna_ext_software = Slot(uri=DEFAULT_.trna_ext_software, name="trna_ext_software", curie=DEFAULT_.curie('trna_ext_software'), - model_uri=DEFAULT_.trna_ext_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.trna_ext_software]) - -slots.compl_score = Slot(uri=DEFAULT_.compl_score, name="compl_score", curie=DEFAULT_.curie('compl_score'), - model_uri=DEFAULT_.compl_score, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.compl_score]) - -slots.compl_software = Slot(uri=DEFAULT_.compl_software, name="compl_software", curie=DEFAULT_.curie('compl_software'), - model_uri=DEFAULT_.compl_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.compl_software]) - -slots.compl_appr = Slot(uri=DEFAULT_.compl_appr, name="compl_appr", curie=DEFAULT_.curie('compl_appr'), - model_uri=DEFAULT_.compl_appr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.compl_appr], - pattern=re.compile(r'[marker gene|reference based|other]')) - -slots.contam_score = Slot(uri=DEFAULT_.contam_score, name="contam_score", curie=DEFAULT_.curie('contam_score'), - model_uri=DEFAULT_.contam_score, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.contam_score], - pattern=re.compile(r'\d+[.\d+] percentage')) - -slots.contam_screen_input = Slot(uri=DEFAULT_.contam_screen_input, name="contam_screen_input", curie=DEFAULT_.curie('contam_screen_input'), - model_uri=DEFAULT_.contam_screen_input, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.contam_screen_input], - pattern=re.compile(r'[reads| contigs]')) - -slots.contam_screen_param = Slot(uri=DEFAULT_.contam_screen_param, name="contam_screen_param", curie=DEFAULT_.curie('contam_screen_param'), - model_uri=DEFAULT_.contam_screen_param, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.contam_screen_param]) - -slots.decontam_software = Slot(uri=DEFAULT_.decontam_software, name="decontam_software", curie=DEFAULT_.curie('decontam_software'), - model_uri=DEFAULT_.decontam_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.decontam_software], - pattern=re.compile(r'[checkm\/refinem|anvi\'o|prodege|bbtools:decontaminate.sh|acdc|combination]')) - -slots.sort_tech = Slot(uri=DEFAULT_.sort_tech, name="sort_tech", curie=DEFAULT_.curie('sort_tech'), - model_uri=DEFAULT_.sort_tech, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sort_tech], - pattern=re.compile(r'[flow cytometric cell sorting|microfluidics|lazer\-tweezing|optical manipulation|micromanipulation|other]')) - -slots.single_cell_lysis_appr = Slot(uri=DEFAULT_.single_cell_lysis_appr, name="single_cell_lysis_appr", curie=DEFAULT_.curie('single_cell_lysis_appr'), - model_uri=DEFAULT_.single_cell_lysis_appr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.single_cell_lysis_appr], - pattern=re.compile(r'[chemical|enzymatic|physical|combination]')) - -slots.single_cell_lysis_prot = Slot(uri=DEFAULT_.single_cell_lysis_prot, name="single_cell_lysis_prot", curie=DEFAULT_.curie('single_cell_lysis_prot'), - model_uri=DEFAULT_.single_cell_lysis_prot, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.single_cell_lysis_prot]) - -slots.wga_amp_appr = Slot(uri=DEFAULT_.wga_amp_appr, name="wga_amp_appr", curie=DEFAULT_.curie('wga_amp_appr'), - model_uri=DEFAULT_.wga_amp_appr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wga_amp_appr], - pattern=re.compile(r'[pcr based|mda based]')) - -slots.wga_amp_kit = Slot(uri=DEFAULT_.wga_amp_kit, name="wga_amp_kit", curie=DEFAULT_.curie('wga_amp_kit'), - model_uri=DEFAULT_.wga_amp_kit, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wga_amp_kit]) - -slots.bin_param = Slot(uri=DEFAULT_.bin_param, name="bin_param", curie=DEFAULT_.curie('bin_param'), - model_uri=DEFAULT_.bin_param, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.bin_param], - pattern=re.compile(r'[homology search|kmer|coverage|codon usage|combination]')) - -slots.bin_software = Slot(uri=DEFAULT_.bin_software, name="bin_software", curie=DEFAULT_.curie('bin_software'), - model_uri=DEFAULT_.bin_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.bin_software], - pattern=re.compile(r'[metabat|maxbin|concoct|groupm|esom|metawatt|combination|other]')) - -slots.reassembly_bin = Slot(uri=DEFAULT_.reassembly_bin, name="reassembly_bin", curie=DEFAULT_.curie('reassembly_bin'), - model_uri=DEFAULT_.reassembly_bin, domain=None, range=Optional[Union[dict, BooleanValue]], mappings = [MIXS.reassembly_bin], - pattern=re.compile(r'[true|false]')) - -slots.mag_cov_software = Slot(uri=DEFAULT_.mag_cov_software, name="mag_cov_software", curie=DEFAULT_.curie('mag_cov_software'), - model_uri=DEFAULT_.mag_cov_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.mag_cov_software], - pattern=re.compile(r'[bwa|bbmap|bowtie|other]')) - -slots.vir_ident_software = Slot(uri=DEFAULT_.vir_ident_software, name="vir_ident_software", curie=DEFAULT_.curie('vir_ident_software'), - model_uri=DEFAULT_.vir_ident_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.vir_ident_software]) - -slots.pred_genome_type = Slot(uri=DEFAULT_.pred_genome_type, name="pred_genome_type", curie=DEFAULT_.curie('pred_genome_type'), - model_uri=DEFAULT_.pred_genome_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pred_genome_type], - pattern=re.compile(r'[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (\-)|mixed|uncharacterized]')) - -slots.pred_genome_struc = Slot(uri=DEFAULT_.pred_genome_struc, name="pred_genome_struc", curie=DEFAULT_.curie('pred_genome_struc'), - model_uri=DEFAULT_.pred_genome_struc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pred_genome_struc], - pattern=re.compile(r'[segmented|non\-segmented|undetermined]')) - -slots.detec_type = Slot(uri=DEFAULT_.detec_type, name="detec_type", curie=DEFAULT_.curie('detec_type'), - model_uri=DEFAULT_.detec_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.detec_type], - pattern=re.compile(r'[independent sequence (UViG)|provirus (UpViG)]')) - -slots.votu_class_appr = Slot(uri=DEFAULT_.votu_class_appr, name="votu_class_appr", curie=DEFAULT_.curie('votu_class_appr'), - model_uri=DEFAULT_.votu_class_appr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.votu_class_appr]) - -slots.votu_seq_comp_appr = Slot(uri=DEFAULT_.votu_seq_comp_appr, name="votu_seq_comp_appr", curie=DEFAULT_.curie('votu_seq_comp_appr'), - model_uri=DEFAULT_.votu_seq_comp_appr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.votu_seq_comp_appr]) - -slots.votu_db = Slot(uri=DEFAULT_.votu_db, name="votu_db", curie=DEFAULT_.curie('votu_db'), - model_uri=DEFAULT_.votu_db, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.votu_db]) - -slots.host_pred_appr = Slot(uri=DEFAULT_.host_pred_appr, name="host_pred_appr", curie=DEFAULT_.curie('host_pred_appr'), - model_uri=DEFAULT_.host_pred_appr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_pred_appr], - pattern=re.compile(r'[provirus|host sequence similarity|CRISPR spacer match|kmer similarity|co\-occurrence|combination|other]')) - -slots.host_pred_est_acc = Slot(uri=DEFAULT_.host_pred_est_acc, name="host_pred_est_acc", curie=DEFAULT_.curie('host_pred_est_acc'), - model_uri=DEFAULT_.host_pred_est_acc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_pred_est_acc]) - -slots.mixs_url = Slot(uri=DEFAULT_.mixs_url, name="mixs_url", curie=DEFAULT_.curie('mixs_url'), - model_uri=DEFAULT_.mixs_url, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.mixs_url]) - -slots.sop = Slot(uri=DEFAULT_.sop, name="sop", curie=DEFAULT_.curie('sop'), - model_uri=DEFAULT_.sop, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sop]) - -slots.barometric_press = Slot(uri=DEFAULT_.barometric_press, name="barometric_press", curie=DEFAULT_.curie('barometric_press'), - model_uri=DEFAULT_.barometric_press, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.barometric_press], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.carb_dioxide = Slot(uri=DEFAULT_.carb_dioxide, name="carb_dioxide", curie=DEFAULT_.curie('carb_dioxide'), - model_uri=DEFAULT_.carb_dioxide, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.carb_dioxide], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.carb_monoxide = Slot(uri=DEFAULT_.carb_monoxide, name="carb_monoxide", curie=DEFAULT_.curie('carb_monoxide'), - model_uri=DEFAULT_.carb_monoxide, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.carb_monoxide], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.chem_administration = Slot(uri=DEFAULT_.chem_administration, name="chem_administration", curie=DEFAULT_.curie('chem_administration'), - model_uri=DEFAULT_.chem_administration, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.chem_administration]) - -slots.humidity = Slot(uri=DEFAULT_.humidity, name="humidity", curie=DEFAULT_.curie('humidity'), - model_uri=DEFAULT_.humidity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.humidity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.methane = Slot(uri=DEFAULT_.methane, name="methane", curie=DEFAULT_.curie('methane'), - model_uri=DEFAULT_.methane, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.methane], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.misc_param = Slot(uri=DEFAULT_.misc_param, name="misc_param", curie=DEFAULT_.curie('misc_param'), - model_uri=DEFAULT_.misc_param, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.misc_param]) - -slots.organism_count = Slot(uri=DEFAULT_.organism_count, name="organism_count", curie=DEFAULT_.curie('organism_count'), - model_uri=DEFAULT_.organism_count, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.organism_count]) - -slots.oxygen = Slot(uri=DEFAULT_.oxygen, name="oxygen", curie=DEFAULT_.curie('oxygen'), - model_uri=DEFAULT_.oxygen, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.oxygen], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.oxy_stat_samp = Slot(uri=DEFAULT_.oxy_stat_samp, name="oxy_stat_samp", curie=DEFAULT_.curie('oxy_stat_samp'), - model_uri=DEFAULT_.oxy_stat_samp, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.oxy_stat_samp], - pattern=re.compile(r'[aerobic|anaerobic|other]')) - -slots.perturbation = Slot(uri=DEFAULT_.perturbation, name="perturbation", curie=DEFAULT_.curie('perturbation'), - model_uri=DEFAULT_.perturbation, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.perturbation]) - -slots.pollutants = Slot(uri=DEFAULT_.pollutants, name="pollutants", curie=DEFAULT_.curie('pollutants'), - model_uri=DEFAULT_.pollutants, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.pollutants]) - -slots.resp_part_matter = Slot(uri=DEFAULT_.resp_part_matter, name="resp_part_matter", curie=DEFAULT_.curie('resp_part_matter'), - model_uri=DEFAULT_.resp_part_matter, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.resp_part_matter]) - -slots.samp_salinity = Slot(uri=DEFAULT_.samp_salinity, name="samp_salinity", curie=DEFAULT_.curie('samp_salinity'), - model_uri=DEFAULT_.samp_salinity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_salinity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.samp_store_dur = Slot(uri=DEFAULT_.samp_store_dur, name="samp_store_dur", curie=DEFAULT_.curie('samp_store_dur'), - model_uri=DEFAULT_.samp_store_dur, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_store_dur]) - -slots.samp_store_loc = Slot(uri=DEFAULT_.samp_store_loc, name="samp_store_loc", curie=DEFAULT_.curie('samp_store_loc'), - model_uri=DEFAULT_.samp_store_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_store_loc]) - -slots.samp_store_temp = Slot(uri=DEFAULT_.samp_store_temp, name="samp_store_temp", curie=DEFAULT_.curie('samp_store_temp'), - model_uri=DEFAULT_.samp_store_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_store_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.samp_vol_we_dna_ext = Slot(uri=DEFAULT_.samp_vol_we_dna_ext, name="samp_vol_we_dna_ext", curie=DEFAULT_.curie('samp_vol_we_dna_ext'), - model_uri=DEFAULT_.samp_vol_we_dna_ext, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_vol_we_dna_ext], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.solar_irradiance = Slot(uri=DEFAULT_.solar_irradiance, name="solar_irradiance", curie=DEFAULT_.curie('solar_irradiance'), - model_uri=DEFAULT_.solar_irradiance, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.solar_irradiance], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.temp = Slot(uri=DEFAULT_.temp, name="temp", curie=DEFAULT_.curie('temp'), - model_uri=DEFAULT_.temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.ventilation_rate = Slot(uri=DEFAULT_.ventilation_rate, name="ventilation_rate", curie=DEFAULT_.curie('ventilation_rate'), - model_uri=DEFAULT_.ventilation_rate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.ventilation_rate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.ventilation_type = Slot(uri=DEFAULT_.ventilation_type, name="ventilation_type", curie=DEFAULT_.curie('ventilation_type'), - model_uri=DEFAULT_.ventilation_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ventilation_type]) - -slots.volatile_org_comp = Slot(uri=DEFAULT_.volatile_org_comp, name="volatile_org_comp", curie=DEFAULT_.curie('volatile_org_comp'), - model_uri=DEFAULT_.volatile_org_comp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.volatile_org_comp]) - -slots.wind_direction = Slot(uri=DEFAULT_.wind_direction, name="wind_direction", curie=DEFAULT_.curie('wind_direction'), - model_uri=DEFAULT_.wind_direction, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wind_direction]) - -slots.wind_speed = Slot(uri=DEFAULT_.wind_speed, name="wind_speed", curie=DEFAULT_.curie('wind_speed'), - model_uri=DEFAULT_.wind_speed, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.wind_speed], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.surf_material = Slot(uri=DEFAULT_.surf_material, name="surf_material", curie=DEFAULT_.curie('surf_material'), - model_uri=DEFAULT_.surf_material, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.surf_material], - pattern=re.compile(r'[concrete|wood|stone|tile|plastic|glass|vinyl|metal|carpet|stainless steel|paint|cinder blocks|hay bales|stucco|adobe]')) - -slots.surf_air_cont = Slot(uri=DEFAULT_.surf_air_cont, name="surf_air_cont", curie=DEFAULT_.curie('surf_air_cont'), - model_uri=DEFAULT_.surf_air_cont, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.surf_air_cont], - pattern=re.compile(r'[dust|organic matter|particulate matter|volatile organic compounds|biological contaminants|radon|nutrients|biocides]')) - -slots.rel_air_humidity = Slot(uri=DEFAULT_.rel_air_humidity, name="rel_air_humidity", curie=DEFAULT_.curie('rel_air_humidity'), - model_uri=DEFAULT_.rel_air_humidity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.rel_air_humidity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.abs_air_humidity = Slot(uri=DEFAULT_.abs_air_humidity, name="abs_air_humidity", curie=DEFAULT_.curie('abs_air_humidity'), - model_uri=DEFAULT_.abs_air_humidity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.abs_air_humidity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.surf_humidity = Slot(uri=DEFAULT_.surf_humidity, name="surf_humidity", curie=DEFAULT_.curie('surf_humidity'), - model_uri=DEFAULT_.surf_humidity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.surf_humidity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.air_temp = Slot(uri=DEFAULT_.air_temp, name="air_temp", curie=DEFAULT_.curie('air_temp'), - model_uri=DEFAULT_.air_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.air_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.surf_temp = Slot(uri=DEFAULT_.surf_temp, name="surf_temp", curie=DEFAULT_.curie('surf_temp'), - model_uri=DEFAULT_.surf_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.surf_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.surf_moisture_ph = Slot(uri=DEFAULT_.surf_moisture_ph, name="surf_moisture_ph", curie=DEFAULT_.curie('surf_moisture_ph'), - model_uri=DEFAULT_.surf_moisture_ph, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.surf_moisture_ph], - pattern=re.compile(r'\d+[.\d+]')) - -slots.build_occup_type = Slot(uri=DEFAULT_.build_occup_type, name="build_occup_type", curie=DEFAULT_.curie('build_occup_type'), - model_uri=DEFAULT_.build_occup_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.build_occup_type], - pattern=re.compile(r'[office|market|restaurant|residence|school|residential|commercial|low rise|high rise|wood framed|office|health care|school|airport|sports complex]')) - -slots.surf_moisture = Slot(uri=DEFAULT_.surf_moisture, name="surf_moisture", curie=DEFAULT_.curie('surf_moisture'), - model_uri=DEFAULT_.surf_moisture, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.surf_moisture], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.dew_point = Slot(uri=DEFAULT_.dew_point, name="dew_point", curie=DEFAULT_.curie('dew_point'), - model_uri=DEFAULT_.dew_point, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.dew_point], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.indoor_space = Slot(uri=DEFAULT_.indoor_space, name="indoor_space", curie=DEFAULT_.curie('indoor_space'), - model_uri=DEFAULT_.indoor_space, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.indoor_space], - pattern=re.compile(r'[bedroom|office|bathroom|foyer|kitchen|locker room|hallway|elevator]')) - -slots.indoor_surf = Slot(uri=DEFAULT_.indoor_surf, name="indoor_surf", curie=DEFAULT_.curie('indoor_surf'), - model_uri=DEFAULT_.indoor_surf, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.indoor_surf], - pattern=re.compile(r'[counter top|window|wall|cabinet|ceiling|door|shelving|vent cover]')) - -slots.filter_type = Slot(uri=DEFAULT_.filter_type, name="filter_type", curie=DEFAULT_.curie('filter_type'), - model_uri=DEFAULT_.filter_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.filter_type], - pattern=re.compile(r'[particulate air filter|chemical air filter|low\-MERV pleated media|HEPA|electrostatic|gas\-phase or ultraviolet air treatments]')) - -slots.heat_cool_type = Slot(uri=DEFAULT_.heat_cool_type, name="heat_cool_type", curie=DEFAULT_.curie('heat_cool_type'), - model_uri=DEFAULT_.heat_cool_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.heat_cool_type], - pattern=re.compile(r'[radiant system|heat pump|forced air system|steam forced heat|wood stove]')) - -slots.substructure_type = Slot(uri=DEFAULT_.substructure_type, name="substructure_type", curie=DEFAULT_.curie('substructure_type'), - model_uri=DEFAULT_.substructure_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.substructure_type], - pattern=re.compile(r'[crawlspace|slab on grade|basement]')) - -slots.building_setting = Slot(uri=DEFAULT_.building_setting, name="building_setting", curie=DEFAULT_.curie('building_setting'), - model_uri=DEFAULT_.building_setting, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.building_setting], - pattern=re.compile(r'[urban|suburban|exurban|rural]')) - -slots.light_type = Slot(uri=DEFAULT_.light_type, name="light_type", curie=DEFAULT_.curie('light_type'), - model_uri=DEFAULT_.light_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.light_type], - pattern=re.compile(r'[natural light|electric light|desk lamp|flourescent lights|natural light|none]')) - -slots.samp_sort_meth = Slot(uri=DEFAULT_.samp_sort_meth, name="samp_sort_meth", curie=DEFAULT_.curie('samp_sort_meth'), - model_uri=DEFAULT_.samp_sort_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_sort_meth]) - -slots.space_typ_state = Slot(uri=DEFAULT_.space_typ_state, name="space_typ_state", curie=DEFAULT_.curie('space_typ_state'), - model_uri=DEFAULT_.space_typ_state, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.space_typ_state], - pattern=re.compile(r'[typically occupied|typically unoccupied]')) - -slots.typ_occup_density = Slot(uri=DEFAULT_.typ_occup_density, name="typ_occup_density", curie=DEFAULT_.curie('typ_occup_density'), - model_uri=DEFAULT_.typ_occup_density, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.typ_occup_density], - pattern=re.compile(r'\d+[.\d+]')) - -slots.occup_samp = Slot(uri=DEFAULT_.occup_samp, name="occup_samp", curie=DEFAULT_.curie('occup_samp'), - model_uri=DEFAULT_.occup_samp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.occup_samp]) - -slots.occup_density_samp = Slot(uri=DEFAULT_.occup_density_samp, name="occup_density_samp", curie=DEFAULT_.curie('occup_density_samp'), - model_uri=DEFAULT_.occup_density_samp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.occup_density_samp], - pattern=re.compile(r'\d+[.\d+]')) - -slots.address = Slot(uri=DEFAULT_.address, name="address", curie=DEFAULT_.curie('address'), - model_uri=DEFAULT_.address, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.address]) - -slots.adj_room = Slot(uri=DEFAULT_.adj_room, name="adj_room", curie=DEFAULT_.curie('adj_room'), - model_uri=DEFAULT_.adj_room, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.adj_room]) - -slots.aero_struc = Slot(uri=DEFAULT_.aero_struc, name="aero_struc", curie=DEFAULT_.curie('aero_struc'), - model_uri=DEFAULT_.aero_struc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.aero_struc], - pattern=re.compile(r'[plane|glider]')) - -slots.amount_light = Slot(uri=DEFAULT_.amount_light, name="amount_light", curie=DEFAULT_.curie('amount_light'), - model_uri=DEFAULT_.amount_light, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.amount_light], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.arch_struc = Slot(uri=DEFAULT_.arch_struc, name="arch_struc", curie=DEFAULT_.curie('arch_struc'), - model_uri=DEFAULT_.arch_struc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.arch_struc], - pattern=re.compile(r'[building|shed|home]')) - -slots.avg_occup = Slot(uri=DEFAULT_.avg_occup, name="avg_occup", curie=DEFAULT_.curie('avg_occup'), - model_uri=DEFAULT_.avg_occup, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.avg_occup], - pattern=re.compile(r'\d+[.\d+]')) - -slots.avg_dew_point = Slot(uri=DEFAULT_.avg_dew_point, name="avg_dew_point", curie=DEFAULT_.curie('avg_dew_point'), - model_uri=DEFAULT_.avg_dew_point, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.avg_dew_point], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.avg_temp = Slot(uri=DEFAULT_.avg_temp, name="avg_temp", curie=DEFAULT_.curie('avg_temp'), - model_uri=DEFAULT_.avg_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.avg_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.bathroom_count = Slot(uri=DEFAULT_.bathroom_count, name="bathroom_count", curie=DEFAULT_.curie('bathroom_count'), - model_uri=DEFAULT_.bathroom_count, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.bathroom_count]) - -slots.bedroom_count = Slot(uri=DEFAULT_.bedroom_count, name="bedroom_count", curie=DEFAULT_.curie('bedroom_count'), - model_uri=DEFAULT_.bedroom_count, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.bedroom_count]) - -slots.built_struc_age = Slot(uri=DEFAULT_.built_struc_age, name="built_struc_age", curie=DEFAULT_.curie('built_struc_age'), - model_uri=DEFAULT_.built_struc_age, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.built_struc_age], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.built_struc_set = Slot(uri=DEFAULT_.built_struc_set, name="built_struc_set", curie=DEFAULT_.curie('built_struc_set'), - model_uri=DEFAULT_.built_struc_set, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.built_struc_set], - pattern=re.compile(r'[urban|rural]')) - -slots.built_struc_type = Slot(uri=DEFAULT_.built_struc_type, name="built_struc_type", curie=DEFAULT_.curie('built_struc_type'), - model_uri=DEFAULT_.built_struc_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.built_struc_type]) - -slots.ceil_area = Slot(uri=DEFAULT_.ceil_area, name="ceil_area", curie=DEFAULT_.curie('ceil_area'), - model_uri=DEFAULT_.ceil_area, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.ceil_area], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.ceil_cond = Slot(uri=DEFAULT_.ceil_cond, name="ceil_cond", curie=DEFAULT_.curie('ceil_cond'), - model_uri=DEFAULT_.ceil_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ceil_cond], - pattern=re.compile(r'[new|visible wear|needs repair|damaged|rupture]')) - -slots.ceil_finish_mat = Slot(uri=DEFAULT_.ceil_finish_mat, name="ceil_finish_mat", curie=DEFAULT_.curie('ceil_finish_mat'), - model_uri=DEFAULT_.ceil_finish_mat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ceil_finish_mat], - pattern=re.compile(r'[drywall|mineral fibre|tiles|PVC|plasterboard|metal|fiberglass|stucco|mineral wool\/calcium silicate|wood]')) - -slots.ceil_water_mold = Slot(uri=DEFAULT_.ceil_water_mold, name="ceil_water_mold", curie=DEFAULT_.curie('ceil_water_mold'), - model_uri=DEFAULT_.ceil_water_mold, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ceil_water_mold], - pattern=re.compile(r'[presence of mold visible|no presence of mold visible]')) - -slots.ceil_struc = Slot(uri=DEFAULT_.ceil_struc, name="ceil_struc", curie=DEFAULT_.curie('ceil_struc'), - model_uri=DEFAULT_.ceil_struc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ceil_struc], - pattern=re.compile(r'[wood frame|concrete]')) - -slots.ceil_texture = Slot(uri=DEFAULT_.ceil_texture, name="ceil_texture", curie=DEFAULT_.curie('ceil_texture'), - model_uri=DEFAULT_.ceil_texture, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ceil_texture], - pattern=re.compile(r'[crows feet|crows\-foot stomp|double skip|hawk and trowel|knockdown|popcorn|orange peel|rosebud stomp|Santa\-Fe texture|skip trowel|smooth|stomp knockdown|swirl]')) - -slots.ceil_thermal_mass = Slot(uri=DEFAULT_.ceil_thermal_mass, name="ceil_thermal_mass", curie=DEFAULT_.curie('ceil_thermal_mass'), - model_uri=DEFAULT_.ceil_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.ceil_thermal_mass], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.ceil_type = Slot(uri=DEFAULT_.ceil_type, name="ceil_type", curie=DEFAULT_.curie('ceil_type'), - model_uri=DEFAULT_.ceil_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ceil_type], - pattern=re.compile(r'[cathedral|dropped|concave|barrel\-shaped|coffered|cove|stretched]')) - -slots.cool_syst_id = Slot(uri=DEFAULT_.cool_syst_id, name="cool_syst_id", curie=DEFAULT_.curie('cool_syst_id'), - model_uri=DEFAULT_.cool_syst_id, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.cool_syst_id]) - -slots.date_last_rain = Slot(uri=DEFAULT_.date_last_rain, name="date_last_rain", curie=DEFAULT_.curie('date_last_rain'), - model_uri=DEFAULT_.date_last_rain, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.date_last_rain]) - -slots.build_docs = Slot(uri=DEFAULT_.build_docs, name="build_docs", curie=DEFAULT_.curie('build_docs'), - model_uri=DEFAULT_.build_docs, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.build_docs], - pattern=re.compile(r'[building information model|commissioning report|complaint logs|contract administration|cost estimate|janitorial schedules or logs|maintenance plans|schedule|sections|shop drawings|submittals|ventilation system|windows] ')) - -slots.door_size = Slot(uri=DEFAULT_.door_size, name="door_size", curie=DEFAULT_.curie('door_size'), - model_uri=DEFAULT_.door_size, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.door_size], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.door_cond = Slot(uri=DEFAULT_.door_cond, name="door_cond", curie=DEFAULT_.curie('door_cond'), - model_uri=DEFAULT_.door_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_cond], - pattern=re.compile(r'[damaged|needs repair|new|rupture|visible wear]')) - -slots.door_direct = Slot(uri=DEFAULT_.door_direct, name="door_direct", curie=DEFAULT_.curie('door_direct'), - model_uri=DEFAULT_.door_direct, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_direct], - pattern=re.compile(r'[inward|outward|sideways]')) - -slots.door_loc = Slot(uri=DEFAULT_.door_loc, name="door_loc", curie=DEFAULT_.curie('door_loc'), - model_uri=DEFAULT_.door_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_loc], - pattern=re.compile(r'[north|south|east|west]')) - -slots.door_mat = Slot(uri=DEFAULT_.door_mat, name="door_mat", curie=DEFAULT_.curie('door_mat'), - model_uri=DEFAULT_.door_mat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_mat], - pattern=re.compile(r'[aluminum|cellular PVC|engineered plastic|fiberboard|fiberglass|metal|thermoplastic alloy|vinyl|wood|wood\/plastic composite]')) - -slots.door_move = Slot(uri=DEFAULT_.door_move, name="door_move", curie=DEFAULT_.curie('door_move'), - model_uri=DEFAULT_.door_move, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_move], - pattern=re.compile(r'[collapsible|folding|revolving|rolling shutter|sliding|swinging] ')) - -slots.door_water_mold = Slot(uri=DEFAULT_.door_water_mold, name="door_water_mold", curie=DEFAULT_.curie('door_water_mold'), - model_uri=DEFAULT_.door_water_mold, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_water_mold], - pattern=re.compile(r'[presence of mold visible|no presence of mold visible]')) - -slots.door_type = Slot(uri=DEFAULT_.door_type, name="door_type", curie=DEFAULT_.curie('door_type'), - model_uri=DEFAULT_.door_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_type], - pattern=re.compile(r'[composite|metal|wooden]')) - -slots.door_comp_type = Slot(uri=DEFAULT_.door_comp_type, name="door_comp_type", curie=DEFAULT_.curie('door_comp_type'), - model_uri=DEFAULT_.door_comp_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_comp_type], - pattern=re.compile(r'[metal covered|revolving|sliding|telescopic]')) - -slots.door_type_metal = Slot(uri=DEFAULT_.door_type_metal, name="door_type_metal", curie=DEFAULT_.curie('door_type_metal'), - model_uri=DEFAULT_.door_type_metal, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_type_metal], - pattern=re.compile(r'[collapsible|corrugated steel|hollow|rolling shutters|steel plate]')) - -slots.door_type_wood = Slot(uri=DEFAULT_.door_type_wood, name="door_type_wood", curie=DEFAULT_.curie('door_type_wood'), - model_uri=DEFAULT_.door_type_wood, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_type_wood], - pattern=re.compile(r'[bettened and ledged|battened|ledged and braced|battened|ledged and framed|battened|ledged, braced and frame|framed and paneled|glashed or sash|flush|louvered|wire gauged]')) - -slots.drawings = Slot(uri=DEFAULT_.drawings, name="drawings", curie=DEFAULT_.curie('drawings'), - model_uri=DEFAULT_.drawings, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.drawings], - pattern=re.compile(r'[operation|as built|construction|bid|design|building navigation map|diagram|sketch]')) - -slots.elevator = Slot(uri=DEFAULT_.elevator, name="elevator", curie=DEFAULT_.curie('elevator'), - model_uri=DEFAULT_.elevator, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.elevator]) - -slots.escalator = Slot(uri=DEFAULT_.escalator, name="escalator", curie=DEFAULT_.curie('escalator'), - model_uri=DEFAULT_.escalator, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.escalator]) - -slots.exp_duct = Slot(uri=DEFAULT_.exp_duct, name="exp_duct", curie=DEFAULT_.curie('exp_duct'), - model_uri=DEFAULT_.exp_duct, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.exp_duct], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.exp_pipe = Slot(uri=DEFAULT_.exp_pipe, name="exp_pipe", curie=DEFAULT_.curie('exp_pipe'), - model_uri=DEFAULT_.exp_pipe, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.exp_pipe]) - -slots.ext_door = Slot(uri=DEFAULT_.ext_door, name="ext_door", curie=DEFAULT_.curie('ext_door'), - model_uri=DEFAULT_.ext_door, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ext_door]) - -slots.fireplace_type = Slot(uri=DEFAULT_.fireplace_type, name="fireplace_type", curie=DEFAULT_.curie('fireplace_type'), - model_uri=DEFAULT_.fireplace_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.fireplace_type], - pattern=re.compile(r'[gas burning|wood burning]')) - -slots.floor_age = Slot(uri=DEFAULT_.floor_age, name="floor_age", curie=DEFAULT_.curie('floor_age'), - model_uri=DEFAULT_.floor_age, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.floor_age], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.floor_area = Slot(uri=DEFAULT_.floor_area, name="floor_area", curie=DEFAULT_.curie('floor_area'), - model_uri=DEFAULT_.floor_area, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.floor_area], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.floor_cond = Slot(uri=DEFAULT_.floor_cond, name="floor_cond", curie=DEFAULT_.curie('floor_cond'), - model_uri=DEFAULT_.floor_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.floor_cond], - pattern=re.compile(r'[new|visible wear|needs repair|damaged|rupture]')) - -slots.floor_count = Slot(uri=DEFAULT_.floor_count, name="floor_count", curie=DEFAULT_.curie('floor_count'), - model_uri=DEFAULT_.floor_count, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.floor_count]) - -slots.floor_finish_mat = Slot(uri=DEFAULT_.floor_finish_mat, name="floor_finish_mat", curie=DEFAULT_.curie('floor_finish_mat'), - model_uri=DEFAULT_.floor_finish_mat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.floor_finish_mat], - pattern=re.compile(r'[tile|wood strip or parquet|carpet|rug|laminate wood|lineoleum|vinyl composition tile|sheet vinyl|stone|bamboo|cork|terrazo|concrete|none;specify unfinished|sealed|clear finish|paint]')) - -slots.floor_water_mold = Slot(uri=DEFAULT_.floor_water_mold, name="floor_water_mold", curie=DEFAULT_.curie('floor_water_mold'), - model_uri=DEFAULT_.floor_water_mold, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.floor_water_mold], - pattern=re.compile(r'[mold odor|wet floor|water stains|wall discoloration|floor discoloration|ceiling discoloration|peeling paint or wallpaper|bulging walls|condensation]')) - -slots.floor_struc = Slot(uri=DEFAULT_.floor_struc, name="floor_struc", curie=DEFAULT_.curie('floor_struc'), - model_uri=DEFAULT_.floor_struc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.floor_struc], - pattern=re.compile(r'[balcony|floating floor|glass floor|raised floor|sprung floor|wood\-framed|concrete]')) - -slots.floor_thermal_mass = Slot(uri=DEFAULT_.floor_thermal_mass, name="floor_thermal_mass", curie=DEFAULT_.curie('floor_thermal_mass'), - model_uri=DEFAULT_.floor_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.floor_thermal_mass], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.freq_clean = Slot(uri=DEFAULT_.freq_clean, name="freq_clean", curie=DEFAULT_.curie('freq_clean'), - model_uri=DEFAULT_.freq_clean, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.freq_clean]) - -slots.freq_cook = Slot(uri=DEFAULT_.freq_cook, name="freq_cook", curie=DEFAULT_.curie('freq_cook'), - model_uri=DEFAULT_.freq_cook, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.freq_cook]) - -slots.furniture = Slot(uri=DEFAULT_.furniture, name="furniture", curie=DEFAULT_.curie('furniture'), - model_uri=DEFAULT_.furniture, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.furniture], - pattern=re.compile(r'[cabinet|chair|desks]')) - -slots.gender_restroom = Slot(uri=DEFAULT_.gender_restroom, name="gender_restroom", curie=DEFAULT_.curie('gender_restroom'), - model_uri=DEFAULT_.gender_restroom, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.gender_restroom], - pattern=re.compile(r'[male|female]')) - -slots.hall_count = Slot(uri=DEFAULT_.hall_count, name="hall_count", curie=DEFAULT_.curie('hall_count'), - model_uri=DEFAULT_.hall_count, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.hall_count]) - -slots.handidness = Slot(uri=DEFAULT_.handidness, name="handidness", curie=DEFAULT_.curie('handidness'), - model_uri=DEFAULT_.handidness, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.handidness], - pattern=re.compile(r'[ambidexterity|left handedness|mixed\-handedness|right handedness]')) - -slots.heat_deliv_loc = Slot(uri=DEFAULT_.heat_deliv_loc, name="heat_deliv_loc", curie=DEFAULT_.curie('heat_deliv_loc'), - model_uri=DEFAULT_.heat_deliv_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.heat_deliv_loc], - pattern=re.compile(r'[north|south|east|west]')) - -slots.heat_system_deliv_meth = Slot(uri=DEFAULT_.heat_system_deliv_meth, name="heat_system_deliv_meth", curie=DEFAULT_.curie('heat_system_deliv_meth'), - model_uri=DEFAULT_.heat_system_deliv_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.heat_system_deliv_meth], - pattern=re.compile(r'[conductive|radiant]')) - -slots.heat_system_id = Slot(uri=DEFAULT_.heat_system_id, name="heat_system_id", curie=DEFAULT_.curie('heat_system_id'), - model_uri=DEFAULT_.heat_system_id, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.heat_system_id]) - -slots.height_carper_fiber = Slot(uri=DEFAULT_.height_carper_fiber, name="height_carper_fiber", curie=DEFAULT_.curie('height_carper_fiber'), - model_uri=DEFAULT_.height_carper_fiber, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.height_carper_fiber], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.inside_lux = Slot(uri=DEFAULT_.inside_lux, name="inside_lux", curie=DEFAULT_.curie('inside_lux'), - model_uri=DEFAULT_.inside_lux, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.inside_lux], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.int_wall_cond = Slot(uri=DEFAULT_.int_wall_cond, name="int_wall_cond", curie=DEFAULT_.curie('int_wall_cond'), - model_uri=DEFAULT_.int_wall_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.int_wall_cond], - pattern=re.compile(r'[new|visible wear|needs repair|damaged|rupture]')) - -slots.last_clean = Slot(uri=DEFAULT_.last_clean, name="last_clean", curie=DEFAULT_.curie('last_clean'), - model_uri=DEFAULT_.last_clean, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.last_clean]) - -slots.max_occup = Slot(uri=DEFAULT_.max_occup, name="max_occup", curie=DEFAULT_.curie('max_occup'), - model_uri=DEFAULT_.max_occup, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.max_occup]) - -slots.mech_struc = Slot(uri=DEFAULT_.mech_struc, name="mech_struc", curie=DEFAULT_.curie('mech_struc'), - model_uri=DEFAULT_.mech_struc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.mech_struc], - pattern=re.compile(r'[subway|coach|carriage|elevator|escalator|boat|train|car|bus]')) - -slots.number_plants = Slot(uri=DEFAULT_.number_plants, name="number_plants", curie=DEFAULT_.curie('number_plants'), - model_uri=DEFAULT_.number_plants, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.number_plants]) - -slots.number_pets = Slot(uri=DEFAULT_.number_pets, name="number_pets", curie=DEFAULT_.curie('number_pets'), - model_uri=DEFAULT_.number_pets, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.number_pets]) - -slots.number_resident = Slot(uri=DEFAULT_.number_resident, name="number_resident", curie=DEFAULT_.curie('number_resident'), - model_uri=DEFAULT_.number_resident, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.number_resident]) - -slots.occup_document = Slot(uri=DEFAULT_.occup_document, name="occup_document", curie=DEFAULT_.curie('occup_document'), - model_uri=DEFAULT_.occup_document, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.occup_document], - pattern=re.compile(r'[automated count|estimate|manual count|videos]')) - -slots.ext_wall_orient = Slot(uri=DEFAULT_.ext_wall_orient, name="ext_wall_orient", curie=DEFAULT_.curie('ext_wall_orient'), - model_uri=DEFAULT_.ext_wall_orient, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ext_wall_orient], - pattern=re.compile(r'[north|south|east|west|northeast|southeast|southwest|northwest]')) - -slots.ext_window_orient = Slot(uri=DEFAULT_.ext_window_orient, name="ext_window_orient", curie=DEFAULT_.curie('ext_window_orient'), - model_uri=DEFAULT_.ext_window_orient, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ext_window_orient], - pattern=re.compile(r'[north|south|east|west|northeast|southeast|southwest|northwest]')) - -slots.rel_humidity_out = Slot(uri=DEFAULT_.rel_humidity_out, name="rel_humidity_out", curie=DEFAULT_.curie('rel_humidity_out'), - model_uri=DEFAULT_.rel_humidity_out, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.rel_humidity_out], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.pres_animal = Slot(uri=DEFAULT_.pres_animal, name="pres_animal", curie=DEFAULT_.curie('pres_animal'), - model_uri=DEFAULT_.pres_animal, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pres_animal]) - -slots.quad_pos = Slot(uri=DEFAULT_.quad_pos, name="quad_pos", curie=DEFAULT_.curie('quad_pos'), - model_uri=DEFAULT_.quad_pos, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.quad_pos], - pattern=re.compile(r'[North side|West side|South side|East side]')) - -slots.rel_samp_loc = Slot(uri=DEFAULT_.rel_samp_loc, name="rel_samp_loc", curie=DEFAULT_.curie('rel_samp_loc'), - model_uri=DEFAULT_.rel_samp_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.rel_samp_loc], - pattern=re.compile(r'[edge of car|center of car|under a seat]')) - -slots.room_air_exch_rate = Slot(uri=DEFAULT_.room_air_exch_rate, name="room_air_exch_rate", curie=DEFAULT_.curie('room_air_exch_rate'), - model_uri=DEFAULT_.room_air_exch_rate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.room_air_exch_rate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.room_architec_element = Slot(uri=DEFAULT_.room_architec_element, name="room_architec_element", curie=DEFAULT_.curie('room_architec_element'), - model_uri=DEFAULT_.room_architec_element, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_architec_element]) - -slots.room_condt = Slot(uri=DEFAULT_.room_condt, name="room_condt", curie=DEFAULT_.curie('room_condt'), - model_uri=DEFAULT_.room_condt, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_condt], - pattern=re.compile(r'[new|visible wear|needs repair|damaged|rupture|visible signs of mold\/mildew]')) - -slots.room_count = Slot(uri=DEFAULT_.room_count, name="room_count", curie=DEFAULT_.curie('room_count'), - model_uri=DEFAULT_.room_count, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_count]) - -slots.room_dim = Slot(uri=DEFAULT_.room_dim, name="room_dim", curie=DEFAULT_.curie('room_dim'), - model_uri=DEFAULT_.room_dim, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.room_dim]) - -slots.room_door_dist = Slot(uri=DEFAULT_.room_door_dist, name="room_door_dist", curie=DEFAULT_.curie('room_door_dist'), - model_uri=DEFAULT_.room_door_dist, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.room_door_dist]) - -slots.room_loc = Slot(uri=DEFAULT_.room_loc, name="room_loc", curie=DEFAULT_.curie('room_loc'), - model_uri=DEFAULT_.room_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_loc], - pattern=re.compile(r'[corner room|interior room|exterior wall]')) - -slots.room_moist_damage_hist = Slot(uri=DEFAULT_.room_moist_damage_hist, name="room_moist_damage_hist", curie=DEFAULT_.curie('room_moist_damage_hist'), - model_uri=DEFAULT_.room_moist_damage_hist, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_moist_damage_hist]) - -slots.room_net_area = Slot(uri=DEFAULT_.room_net_area, name="room_net_area", curie=DEFAULT_.curie('room_net_area'), - model_uri=DEFAULT_.room_net_area, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.room_net_area]) - -slots.room_occup = Slot(uri=DEFAULT_.room_occup, name="room_occup", curie=DEFAULT_.curie('room_occup'), - model_uri=DEFAULT_.room_occup, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.room_occup]) - -slots.room_samp_pos = Slot(uri=DEFAULT_.room_samp_pos, name="room_samp_pos", curie=DEFAULT_.curie('room_samp_pos'), - model_uri=DEFAULT_.room_samp_pos, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_samp_pos], - pattern=re.compile(r'[north corner|south corner|west corner|east corner|northeast corner|northwest corner|southeast corner|southwest corner|center]')) - -slots.room_type = Slot(uri=DEFAULT_.room_type, name="room_type", curie=DEFAULT_.curie('room_type'), - model_uri=DEFAULT_.room_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_type], - pattern=re.compile(r'[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail room|private office|open office|stairwell|,restroom|lobby|vestibule|mechanical or electrical room|data center|laboratory_wet|laboratory_dry|gymnasium|natatorium|auditorium|lockers|cafe|warehouse]')) - -slots.room_vol = Slot(uri=DEFAULT_.room_vol, name="room_vol", curie=DEFAULT_.curie('room_vol'), - model_uri=DEFAULT_.room_vol, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.room_vol]) - -slots.room_window_count = Slot(uri=DEFAULT_.room_window_count, name="room_window_count", curie=DEFAULT_.curie('room_window_count'), - model_uri=DEFAULT_.room_window_count, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_window_count]) - -slots.room_connected = Slot(uri=DEFAULT_.room_connected, name="room_connected", curie=DEFAULT_.curie('room_connected'), - model_uri=DEFAULT_.room_connected, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_connected], - pattern=re.compile(r'[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail room|office|stairwell]')) - -slots.room_hallway = Slot(uri=DEFAULT_.room_hallway, name="room_hallway", curie=DEFAULT_.curie('room_hallway'), - model_uri=DEFAULT_.room_hallway, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_hallway]) - -slots.room_door_share = Slot(uri=DEFAULT_.room_door_share, name="room_door_share", curie=DEFAULT_.curie('room_door_share'), - model_uri=DEFAULT_.room_door_share, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_door_share]) - -slots.room_wall_share = Slot(uri=DEFAULT_.room_wall_share, name="room_wall_share", curie=DEFAULT_.curie('room_wall_share'), - model_uri=DEFAULT_.room_wall_share, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_wall_share]) - -slots.samp_weather = Slot(uri=DEFAULT_.samp_weather, name="samp_weather", curie=DEFAULT_.curie('samp_weather'), - model_uri=DEFAULT_.samp_weather, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_weather], - pattern=re.compile(r'[clear sky|cloudy|foggy|hail|rain|snow|sleet|sunny|windy]')) - -slots.samp_floor = Slot(uri=DEFAULT_.samp_floor, name="samp_floor", curie=DEFAULT_.curie('samp_floor'), - model_uri=DEFAULT_.samp_floor, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_floor]) - -slots.samp_room_id = Slot(uri=DEFAULT_.samp_room_id, name="samp_room_id", curie=DEFAULT_.curie('samp_room_id'), - model_uri=DEFAULT_.samp_room_id, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_room_id]) - -slots.samp_time_out = Slot(uri=DEFAULT_.samp_time_out, name="samp_time_out", curie=DEFAULT_.curie('samp_time_out'), - model_uri=DEFAULT_.samp_time_out, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_time_out], - pattern=re.compile(r'\d+[.\d+]')) - -slots.season = Slot(uri=DEFAULT_.season, name="season", curie=DEFAULT_.curie('season'), - model_uri=DEFAULT_.season, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.season], - pattern=re.compile(r'[Spring|Summer|Fall|Winter]')) - -slots.season_use = Slot(uri=DEFAULT_.season_use, name="season_use", curie=DEFAULT_.curie('season_use'), - model_uri=DEFAULT_.season_use, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.season_use], - pattern=re.compile(r'[Spring|Summer|Fall|Winter]')) - -slots.shading_device_cond = Slot(uri=DEFAULT_.shading_device_cond, name="shading_device_cond", curie=DEFAULT_.curie('shading_device_cond'), - model_uri=DEFAULT_.shading_device_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.shading_device_cond], - pattern=re.compile(r'[damaged|needs repair|new|rupture|visible wear]')) - -slots.shading_device_loc = Slot(uri=DEFAULT_.shading_device_loc, name="shading_device_loc", curie=DEFAULT_.curie('shading_device_loc'), - model_uri=DEFAULT_.shading_device_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.shading_device_loc], - pattern=re.compile(r'[exterior|interior]')) - -slots.shading_device_mat = Slot(uri=DEFAULT_.shading_device_mat, name="shading_device_mat", curie=DEFAULT_.curie('shading_device_mat'), - model_uri=DEFAULT_.shading_device_mat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.shading_device_mat]) - -slots.shading_device_water_mold = Slot(uri=DEFAULT_.shading_device_water_mold, name="shading_device_water_mold", curie=DEFAULT_.curie('shading_device_water_mold'), - model_uri=DEFAULT_.shading_device_water_mold, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.shading_device_water_mold], - pattern=re.compile(r'[presence of mold visible|no presence of mold visible]')) - -slots.shading_device_type = Slot(uri=DEFAULT_.shading_device_type, name="shading_device_type", curie=DEFAULT_.curie('shading_device_type'), - model_uri=DEFAULT_.shading_device_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.shading_device_type], - pattern=re.compile(r'[bahama shutters|exterior roll blind|gambrel awning|hood awning|porchroller awning|sarasota shutters|slatted aluminum|solid aluminum awning|sun screen|tree|trellis|venetian awning]')) - -slots.specific_humidity = Slot(uri=DEFAULT_.specific_humidity, name="specific_humidity", curie=DEFAULT_.curie('specific_humidity'), - model_uri=DEFAULT_.specific_humidity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.specific_humidity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.specific = Slot(uri=DEFAULT_.specific, name="specific", curie=DEFAULT_.curie('specific'), - model_uri=DEFAULT_.specific, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.specific], - pattern=re.compile(r'[operation|as built|construction|bid|design|photos]')) - -slots.temp_out = Slot(uri=DEFAULT_.temp_out, name="temp_out", curie=DEFAULT_.curie('temp_out'), - model_uri=DEFAULT_.temp_out, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.temp_out], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.train_line = Slot(uri=DEFAULT_.train_line, name="train_line", curie=DEFAULT_.curie('train_line'), - model_uri=DEFAULT_.train_line, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.train_line], - pattern=re.compile(r'[red|green|orange]')) - -slots.train_stat_loc = Slot(uri=DEFAULT_.train_stat_loc, name="train_stat_loc", curie=DEFAULT_.curie('train_stat_loc'), - model_uri=DEFAULT_.train_stat_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.train_stat_loc], - pattern=re.compile(r'[south station above ground|south station underground|south station amtrak|forest hills|riverside]')) - -slots.train_stop_loc = Slot(uri=DEFAULT_.train_stop_loc, name="train_stop_loc", curie=DEFAULT_.curie('train_stop_loc'), - model_uri=DEFAULT_.train_stop_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.train_stop_loc], - pattern=re.compile(r'[end|mid|downtown]')) - -slots.vis_media = Slot(uri=DEFAULT_.vis_media, name="vis_media", curie=DEFAULT_.curie('vis_media'), - model_uri=DEFAULT_.vis_media, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.vis_media], - pattern=re.compile(r'[photos|videos|commonly of the building|site context (adjacent buildings, vegetation, terrain, streets)|interiors|equipment|3D scans]')) - -slots.wall_area = Slot(uri=DEFAULT_.wall_area, name="wall_area", curie=DEFAULT_.curie('wall_area'), - model_uri=DEFAULT_.wall_area, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.wall_area], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.wall_const_type = Slot(uri=DEFAULT_.wall_const_type, name="wall_const_type", curie=DEFAULT_.curie('wall_const_type'), - model_uri=DEFAULT_.wall_const_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wall_const_type], - pattern=re.compile(r'[frame construction|joisted masonry|light noncombustible|masonry noncombustible|modified fire resistive|fire resistive]')) - -slots.wall_finish_mat = Slot(uri=DEFAULT_.wall_finish_mat, name="wall_finish_mat", curie=DEFAULT_.curie('wall_finish_mat'), - model_uri=DEFAULT_.wall_finish_mat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wall_finish_mat], - pattern=re.compile(r'[plaster|gypsum plaster|veneer plaster|gypsum board|tile|terrazzo|stone facing|acoustical treatment|wood|metal|masonry]')) - -slots.wall_height = Slot(uri=DEFAULT_.wall_height, name="wall_height", curie=DEFAULT_.curie('wall_height'), - model_uri=DEFAULT_.wall_height, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.wall_height], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.wall_loc = Slot(uri=DEFAULT_.wall_loc, name="wall_loc", curie=DEFAULT_.curie('wall_loc'), - model_uri=DEFAULT_.wall_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wall_loc], - pattern=re.compile(r'[north|south|east|west]')) - -slots.wall_water_mold = Slot(uri=DEFAULT_.wall_water_mold, name="wall_water_mold", curie=DEFAULT_.curie('wall_water_mold'), - model_uri=DEFAULT_.wall_water_mold, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wall_water_mold], - pattern=re.compile(r'[presence of mold visible|no presence of mold visible]')) - -slots.wall_surf_treatment = Slot(uri=DEFAULT_.wall_surf_treatment, name="wall_surf_treatment", curie=DEFAULT_.curie('wall_surf_treatment'), - model_uri=DEFAULT_.wall_surf_treatment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wall_surf_treatment], - pattern=re.compile(r'[painted|wall paper|no treatment|paneling|stucco|fabric]')) - -slots.wall_texture = Slot(uri=DEFAULT_.wall_texture, name="wall_texture", curie=DEFAULT_.curie('wall_texture'), - model_uri=DEFAULT_.wall_texture, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wall_texture], - pattern=re.compile(r'[crows feet|crows\-foot stomp|double skip|hawk and trowel|knockdown|popcorn|orange peel|rosebud stomp|Santa\-Fe texture|skip trowel|smooth|stomp knockdown|swirl]')) - -slots.wall_thermal_mass = Slot(uri=DEFAULT_.wall_thermal_mass, name="wall_thermal_mass", curie=DEFAULT_.curie('wall_thermal_mass'), - model_uri=DEFAULT_.wall_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.wall_thermal_mass], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.water_feat_size = Slot(uri=DEFAULT_.water_feat_size, name="water_feat_size", curie=DEFAULT_.curie('water_feat_size'), - model_uri=DEFAULT_.water_feat_size, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.water_feat_size], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.water_feat_type = Slot(uri=DEFAULT_.water_feat_type, name="water_feat_type", curie=DEFAULT_.curie('water_feat_type'), - model_uri=DEFAULT_.water_feat_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.water_feat_type], - pattern=re.compile(r'[fountain|pool|standing feature|stream|waterfall]')) - -slots.weekday = Slot(uri=DEFAULT_.weekday, name="weekday", curie=DEFAULT_.curie('weekday'), - model_uri=DEFAULT_.weekday, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.weekday], - pattern=re.compile(r'[Monday|Tuesday|Wednesday|Thursday|Friday|Saturday|Sunday]')) - -slots.window_size = Slot(uri=DEFAULT_.window_size, name="window_size", curie=DEFAULT_.curie('window_size'), - model_uri=DEFAULT_.window_size, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.window_size], - pattern=re.compile(r'\d+[.\d+] \S+ x \d+[.\d+] \S+')) - -slots.window_cond = Slot(uri=DEFAULT_.window_cond, name="window_cond", curie=DEFAULT_.curie('window_cond'), - model_uri=DEFAULT_.window_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_cond], - pattern=re.compile(r'[damaged|needs repair|new|rupture|visible wear]')) - -slots.window_cover = Slot(uri=DEFAULT_.window_cover, name="window_cover", curie=DEFAULT_.curie('window_cover'), - model_uri=DEFAULT_.window_cover, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_cover], - pattern=re.compile(r'[blinds|curtains|none]')) - -slots.window_horiz_pos = Slot(uri=DEFAULT_.window_horiz_pos, name="window_horiz_pos", curie=DEFAULT_.curie('window_horiz_pos'), - model_uri=DEFAULT_.window_horiz_pos, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_horiz_pos], - pattern=re.compile(r'[left|middle|right]')) - -slots.window_loc = Slot(uri=DEFAULT_.window_loc, name="window_loc", curie=DEFAULT_.curie('window_loc'), - model_uri=DEFAULT_.window_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_loc], - pattern=re.compile(r'[north|south|east|west]')) - -slots.window_mat = Slot(uri=DEFAULT_.window_mat, name="window_mat", curie=DEFAULT_.curie('window_mat'), - model_uri=DEFAULT_.window_mat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_mat], - pattern=re.compile(r'[clad|fiberglass|metal|vinyl|wood]')) - -slots.window_open_freq = Slot(uri=DEFAULT_.window_open_freq, name="window_open_freq", curie=DEFAULT_.curie('window_open_freq'), - model_uri=DEFAULT_.window_open_freq, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_open_freq]) - -slots.window_water_mold = Slot(uri=DEFAULT_.window_water_mold, name="window_water_mold", curie=DEFAULT_.curie('window_water_mold'), - model_uri=DEFAULT_.window_water_mold, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_water_mold], - pattern=re.compile(r'[presence of mold visible|no presence of mold visible]')) - -slots.window_status = Slot(uri=DEFAULT_.window_status, name="window_status", curie=DEFAULT_.curie('window_status'), - model_uri=DEFAULT_.window_status, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_status], - pattern=re.compile(r'[closed|open]')) - -slots.window_type = Slot(uri=DEFAULT_.window_type, name="window_type", curie=DEFAULT_.curie('window_type'), - model_uri=DEFAULT_.window_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_type], - pattern=re.compile(r'[single\-hung sash window|horizontal sash window|fixed window] ')) - -slots.window_vert_pos = Slot(uri=DEFAULT_.window_vert_pos, name="window_vert_pos", curie=DEFAULT_.curie('window_vert_pos'), - model_uri=DEFAULT_.window_vert_pos, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_vert_pos], - pattern=re.compile(r'[bottom|middle|top|low|middle|high]')) - -slots.ances_data = Slot(uri=DEFAULT_.ances_data, name="ances_data", curie=DEFAULT_.curie('ances_data'), - model_uri=DEFAULT_.ances_data, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ances_data]) - -slots.biol_stat = Slot(uri=DEFAULT_.biol_stat, name="biol_stat", curie=DEFAULT_.curie('biol_stat'), - model_uri=DEFAULT_.biol_stat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.biol_stat], - pattern=re.compile(r'[wild|natural|semi\-natural|inbred line|breeder\'s line|hybrid|clonal selection|mutant]')) - -slots.genetic_mod = Slot(uri=DEFAULT_.genetic_mod, name="genetic_mod", curie=DEFAULT_.curie('genetic_mod'), - model_uri=DEFAULT_.genetic_mod, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.genetic_mod]) - -slots.host_common_name = Slot(uri=DEFAULT_.host_common_name, name="host_common_name", curie=DEFAULT_.curie('host_common_name'), - model_uri=DEFAULT_.host_common_name, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_common_name]) - -slots.samp_capt_status = Slot(uri=DEFAULT_.samp_capt_status, name="samp_capt_status", curie=DEFAULT_.curie('samp_capt_status'), - model_uri=DEFAULT_.samp_capt_status, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_capt_status], - pattern=re.compile(r'[active surveillance in response to an outbreak|active surveillance not initiated by an outbreak|farm sample|market sample|other]')) - -slots.samp_dis_stage = Slot(uri=DEFAULT_.samp_dis_stage, name="samp_dis_stage", curie=DEFAULT_.curie('samp_dis_stage'), - model_uri=DEFAULT_.samp_dis_stage, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_dis_stage]) - -slots.host_taxid = Slot(uri=DEFAULT_.host_taxid, name="host_taxid", curie=DEFAULT_.curie('host_taxid'), - model_uri=DEFAULT_.host_taxid, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_taxid]) - -slots.host_subject_id = Slot(uri=DEFAULT_.host_subject_id, name="host_subject_id", curie=DEFAULT_.curie('host_subject_id'), - model_uri=DEFAULT_.host_subject_id, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_subject_id]) - -slots.host_age = Slot(uri=DEFAULT_.host_age, name="host_age", curie=DEFAULT_.curie('host_age'), - model_uri=DEFAULT_.host_age, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_age], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_life_stage = Slot(uri=DEFAULT_.host_life_stage, name="host_life_stage", curie=DEFAULT_.curie('host_life_stage'), - model_uri=DEFAULT_.host_life_stage, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_life_stage]) - -slots.host_sex = Slot(uri=DEFAULT_.host_sex, name="host_sex", curie=DEFAULT_.curie('host_sex'), - model_uri=DEFAULT_.host_sex, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_sex], - pattern=re.compile(r'[male|female|neuter|hermaphrodite|not determined]')) - -slots.host_disease_stat = Slot(uri=DEFAULT_.host_disease_stat, name="host_disease_stat", curie=DEFAULT_.curie('host_disease_stat'), - model_uri=DEFAULT_.host_disease_stat, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.host_disease_stat]) - -slots.host_body_habitat = Slot(uri=DEFAULT_.host_body_habitat, name="host_body_habitat", curie=DEFAULT_.curie('host_body_habitat'), - model_uri=DEFAULT_.host_body_habitat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_body_habitat]) - -slots.host_body_site = Slot(uri=DEFAULT_.host_body_site, name="host_body_site", curie=DEFAULT_.curie('host_body_site'), - model_uri=DEFAULT_.host_body_site, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.host_body_site], - pattern=re.compile(r'.* \S+:\S+')) - -slots.host_body_product = Slot(uri=DEFAULT_.host_body_product, name="host_body_product", curie=DEFAULT_.curie('host_body_product'), - model_uri=DEFAULT_.host_body_product, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.host_body_product], - pattern=re.compile(r'.* \S+:\S+')) - -slots.host_tot_mass = Slot(uri=DEFAULT_.host_tot_mass, name="host_tot_mass", curie=DEFAULT_.curie('host_tot_mass'), - model_uri=DEFAULT_.host_tot_mass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_tot_mass], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_height = Slot(uri=DEFAULT_.host_height, name="host_height", curie=DEFAULT_.curie('host_height'), - model_uri=DEFAULT_.host_height, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_height], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_length = Slot(uri=DEFAULT_.host_length, name="host_length", curie=DEFAULT_.curie('host_length'), - model_uri=DEFAULT_.host_length, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_length], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_diet = Slot(uri=DEFAULT_.host_diet, name="host_diet", curie=DEFAULT_.curie('host_diet'), - model_uri=DEFAULT_.host_diet, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_diet]) - -slots.host_last_meal = Slot(uri=DEFAULT_.host_last_meal, name="host_last_meal", curie=DEFAULT_.curie('host_last_meal'), - model_uri=DEFAULT_.host_last_meal, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_last_meal]) - -slots.host_growth_cond = Slot(uri=DEFAULT_.host_growth_cond, name="host_growth_cond", curie=DEFAULT_.curie('host_growth_cond'), - model_uri=DEFAULT_.host_growth_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_growth_cond]) - -slots.host_substrate = Slot(uri=DEFAULT_.host_substrate, name="host_substrate", curie=DEFAULT_.curie('host_substrate'), - model_uri=DEFAULT_.host_substrate, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_substrate]) - -slots.host_family_relationship = Slot(uri=DEFAULT_.host_family_relationship, name="host_family_relationship", curie=DEFAULT_.curie('host_family_relationship'), - model_uri=DEFAULT_.host_family_relationship, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_family_relationship]) - -slots.host_infra_specific_name = Slot(uri=DEFAULT_.host_infra_specific_name, name="host_infra_specific_name", curie=DEFAULT_.curie('host_infra_specific_name'), - model_uri=DEFAULT_.host_infra_specific_name, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_infra_specific_name]) - -slots.host_infra_specific_rank = Slot(uri=DEFAULT_.host_infra_specific_rank, name="host_infra_specific_rank", curie=DEFAULT_.curie('host_infra_specific_rank'), - model_uri=DEFAULT_.host_infra_specific_rank, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_infra_specific_rank]) - -slots.host_genotype = Slot(uri=DEFAULT_.host_genotype, name="host_genotype", curie=DEFAULT_.curie('host_genotype'), - model_uri=DEFAULT_.host_genotype, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_genotype]) - -slots.host_phenotype = Slot(uri=DEFAULT_.host_phenotype, name="host_phenotype", curie=DEFAULT_.curie('host_phenotype'), - model_uri=DEFAULT_.host_phenotype, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.host_phenotype], - pattern=re.compile(r'.* \S+:\S+')) - -slots.host_body_temp = Slot(uri=DEFAULT_.host_body_temp, name="host_body_temp", curie=DEFAULT_.curie('host_body_temp'), - model_uri=DEFAULT_.host_body_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_body_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_dry_mass = Slot(uri=DEFAULT_.host_dry_mass, name="host_dry_mass", curie=DEFAULT_.curie('host_dry_mass'), - model_uri=DEFAULT_.host_dry_mass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_dry_mass], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_blood_press_diast = Slot(uri=DEFAULT_.host_blood_press_diast, name="host_blood_press_diast", curie=DEFAULT_.curie('host_blood_press_diast'), - model_uri=DEFAULT_.host_blood_press_diast, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_blood_press_diast], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_blood_press_syst = Slot(uri=DEFAULT_.host_blood_press_syst, name="host_blood_press_syst", curie=DEFAULT_.curie('host_blood_press_syst'), - model_uri=DEFAULT_.host_blood_press_syst, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_blood_press_syst], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_color = Slot(uri=DEFAULT_.host_color, name="host_color", curie=DEFAULT_.curie('host_color'), - model_uri=DEFAULT_.host_color, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_color]) - -slots.host_shape = Slot(uri=DEFAULT_.host_shape, name="host_shape", curie=DEFAULT_.curie('host_shape'), - model_uri=DEFAULT_.host_shape, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_shape]) - -slots.gravidity = Slot(uri=DEFAULT_.gravidity, name="gravidity", curie=DEFAULT_.curie('gravidity'), - model_uri=DEFAULT_.gravidity, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.gravidity]) - -slots.ihmc_medication_code = Slot(uri=DEFAULT_.ihmc_medication_code, name="ihmc_medication_code", curie=DEFAULT_.curie('ihmc_medication_code'), - model_uri=DEFAULT_.ihmc_medication_code, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ihmc_medication_code]) - -slots.smoker = Slot(uri=DEFAULT_.smoker, name="smoker", curie=DEFAULT_.curie('smoker'), - model_uri=DEFAULT_.smoker, domain=None, range=Optional[Union[dict, BooleanValue]], mappings = [MIXS.smoker], - pattern=re.compile(r'[true|false]')) - -slots.host_hiv_stat = Slot(uri=DEFAULT_.host_hiv_stat, name="host_hiv_stat", curie=DEFAULT_.curie('host_hiv_stat'), - model_uri=DEFAULT_.host_hiv_stat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_hiv_stat], - pattern=re.compile(r'[true|false];[true|false]')) - -slots.drug_usage = Slot(uri=DEFAULT_.drug_usage, name="drug_usage", curie=DEFAULT_.curie('drug_usage'), - model_uri=DEFAULT_.drug_usage, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.drug_usage]) - -slots.host_body_mass_index = Slot(uri=DEFAULT_.host_body_mass_index, name="host_body_mass_index", curie=DEFAULT_.curie('host_body_mass_index'), - model_uri=DEFAULT_.host_body_mass_index, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_body_mass_index], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diet_last_six_month = Slot(uri=DEFAULT_.diet_last_six_month, name="diet_last_six_month", curie=DEFAULT_.curie('diet_last_six_month'), - model_uri=DEFAULT_.diet_last_six_month, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.diet_last_six_month]) - -slots.weight_loss_3_month = Slot(uri=DEFAULT_.weight_loss_3_month, name="weight_loss_3_month", curie=DEFAULT_.curie('weight_loss_3_month'), - model_uri=DEFAULT_.weight_loss_3_month, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.weight_loss_3_month], - pattern=re.compile(r'[true|false];\d+[.\d+] \S+')) - -slots.ihmc_ethnicity = Slot(uri=DEFAULT_.ihmc_ethnicity, name="ihmc_ethnicity", curie=DEFAULT_.curie('ihmc_ethnicity'), - model_uri=DEFAULT_.ihmc_ethnicity, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ihmc_ethnicity]) - -slots.host_occupation = Slot(uri=DEFAULT_.host_occupation, name="host_occupation", curie=DEFAULT_.curie('host_occupation'), - model_uri=DEFAULT_.host_occupation, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_occupation]) - -slots.pet_farm_animal = Slot(uri=DEFAULT_.pet_farm_animal, name="pet_farm_animal", curie=DEFAULT_.curie('pet_farm_animal'), - model_uri=DEFAULT_.pet_farm_animal, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pet_farm_animal]) - -slots.travel_out_six_month = Slot(uri=DEFAULT_.travel_out_six_month, name="travel_out_six_month", curie=DEFAULT_.curie('travel_out_six_month'), - model_uri=DEFAULT_.travel_out_six_month, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.travel_out_six_month]) - -slots.twin_sibling = Slot(uri=DEFAULT_.twin_sibling, name="twin_sibling", curie=DEFAULT_.curie('twin_sibling'), - model_uri=DEFAULT_.twin_sibling, domain=None, range=Optional[Union[dict, BooleanValue]], mappings = [MIXS.twin_sibling], - pattern=re.compile(r'[true|false]')) - -slots.medic_hist_perform = Slot(uri=DEFAULT_.medic_hist_perform, name="medic_hist_perform", curie=DEFAULT_.curie('medic_hist_perform'), - model_uri=DEFAULT_.medic_hist_perform, domain=None, range=Optional[Union[dict, BooleanValue]], mappings = [MIXS.medic_hist_perform], - pattern=re.compile(r'[true|false]')) - -slots.study_complt_stat = Slot(uri=DEFAULT_.study_complt_stat, name="study_complt_stat", curie=DEFAULT_.curie('study_complt_stat'), - model_uri=DEFAULT_.study_complt_stat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.study_complt_stat], - pattern=re.compile(r'[true|false];[adverse event|non\-compliance|lost to follow up|other\-specify]')) - -slots.pulmonary_disord = Slot(uri=DEFAULT_.pulmonary_disord, name="pulmonary_disord", curie=DEFAULT_.curie('pulmonary_disord'), - model_uri=DEFAULT_.pulmonary_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pulmonary_disord]) - -slots.nose_throat_disord = Slot(uri=DEFAULT_.nose_throat_disord, name="nose_throat_disord", curie=DEFAULT_.curie('nose_throat_disord'), - model_uri=DEFAULT_.nose_throat_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.nose_throat_disord]) - -slots.blood_blood_disord = Slot(uri=DEFAULT_.blood_blood_disord, name="blood_blood_disord", curie=DEFAULT_.curie('blood_blood_disord'), - model_uri=DEFAULT_.blood_blood_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.blood_blood_disord]) - -slots.host_pulse = Slot(uri=DEFAULT_.host_pulse, name="host_pulse", curie=DEFAULT_.curie('host_pulse'), - model_uri=DEFAULT_.host_pulse, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_pulse], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.gestation_state = Slot(uri=DEFAULT_.gestation_state, name="gestation_state", curie=DEFAULT_.curie('gestation_state'), - model_uri=DEFAULT_.gestation_state, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.gestation_state]) - -slots.maternal_health_stat = Slot(uri=DEFAULT_.maternal_health_stat, name="maternal_health_stat", curie=DEFAULT_.curie('maternal_health_stat'), - model_uri=DEFAULT_.maternal_health_stat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.maternal_health_stat]) - -slots.foetal_health_stat = Slot(uri=DEFAULT_.foetal_health_stat, name="foetal_health_stat", curie=DEFAULT_.curie('foetal_health_stat'), - model_uri=DEFAULT_.foetal_health_stat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.foetal_health_stat]) - -slots.amniotic_fluid_color = Slot(uri=DEFAULT_.amniotic_fluid_color, name="amniotic_fluid_color", curie=DEFAULT_.curie('amniotic_fluid_color'), - model_uri=DEFAULT_.amniotic_fluid_color, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.amniotic_fluid_color]) - -slots.kidney_disord = Slot(uri=DEFAULT_.kidney_disord, name="kidney_disord", curie=DEFAULT_.curie('kidney_disord'), - model_uri=DEFAULT_.kidney_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.kidney_disord]) - -slots.urogenit_tract_disor = Slot(uri=DEFAULT_.urogenit_tract_disor, name="urogenit_tract_disor", curie=DEFAULT_.curie('urogenit_tract_disor'), - model_uri=DEFAULT_.urogenit_tract_disor, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.urogenit_tract_disor]) - -slots.urine_collect_meth = Slot(uri=DEFAULT_.urine_collect_meth, name="urine_collect_meth", curie=DEFAULT_.curie('urine_collect_meth'), - model_uri=DEFAULT_.urine_collect_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.urine_collect_meth], - pattern=re.compile(r'[clean catch|catheter]')) - -slots.gastrointest_disord = Slot(uri=DEFAULT_.gastrointest_disord, name="gastrointest_disord", curie=DEFAULT_.curie('gastrointest_disord'), - model_uri=DEFAULT_.gastrointest_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.gastrointest_disord]) - -slots.liver_disord = Slot(uri=DEFAULT_.liver_disord, name="liver_disord", curie=DEFAULT_.curie('liver_disord'), - model_uri=DEFAULT_.liver_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.liver_disord]) - -slots.special_diet = Slot(uri=DEFAULT_.special_diet, name="special_diet", curie=DEFAULT_.curie('special_diet'), - model_uri=DEFAULT_.special_diet, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.special_diet], - pattern=re.compile(r'[low carb|reduced calorie|vegetarian|other(to be specified)]')) - -slots.nose_mouth_teeth_throat_disord = Slot(uri=DEFAULT_.nose_mouth_teeth_throat_disord, name="nose_mouth_teeth_throat_disord", curie=DEFAULT_.curie('nose_mouth_teeth_throat_disord'), - model_uri=DEFAULT_.nose_mouth_teeth_throat_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.nose_mouth_teeth_throat_disord]) - -slots.time_last_toothbrush = Slot(uri=DEFAULT_.time_last_toothbrush, name="time_last_toothbrush", curie=DEFAULT_.curie('time_last_toothbrush'), - model_uri=DEFAULT_.time_last_toothbrush, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.time_last_toothbrush]) - -slots.dermatology_disord = Slot(uri=DEFAULT_.dermatology_disord, name="dermatology_disord", curie=DEFAULT_.curie('dermatology_disord'), - model_uri=DEFAULT_.dermatology_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.dermatology_disord]) - -slots.time_since_last_wash = Slot(uri=DEFAULT_.time_since_last_wash, name="time_since_last_wash", curie=DEFAULT_.curie('time_since_last_wash'), - model_uri=DEFAULT_.time_since_last_wash, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.time_since_last_wash]) - -slots.dominant_hand = Slot(uri=DEFAULT_.dominant_hand, name="dominant_hand", curie=DEFAULT_.curie('dominant_hand'), - model_uri=DEFAULT_.dominant_hand, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.dominant_hand], - pattern=re.compile(r'[left|right|ambidextrous]')) - -slots.menarche = Slot(uri=DEFAULT_.menarche, name="menarche", curie=DEFAULT_.curie('menarche'), - model_uri=DEFAULT_.menarche, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.menarche]) - -slots.sexual_act = Slot(uri=DEFAULT_.sexual_act, name="sexual_act", curie=DEFAULT_.curie('sexual_act'), - model_uri=DEFAULT_.sexual_act, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sexual_act]) - -slots.pregnancy = Slot(uri=DEFAULT_.pregnancy, name="pregnancy", curie=DEFAULT_.curie('pregnancy'), - model_uri=DEFAULT_.pregnancy, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.pregnancy]) - -slots.douche = Slot(uri=DEFAULT_.douche, name="douche", curie=DEFAULT_.curie('douche'), - model_uri=DEFAULT_.douche, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.douche]) - -slots.birth_control = Slot(uri=DEFAULT_.birth_control, name="birth_control", curie=DEFAULT_.curie('birth_control'), - model_uri=DEFAULT_.birth_control, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.birth_control]) - -slots.menopause = Slot(uri=DEFAULT_.menopause, name="menopause", curie=DEFAULT_.curie('menopause'), - model_uri=DEFAULT_.menopause, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.menopause]) - -slots.hrt = Slot(uri=DEFAULT_.hrt, name="hrt", curie=DEFAULT_.curie('hrt'), - model_uri=DEFAULT_.hrt, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.hrt]) - -slots.hysterectomy = Slot(uri=DEFAULT_.hysterectomy, name="hysterectomy", curie=DEFAULT_.curie('hysterectomy'), - model_uri=DEFAULT_.hysterectomy, domain=None, range=Optional[Union[dict, BooleanValue]], mappings = [MIXS.hysterectomy], - pattern=re.compile(r'[true|false]')) - -slots.gynecologic_disord = Slot(uri=DEFAULT_.gynecologic_disord, name="gynecologic_disord", curie=DEFAULT_.curie('gynecologic_disord'), - model_uri=DEFAULT_.gynecologic_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.gynecologic_disord]) - -slots.urogenit_disord = Slot(uri=DEFAULT_.urogenit_disord, name="urogenit_disord", curie=DEFAULT_.curie('urogenit_disord'), - model_uri=DEFAULT_.urogenit_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.urogenit_disord]) - -slots.hcr = Slot(uri=DEFAULT_.hcr, name="hcr", curie=DEFAULT_.curie('hcr'), - model_uri=DEFAULT_.hcr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.hcr], - pattern=re.compile(r'[Oil Reservoir|Gas Reservoir|Oil Sand|Coalbed|Shale|Tight Oil Reservoir|Tight Gas Reservoir|other]')) - -slots.hc_produced = Slot(uri=DEFAULT_.hc_produced, name="hc_produced", curie=DEFAULT_.curie('hc_produced'), - model_uri=DEFAULT_.hc_produced, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.hc_produced], - pattern=re.compile(r'[Oil|Gas\-Condensate|Gas|Bitumen|Coalbed Methane|other]')) - -slots.basin = Slot(uri=DEFAULT_.basin, name="basin", curie=DEFAULT_.curie('basin'), - model_uri=DEFAULT_.basin, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.basin]) - -slots.field = Slot(uri=DEFAULT_.field, name="field", curie=DEFAULT_.curie('field'), - model_uri=DEFAULT_.field, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.field]) - -slots.reservoir = Slot(uri=DEFAULT_.reservoir, name="reservoir", curie=DEFAULT_.curie('reservoir'), - model_uri=DEFAULT_.reservoir, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.reservoir]) - -slots.hcr_temp = Slot(uri=DEFAULT_.hcr_temp, name="hcr_temp", curie=DEFAULT_.curie('hcr_temp'), - model_uri=DEFAULT_.hcr_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.hcr_temp], - pattern=re.compile(r'\d+[.\d+] \- \d+[.\d+] \S+')) - -slots.tvdss_of_hcr_temp = Slot(uri=DEFAULT_.tvdss_of_hcr_temp, name="tvdss_of_hcr_temp", curie=DEFAULT_.curie('tvdss_of_hcr_temp'), - model_uri=DEFAULT_.tvdss_of_hcr_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tvdss_of_hcr_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.hcr_pressure = Slot(uri=DEFAULT_.hcr_pressure, name="hcr_pressure", curie=DEFAULT_.curie('hcr_pressure'), - model_uri=DEFAULT_.hcr_pressure, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.hcr_pressure], - pattern=re.compile(r'\d+[.\d+] \- \d+[.\d+] \S+')) - -slots.tvdss_of_hcr_pressure = Slot(uri=DEFAULT_.tvdss_of_hcr_pressure, name="tvdss_of_hcr_pressure", curie=DEFAULT_.curie('tvdss_of_hcr_pressure'), - model_uri=DEFAULT_.tvdss_of_hcr_pressure, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tvdss_of_hcr_pressure], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.permeability = Slot(uri=DEFAULT_.permeability, name="permeability", curie=DEFAULT_.curie('permeability'), - model_uri=DEFAULT_.permeability, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.permeability]) - -slots.porosity = Slot(uri=DEFAULT_.porosity, name="porosity", curie=DEFAULT_.curie('porosity'), - model_uri=DEFAULT_.porosity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.porosity], - pattern=re.compile(r'\d+[.\d+] \- \d+[.\d+] \S+')) - -slots.lithology = Slot(uri=DEFAULT_.lithology, name="lithology", curie=DEFAULT_.curie('lithology'), - model_uri=DEFAULT_.lithology, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.lithology], - pattern=re.compile(r'[Basement|Chalk|Chert|Coal|Conglomerate|Diatomite|Dolomite|Limestone|Sandstone|Shale|Siltstone|Volcanic|other]')) - -slots.depos_env = Slot(uri=DEFAULT_.depos_env, name="depos_env", curie=DEFAULT_.curie('depos_env'), - model_uri=DEFAULT_.depos_env, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.depos_env], - pattern=re.compile(r'[Continental \- Alluvial|Continental \- Aeolian|Continental \- Fluvial|Continental \- Lacustrine|Transitional \- Deltaic|Transitional \- Tidal|Transitional \- Lagoonal|Transitional \- Beach|Transitional \- Lake|Marine \- Shallow|Marine \- Deep|Marine \- Reef|Other \- Evaporite|Other \- Glacial|Other \- Volcanic|other]')) - -slots.hcr_geol_age = Slot(uri=DEFAULT_.hcr_geol_age, name="hcr_geol_age", curie=DEFAULT_.curie('hcr_geol_age'), - model_uri=DEFAULT_.hcr_geol_age, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.hcr_geol_age], - pattern=re.compile(r'[Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other]')) - -slots.owc_tvdss = Slot(uri=DEFAULT_.owc_tvdss, name="owc_tvdss", curie=DEFAULT_.curie('owc_tvdss'), - model_uri=DEFAULT_.owc_tvdss, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.owc_tvdss], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.hcr_fw_salinity = Slot(uri=DEFAULT_.hcr_fw_salinity, name="hcr_fw_salinity", curie=DEFAULT_.curie('hcr_fw_salinity'), - model_uri=DEFAULT_.hcr_fw_salinity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.hcr_fw_salinity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.sulfate_fw = Slot(uri=DEFAULT_.sulfate_fw, name="sulfate_fw", curie=DEFAULT_.curie('sulfate_fw'), - model_uri=DEFAULT_.sulfate_fw, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.sulfate_fw], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.vfa_fw = Slot(uri=DEFAULT_.vfa_fw, name="vfa_fw", curie=DEFAULT_.curie('vfa_fw'), - model_uri=DEFAULT_.vfa_fw, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.vfa_fw], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.sr_kerog_type = Slot(uri=DEFAULT_.sr_kerog_type, name="sr_kerog_type", curie=DEFAULT_.curie('sr_kerog_type'), - model_uri=DEFAULT_.sr_kerog_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sr_kerog_type], - pattern=re.compile(r'[Type I|Type II|Type III|Type IV|other]')) - -slots.sr_lithology = Slot(uri=DEFAULT_.sr_lithology, name="sr_lithology", curie=DEFAULT_.curie('sr_lithology'), - model_uri=DEFAULT_.sr_lithology, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sr_lithology], - pattern=re.compile(r'[Clastic|Carbonate|Coal|Biosilicieous|other]')) - -slots.sr_dep_env = Slot(uri=DEFAULT_.sr_dep_env, name="sr_dep_env", curie=DEFAULT_.curie('sr_dep_env'), - model_uri=DEFAULT_.sr_dep_env, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sr_dep_env], - pattern=re.compile(r'[Lacustine|Fluvioldeltaic|Fluviomarine|Marine|other]')) - -slots.sr_geol_age = Slot(uri=DEFAULT_.sr_geol_age, name="sr_geol_age", curie=DEFAULT_.curie('sr_geol_age'), - model_uri=DEFAULT_.sr_geol_age, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sr_geol_age], - pattern=re.compile(r'[Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other]')) - -slots.samp_well_name = Slot(uri=DEFAULT_.samp_well_name, name="samp_well_name", curie=DEFAULT_.curie('samp_well_name'), - model_uri=DEFAULT_.samp_well_name, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_well_name]) - -slots.win = Slot(uri=DEFAULT_.win, name="win", curie=DEFAULT_.curie('win'), - model_uri=DEFAULT_.win, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.win]) - -slots.samp_type = Slot(uri=DEFAULT_.samp_type, name="samp_type", curie=DEFAULT_.curie('samp_type'), - model_uri=DEFAULT_.samp_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_type], - pattern=re.compile(r'[core|rock trimmings|drill cuttings|piping section|coupon|pigging debris|solid deposit|produced fluid|produced water|injected water|water from treatment plant|fresh water|sea water|drilling fluid|procedural blank|positive control|negative control|other]')) - -slots.samp_subtype = Slot(uri=DEFAULT_.samp_subtype, name="samp_subtype", curie=DEFAULT_.curie('samp_subtype'), - model_uri=DEFAULT_.samp_subtype, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_subtype], - pattern=re.compile(r'[oil phase|water phase|biofilm|not applicable|other]')) - -slots.pressure = Slot(uri=DEFAULT_.pressure, name="pressure", curie=DEFAULT_.curie('pressure'), - model_uri=DEFAULT_.pressure, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.pressure], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.samp_tvdss = Slot(uri=DEFAULT_.samp_tvdss, name="samp_tvdss", curie=DEFAULT_.curie('samp_tvdss'), - model_uri=DEFAULT_.samp_tvdss, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_tvdss], - pattern=re.compile(r'\d+[.\d+]\-\d+[.\d+] \S+')) - -slots.samp_md = Slot(uri=DEFAULT_.samp_md, name="samp_md", curie=DEFAULT_.curie('samp_md'), - model_uri=DEFAULT_.samp_md, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_md], - pattern=re.compile(r'\d+[.\d+] \S+;[GL|DF|RT|KB|MSL|other]')) - -slots.samp_transport_cond = Slot(uri=DEFAULT_.samp_transport_cond, name="samp_transport_cond", curie=DEFAULT_.curie('samp_transport_cond'), - model_uri=DEFAULT_.samp_transport_cond, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_transport_cond], - pattern=re.compile(r'\d+[.\d+] \S+;\d+[.\d+] \S+')) - -slots.organism_count_qpcr_info = Slot(uri=DEFAULT_.organism_count_qpcr_info, name="organism_count_qpcr_info", curie=DEFAULT_.curie('organism_count_qpcr_info'), - model_uri=DEFAULT_.organism_count_qpcr_info, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.organism_count_qpcr_info]) - -slots.ph = Slot(uri=DEFAULT_.ph, name="ph", curie=DEFAULT_.curie('ph'), - model_uri=DEFAULT_.ph, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.ph], - pattern=re.compile(r'\d+[.\d+]')) - -slots.alkalinity = Slot(uri=DEFAULT_.alkalinity, name="alkalinity", curie=DEFAULT_.curie('alkalinity'), - model_uri=DEFAULT_.alkalinity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.alkalinity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.alkalinity_method = Slot(uri=DEFAULT_.alkalinity_method, name="alkalinity_method", curie=DEFAULT_.curie('alkalinity_method'), - model_uri=DEFAULT_.alkalinity_method, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.alkalinity_method]) - -slots.sulfate = Slot(uri=DEFAULT_.sulfate, name="sulfate", curie=DEFAULT_.curie('sulfate'), - model_uri=DEFAULT_.sulfate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.sulfate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.sulfide = Slot(uri=DEFAULT_.sulfide, name="sulfide", curie=DEFAULT_.curie('sulfide'), - model_uri=DEFAULT_.sulfide, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.sulfide], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_sulfur = Slot(uri=DEFAULT_.tot_sulfur, name="tot_sulfur", curie=DEFAULT_.curie('tot_sulfur'), - model_uri=DEFAULT_.tot_sulfur, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_sulfur], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.nitrate = Slot(uri=DEFAULT_.nitrate, name="nitrate", curie=DEFAULT_.curie('nitrate'), - model_uri=DEFAULT_.nitrate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.nitrate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.nitrite = Slot(uri=DEFAULT_.nitrite, name="nitrite", curie=DEFAULT_.curie('nitrite'), - model_uri=DEFAULT_.nitrite, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.nitrite], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.ammonium = Slot(uri=DEFAULT_.ammonium, name="ammonium", curie=DEFAULT_.curie('ammonium'), - model_uri=DEFAULT_.ammonium, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.ammonium], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_nitro = Slot(uri=DEFAULT_.tot_nitro, name="tot_nitro", curie=DEFAULT_.curie('tot_nitro'), - model_uri=DEFAULT_.tot_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_iron = Slot(uri=DEFAULT_.diss_iron, name="diss_iron", curie=DEFAULT_.curie('diss_iron'), - model_uri=DEFAULT_.diss_iron, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_iron], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.sodium = Slot(uri=DEFAULT_.sodium, name="sodium", curie=DEFAULT_.curie('sodium'), - model_uri=DEFAULT_.sodium, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.sodium], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.chloride = Slot(uri=DEFAULT_.chloride, name="chloride", curie=DEFAULT_.curie('chloride'), - model_uri=DEFAULT_.chloride, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.chloride], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.potassium = Slot(uri=DEFAULT_.potassium, name="potassium", curie=DEFAULT_.curie('potassium'), - model_uri=DEFAULT_.potassium, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.potassium], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.magnesium = Slot(uri=DEFAULT_.magnesium, name="magnesium", curie=DEFAULT_.curie('magnesium'), - model_uri=DEFAULT_.magnesium, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.magnesium], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.calcium = Slot(uri=DEFAULT_.calcium, name="calcium", curie=DEFAULT_.curie('calcium'), - model_uri=DEFAULT_.calcium, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.calcium], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_iron = Slot(uri=DEFAULT_.tot_iron, name="tot_iron", curie=DEFAULT_.curie('tot_iron'), - model_uri=DEFAULT_.tot_iron, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_iron], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_org_carb = Slot(uri=DEFAULT_.diss_org_carb, name="diss_org_carb", curie=DEFAULT_.curie('diss_org_carb'), - model_uri=DEFAULT_.diss_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_org_carb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_inorg_carb = Slot(uri=DEFAULT_.diss_inorg_carb, name="diss_inorg_carb", curie=DEFAULT_.curie('diss_inorg_carb'), - model_uri=DEFAULT_.diss_inorg_carb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_inorg_carb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_inorg_phosp = Slot(uri=DEFAULT_.diss_inorg_phosp, name="diss_inorg_phosp", curie=DEFAULT_.curie('diss_inorg_phosp'), - model_uri=DEFAULT_.diss_inorg_phosp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_inorg_phosp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_phosp = Slot(uri=DEFAULT_.tot_phosp, name="tot_phosp", curie=DEFAULT_.curie('tot_phosp'), - model_uri=DEFAULT_.tot_phosp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_phosp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.suspend_solids = Slot(uri=DEFAULT_.suspend_solids, name="suspend_solids", curie=DEFAULT_.curie('suspend_solids'), - model_uri=DEFAULT_.suspend_solids, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.suspend_solids]) - -slots.density = Slot(uri=DEFAULT_.density, name="density", curie=DEFAULT_.curie('density'), - model_uri=DEFAULT_.density, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.density], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_carb_dioxide = Slot(uri=DEFAULT_.diss_carb_dioxide, name="diss_carb_dioxide", curie=DEFAULT_.curie('diss_carb_dioxide'), - model_uri=DEFAULT_.diss_carb_dioxide, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_carb_dioxide], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_oxygen_fluid = Slot(uri=DEFAULT_.diss_oxygen_fluid, name="diss_oxygen_fluid", curie=DEFAULT_.curie('diss_oxygen_fluid'), - model_uri=DEFAULT_.diss_oxygen_fluid, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_oxygen_fluid], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.vfa = Slot(uri=DEFAULT_.vfa, name="vfa", curie=DEFAULT_.curie('vfa'), - model_uri=DEFAULT_.vfa, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.vfa], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.benzene = Slot(uri=DEFAULT_.benzene, name="benzene", curie=DEFAULT_.curie('benzene'), - model_uri=DEFAULT_.benzene, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.benzene], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.toluene = Slot(uri=DEFAULT_.toluene, name="toluene", curie=DEFAULT_.curie('toluene'), - model_uri=DEFAULT_.toluene, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.toluene], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.ethylbenzene = Slot(uri=DEFAULT_.ethylbenzene, name="ethylbenzene", curie=DEFAULT_.curie('ethylbenzene'), - model_uri=DEFAULT_.ethylbenzene, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.ethylbenzene], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.xylene = Slot(uri=DEFAULT_.xylene, name="xylene", curie=DEFAULT_.curie('xylene'), - model_uri=DEFAULT_.xylene, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.xylene], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.api = Slot(uri=DEFAULT_.api, name="api", curie=DEFAULT_.curie('api'), - model_uri=DEFAULT_.api, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.api], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tan = Slot(uri=DEFAULT_.tan, name="tan", curie=DEFAULT_.curie('tan'), - model_uri=DEFAULT_.tan, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tan], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.viscosity = Slot(uri=DEFAULT_.viscosity, name="viscosity", curie=DEFAULT_.curie('viscosity'), - model_uri=DEFAULT_.viscosity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.viscosity], - pattern=re.compile(r'\d+[.\d+] \S+;\d+[.\d+] \S+')) - -slots.pour_point = Slot(uri=DEFAULT_.pour_point, name="pour_point", curie=DEFAULT_.curie('pour_point'), - model_uri=DEFAULT_.pour_point, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.pour_point], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.saturates_pc = Slot(uri=DEFAULT_.saturates_pc, name="saturates_pc", curie=DEFAULT_.curie('saturates_pc'), - model_uri=DEFAULT_.saturates_pc, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.saturates_pc]) - -slots.aromatics_pc = Slot(uri=DEFAULT_.aromatics_pc, name="aromatics_pc", curie=DEFAULT_.curie('aromatics_pc'), - model_uri=DEFAULT_.aromatics_pc, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.aromatics_pc]) - -slots.resins_pc = Slot(uri=DEFAULT_.resins_pc, name="resins_pc", curie=DEFAULT_.curie('resins_pc'), - model_uri=DEFAULT_.resins_pc, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.resins_pc]) - -slots.asphaltenes_pc = Slot(uri=DEFAULT_.asphaltenes_pc, name="asphaltenes_pc", curie=DEFAULT_.curie('asphaltenes_pc'), - model_uri=DEFAULT_.asphaltenes_pc, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.asphaltenes_pc]) - -slots.additional_info = Slot(uri=DEFAULT_.additional_info, name="additional_info", curie=DEFAULT_.curie('additional_info'), - model_uri=DEFAULT_.additional_info, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.additional_info]) - -slots.prod_start_date = Slot(uri=DEFAULT_.prod_start_date, name="prod_start_date", curie=DEFAULT_.curie('prod_start_date'), - model_uri=DEFAULT_.prod_start_date, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.prod_start_date]) - -slots.prod_rate = Slot(uri=DEFAULT_.prod_rate, name="prod_rate", curie=DEFAULT_.curie('prod_rate'), - model_uri=DEFAULT_.prod_rate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.prod_rate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.water_production_rate = Slot(uri=DEFAULT_.water_production_rate, name="water_production_rate", curie=DEFAULT_.curie('water_production_rate'), - model_uri=DEFAULT_.water_production_rate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.water_production_rate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.water_cut = Slot(uri=DEFAULT_.water_cut, name="water_cut", curie=DEFAULT_.curie('water_cut'), - model_uri=DEFAULT_.water_cut, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.water_cut], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.iwf = Slot(uri=DEFAULT_.iwf, name="iwf", curie=DEFAULT_.curie('iwf'), - model_uri=DEFAULT_.iwf, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.iwf], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.add_recov_method = Slot(uri=DEFAULT_.add_recov_method, name="add_recov_method", curie=DEFAULT_.curie('add_recov_method'), - model_uri=DEFAULT_.add_recov_method, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.add_recov_method]) - -slots.iw_bt_date_well = Slot(uri=DEFAULT_.iw_bt_date_well, name="iw_bt_date_well", curie=DEFAULT_.curie('iw_bt_date_well'), - model_uri=DEFAULT_.iw_bt_date_well, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.iw_bt_date_well]) - -slots.biocide = Slot(uri=DEFAULT_.biocide, name="biocide", curie=DEFAULT_.curie('biocide'), - model_uri=DEFAULT_.biocide, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.biocide]) - -slots.biocide_admin_method = Slot(uri=DEFAULT_.biocide_admin_method, name="biocide_admin_method", curie=DEFAULT_.curie('biocide_admin_method'), - model_uri=DEFAULT_.biocide_admin_method, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.biocide_admin_method]) - -slots.chem_treatment = Slot(uri=DEFAULT_.chem_treatment, name="chem_treatment", curie=DEFAULT_.curie('chem_treatment'), - model_uri=DEFAULT_.chem_treatment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.chem_treatment]) - -slots.chem_treatment_method = Slot(uri=DEFAULT_.chem_treatment_method, name="chem_treatment_method", curie=DEFAULT_.curie('chem_treatment_method'), - model_uri=DEFAULT_.chem_treatment_method, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.chem_treatment_method]) - -slots.samp_loc_corr_rate = Slot(uri=DEFAULT_.samp_loc_corr_rate, name="samp_loc_corr_rate", curie=DEFAULT_.curie('samp_loc_corr_rate'), - model_uri=DEFAULT_.samp_loc_corr_rate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_loc_corr_rate], - pattern=re.compile(r'\d+[.\d+] \- \d+[.\d+] \S+')) - -slots.samp_collection_point = Slot(uri=DEFAULT_.samp_collection_point, name="samp_collection_point", curie=DEFAULT_.curie('samp_collection_point'), - model_uri=DEFAULT_.samp_collection_point, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_collection_point], - pattern=re.compile(r'[well|test well|drilling rig|wellhead|separator|storage tank|other]')) - -slots.samp_preserv = Slot(uri=DEFAULT_.samp_preserv, name="samp_preserv", curie=DEFAULT_.curie('samp_preserv'), - model_uri=DEFAULT_.samp_preserv, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_preserv]) - -slots.alkyl_diethers = Slot(uri=DEFAULT_.alkyl_diethers, name="alkyl_diethers", curie=DEFAULT_.curie('alkyl_diethers'), - model_uri=DEFAULT_.alkyl_diethers, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.alkyl_diethers], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.aminopept_act = Slot(uri=DEFAULT_.aminopept_act, name="aminopept_act", curie=DEFAULT_.curie('aminopept_act'), - model_uri=DEFAULT_.aminopept_act, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.aminopept_act], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.bacteria_carb_prod = Slot(uri=DEFAULT_.bacteria_carb_prod, name="bacteria_carb_prod", curie=DEFAULT_.curie('bacteria_carb_prod'), - model_uri=DEFAULT_.bacteria_carb_prod, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.bacteria_carb_prod], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.biomass = Slot(uri=DEFAULT_.biomass, name="biomass", curie=DEFAULT_.curie('biomass'), - model_uri=DEFAULT_.biomass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.biomass]) - -slots.bishomohopanol = Slot(uri=DEFAULT_.bishomohopanol, name="bishomohopanol", curie=DEFAULT_.curie('bishomohopanol'), - model_uri=DEFAULT_.bishomohopanol, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.bishomohopanol], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.bromide = Slot(uri=DEFAULT_.bromide, name="bromide", curie=DEFAULT_.curie('bromide'), - model_uri=DEFAULT_.bromide, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.bromide], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.carb_nitro_ratio = Slot(uri=DEFAULT_.carb_nitro_ratio, name="carb_nitro_ratio", curie=DEFAULT_.curie('carb_nitro_ratio'), - model_uri=DEFAULT_.carb_nitro_ratio, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.carb_nitro_ratio], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.chlorophyll = Slot(uri=DEFAULT_.chlorophyll, name="chlorophyll", curie=DEFAULT_.curie('chlorophyll'), - model_uri=DEFAULT_.chlorophyll, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.chlorophyll], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diether_lipids = Slot(uri=DEFAULT_.diether_lipids, name="diether_lipids", curie=DEFAULT_.curie('diether_lipids'), - model_uri=DEFAULT_.diether_lipids, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diether_lipids]) - -slots.diss_hydrogen = Slot(uri=DEFAULT_.diss_hydrogen, name="diss_hydrogen", curie=DEFAULT_.curie('diss_hydrogen'), - model_uri=DEFAULT_.diss_hydrogen, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_hydrogen], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_org_nitro = Slot(uri=DEFAULT_.diss_org_nitro, name="diss_org_nitro", curie=DEFAULT_.curie('diss_org_nitro'), - model_uri=DEFAULT_.diss_org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_org_nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_oxygen = Slot(uri=DEFAULT_.diss_oxygen, name="diss_oxygen", curie=DEFAULT_.curie('diss_oxygen'), - model_uri=DEFAULT_.diss_oxygen, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_oxygen], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.glucosidase_act = Slot(uri=DEFAULT_.glucosidase_act, name="glucosidase_act", curie=DEFAULT_.curie('glucosidase_act'), - model_uri=DEFAULT_.glucosidase_act, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.glucosidase_act], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.mean_frict_vel = Slot(uri=DEFAULT_.mean_frict_vel, name="mean_frict_vel", curie=DEFAULT_.curie('mean_frict_vel'), - model_uri=DEFAULT_.mean_frict_vel, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.mean_frict_vel], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.mean_peak_frict_vel = Slot(uri=DEFAULT_.mean_peak_frict_vel, name="mean_peak_frict_vel", curie=DEFAULT_.curie('mean_peak_frict_vel'), - model_uri=DEFAULT_.mean_peak_frict_vel, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.mean_peak_frict_vel], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.n_alkanes = Slot(uri=DEFAULT_.n_alkanes, name="n_alkanes", curie=DEFAULT_.curie('n_alkanes'), - model_uri=DEFAULT_.n_alkanes, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.n_alkanes]) - -slots.nitro = Slot(uri=DEFAULT_.nitro, name="nitro", curie=DEFAULT_.curie('nitro'), - model_uri=DEFAULT_.nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.org_carb = Slot(uri=DEFAULT_.org_carb, name="org_carb", curie=DEFAULT_.curie('org_carb'), - model_uri=DEFAULT_.org_carb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.org_carb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.org_matter = Slot(uri=DEFAULT_.org_matter, name="org_matter", curie=DEFAULT_.curie('org_matter'), - model_uri=DEFAULT_.org_matter, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.org_matter], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.org_nitro = Slot(uri=DEFAULT_.org_nitro, name="org_nitro", curie=DEFAULT_.curie('org_nitro'), - model_uri=DEFAULT_.org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.org_nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.part_org_carb = Slot(uri=DEFAULT_.part_org_carb, name="part_org_carb", curie=DEFAULT_.curie('part_org_carb'), - model_uri=DEFAULT_.part_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.part_org_carb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.petroleum_hydrocarb = Slot(uri=DEFAULT_.petroleum_hydrocarb, name="petroleum_hydrocarb", curie=DEFAULT_.curie('petroleum_hydrocarb'), - model_uri=DEFAULT_.petroleum_hydrocarb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.petroleum_hydrocarb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.phaeopigments = Slot(uri=DEFAULT_.phaeopigments, name="phaeopigments", curie=DEFAULT_.curie('phaeopigments'), - model_uri=DEFAULT_.phaeopigments, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.phaeopigments]) - -slots.phosphate = Slot(uri=DEFAULT_.phosphate, name="phosphate", curie=DEFAULT_.curie('phosphate'), - model_uri=DEFAULT_.phosphate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.phosphate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.phosplipid_fatt_acid = Slot(uri=DEFAULT_.phosplipid_fatt_acid, name="phosplipid_fatt_acid", curie=DEFAULT_.curie('phosplipid_fatt_acid'), - model_uri=DEFAULT_.phosplipid_fatt_acid, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.phosplipid_fatt_acid]) - -slots.redox_potential = Slot(uri=DEFAULT_.redox_potential, name="redox_potential", curie=DEFAULT_.curie('redox_potential'), - model_uri=DEFAULT_.redox_potential, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.redox_potential], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.salinity = Slot(uri=DEFAULT_.salinity, name="salinity", curie=DEFAULT_.curie('salinity'), - model_uri=DEFAULT_.salinity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.salinity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.silicate = Slot(uri=DEFAULT_.silicate, name="silicate", curie=DEFAULT_.curie('silicate'), - model_uri=DEFAULT_.silicate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.silicate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_carb = Slot(uri=DEFAULT_.tot_carb, name="tot_carb", curie=DEFAULT_.curie('tot_carb'), - model_uri=DEFAULT_.tot_carb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_carb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_nitro_content = Slot(uri=DEFAULT_.tot_nitro_content, name="tot_nitro_content", curie=DEFAULT_.curie('tot_nitro_content'), - model_uri=DEFAULT_.tot_nitro_content, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_nitro_content], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_org_carb = Slot(uri=DEFAULT_.tot_org_carb, name="tot_org_carb", curie=DEFAULT_.curie('tot_org_carb'), - model_uri=DEFAULT_.tot_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_org_carb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.turbidity = Slot(uri=DEFAULT_.turbidity, name="turbidity", curie=DEFAULT_.curie('turbidity'), - model_uri=DEFAULT_.turbidity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.turbidity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.water_content = Slot(uri=DEFAULT_.water_content, name="water_content", curie=DEFAULT_.curie('water_content'), - model_uri=DEFAULT_.water_content, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.water_content], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.water_current = Slot(uri=DEFAULT_.water_current, name="water_current", curie=DEFAULT_.curie('water_current'), - model_uri=DEFAULT_.water_current, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.water_current], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.air_temp_regm = Slot(uri=DEFAULT_.air_temp_regm, name="air_temp_regm", curie=DEFAULT_.curie('air_temp_regm'), - model_uri=DEFAULT_.air_temp_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.air_temp_regm]) - -slots.antibiotic_regm = Slot(uri=DEFAULT_.antibiotic_regm, name="antibiotic_regm", curie=DEFAULT_.curie('antibiotic_regm'), - model_uri=DEFAULT_.antibiotic_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.antibiotic_regm]) - -slots.biotic_regm = Slot(uri=DEFAULT_.biotic_regm, name="biotic_regm", curie=DEFAULT_.curie('biotic_regm'), - model_uri=DEFAULT_.biotic_regm, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.biotic_regm]) - -slots.chem_mutagen = Slot(uri=DEFAULT_.chem_mutagen, name="chem_mutagen", curie=DEFAULT_.curie('chem_mutagen'), - model_uri=DEFAULT_.chem_mutagen, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.chem_mutagen]) - -slots.climate_environment = Slot(uri=DEFAULT_.climate_environment, name="climate_environment", curie=DEFAULT_.curie('climate_environment'), - model_uri=DEFAULT_.climate_environment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.climate_environment]) - -slots.cult_root_med = Slot(uri=DEFAULT_.cult_root_med, name="cult_root_med", curie=DEFAULT_.curie('cult_root_med'), - model_uri=DEFAULT_.cult_root_med, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.cult_root_med]) - -slots.fertilizer_regm = Slot(uri=DEFAULT_.fertilizer_regm, name="fertilizer_regm", curie=DEFAULT_.curie('fertilizer_regm'), - model_uri=DEFAULT_.fertilizer_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.fertilizer_regm]) - -slots.fungicide_regm = Slot(uri=DEFAULT_.fungicide_regm, name="fungicide_regm", curie=DEFAULT_.curie('fungicide_regm'), - model_uri=DEFAULT_.fungicide_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.fungicide_regm]) - -slots.gaseous_environment = Slot(uri=DEFAULT_.gaseous_environment, name="gaseous_environment", curie=DEFAULT_.curie('gaseous_environment'), - model_uri=DEFAULT_.gaseous_environment, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.gaseous_environment]) - -slots.gravity = Slot(uri=DEFAULT_.gravity, name="gravity", curie=DEFAULT_.curie('gravity'), - model_uri=DEFAULT_.gravity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.gravity]) - -slots.growth_facil = Slot(uri=DEFAULT_.growth_facil, name="growth_facil", curie=DEFAULT_.curie('growth_facil'), - model_uri=DEFAULT_.growth_facil, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.growth_facil]) - -slots.growth_habit = Slot(uri=DEFAULT_.growth_habit, name="growth_habit", curie=DEFAULT_.curie('growth_habit'), - model_uri=DEFAULT_.growth_habit, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.growth_habit], - pattern=re.compile(r'[erect|semi\-erect|spreading|prostrate] ')) - -slots.growth_hormone_regm = Slot(uri=DEFAULT_.growth_hormone_regm, name="growth_hormone_regm", curie=DEFAULT_.curie('growth_hormone_regm'), - model_uri=DEFAULT_.growth_hormone_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.growth_hormone_regm]) - -slots.herbicide_regm = Slot(uri=DEFAULT_.herbicide_regm, name="herbicide_regm", curie=DEFAULT_.curie('herbicide_regm'), - model_uri=DEFAULT_.herbicide_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.herbicide_regm]) - -slots.host_wet_mass = Slot(uri=DEFAULT_.host_wet_mass, name="host_wet_mass", curie=DEFAULT_.curie('host_wet_mass'), - model_uri=DEFAULT_.host_wet_mass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_wet_mass], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.humidity_regm = Slot(uri=DEFAULT_.humidity_regm, name="humidity_regm", curie=DEFAULT_.curie('humidity_regm'), - model_uri=DEFAULT_.humidity_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.humidity_regm]) - -slots.light_regm = Slot(uri=DEFAULT_.light_regm, name="light_regm", curie=DEFAULT_.curie('light_regm'), - model_uri=DEFAULT_.light_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.light_regm]) - -slots.mechanical_damage = Slot(uri=DEFAULT_.mechanical_damage, name="mechanical_damage", curie=DEFAULT_.curie('mechanical_damage'), - model_uri=DEFAULT_.mechanical_damage, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.mechanical_damage]) - -slots.mineral_nutr_regm = Slot(uri=DEFAULT_.mineral_nutr_regm, name="mineral_nutr_regm", curie=DEFAULT_.curie('mineral_nutr_regm'), - model_uri=DEFAULT_.mineral_nutr_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.mineral_nutr_regm]) - -slots.non_mineral_nutr_regm = Slot(uri=DEFAULT_.non_mineral_nutr_regm, name="non_mineral_nutr_regm", curie=DEFAULT_.curie('non_mineral_nutr_regm'), - model_uri=DEFAULT_.non_mineral_nutr_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.non_mineral_nutr_regm]) - -slots.ph_regm = Slot(uri=DEFAULT_.ph_regm, name="ph_regm", curie=DEFAULT_.curie('ph_regm'), - model_uri=DEFAULT_.ph_regm, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ph_regm]) - -slots.pesticide_regm = Slot(uri=DEFAULT_.pesticide_regm, name="pesticide_regm", curie=DEFAULT_.curie('pesticide_regm'), - model_uri=DEFAULT_.pesticide_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.pesticide_regm]) - -slots.plant_growth_med = Slot(uri=DEFAULT_.plant_growth_med, name="plant_growth_med", curie=DEFAULT_.curie('plant_growth_med'), - model_uri=DEFAULT_.plant_growth_med, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.plant_growth_med], - pattern=re.compile(r'.* \S+:\S+')) - -slots.plant_product = Slot(uri=DEFAULT_.plant_product, name="plant_product", curie=DEFAULT_.curie('plant_product'), - model_uri=DEFAULT_.plant_product, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.plant_product]) - -slots.plant_sex = Slot(uri=DEFAULT_.plant_sex, name="plant_sex", curie=DEFAULT_.curie('plant_sex'), - model_uri=DEFAULT_.plant_sex, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.plant_sex], - pattern=re.compile(r'[Androdioecious|Androecious|Androgynous|Androgynomonoecious|Andromonoecious|Bisexual|Dichogamous|Diclinous|Dioecious|Gynodioecious|Gynoecious|Gynomonoecious|Hermaphroditic|Imperfect|Monoclinous|Monoecious|Perfect|Polygamodioecious|Polygamomonoecious|Polygamous|Protandrous|Protogynous|Subandroecious|Subdioecious|Subgynoecious|Synoecious|Trimonoecious|Trioecious|Unisexual]')) - -slots.plant_struc = Slot(uri=DEFAULT_.plant_struc, name="plant_struc", curie=DEFAULT_.curie('plant_struc'), - model_uri=DEFAULT_.plant_struc, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.plant_struc], - pattern=re.compile(r'.* \S+:\S+')) - -slots.radiation_regm = Slot(uri=DEFAULT_.radiation_regm, name="radiation_regm", curie=DEFAULT_.curie('radiation_regm'), - model_uri=DEFAULT_.radiation_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.radiation_regm]) - -slots.rainfall_regm = Slot(uri=DEFAULT_.rainfall_regm, name="rainfall_regm", curie=DEFAULT_.curie('rainfall_regm'), - model_uri=DEFAULT_.rainfall_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.rainfall_regm]) - -slots.root_cond = Slot(uri=DEFAULT_.root_cond, name="root_cond", curie=DEFAULT_.curie('root_cond'), - model_uri=DEFAULT_.root_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.root_cond]) - -slots.root_med_carbon = Slot(uri=DEFAULT_.root_med_carbon, name="root_med_carbon", curie=DEFAULT_.curie('root_med_carbon'), - model_uri=DEFAULT_.root_med_carbon, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.root_med_carbon]) - -slots.root_med_macronutr = Slot(uri=DEFAULT_.root_med_macronutr, name="root_med_macronutr", curie=DEFAULT_.curie('root_med_macronutr'), - model_uri=DEFAULT_.root_med_macronutr, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.root_med_macronutr]) - -slots.root_med_micronutr = Slot(uri=DEFAULT_.root_med_micronutr, name="root_med_micronutr", curie=DEFAULT_.curie('root_med_micronutr'), - model_uri=DEFAULT_.root_med_micronutr, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.root_med_micronutr]) - -slots.root_med_suppl = Slot(uri=DEFAULT_.root_med_suppl, name="root_med_suppl", curie=DEFAULT_.curie('root_med_suppl'), - model_uri=DEFAULT_.root_med_suppl, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.root_med_suppl]) - -slots.root_med_ph = Slot(uri=DEFAULT_.root_med_ph, name="root_med_ph", curie=DEFAULT_.curie('root_med_ph'), - model_uri=DEFAULT_.root_med_ph, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.root_med_ph], - pattern=re.compile(r'\d+[.\d+]')) - -slots.root_med_regl = Slot(uri=DEFAULT_.root_med_regl, name="root_med_regl", curie=DEFAULT_.curie('root_med_regl'), - model_uri=DEFAULT_.root_med_regl, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.root_med_regl]) - -slots.root_med_solid = Slot(uri=DEFAULT_.root_med_solid, name="root_med_solid", curie=DEFAULT_.curie('root_med_solid'), - model_uri=DEFAULT_.root_med_solid, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.root_med_solid]) - -slots.salt_regm = Slot(uri=DEFAULT_.salt_regm, name="salt_regm", curie=DEFAULT_.curie('salt_regm'), - model_uri=DEFAULT_.salt_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.salt_regm]) - -slots.season_environment = Slot(uri=DEFAULT_.season_environment, name="season_environment", curie=DEFAULT_.curie('season_environment'), - model_uri=DEFAULT_.season_environment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.season_environment]) - -slots.standing_water_regm = Slot(uri=DEFAULT_.standing_water_regm, name="standing_water_regm", curie=DEFAULT_.curie('standing_water_regm'), - model_uri=DEFAULT_.standing_water_regm, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.standing_water_regm]) - -slots.tiss_cult_growth_med = Slot(uri=DEFAULT_.tiss_cult_growth_med, name="tiss_cult_growth_med", curie=DEFAULT_.curie('tiss_cult_growth_med'), - model_uri=DEFAULT_.tiss_cult_growth_med, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tiss_cult_growth_med]) - -slots.water_temp_regm = Slot(uri=DEFAULT_.water_temp_regm, name="water_temp_regm", curie=DEFAULT_.curie('water_temp_regm'), - model_uri=DEFAULT_.water_temp_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.water_temp_regm]) - -slots.watering_regm = Slot(uri=DEFAULT_.watering_regm, name="watering_regm", curie=DEFAULT_.curie('watering_regm'), - model_uri=DEFAULT_.watering_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.watering_regm]) - -slots.particle_class = Slot(uri=DEFAULT_.particle_class, name="particle_class", curie=DEFAULT_.curie('particle_class'), - model_uri=DEFAULT_.particle_class, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.particle_class]) - -slots.sediment_type = Slot(uri=DEFAULT_.sediment_type, name="sediment_type", curie=DEFAULT_.curie('sediment_type'), - model_uri=DEFAULT_.sediment_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sediment_type], - pattern=re.compile(r'[biogenous|cosmogenous|hydrogenous|lithogenous]')) - -slots.tidal_stage = Slot(uri=DEFAULT_.tidal_stage, name="tidal_stage", curie=DEFAULT_.curie('tidal_stage'), - model_uri=DEFAULT_.tidal_stage, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tidal_stage], - pattern=re.compile(r'[low tide|ebb tide|flood tide|high tide]')) - -slots.tot_depth_water_col = Slot(uri=DEFAULT_.tot_depth_water_col, name="tot_depth_water_col", curie=DEFAULT_.curie('tot_depth_water_col'), - model_uri=DEFAULT_.tot_depth_water_col, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_depth_water_col], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.cur_land_use = Slot(uri=DEFAULT_.cur_land_use, name="cur_land_use", curie=DEFAULT_.curie('cur_land_use'), - model_uri=DEFAULT_.cur_land_use, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.cur_land_use], - pattern=re.compile(r'[cities|farmstead|industrial areas|roads\/railroads|rock|sand|gravel|mudflats|salt flats|badlands|permanent snow or ice|saline seeps|mines\/quarries|oil waste areas|small grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands (grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands used for livestock grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub land (e.g. mesquite,sage\-brush,creosote bush,shrub oak,eucalyptus)|successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub crops (blueberries,nursery ornamentals,filberts)|vine crops (grapes)|conifers (e.g. pine,spruce,fir,cypress)|hardwoods (e.g. oak,hickory,elm,aspen)|intermixed hardwood and conifers|tropical (e.g. mangrove,palms)|rainforest (evergreen forest receiving >406 cm annual rainfall)|swamp (permanent or semi\-permanent water body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery trees)]')) - -slots.cur_vegetation = Slot(uri=DEFAULT_.cur_vegetation, name="cur_vegetation", curie=DEFAULT_.curie('cur_vegetation'), - model_uri=DEFAULT_.cur_vegetation, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.cur_vegetation]) - -slots.cur_vegetation_meth = Slot(uri=DEFAULT_.cur_vegetation_meth, name="cur_vegetation_meth", curie=DEFAULT_.curie('cur_vegetation_meth'), - model_uri=DEFAULT_.cur_vegetation_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.cur_vegetation_meth]) - -slots.previous_land_use = Slot(uri=DEFAULT_.previous_land_use, name="previous_land_use", curie=DEFAULT_.curie('previous_land_use'), - model_uri=DEFAULT_.previous_land_use, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.previous_land_use]) - -slots.previous_land_use_meth = Slot(uri=DEFAULT_.previous_land_use_meth, name="previous_land_use_meth", curie=DEFAULT_.curie('previous_land_use_meth'), - model_uri=DEFAULT_.previous_land_use_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.previous_land_use_meth]) - -slots.crop_rotation = Slot(uri=DEFAULT_.crop_rotation, name="crop_rotation", curie=DEFAULT_.curie('crop_rotation'), - model_uri=DEFAULT_.crop_rotation, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.crop_rotation]) - -slots.agrochem_addition = Slot(uri=DEFAULT_.agrochem_addition, name="agrochem_addition", curie=DEFAULT_.curie('agrochem_addition'), - model_uri=DEFAULT_.agrochem_addition, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.agrochem_addition]) - -slots.tillage = Slot(uri=DEFAULT_.tillage, name="tillage", curie=DEFAULT_.curie('tillage'), - model_uri=DEFAULT_.tillage, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tillage], - pattern=re.compile(r'[drill|cutting disc|ridge till|strip tillage|zonal tillage|chisel|tined|mouldboard|disc plough]')) - -slots.fire = Slot(uri=DEFAULT_.fire, name="fire", curie=DEFAULT_.curie('fire'), - model_uri=DEFAULT_.fire, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.fire]) - -slots.flooding = Slot(uri=DEFAULT_.flooding, name="flooding", curie=DEFAULT_.curie('flooding'), - model_uri=DEFAULT_.flooding, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.flooding]) - -slots.extreme_event = Slot(uri=DEFAULT_.extreme_event, name="extreme_event", curie=DEFAULT_.curie('extreme_event'), - model_uri=DEFAULT_.extreme_event, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.extreme_event]) - -slots.horizon = Slot(uri=DEFAULT_.horizon, name="horizon", curie=DEFAULT_.curie('horizon'), - model_uri=DEFAULT_.horizon, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.horizon], - pattern=re.compile(r'[O horizon|A horizon|E horizon|B horizon|C horizon|R layer|Permafrost]')) - -slots.horizon_meth = Slot(uri=DEFAULT_.horizon_meth, name="horizon_meth", curie=DEFAULT_.curie('horizon_meth'), - model_uri=DEFAULT_.horizon_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.horizon_meth]) - -slots.sieving = Slot(uri=DEFAULT_.sieving, name="sieving", curie=DEFAULT_.curie('sieving'), - model_uri=DEFAULT_.sieving, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.sieving]) - -slots.water_content_soil_meth = Slot(uri=DEFAULT_.water_content_soil_meth, name="water_content_soil_meth", curie=DEFAULT_.curie('water_content_soil_meth'), - model_uri=DEFAULT_.water_content_soil_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.water_content_soil_meth]) - -slots.pool_dna_extracts = Slot(uri=DEFAULT_.pool_dna_extracts, name="pool_dna_extracts", curie=DEFAULT_.curie('pool_dna_extracts'), - model_uri=DEFAULT_.pool_dna_extracts, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pool_dna_extracts]) - -slots.store_cond = Slot(uri=DEFAULT_.store_cond, name="store_cond", curie=DEFAULT_.curie('store_cond'), - model_uri=DEFAULT_.store_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.store_cond]) - -slots.link_climate_info = Slot(uri=DEFAULT_.link_climate_info, name="link_climate_info", curie=DEFAULT_.curie('link_climate_info'), - model_uri=DEFAULT_.link_climate_info, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.link_climate_info]) - -slots.annual_temp = Slot(uri=DEFAULT_.annual_temp, name="annual_temp", curie=DEFAULT_.curie('annual_temp'), - model_uri=DEFAULT_.annual_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.annual_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.season_temp = Slot(uri=DEFAULT_.season_temp, name="season_temp", curie=DEFAULT_.curie('season_temp'), - model_uri=DEFAULT_.season_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.season_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.annual_precpt = Slot(uri=DEFAULT_.annual_precpt, name="annual_precpt", curie=DEFAULT_.curie('annual_precpt'), - model_uri=DEFAULT_.annual_precpt, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.annual_precpt], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.season_precpt = Slot(uri=DEFAULT_.season_precpt, name="season_precpt", curie=DEFAULT_.curie('season_precpt'), - model_uri=DEFAULT_.season_precpt, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.season_precpt], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.link_class_info = Slot(uri=DEFAULT_.link_class_info, name="link_class_info", curie=DEFAULT_.curie('link_class_info'), - model_uri=DEFAULT_.link_class_info, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.link_class_info]) - -slots.fao_class = Slot(uri=DEFAULT_.fao_class, name="fao_class", curie=DEFAULT_.curie('fao_class'), - model_uri=DEFAULT_.fao_class, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.fao_class], - pattern=re.compile(r'[Acrisols|Andosols|Arenosols|Cambisols|Chernozems|Ferralsols|Fluvisols|Gleysols|Greyzems|Gypsisols|Histosols|Kastanozems|Lithosols|Luvisols|Nitosols|Phaeozems|Planosols|Podzols|Podzoluvisols|Rankers|Regosols|Rendzinas|Solonchaks|Solonetz|Vertisols|Yermosols]')) - -slots.local_class = Slot(uri=DEFAULT_.local_class, name="local_class", curie=DEFAULT_.curie('local_class'), - model_uri=DEFAULT_.local_class, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.local_class]) - -slots.local_class_meth = Slot(uri=DEFAULT_.local_class_meth, name="local_class_meth", curie=DEFAULT_.curie('local_class_meth'), - model_uri=DEFAULT_.local_class_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.local_class_meth]) - -slots.soil_type = Slot(uri=DEFAULT_.soil_type, name="soil_type", curie=DEFAULT_.curie('soil_type'), - model_uri=DEFAULT_.soil_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.soil_type]) - -slots.soil_type_meth = Slot(uri=DEFAULT_.soil_type_meth, name="soil_type_meth", curie=DEFAULT_.curie('soil_type_meth'), - model_uri=DEFAULT_.soil_type_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.soil_type_meth]) - -slots.slope_gradient = Slot(uri=DEFAULT_.slope_gradient, name="slope_gradient", curie=DEFAULT_.curie('slope_gradient'), - model_uri=DEFAULT_.slope_gradient, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.slope_gradient], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.slope_aspect = Slot(uri=DEFAULT_.slope_aspect, name="slope_aspect", curie=DEFAULT_.curie('slope_aspect'), - model_uri=DEFAULT_.slope_aspect, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.slope_aspect], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.profile_position = Slot(uri=DEFAULT_.profile_position, name="profile_position", curie=DEFAULT_.curie('profile_position'), - model_uri=DEFAULT_.profile_position, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.profile_position], - pattern=re.compile(r'[summit|shoulder|backslope|footslope|toeslope]')) - -slots.drainage_class = Slot(uri=DEFAULT_.drainage_class, name="drainage_class", curie=DEFAULT_.curie('drainage_class'), - model_uri=DEFAULT_.drainage_class, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.drainage_class], - pattern=re.compile(r'[very poorly|poorly|somewhat poorly|moderately well|well|excessively drained]')) - -slots.texture = Slot(uri=DEFAULT_.texture, name="texture", curie=DEFAULT_.curie('texture'), - model_uri=DEFAULT_.texture, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.texture], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.texture_meth = Slot(uri=DEFAULT_.texture_meth, name="texture_meth", curie=DEFAULT_.curie('texture_meth'), - model_uri=DEFAULT_.texture_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.texture_meth]) - -slots.ph_meth = Slot(uri=DEFAULT_.ph_meth, name="ph_meth", curie=DEFAULT_.curie('ph_meth'), - model_uri=DEFAULT_.ph_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ph_meth]) - -slots.tot_org_c_meth = Slot(uri=DEFAULT_.tot_org_c_meth, name="tot_org_c_meth", curie=DEFAULT_.curie('tot_org_c_meth'), - model_uri=DEFAULT_.tot_org_c_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tot_org_c_meth]) - -slots.tot_nitro_content_meth = Slot(uri=DEFAULT_.tot_nitro_content_meth, name="tot_nitro_content_meth", curie=DEFAULT_.curie('tot_nitro_content_meth'), - model_uri=DEFAULT_.tot_nitro_content_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tot_nitro_content_meth]) - -slots.microbial_biomass = Slot(uri=DEFAULT_.microbial_biomass, name="microbial_biomass", curie=DEFAULT_.curie('microbial_biomass'), - model_uri=DEFAULT_.microbial_biomass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.microbial_biomass], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.microbial_biomass_meth = Slot(uri=DEFAULT_.microbial_biomass_meth, name="microbial_biomass_meth", curie=DEFAULT_.curie('microbial_biomass_meth'), - model_uri=DEFAULT_.microbial_biomass_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.microbial_biomass_meth]) - -slots.link_addit_analys = Slot(uri=DEFAULT_.link_addit_analys, name="link_addit_analys", curie=DEFAULT_.curie('link_addit_analys'), - model_uri=DEFAULT_.link_addit_analys, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.link_addit_analys]) - -slots.extreme_salinity = Slot(uri=DEFAULT_.extreme_salinity, name="extreme_salinity", curie=DEFAULT_.curie('extreme_salinity'), - model_uri=DEFAULT_.extreme_salinity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.extreme_salinity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.salinity_meth = Slot(uri=DEFAULT_.salinity_meth, name="salinity_meth", curie=DEFAULT_.curie('salinity_meth'), - model_uri=DEFAULT_.salinity_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.salinity_meth]) - -slots.heavy_metals = Slot(uri=DEFAULT_.heavy_metals, name="heavy_metals", curie=DEFAULT_.curie('heavy_metals'), - model_uri=DEFAULT_.heavy_metals, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.heavy_metals]) - -slots.heavy_metals_meth = Slot(uri=DEFAULT_.heavy_metals_meth, name="heavy_metals_meth", curie=DEFAULT_.curie('heavy_metals_meth'), - model_uri=DEFAULT_.heavy_metals_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.heavy_metals_meth]) - -slots.al_sat = Slot(uri=DEFAULT_.al_sat, name="al_sat", curie=DEFAULT_.curie('al_sat'), - model_uri=DEFAULT_.al_sat, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.al_sat], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.al_sat_meth = Slot(uri=DEFAULT_.al_sat_meth, name="al_sat_meth", curie=DEFAULT_.curie('al_sat_meth'), - model_uri=DEFAULT_.al_sat_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.al_sat_meth]) - -slots.biochem_oxygen_dem = Slot(uri=DEFAULT_.biochem_oxygen_dem, name="biochem_oxygen_dem", curie=DEFAULT_.curie('biochem_oxygen_dem'), - model_uri=DEFAULT_.biochem_oxygen_dem, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.biochem_oxygen_dem], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.chem_oxygen_dem = Slot(uri=DEFAULT_.chem_oxygen_dem, name="chem_oxygen_dem", curie=DEFAULT_.curie('chem_oxygen_dem'), - model_uri=DEFAULT_.chem_oxygen_dem, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.chem_oxygen_dem], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.efficiency_percent = Slot(uri=DEFAULT_.efficiency_percent, name="efficiency_percent", curie=DEFAULT_.curie('efficiency_percent'), - model_uri=DEFAULT_.efficiency_percent, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.efficiency_percent], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.emulsions = Slot(uri=DEFAULT_.emulsions, name="emulsions", curie=DEFAULT_.curie('emulsions'), - model_uri=DEFAULT_.emulsions, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.emulsions]) - -slots.gaseous_substances = Slot(uri=DEFAULT_.gaseous_substances, name="gaseous_substances", curie=DEFAULT_.curie('gaseous_substances'), - model_uri=DEFAULT_.gaseous_substances, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.gaseous_substances]) - -slots.indust_eff_percent = Slot(uri=DEFAULT_.indust_eff_percent, name="indust_eff_percent", curie=DEFAULT_.curie('indust_eff_percent'), - model_uri=DEFAULT_.indust_eff_percent, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.indust_eff_percent], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.inorg_particles = Slot(uri=DEFAULT_.inorg_particles, name="inorg_particles", curie=DEFAULT_.curie('inorg_particles'), - model_uri=DEFAULT_.inorg_particles, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.inorg_particles]) - -slots.org_particles = Slot(uri=DEFAULT_.org_particles, name="org_particles", curie=DEFAULT_.curie('org_particles'), - model_uri=DEFAULT_.org_particles, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.org_particles]) - -slots.pre_treatment = Slot(uri=DEFAULT_.pre_treatment, name="pre_treatment", curie=DEFAULT_.curie('pre_treatment'), - model_uri=DEFAULT_.pre_treatment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pre_treatment]) - -slots.primary_treatment = Slot(uri=DEFAULT_.primary_treatment, name="primary_treatment", curie=DEFAULT_.curie('primary_treatment'), - model_uri=DEFAULT_.primary_treatment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.primary_treatment]) - -slots.reactor_type = Slot(uri=DEFAULT_.reactor_type, name="reactor_type", curie=DEFAULT_.curie('reactor_type'), - model_uri=DEFAULT_.reactor_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.reactor_type]) - -slots.secondary_treatment = Slot(uri=DEFAULT_.secondary_treatment, name="secondary_treatment", curie=DEFAULT_.curie('secondary_treatment'), - model_uri=DEFAULT_.secondary_treatment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.secondary_treatment]) - -slots.sewage_type = Slot(uri=DEFAULT_.sewage_type, name="sewage_type", curie=DEFAULT_.curie('sewage_type'), - model_uri=DEFAULT_.sewage_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sewage_type]) - -slots.sludge_retent_time = Slot(uri=DEFAULT_.sludge_retent_time, name="sludge_retent_time", curie=DEFAULT_.curie('sludge_retent_time'), - model_uri=DEFAULT_.sludge_retent_time, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.sludge_retent_time], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.soluble_inorg_mat = Slot(uri=DEFAULT_.soluble_inorg_mat, name="soluble_inorg_mat", curie=DEFAULT_.curie('soluble_inorg_mat'), - model_uri=DEFAULT_.soluble_inorg_mat, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.soluble_inorg_mat]) - -slots.soluble_org_mat = Slot(uri=DEFAULT_.soluble_org_mat, name="soluble_org_mat", curie=DEFAULT_.curie('soluble_org_mat'), - model_uri=DEFAULT_.soluble_org_mat, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.soluble_org_mat]) - -slots.tertiary_treatment = Slot(uri=DEFAULT_.tertiary_treatment, name="tertiary_treatment", curie=DEFAULT_.curie('tertiary_treatment'), - model_uri=DEFAULT_.tertiary_treatment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tertiary_treatment]) - -slots.tot_phosphate = Slot(uri=DEFAULT_.tot_phosphate, name="tot_phosphate", curie=DEFAULT_.curie('tot_phosphate'), - model_uri=DEFAULT_.tot_phosphate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_phosphate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.wastewater_type = Slot(uri=DEFAULT_.wastewater_type, name="wastewater_type", curie=DEFAULT_.curie('wastewater_type'), - model_uri=DEFAULT_.wastewater_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wastewater_type]) - -slots.atmospheric_data = Slot(uri=DEFAULT_.atmospheric_data, name="atmospheric_data", curie=DEFAULT_.curie('atmospheric_data'), - model_uri=DEFAULT_.atmospheric_data, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.atmospheric_data]) - -slots.bac_prod = Slot(uri=DEFAULT_.bac_prod, name="bac_prod", curie=DEFAULT_.curie('bac_prod'), - model_uri=DEFAULT_.bac_prod, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.bac_prod], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.bac_resp = Slot(uri=DEFAULT_.bac_resp, name="bac_resp", curie=DEFAULT_.curie('bac_resp'), - model_uri=DEFAULT_.bac_resp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.bac_resp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.conduc = Slot(uri=DEFAULT_.conduc, name="conduc", curie=DEFAULT_.curie('conduc'), - model_uri=DEFAULT_.conduc, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.conduc], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_inorg_nitro = Slot(uri=DEFAULT_.diss_inorg_nitro, name="diss_inorg_nitro", curie=DEFAULT_.curie('diss_inorg_nitro'), - model_uri=DEFAULT_.diss_inorg_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_inorg_nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.down_par = Slot(uri=DEFAULT_.down_par, name="down_par", curie=DEFAULT_.curie('down_par'), - model_uri=DEFAULT_.down_par, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.down_par], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.fluor = Slot(uri=DEFAULT_.fluor, name="fluor", curie=DEFAULT_.curie('fluor'), - model_uri=DEFAULT_.fluor, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.fluor], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.light_intensity = Slot(uri=DEFAULT_.light_intensity, name="light_intensity", curie=DEFAULT_.curie('light_intensity'), - model_uri=DEFAULT_.light_intensity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.light_intensity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.part_org_nitro = Slot(uri=DEFAULT_.part_org_nitro, name="part_org_nitro", curie=DEFAULT_.curie('part_org_nitro'), - model_uri=DEFAULT_.part_org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.part_org_nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.photon_flux = Slot(uri=DEFAULT_.photon_flux, name="photon_flux", curie=DEFAULT_.curie('photon_flux'), - model_uri=DEFAULT_.photon_flux, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.photon_flux], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.primary_prod = Slot(uri=DEFAULT_.primary_prod, name="primary_prod", curie=DEFAULT_.curie('primary_prod'), - model_uri=DEFAULT_.primary_prod, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.primary_prod], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.size_frac_low = Slot(uri=DEFAULT_.size_frac_low, name="size_frac_low", curie=DEFAULT_.curie('size_frac_low'), - model_uri=DEFAULT_.size_frac_low, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.size_frac_low], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.size_frac_up = Slot(uri=DEFAULT_.size_frac_up, name="size_frac_up", curie=DEFAULT_.curie('size_frac_up'), - model_uri=DEFAULT_.size_frac_up, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.size_frac_up], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.soluble_react_phosp = Slot(uri=DEFAULT_.soluble_react_phosp, name="soluble_react_phosp", curie=DEFAULT_.curie('soluble_react_phosp'), - model_uri=DEFAULT_.soluble_react_phosp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.soluble_react_phosp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.suspend_part_matter = Slot(uri=DEFAULT_.suspend_part_matter, name="suspend_part_matter", curie=DEFAULT_.curie('suspend_part_matter'), - model_uri=DEFAULT_.suspend_part_matter, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.suspend_part_matter], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_diss_nitro = Slot(uri=DEFAULT_.tot_diss_nitro, name="tot_diss_nitro", curie=DEFAULT_.curie('tot_diss_nitro'), - model_uri=DEFAULT_.tot_diss_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_diss_nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_inorg_nitro = Slot(uri=DEFAULT_.tot_inorg_nitro, name="tot_inorg_nitro", curie=DEFAULT_.curie('tot_inorg_nitro'), - model_uri=DEFAULT_.tot_inorg_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_inorg_nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_part_carb = Slot(uri=DEFAULT_.tot_part_carb, name="tot_part_carb", curie=DEFAULT_.curie('tot_part_carb'), - model_uri=DEFAULT_.tot_part_carb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_part_carb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.language = Slot(uri=NMDC.language, name="language", curie=NMDC.curie('language'), - model_uri=DEFAULT_.language, domain=None, range=Optional[str]) - -slots.attribute = Slot(uri=NMDC.attribute, name="attribute", curie=NMDC.curie('attribute'), - model_uri=DEFAULT_.attribute, domain=None, range=Optional[str]) - -slots.has_raw_value = Slot(uri=NMDC.has_raw_value, name="has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.has_raw_value, domain=AttributeValue, range=Optional[str]) - -slots.has_unit = Slot(uri=NMDC.has_unit, name="has unit", curie=NMDC.curie('has_unit'), - model_uri=DEFAULT_.has_unit, domain=None, range=Optional[str], mappings = [QUD.unit, SCHEMA.unitCode]) - -slots.has_numeric_value = Slot(uri=NMDC.has_numeric_value, name="has numeric value", curie=NMDC.curie('has_numeric_value'), - model_uri=DEFAULT_.has_numeric_value, domain=None, range=Optional[float], mappings = [QUD.quantityValue, SCHEMA.value]) - -slots.has_minimum_numeric_value = Slot(uri=NMDC.has_minimum_numeric_value, name="has minimum numeric value", curie=NMDC.curie('has_minimum_numeric_value'), - model_uri=DEFAULT_.has_minimum_numeric_value, domain=None, range=Optional[float]) - -slots.has_maximum_numeric_value = Slot(uri=NMDC.has_maximum_numeric_value, name="has maximum numeric value", curie=NMDC.curie('has_maximum_numeric_value'), - model_uri=DEFAULT_.has_maximum_numeric_value, domain=None, range=Optional[float]) - -slots.has_boolean_value = Slot(uri=NMDC.has_boolean_value, name="has boolean value", curie=NMDC.curie('has_boolean_value'), - model_uri=DEFAULT_.has_boolean_value, domain=None, range=Optional[Union[bool, Bool]]) - -slots.latitude = Slot(uri=WGS.lat, name="latitude", curie=WGS.curie('lat'), - model_uri=DEFAULT_.latitude, domain=GeolocationValue, range=Optional[float], mappings = [SCHEMA.latitude]) - -slots.longitude = Slot(uri=WGS.long, name="longitude", curie=WGS.curie('long'), - model_uri=DEFAULT_.longitude, domain=GeolocationValue, range=Optional[float], mappings = [SCHEMA.longitude]) - -slots.term = Slot(uri=RDF.type, name="term", curie=RDF.curie('type'), - model_uri=DEFAULT_.term, domain=ControlledTermValue, range=Optional[Union[dict, OntologyClass]]) - -slots.orcid = Slot(uri=NMDC.orcid, name="orcid", curie=NMDC.curie('orcid'), - model_uri=DEFAULT_.orcid, domain=PersonValue, range=Optional[str]) - -slots.email = Slot(uri=SCHEMA.email, name="email", curie=SCHEMA.curie('email'), - model_uri=DEFAULT_.email, domain=None, range=Optional[str]) - -slots.alternate_emails = Slot(uri=NMDC.alternate_emails, name="alternate emails", curie=NMDC.curie('alternate_emails'), - model_uri=DEFAULT_.alternate_emails, domain=None, range=Optional[str]) - -slots.profile_image_url = Slot(uri=NMDC.profile_image_url, name="profile image url", curie=NMDC.curie('profile_image_url'), - model_uri=DEFAULT_.profile_image_url, domain=PersonValue, range=Optional[str]) - -slots.has_input = Slot(uri=NMDC.has_input, name="has input", curie=NMDC.curie('has_input'), - model_uri=DEFAULT_.has_input, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) - -slots.has_output = Slot(uri=NMDC.has_output, name="has output", curie=NMDC.curie('has_output'), - model_uri=DEFAULT_.has_output, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) - -slots.part_of = Slot(uri=DCTERMS.isPartOf, name="part of", curie=DCTERMS.curie('isPartOf'), - model_uri=DEFAULT_.part_of, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) - -slots.execution_resource = Slot(uri=NMDC.execution_resource, name="execution resource", curie=NMDC.curie('execution_resource'), - model_uri=DEFAULT_.execution_resource, domain=None, range=Optional[str]) - -slots.url = Slot(uri=NMDC.url, name="url", curie=NMDC.curie('url'), - model_uri=DEFAULT_.url, domain=None, range=Optional[str]) - -slots.display_order = Slot(uri=NMDC.display_order, name="display order", curie=NMDC.curie('display_order'), - model_uri=DEFAULT_.display_order, domain=None, range=Optional[str]) - -slots.git_url = Slot(uri=NMDC.git_url, name="git url", curie=NMDC.curie('git_url'), - model_uri=DEFAULT_.git_url, domain=None, range=Optional[str]) - -slots.file_size_bytes = Slot(uri=NMDC.file_size_bytes, name="file size bytes", curie=NMDC.curie('file_size_bytes'), - model_uri=DEFAULT_.file_size_bytes, domain=None, range=Optional[int]) - -slots.md5_checksum = Slot(uri=NMDC.md5_checksum, name="md5 checksum", curie=NMDC.curie('md5_checksum'), - model_uri=DEFAULT_.md5_checksum, domain=None, range=Optional[str]) - -slots.abstract = Slot(uri=NMDC.abstract, name="abstract", curie=NMDC.curie('abstract'), - model_uri=DEFAULT_.abstract, domain=None, range=Optional[str]) - -slots.keywords = Slot(uri=NMDC.keywords, name="keywords", curie=NMDC.curie('keywords'), - model_uri=DEFAULT_.keywords, domain=None, range=Optional[Union[str, List[str]]], mappings = [DCTERMS.subject]) - -slots.objective = Slot(uri=NMDC.objective, name="objective", curie=NMDC.curie('objective'), - model_uri=DEFAULT_.objective, domain=None, range=Optional[str], mappings = [SIO["000337"]]) - -slots.websites = Slot(uri=NMDC.websites, name="websites", curie=NMDC.curie('websites'), - model_uri=DEFAULT_.websites, domain=None, range=Optional[Union[str, List[str]]]) - -slots.publications = Slot(uri=NMDC.publications, name="publications", curie=NMDC.curie('publications'), - model_uri=DEFAULT_.publications, domain=None, range=Optional[Union[str, List[str]]]) - -slots.id = Slot(uri=NMDC.id, name="id", curie=NMDC.curie('id'), - model_uri=DEFAULT_.id, domain=None, range=URIRef) - -slots.name = Slot(uri=NMDC.name, name="name", curie=NMDC.curie('name'), - model_uri=DEFAULT_.name, domain=None, range=Optional[str]) - -slots.description = Slot(uri=DCTERMS.description, name="description", curie=DCTERMS.curie('description'), - model_uri=DEFAULT_.description, domain=None, range=Optional[str]) - -slots.type = Slot(uri=NMDC.type, name="type", curie=NMDC.curie('type'), - model_uri=DEFAULT_.type, domain=None, range=Optional[str]) - -slots.title = Slot(uri=NMDC.title, name="title", curie=NMDC.curie('title'), - model_uri=DEFAULT_.title, domain=None, range=Optional[str]) - -slots.alternative_titles = Slot(uri=NMDC.alternative_titles, name="alternative titles", curie=NMDC.curie('alternative_titles'), - model_uri=DEFAULT_.alternative_titles, domain=None, range=Optional[Union[str, List[str]]]) - -slots.alternative_names = Slot(uri=NMDC.alternative_names, name="alternative names", curie=NMDC.curie('alternative_names'), - model_uri=DEFAULT_.alternative_names, domain=None, range=Optional[Union[str, List[str]]]) - -slots.alternative_descriptions = Slot(uri=NMDC.alternative_descriptions, name="alternative descriptions", curie=NMDC.curie('alternative_descriptions'), - model_uri=DEFAULT_.alternative_descriptions, domain=None, range=Optional[Union[str, List[str]]]) - -slots.alternative_identifiers = Slot(uri=NMDC.alternative_identifiers, name="alternative identifiers", curie=NMDC.curie('alternative_identifiers'), - model_uri=DEFAULT_.alternative_identifiers, domain=None, range=Optional[Union[str, List[str]]]) - -slots.started_at_time = Slot(uri=NMDC.started_at_time, name="started at time", curie=NMDC.curie('started_at_time'), - model_uri=DEFAULT_.started_at_time, domain=None, range=Optional[Union[str, XSDDateTime]], mappings = [PROV.startedAtTime], - pattern=re.compile(r'^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$')) - -slots.ended_at_time = Slot(uri=NMDC.ended_at_time, name="ended at time", curie=NMDC.curie('ended_at_time'), - model_uri=DEFAULT_.ended_at_time, domain=None, range=Optional[Union[str, XSDDateTime]], mappings = [PROV.endedAtTime], - pattern=re.compile(r'^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$')) - -slots.was_informed_by = Slot(uri=NMDC.was_informed_by, name="was informed by", curie=NMDC.curie('was_informed_by'), - model_uri=DEFAULT_.was_informed_by, domain=None, range=Optional[Union[str, ActivityId]], mappings = [PROV.wasInformedBy]) - -slots.was_associated_with = Slot(uri=NMDC.was_associated_with, name="was associated with", curie=NMDC.curie('was_associated_with'), - model_uri=DEFAULT_.was_associated_with, domain=None, range=Optional[Union[dict, Agent]], mappings = [PROV.wasAssociatedWith]) - -slots.acted_on_behalf_of = Slot(uri=NMDC.acted_on_behalf_of, name="acted on behalf of", curie=NMDC.curie('acted_on_behalf_of'), - model_uri=DEFAULT_.acted_on_behalf_of, domain=None, range=Optional[Union[dict, Agent]], mappings = [PROV.actedOnBehalfOf]) - -slots.was_generated_by = Slot(uri=NMDC.was_generated_by, name="was generated by", curie=NMDC.curie('was_generated_by'), - model_uri=DEFAULT_.was_generated_by, domain=None, range=Optional[Union[str, ActivityId]], mappings = [PROV.wasGeneratedBy]) - -slots.used = Slot(uri=NMDC.used, name="used", curie=NMDC.curie('used'), - model_uri=DEFAULT_.used, domain=Activity, range=Optional[str], mappings = [PROV.used]) - -slots.mAGBin__bin_name = Slot(uri=DEFAULT_.bin_name, name="mAGBin__bin_name", curie=DEFAULT_.curie('bin_name'), - model_uri=DEFAULT_.mAGBin__bin_name, domain=None, range=Optional[str]) - -slots.mAGBin__number_of_contig = Slot(uri=DEFAULT_.number_of_contig, name="mAGBin__number_of_contig", curie=DEFAULT_.curie('number_of_contig'), - model_uri=DEFAULT_.mAGBin__number_of_contig, domain=None, range=Optional[int]) - -slots.mAGBin__completeness = Slot(uri=DEFAULT_.completeness, name="mAGBin__completeness", curie=DEFAULT_.curie('completeness'), - model_uri=DEFAULT_.mAGBin__completeness, domain=None, range=Optional[float]) - -slots.mAGBin__contamination = Slot(uri=DEFAULT_.contamination, name="mAGBin__contamination", curie=DEFAULT_.curie('contamination'), - model_uri=DEFAULT_.mAGBin__contamination, domain=None, range=Optional[float]) - -slots.mAGBin__gene_count = Slot(uri=DEFAULT_.gene_count, name="mAGBin__gene_count", curie=DEFAULT_.curie('gene_count'), - model_uri=DEFAULT_.mAGBin__gene_count, domain=None, range=Optional[int]) - -slots.mAGBin__bin_quality = Slot(uri=DEFAULT_.bin_quality, name="mAGBin__bin_quality", curie=DEFAULT_.curie('bin_quality'), - model_uri=DEFAULT_.mAGBin__bin_quality, domain=None, range=Optional[str]) - -slots.mAGBin__num_16s = Slot(uri=DEFAULT_.num_16s, name="mAGBin__num_16s", curie=DEFAULT_.curie('num_16s'), - model_uri=DEFAULT_.mAGBin__num_16s, domain=None, range=Optional[int]) - -slots.mAGBin__num_5s = Slot(uri=DEFAULT_.num_5s, name="mAGBin__num_5s", curie=DEFAULT_.curie('num_5s'), - model_uri=DEFAULT_.mAGBin__num_5s, domain=None, range=Optional[int]) - -slots.mAGBin__num_23s = Slot(uri=DEFAULT_.num_23s, name="mAGBin__num_23s", curie=DEFAULT_.curie('num_23s'), - model_uri=DEFAULT_.mAGBin__num_23s, domain=None, range=Optional[int]) - -slots.mAGBin__num_tRNA = Slot(uri=DEFAULT_.num_tRNA, name="mAGBin__num_tRNA", curie=DEFAULT_.curie('num_tRNA'), - model_uri=DEFAULT_.mAGBin__num_tRNA, domain=None, range=Optional[int]) - -slots.mAGBin__gtdbtk_domain = Slot(uri=DEFAULT_.gtdbtk_domain, name="mAGBin__gtdbtk_domain", curie=DEFAULT_.curie('gtdbtk_domain'), - model_uri=DEFAULT_.mAGBin__gtdbtk_domain, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_phylum = Slot(uri=DEFAULT_.gtdbtk_phylum, name="mAGBin__gtdbtk_phylum", curie=DEFAULT_.curie('gtdbtk_phylum'), - model_uri=DEFAULT_.mAGBin__gtdbtk_phylum, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_class = Slot(uri=DEFAULT_.gtdbtk_class, name="mAGBin__gtdbtk_class", curie=DEFAULT_.curie('gtdbtk_class'), - model_uri=DEFAULT_.mAGBin__gtdbtk_class, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_order = Slot(uri=DEFAULT_.gtdbtk_order, name="mAGBin__gtdbtk_order", curie=DEFAULT_.curie('gtdbtk_order'), - model_uri=DEFAULT_.mAGBin__gtdbtk_order, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_family = Slot(uri=DEFAULT_.gtdbtk_family, name="mAGBin__gtdbtk_family", curie=DEFAULT_.curie('gtdbtk_family'), - model_uri=DEFAULT_.mAGBin__gtdbtk_family, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_genus = Slot(uri=DEFAULT_.gtdbtk_genus, name="mAGBin__gtdbtk_genus", curie=DEFAULT_.curie('gtdbtk_genus'), - model_uri=DEFAULT_.mAGBin__gtdbtk_genus, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_species = Slot(uri=DEFAULT_.gtdbtk_species, name="mAGBin__gtdbtk_species", curie=DEFAULT_.curie('gtdbtk_species'), - model_uri=DEFAULT_.mAGBin__gtdbtk_species, domain=None, range=Optional[str]) - -slots.metabolite_quantified = Slot(uri=DEFAULT_.metabolite_quantified, name="metabolite quantified", curie=DEFAULT_.curie('metabolite_quantified'), - model_uri=DEFAULT_.metabolite_quantified, domain=None, range=Optional[Union[str, ChemicalEntityId]]) - -slots.highest_similarity_score = Slot(uri=DEFAULT_.highest_similarity_score, name="highest similarity score", curie=DEFAULT_.curie('highest_similarity_score'), - model_uri=DEFAULT_.highest_similarity_score, domain=None, range=Optional[float]) - -slots.peptide_sequence = Slot(uri=DEFAULT_.peptide_sequence, name="peptide sequence", curie=DEFAULT_.curie('peptide_sequence'), - model_uri=DEFAULT_.peptide_sequence, domain=None, range=Optional[str]) - -slots.best_protein = Slot(uri=DEFAULT_.best_protein, name="best protein", curie=DEFAULT_.curie('best_protein'), - model_uri=DEFAULT_.best_protein, domain=None, range=Optional[Union[str, GeneProductId]]) - -slots.all_proteins = Slot(uri=DEFAULT_.all_proteins, name="all proteins", curie=DEFAULT_.curie('all_proteins'), - model_uri=DEFAULT_.all_proteins, domain=None, range=Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]]) - -slots.min_q_value = Slot(uri=DEFAULT_.min_q_value, name="min_q_value", curie=DEFAULT_.curie('min_q_value'), - model_uri=DEFAULT_.min_q_value, domain=None, range=Optional[float]) - -slots.peptide_spectral_count = Slot(uri=DEFAULT_.peptide_spectral_count, name="peptide_spectral_count", curie=DEFAULT_.curie('peptide_spectral_count'), - model_uri=DEFAULT_.peptide_spectral_count, domain=None, range=Optional[int]) - -slots.peptide_sum_masic_abundance = Slot(uri=DEFAULT_.peptide_sum_masic_abundance, name="peptide_sum_masic_abundance", curie=DEFAULT_.curie('peptide_sum_masic_abundance'), - model_uri=DEFAULT_.peptide_sum_masic_abundance, domain=None, range=Optional[int]) - -slots.peptide_sequence_count = Slot(uri=DEFAULT_.peptide_sequence_count, name="peptide_sequence_count", curie=DEFAULT_.curie('peptide_sequence_count'), - model_uri=DEFAULT_.peptide_sequence_count, domain=None, range=Optional[int]) - -slots.protein_spectral_count = Slot(uri=DEFAULT_.protein_spectral_count, name="protein_spectral_count", curie=DEFAULT_.curie('protein_spectral_count'), - model_uri=DEFAULT_.protein_spectral_count, domain=None, range=Optional[int]) - -slots.protein_sum_masic_abundance = Slot(uri=DEFAULT_.protein_sum_masic_abundance, name="protein_sum_masic_abundance", curie=DEFAULT_.curie('protein_sum_masic_abundance'), - model_uri=DEFAULT_.protein_sum_masic_abundance, domain=None, range=Optional[int]) - -slots.inchi = Slot(uri=DEFAULT_.inchi, name="inchi", curie=DEFAULT_.curie('inchi'), - model_uri=DEFAULT_.inchi, domain=None, range=Optional[str]) - -slots.inchi_key = Slot(uri=DEFAULT_.inchi_key, name="inchi key", curie=DEFAULT_.curie('inchi_key'), - model_uri=DEFAULT_.inchi_key, domain=None, range=Optional[str]) - -slots.smiles = Slot(uri=DEFAULT_.smiles, name="smiles", curie=DEFAULT_.curie('smiles'), - model_uri=DEFAULT_.smiles, domain=None, range=Optional[Union[str, List[str]]]) - -slots.chemical_formula = Slot(uri=DEFAULT_.chemical_formula, name="chemical formula", curie=DEFAULT_.curie('chemical_formula'), - model_uri=DEFAULT_.chemical_formula, domain=None, range=Optional[str]) - -slots.attribute_value_type = Slot(uri=NMDC.type, name="attribute value_type", curie=NMDC.curie('type'), - model_uri=DEFAULT_.attribute_value_type, domain=AttributeValue, range=Optional[str]) - -slots.quantity_value_has_raw_value = Slot(uri=NMDC.has_raw_value, name="quantity value_has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.quantity_value_has_raw_value, domain=QuantityValue, range=Optional[str]) - -slots.quantity_value_has_unit = Slot(uri=NMDC.has_unit, name="quantity value_has unit", curie=NMDC.curie('has_unit'), - model_uri=DEFAULT_.quantity_value_has_unit, domain=QuantityValue, range=Optional[str], mappings = [QUD.unit, SCHEMA.unitCode]) - -slots.quantity_value_has_numeric_value = Slot(uri=NMDC.has_numeric_value, name="quantity value_has numeric value", curie=NMDC.curie('has_numeric_value'), - model_uri=DEFAULT_.quantity_value_has_numeric_value, domain=QuantityValue, range=Optional[float], mappings = [QUD.quantityValue, SCHEMA.value]) - -slots.person_value_orcid = Slot(uri=NMDC.orcid, name="person value_orcid", curie=NMDC.curie('orcid'), - model_uri=DEFAULT_.person_value_orcid, domain=PersonValue, range=Optional[str]) - -slots.person_value_email = Slot(uri=SCHEMA.email, name="person value_email", curie=SCHEMA.curie('email'), - model_uri=DEFAULT_.person_value_email, domain=PersonValue, range=Optional[str]) - -slots.person_value_has_raw_value = Slot(uri=NMDC.has_raw_value, name="person value_has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.person_value_has_raw_value, domain=PersonValue, range=Optional[str]) - -slots.person_value_name = Slot(uri=NMDC.name, name="person value_name", curie=NMDC.curie('name'), - model_uri=DEFAULT_.person_value_name, domain=PersonValue, range=Optional[str]) - -slots.person_id = Slot(uri=NMDC.id, name="person_id", curie=NMDC.curie('id'), - model_uri=DEFAULT_.person_id, domain=Person, range=Union[str, PersonId]) - -slots.metabolite_quantification_metabolite_quantified = Slot(uri=DEFAULT_.metabolite_quantified, name="metabolite quantification_metabolite quantified", curie=DEFAULT_.curie('metabolite_quantified'), - model_uri=DEFAULT_.metabolite_quantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) - -slots.metabolite_quantification_highest_similarity_score = Slot(uri=DEFAULT_.highest_similarity_score, name="metabolite quantification_highest similarity score", curie=DEFAULT_.curie('highest_similarity_score'), - model_uri=DEFAULT_.metabolite_quantification_highest_similarity_score, domain=MetaboliteQuantification, range=Optional[float]) - -slots.peptide_quantification_peptide_sequence = Slot(uri=DEFAULT_.peptide_sequence, name="peptide quantification_peptide sequence", curie=DEFAULT_.curie('peptide_sequence'), - model_uri=DEFAULT_.peptide_quantification_peptide_sequence, domain=PeptideQuantification, range=Optional[str]) - -slots.peptide_quantification_best_protein = Slot(uri=DEFAULT_.best_protein, name="peptide quantification_best protein", curie=DEFAULT_.curie('best_protein'), - model_uri=DEFAULT_.peptide_quantification_best_protein, domain=PeptideQuantification, range=Optional[Union[str, GeneProductId]]) - -slots.peptide_quantification_all_proteins = Slot(uri=DEFAULT_.all_proteins, name="peptide quantification_all proteins", curie=DEFAULT_.curie('all_proteins'), - model_uri=DEFAULT_.peptide_quantification_all_proteins, domain=PeptideQuantification, range=Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]]) - -slots.peptide_quantification_min_q_value = Slot(uri=DEFAULT_.min_q_value, name="peptide quantification_min_q_value", curie=DEFAULT_.curie('min_q_value'), - model_uri=DEFAULT_.peptide_quantification_min_q_value, domain=PeptideQuantification, range=Optional[float]) - -slots.peptide_quantification_peptide_spectral_count = Slot(uri=DEFAULT_.peptide_spectral_count, name="peptide quantification_peptide_spectral_count", curie=DEFAULT_.curie('peptide_spectral_count'), - model_uri=DEFAULT_.peptide_quantification_peptide_spectral_count, domain=PeptideQuantification, range=Optional[int]) - -slots.peptide_quantification_peptide_sum_masic_abundance = Slot(uri=DEFAULT_.peptide_sum_masic_abundance, name="peptide quantification_peptide_sum_masic_abundance", curie=DEFAULT_.curie('peptide_sum_masic_abundance'), - model_uri=DEFAULT_.peptide_quantification_peptide_sum_masic_abundance, domain=PeptideQuantification, range=Optional[int]) - -slots.protein_quantification_best_protein = Slot(uri=DEFAULT_.best_protein, name="protein quantification_best protein", curie=DEFAULT_.curie('best_protein'), - model_uri=DEFAULT_.protein_quantification_best_protein, domain=ProteinQuantification, range=Optional[Union[str, GeneProductId]]) - -slots.protein_quantification_all_proteins = Slot(uri=DEFAULT_.all_proteins, name="protein quantification_all proteins", curie=DEFAULT_.curie('all_proteins'), - model_uri=DEFAULT_.protein_quantification_all_proteins, domain=ProteinQuantification, range=Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]]) - -slots.protein_quantification_peptide_sequence_count = Slot(uri=DEFAULT_.peptide_sequence_count, name="protein quantification_peptide_sequence_count", curie=DEFAULT_.curie('peptide_sequence_count'), - model_uri=DEFAULT_.protein_quantification_peptide_sequence_count, domain=ProteinQuantification, range=Optional[int]) - -slots.protein_quantification_protein_spectral_count = Slot(uri=DEFAULT_.protein_spectral_count, name="protein quantification_protein_spectral_count", curie=DEFAULT_.curie('protein_spectral_count'), - model_uri=DEFAULT_.protein_quantification_protein_spectral_count, domain=ProteinQuantification, range=Optional[int]) - -slots.protein_quantification_protein_sum_masic_abundance = Slot(uri=DEFAULT_.protein_sum_masic_abundance, name="protein quantification_protein_sum_masic_abundance", curie=DEFAULT_.curie('protein_sum_masic_abundance'), - model_uri=DEFAULT_.protein_quantification_protein_sum_masic_abundance, domain=ProteinQuantification, range=Optional[int]) - -slots.chemical_entity_inchi = Slot(uri=DEFAULT_.inchi, name="chemical entity_inchi", curie=DEFAULT_.curie('inchi'), - model_uri=DEFAULT_.chemical_entity_inchi, domain=ChemicalEntity, range=Optional[str]) - -slots.chemical_entity_inchi_key = Slot(uri=DEFAULT_.inchi_key, name="chemical entity_inchi key", curie=DEFAULT_.curie('inchi_key'), - model_uri=DEFAULT_.chemical_entity_inchi_key, domain=ChemicalEntity, range=Optional[str]) - -slots.chemical_entity_smiles = Slot(uri=DEFAULT_.smiles, name="chemical entity_smiles", curie=DEFAULT_.curie('smiles'), - model_uri=DEFAULT_.chemical_entity_smiles, domain=ChemicalEntity, range=Optional[Union[str, List[str]]]) - -slots.chemical_entity_chemical_formula = Slot(uri=DEFAULT_.chemical_formula, name="chemical entity_chemical formula", curie=DEFAULT_.curie('chemical_formula'), - model_uri=DEFAULT_.chemical_entity_chemical_formula, domain=ChemicalEntity, range=Optional[str]) - -slots.geolocation_value_has_raw_value = Slot(uri=NMDC.has_raw_value, name="geolocation value_has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.geolocation_value_has_raw_value, domain=GeolocationValue, range=Optional[str]) diff --git a/nmdc_schema/mixs_new.py b/nmdc_schema/mixs_new.py deleted file mode 100644 index f0376ed9db..0000000000 --- a/nmdc_schema/mixs_new.py +++ /dev/null @@ -1,4656 +0,0 @@ -# Auto generated from mixs_new.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-05-06T11:21:42 -# Schema: mixs-schema -# -# id: https://microbiomedata/schema/mixs -# description: -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import Boolean, Datetime, Double, Float, Integer, String -from linkml_runtime.utils.metamodelcore import Bool, XSDDateTime - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CAS = CurieNamespace('CAS', 'http://identifiers.org/cas/') -CHEBI = CurieNamespace('CHEBI', 'http://purl.obolibrary.org/obo/CHEBI_') -CHEMBL_COMPOUND = CurieNamespace('CHEMBL_COMPOUND', 'http://identifiers.org/chembl.compound/') -DRUGBANK = CurieNamespace('DRUGBANK', 'http://identifiers.org/drugbank/') -HMDB = CurieNamespace('HMDB', 'http://identifiers.org/hmdb/') -KEGG_COMPOUND = CurieNamespace('KEGG_COMPOUND', 'http://identifiers.org/kegg.compound/') -MESH = CurieNamespace('MESH', 'http://identifiers.org/mesh/') -MIXS = CurieNamespace('MIXS', 'https://w3id.org/gensc/') -OBI = CurieNamespace('OBI', 'http://purl.obolibrary.org/obo/OBI_') -PR = CurieNamespace('PR', 'http://purl.obolibrary.org/obo/PR_') -PUBCHEM_COMPOUND = CurieNamespace('PUBCHEM_COMPOUND', 'http://identifiers.org/pubchem.compound/') -UNIPROTKB = CurieNamespace('UniProtKB', 'http://example.org/UNKNOWN/UniProtKB/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -DCTERMS = CurieNamespace('dcterms', 'http://purl.org/dc/terms/') -GTPO = CurieNamespace('gtpo', 'http://example.org/UNKNOWN/gtpo/') -MIXS = CurieNamespace('mixs', 'https://w3id.org/gensc/') -NMDC = CurieNamespace('nmdc', 'https://microbiomedata/meta/') -PROV = CurieNamespace('prov', 'http://www.w3.org/ns/prov#') -QUD = CurieNamespace('qud', 'http://qudt.org/1.1/schema/qudt#') -RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#') -SCHEMA = CurieNamespace('schema', 'http://schema.org/') -SIO = CurieNamespace('sio', 'http://semanticscience.org/resource/SIO_') -SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#') -WGS = CurieNamespace('wgs', 'http://www.w3.org/2003/01/geo/wgs84_pos') -XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#') -DEFAULT_ = CurieNamespace('', 'https://microbiomedata/schema/mixs/') - - -# Types -class Bytes(int): - """ An integer value that corresponds to a size in bytes """ - type_class_uri = XSD.int - type_class_curie = "xsd:int" - type_name = "bytes" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/Bytes") - - -class DecimalDegree(float): - """ A decimal degree expresses latitude or longitude as decimal fractions. """ - type_class_uri = XSD.decimal - type_class_curie = "xsd:decimal" - type_name = "decimal degree" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/DecimalDegree") - - -class LanguageCode(str): - """ A language code conforming to ISO_639-1 """ - type_class_uri = XSD.language - type_class_curie = "xsd:language" - type_name = "language code" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/LanguageCode") - - -class Unit(str): - type_class_uri = XSD.string - type_class_curie = "xsd:string" - type_name = "unit" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/Unit") - - -# Class references -class NamedThingId(extended_str): - pass - - -class OntologyClassId(NamedThingId): - pass - - -class EnvironmentalMaterialTermId(OntologyClassId): - pass - - -class PersonId(NamedThingId): - pass - - -class InstrumentId(NamedThingId): - pass - - -class ChemicalEntityId(OntologyClassId): - pass - - -class GeneProductId(NamedThingId): - pass - - -class ActivityId(extended_str): - pass - - -@dataclass -class NamedThing(YAMLRoot): - """ - a databased entity or concept/class - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.NamedThing - class_class_curie: ClassVar[str] = "nmdc:NamedThing" - class_name: ClassVar[str] = "named thing" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/NamedThing") - - id: Union[str, NamedThingId] = None - name: Optional[str] = None - description: Optional[str] = None - alternative_identifiers: Optional[Union[str, List[str]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedThingId): - self.id = NamedThingId(self.id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.alternative_identifiers, list): - self.alternative_identifiers = [self.alternative_identifiers] if self.alternative_identifiers is not None else [] - self.alternative_identifiers = [v if isinstance(v, str) else str(v) for v in self.alternative_identifiers] - - super().__post_init__(**kwargs) - - -@dataclass -class OntologyClass(NamedThing): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.OntologyClass - class_class_curie: ClassVar[str] = "nmdc:OntologyClass" - class_name: ClassVar[str] = "ontology class" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/OntologyClass") - - id: Union[str, OntologyClassId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OntologyClassId): - self.id = OntologyClassId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class EnvironmentalMaterialTerm(OntologyClass): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.EnvironmentalMaterialTerm - class_class_curie: ClassVar[str] = "nmdc:EnvironmentalMaterialTerm" - class_name: ClassVar[str] = "environmental material term" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/EnvironmentalMaterialTerm") - - id: Union[str, EnvironmentalMaterialTermId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentalMaterialTermId): - self.id = EnvironmentalMaterialTermId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class AttributeValue(YAMLRoot): - """ - The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and - the structured value - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.AttributeValue - class_class_curie: ClassVar[str] = "nmdc:AttributeValue" - class_name: ClassVar[str] = "attribute value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/AttributeValue") - - has_raw_value: Optional[str] = None - was_generated_by: Optional[Union[str, ActivityId]] = None - type: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - if self.was_generated_by is not None and not isinstance(self.was_generated_by, ActivityId): - self.was_generated_by = ActivityId(self.was_generated_by) - - if self.type is not None and not isinstance(self.type, str): - self.type = str(self.type) - - super().__post_init__(**kwargs) - - -@dataclass -class QuantityValue(AttributeValue): - """ - A simple quantity, e.g. 2cm - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.QuantityValue - class_class_curie: ClassVar[str] = "nmdc:QuantityValue" - class_name: ClassVar[str] = "quantity value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/QuantityValue") - - has_unit: Optional[str] = None - has_numeric_value: Optional[float] = None - has_minimum_numeric_value: Optional[float] = None - has_maximum_numeric_value: Optional[float] = None - has_raw_value: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_unit is not None and not isinstance(self.has_unit, str): - self.has_unit = str(self.has_unit) - - if self.has_numeric_value is not None and not isinstance(self.has_numeric_value, float): - self.has_numeric_value = float(self.has_numeric_value) - - if self.has_minimum_numeric_value is not None and not isinstance(self.has_minimum_numeric_value, float): - self.has_minimum_numeric_value = float(self.has_minimum_numeric_value) - - if self.has_maximum_numeric_value is not None and not isinstance(self.has_maximum_numeric_value, float): - self.has_maximum_numeric_value = float(self.has_maximum_numeric_value) - - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - super().__post_init__(**kwargs) - - -@dataclass -class ImageValue(AttributeValue): - """ - An attribute value representing an image. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ImageValue - class_class_curie: ClassVar[str] = "nmdc:ImageValue" - class_name: ClassVar[str] = "image value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ImageValue") - - url: Optional[str] = None - description: Optional[str] = None - display_order: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.url is not None and not isinstance(self.url, str): - self.url = str(self.url) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if self.display_order is not None and not isinstance(self.display_order, str): - self.display_order = str(self.display_order) - - super().__post_init__(**kwargs) - - -@dataclass -class PersonValue(AttributeValue): - """ - An attribute value representing a person - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.PersonValue - class_class_curie: ClassVar[str] = "nmdc:PersonValue" - class_name: ClassVar[str] = "person value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/PersonValue") - - orcid: Optional[str] = None - profile_image_url: Optional[str] = None - email: Optional[str] = None - name: Optional[str] = None - websites: Optional[Union[str, List[str]]] = empty_list() - has_raw_value: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.orcid is not None and not isinstance(self.orcid, str): - self.orcid = str(self.orcid) - - if self.profile_image_url is not None and not isinstance(self.profile_image_url, str): - self.profile_image_url = str(self.profile_image_url) - - if self.email is not None and not isinstance(self.email, str): - self.email = str(self.email) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if not isinstance(self.websites, list): - self.websites = [self.websites] if self.websites is not None else [] - self.websites = [v if isinstance(v, str) else str(v) for v in self.websites] - - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - super().__post_init__(**kwargs) - - -@dataclass -class Person(NamedThing): - """ - represents a person, such as a researcher - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Person - class_class_curie: ClassVar[str] = "nmdc:Person" - class_name: ClassVar[str] = "person" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Person") - - id: Union[str, PersonId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PersonId): - self.id = PersonId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class MAGBin(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.MAGBin - class_class_curie: ClassVar[str] = "nmdc:MAGBin" - class_name: ClassVar[str] = "MAG bin" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/MAGBin") - - type: Optional[str] = None - bin_name: Optional[str] = None - number_of_contig: Optional[int] = None - completeness: Optional[float] = None - contamination: Optional[float] = None - gene_count: Optional[int] = None - bin_quality: Optional[str] = None - num_16s: Optional[int] = None - num_5s: Optional[int] = None - num_23s: Optional[int] = None - num_tRNA: Optional[int] = None - gtdbtk_domain: Optional[str] = None - gtdbtk_phylum: Optional[str] = None - gtdbtk_class: Optional[str] = None - gtdbtk_order: Optional[str] = None - gtdbtk_family: Optional[str] = None - gtdbtk_genus: Optional[str] = None - gtdbtk_species: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.type is not None and not isinstance(self.type, str): - self.type = str(self.type) - - if self.bin_name is not None and not isinstance(self.bin_name, str): - self.bin_name = str(self.bin_name) - - if self.number_of_contig is not None and not isinstance(self.number_of_contig, int): - self.number_of_contig = int(self.number_of_contig) - - if self.completeness is not None and not isinstance(self.completeness, float): - self.completeness = float(self.completeness) - - if self.contamination is not None and not isinstance(self.contamination, float): - self.contamination = float(self.contamination) - - if self.gene_count is not None and not isinstance(self.gene_count, int): - self.gene_count = int(self.gene_count) - - if self.bin_quality is not None and not isinstance(self.bin_quality, str): - self.bin_quality = str(self.bin_quality) - - if self.num_16s is not None and not isinstance(self.num_16s, int): - self.num_16s = int(self.num_16s) - - if self.num_5s is not None and not isinstance(self.num_5s, int): - self.num_5s = int(self.num_5s) - - if self.num_23s is not None and not isinstance(self.num_23s, int): - self.num_23s = int(self.num_23s) - - if self.num_tRNA is not None and not isinstance(self.num_tRNA, int): - self.num_tRNA = int(self.num_tRNA) - - if self.gtdbtk_domain is not None and not isinstance(self.gtdbtk_domain, str): - self.gtdbtk_domain = str(self.gtdbtk_domain) - - if self.gtdbtk_phylum is not None and not isinstance(self.gtdbtk_phylum, str): - self.gtdbtk_phylum = str(self.gtdbtk_phylum) - - if self.gtdbtk_class is not None and not isinstance(self.gtdbtk_class, str): - self.gtdbtk_class = str(self.gtdbtk_class) - - if self.gtdbtk_order is not None and not isinstance(self.gtdbtk_order, str): - self.gtdbtk_order = str(self.gtdbtk_order) - - if self.gtdbtk_family is not None and not isinstance(self.gtdbtk_family, str): - self.gtdbtk_family = str(self.gtdbtk_family) - - if self.gtdbtk_genus is not None and not isinstance(self.gtdbtk_genus, str): - self.gtdbtk_genus = str(self.gtdbtk_genus) - - if self.gtdbtk_species is not None and not isinstance(self.gtdbtk_species, str): - self.gtdbtk_species = str(self.gtdbtk_species) - - super().__post_init__(**kwargs) - - -@dataclass -class Instrument(NamedThing): - """ - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI]. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Instrument - class_class_curie: ClassVar[str] = "nmdc:Instrument" - class_name: ClassVar[str] = "instrument" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Instrument") - - id: Union[str, InstrumentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, InstrumentId): - self.id = InstrumentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class MetaboliteQuantification(YAMLRoot): - """ - This is used to link a metabolomics analysis workflow to a specific metabolite - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.MetaboliteQuantification - class_class_curie: ClassVar[str] = "nmdc:MetaboliteQuantification" - class_name: ClassVar[str] = "metabolite quantification" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/MetaboliteQuantification") - - alternative_identifiers: Optional[Union[str, List[str]]] = empty_list() - metabolite_quantified: Optional[Union[str, ChemicalEntityId]] = None - highest_similarity_score: Optional[float] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.alternative_identifiers, list): - self.alternative_identifiers = [self.alternative_identifiers] if self.alternative_identifiers is not None else [] - self.alternative_identifiers = [v if isinstance(v, str) else str(v) for v in self.alternative_identifiers] - - if self.metabolite_quantified is not None and not isinstance(self.metabolite_quantified, ChemicalEntityId): - self.metabolite_quantified = ChemicalEntityId(self.metabolite_quantified) - - if self.highest_similarity_score is not None and not isinstance(self.highest_similarity_score, float): - self.highest_similarity_score = float(self.highest_similarity_score) - - super().__post_init__(**kwargs) - - -@dataclass -class PeptideQuantification(YAMLRoot): - """ - This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.PeptideQuantification - class_class_curie: ClassVar[str] = "nmdc:PeptideQuantification" - class_name: ClassVar[str] = "peptide quantification" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/PeptideQuantification") - - peptide_sequence: Optional[str] = None - best_protein: Optional[Union[str, GeneProductId]] = None - all_proteins: Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]] = empty_list() - min_q_value: Optional[float] = None - peptide_spectral_count: Optional[int] = None - peptide_sum_masic_abundance: Optional[int] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.peptide_sequence is not None and not isinstance(self.peptide_sequence, str): - self.peptide_sequence = str(self.peptide_sequence) - - if self.best_protein is not None and not isinstance(self.best_protein, GeneProductId): - self.best_protein = GeneProductId(self.best_protein) - - if not isinstance(self.all_proteins, list): - self.all_proteins = [self.all_proteins] if self.all_proteins is not None else [] - self.all_proteins = [v if isinstance(v, GeneProductId) else GeneProductId(v) for v in self.all_proteins] - - if self.min_q_value is not None and not isinstance(self.min_q_value, float): - self.min_q_value = float(self.min_q_value) - - if self.peptide_spectral_count is not None and not isinstance(self.peptide_spectral_count, int): - self.peptide_spectral_count = int(self.peptide_spectral_count) - - if self.peptide_sum_masic_abundance is not None and not isinstance(self.peptide_sum_masic_abundance, int): - self.peptide_sum_masic_abundance = int(self.peptide_sum_masic_abundance) - - super().__post_init__(**kwargs) - - -@dataclass -class ProteinQuantification(YAMLRoot): - """ - This is used to link a metaproteomics analysis workflow to a specific protein - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ProteinQuantification - class_class_curie: ClassVar[str] = "nmdc:ProteinQuantification" - class_name: ClassVar[str] = "protein quantification" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ProteinQuantification") - - best_protein: Optional[Union[str, GeneProductId]] = None - all_proteins: Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]] = empty_list() - peptide_sequence_count: Optional[int] = None - protein_spectral_count: Optional[int] = None - protein_sum_masic_abundance: Optional[int] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.best_protein is not None and not isinstance(self.best_protein, GeneProductId): - self.best_protein = GeneProductId(self.best_protein) - - if not isinstance(self.all_proteins, list): - self.all_proteins = [self.all_proteins] if self.all_proteins is not None else [] - self.all_proteins = [v if isinstance(v, GeneProductId) else GeneProductId(v) for v in self.all_proteins] - - if self.peptide_sequence_count is not None and not isinstance(self.peptide_sequence_count, int): - self.peptide_sequence_count = int(self.peptide_sequence_count) - - if self.protein_spectral_count is not None and not isinstance(self.protein_spectral_count, int): - self.protein_spectral_count = int(self.protein_spectral_count) - - if self.protein_sum_masic_abundance is not None and not isinstance(self.protein_sum_masic_abundance, int): - self.protein_sum_masic_abundance = int(self.protein_sum_masic_abundance) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalEntity(OntologyClass): - """ - An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, - drugs. There may be different terms for distinct acid-base forms, protonation states - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ChemicalEntity - class_class_curie: ClassVar[str] = "nmdc:ChemicalEntity" - class_name: ClassVar[str] = "chemical entity" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ChemicalEntity") - - id: Union[str, ChemicalEntityId] = None - inchi: Optional[str] = None - inchi_key: Optional[str] = None - smiles: Optional[Union[str, List[str]]] = empty_list() - chemical_formula: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalEntityId): - self.id = ChemicalEntityId(self.id) - - if self.inchi is not None and not isinstance(self.inchi, str): - self.inchi = str(self.inchi) - - if self.inchi_key is not None and not isinstance(self.inchi_key, str): - self.inchi_key = str(self.inchi_key) - - if not isinstance(self.smiles, list): - self.smiles = [self.smiles] if self.smiles is not None else [] - self.smiles = [v if isinstance(v, str) else str(v) for v in self.smiles] - - if self.chemical_formula is not None and not isinstance(self.chemical_formula, str): - self.chemical_formula = str(self.chemical_formula) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneProduct(NamedThing): - """ - A molecule encoded by a gene that has an evolved function - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.GeneProduct - class_class_curie: ClassVar[str] = "nmdc:GeneProduct" - class_name: ClassVar[str] = "gene product" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/GeneProduct") - - id: Union[str, GeneProductId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneProductId): - self.id = GeneProductId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class TextValue(AttributeValue): - """ - A basic string value - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.TextValue - class_class_curie: ClassVar[str] = "nmdc:TextValue" - class_name: ClassVar[str] = "text value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/TextValue") - - language: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.language is not None and not isinstance(self.language, str): - self.language = str(self.language) - - super().__post_init__(**kwargs) - - -class UrlValue(AttributeValue): - """ - A value that is a string that conforms to URL syntax - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.UrlValue - class_class_curie: ClassVar[str] = "nmdc:UrlValue" - class_name: ClassVar[str] = "url value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/UrlValue") - - -class TimestampValue(AttributeValue): - """ - A value that is a timestamp. The range should be ISO-8601 - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.TimestampValue - class_class_curie: ClassVar[str] = "nmdc:TimestampValue" - class_name: ClassVar[str] = "timestamp value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/TimestampValue") - - -@dataclass -class IntegerValue(AttributeValue): - """ - A value that is an integer - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.IntegerValue - class_class_curie: ClassVar[str] = "nmdc:IntegerValue" - class_name: ClassVar[str] = "integer value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/IntegerValue") - - has_numeric_value: Optional[float] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_numeric_value is not None and not isinstance(self.has_numeric_value, float): - self.has_numeric_value = float(self.has_numeric_value) - - super().__post_init__(**kwargs) - - -@dataclass -class BooleanValue(AttributeValue): - """ - A value that is a boolean - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.BooleanValue - class_class_curie: ClassVar[str] = "nmdc:BooleanValue" - class_name: ClassVar[str] = "boolean value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/BooleanValue") - - has_boolean_value: Optional[Union[bool, Bool]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_boolean_value is not None and not isinstance(self.has_boolean_value, Bool): - self.has_boolean_value = Bool(self.has_boolean_value) - - super().__post_init__(**kwargs) - - -@dataclass -class ControlledTermValue(AttributeValue): - """ - A controlled term or class from an ontology - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ControlledTermValue - class_class_curie: ClassVar[str] = "nmdc:ControlledTermValue" - class_name: ClassVar[str] = "controlled term value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ControlledTermValue") - - term: Optional[Union[dict, OntologyClass]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.term is not None and not isinstance(self.term, OntologyClass): - self.term = OntologyClass(**as_dict(self.term)) - - super().__post_init__(**kwargs) - - -@dataclass -class GeolocationValue(AttributeValue): - """ - A normalized value for a location on the earth's surface - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.GeolocationValue - class_class_curie: ClassVar[str] = "nmdc:GeolocationValue" - class_name: ClassVar[str] = "geolocation value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/GeolocationValue") - - latitude: Optional[float] = None - longitude: Optional[float] = None - has_raw_value: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.latitude is not None and not isinstance(self.latitude, float): - self.latitude = float(self.latitude) - - if self.longitude is not None and not isinstance(self.longitude, float): - self.longitude = float(self.longitude) - - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - super().__post_init__(**kwargs) - - -@dataclass -class Activity(YAMLRoot): - """ - a provence-generating activity - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Activity - class_class_curie: ClassVar[str] = "nmdc:Activity" - class_name: ClassVar[str] = "activity" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Activity") - - id: Union[str, ActivityId] = None - name: Optional[str] = None - started_at_time: Optional[Union[str, XSDDateTime]] = None - ended_at_time: Optional[Union[str, XSDDateTime]] = None - was_informed_by: Optional[Union[str, ActivityId]] = None - was_associated_with: Optional[Union[dict, "Agent"]] = None - used: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ActivityId): - self.id = ActivityId(self.id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.started_at_time is not None and not isinstance(self.started_at_time, XSDDateTime): - self.started_at_time = XSDDateTime(self.started_at_time) - - if self.ended_at_time is not None and not isinstance(self.ended_at_time, XSDDateTime): - self.ended_at_time = XSDDateTime(self.ended_at_time) - - if self.was_informed_by is not None and not isinstance(self.was_informed_by, ActivityId): - self.was_informed_by = ActivityId(self.was_informed_by) - - if self.was_associated_with is not None and not isinstance(self.was_associated_with, Agent): - self.was_associated_with = Agent(**as_dict(self.was_associated_with)) - - if self.used is not None and not isinstance(self.used, str): - self.used = str(self.used) - - super().__post_init__(**kwargs) - - -@dataclass -class Agent(YAMLRoot): - """ - a provence-generating agent - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Agent - class_class_curie: ClassVar[str] = "nmdc:Agent" - class_name: ClassVar[str] = "agent" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Agent") - - acted_on_behalf_of: Optional[Union[dict, "Agent"]] = None - was_informed_by: Optional[Union[str, ActivityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.acted_on_behalf_of is not None and not isinstance(self.acted_on_behalf_of, Agent): - self.acted_on_behalf_of = Agent(**as_dict(self.acted_on_behalf_of)) - - if self.was_informed_by is not None and not isinstance(self.was_informed_by, ActivityId): - self.was_informed_by = ActivityId(self.was_informed_by) - - super().__post_init__(**kwargs) - - -# Enumerations -class ArchStrucEnum(EnumDefinitionImpl): - - building = PermissibleValue(text="building") - shed = PermissibleValue(text="shed") - home = PermissibleValue(text="home") - - _defn = EnumDefinition( - name="ArchStrucEnum", - ) - -class BiolStatEnum(EnumDefinitionImpl): - - wild = PermissibleValue(text="wild") - natural = PermissibleValue(text="natural") - hybrid = PermissibleValue(text="hybrid") - mutant = PermissibleValue(text="mutant") - - _defn = EnumDefinition( - name="BiolStatEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "semi-natural", - PermissibleValue(text="semi-natural") ) - setattr(cls, "inbred line", - PermissibleValue(text="inbred line") ) - setattr(cls, "breeder's line", - PermissibleValue(text="breeder's line") ) - setattr(cls, "clonal selection", - PermissibleValue(text="clonal selection") ) - -class BioticRelationshipEnum(EnumDefinitionImpl): - - parasite = PermissibleValue(text="parasite") - commensal = PermissibleValue(text="commensal") - symbiont = PermissibleValue(text="symbiont") - - _defn = EnumDefinition( - name="BioticRelationshipEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "free living", - PermissibleValue(text="free living") ) - -class BuildDocsEnum(EnumDefinitionImpl): - - schedule = PermissibleValue(text="schedule") - sections = PermissibleValue(text="sections") - submittals = PermissibleValue(text="submittals") - windows = PermissibleValue(text="windows") - - _defn = EnumDefinition( - name="BuildDocsEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "building information model", - PermissibleValue(text="building information model") ) - setattr(cls, "commissioning report", - PermissibleValue(text="commissioning report") ) - setattr(cls, "complaint logs", - PermissibleValue(text="complaint logs") ) - setattr(cls, "contract administration", - PermissibleValue(text="contract administration") ) - setattr(cls, "cost estimate", - PermissibleValue(text="cost estimate") ) - setattr(cls, "janitorial schedules or logs", - PermissibleValue(text="janitorial schedules or logs") ) - setattr(cls, "maintenance plans", - PermissibleValue(text="maintenance plans") ) - setattr(cls, "shop drawings", - PermissibleValue(text="shop drawings") ) - setattr(cls, "ventilation system", - PermissibleValue(text="ventilation system") ) - -class BuildOccupTypeEnum(EnumDefinitionImpl): - - office = PermissibleValue(text="office") - market = PermissibleValue(text="market") - restaurant = PermissibleValue(text="restaurant") - residence = PermissibleValue(text="residence") - school = PermissibleValue(text="school") - residential = PermissibleValue(text="residential") - commercial = PermissibleValue(text="commercial") - airport = PermissibleValue(text="airport") - - _defn = EnumDefinition( - name="BuildOccupTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "low rise", - PermissibleValue(text="low rise") ) - setattr(cls, "high rise", - PermissibleValue(text="high rise") ) - setattr(cls, "wood framed", - PermissibleValue(text="wood framed") ) - setattr(cls, "health care", - PermissibleValue(text="health care") ) - setattr(cls, "sports complex", - PermissibleValue(text="sports complex") ) - -class BuildingSettingEnum(EnumDefinitionImpl): - - urban = PermissibleValue(text="urban") - suburban = PermissibleValue(text="suburban") - exurban = PermissibleValue(text="exurban") - rural = PermissibleValue(text="rural") - - _defn = EnumDefinition( - name="BuildingSettingEnum", - ) - -class CeilCondEnum(EnumDefinitionImpl): - - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="CeilCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear") ) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair") ) - -class CeilFinishMatEnum(EnumDefinitionImpl): - - drywall = PermissibleValue(text="drywall") - tiles = PermissibleValue(text="tiles") - PVC = PermissibleValue(text="PVC") - plasterboard = PermissibleValue(text="plasterboard") - metal = PermissibleValue(text="metal") - fiberglass = PermissibleValue(text="fiberglass") - stucco = PermissibleValue(text="stucco") - wood = PermissibleValue(text="wood") - - _defn = EnumDefinition( - name="CeilFinishMatEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "mineral fibre", - PermissibleValue(text="mineral fibre") ) - setattr(cls, "mineral wool/calcium silicate", - PermissibleValue(text="mineral wool/calcium silicate") ) - -class CeilTextureEnum(EnumDefinitionImpl): - - knockdown = PermissibleValue(text="knockdown") - popcorn = PermissibleValue(text="popcorn") - smooth = PermissibleValue(text="smooth") - swirl = PermissibleValue(text="swirl") - - _defn = EnumDefinition( - name="CeilTextureEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "crows feet", - PermissibleValue(text="crows feet") ) - setattr(cls, "crows-foot stomp", - PermissibleValue(text="crows-foot stomp") ) - setattr(cls, "double skip", - PermissibleValue(text="double skip") ) - setattr(cls, "hawk and trowel", - PermissibleValue(text="hawk and trowel") ) - setattr(cls, "orange peel", - PermissibleValue(text="orange peel") ) - setattr(cls, "rosebud stomp", - PermissibleValue(text="rosebud stomp") ) - setattr(cls, "Santa-Fe texture", - PermissibleValue(text="Santa-Fe texture") ) - setattr(cls, "skip trowel", - PermissibleValue(text="skip trowel") ) - setattr(cls, "stomp knockdown", - PermissibleValue(text="stomp knockdown") ) - -class CeilTypeEnum(EnumDefinitionImpl): - - cathedral = PermissibleValue(text="cathedral") - dropped = PermissibleValue(text="dropped") - concave = PermissibleValue(text="concave") - coffered = PermissibleValue(text="coffered") - cove = PermissibleValue(text="cove") - stretched = PermissibleValue(text="stretched") - - _defn = EnumDefinition( - name="CeilTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "barrel-shaped", - PermissibleValue(text="barrel-shaped") ) - -class CurLandUseEnum(EnumDefinitionImpl): - - cities = PermissibleValue(text="cities") - farmstead = PermissibleValue(text="farmstead") - rock = PermissibleValue(text="rock") - sand = PermissibleValue(text="sand") - gravel = PermissibleValue(text="gravel") - mudflats = PermissibleValue(text="mudflats") - badlands = PermissibleValue(text="badlands") - rangeland = PermissibleValue(text="rangeland") - hayland = PermissibleValue(text="hayland") - - _defn = EnumDefinition( - name="CurLandUseEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "industrial areas", - PermissibleValue(text="industrial areas") ) - setattr(cls, "roads/railroads", - PermissibleValue(text="roads/railroads") ) - setattr(cls, "salt flats", - PermissibleValue(text="salt flats") ) - setattr(cls, "permanent snow or ice", - PermissibleValue(text="permanent snow or ice") ) - setattr(cls, "saline seeps", - PermissibleValue(text="saline seeps") ) - setattr(cls, "mines/quarries", - PermissibleValue(text="mines/quarries") ) - setattr(cls, "oil waste areas", - PermissibleValue(text="oil waste areas") ) - setattr(cls, "small grains", - PermissibleValue(text="small grains") ) - setattr(cls, "row crops", - PermissibleValue(text="row crops") ) - setattr(cls, "vegetable crops", - PermissibleValue(text="vegetable crops") ) - setattr(cls, "horticultural plants (e.g. tulips)", - PermissibleValue(text="horticultural plants (e.g. tulips)") ) - setattr(cls, "marshlands (grass,sedges,rushes)", - PermissibleValue(text="marshlands (grass,sedges,rushes)") ) - setattr(cls, "tundra (mosses,lichens)", - PermissibleValue(text="tundra (mosses,lichens)") ) - setattr(cls, "pastureland (grasslands used for livestock grazing)", - PermissibleValue(text="pastureland (grasslands used for livestock grazing)") ) - setattr(cls, "meadows (grasses,alfalfa,fescue,bromegrass,timothy)", - PermissibleValue(text="meadows (grasses,alfalfa,fescue,bromegrass,timothy)") ) - setattr(cls, "shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)", - PermissibleValue(text="shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)") ) - setattr(cls, "successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)", - PermissibleValue(text="successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)") ) - setattr(cls, "shrub crops (blueberries,nursery ornamentals,filberts)", - PermissibleValue(text="shrub crops (blueberries,nursery ornamentals,filberts)") ) - setattr(cls, "vine crops (grapes)", - PermissibleValue(text="vine crops (grapes)") ) - setattr(cls, "conifers (e.g. pine,spruce,fir,cypress)", - PermissibleValue(text="conifers (e.g. pine,spruce,fir,cypress)") ) - setattr(cls, "hardwoods (e.g. oak,hickory,elm,aspen)", - PermissibleValue(text="hardwoods (e.g. oak,hickory,elm,aspen)") ) - setattr(cls, "intermixed hardwood and conifers", - PermissibleValue(text="intermixed hardwood and conifers") ) - setattr(cls, "tropical (e.g. mangrove,palms)", - PermissibleValue(text="tropical (e.g. mangrove,palms)") ) - setattr(cls, "rainforest (evergreen forest receiving greater than 406 cm annual rainfall)", - PermissibleValue(text="rainforest (evergreen forest receiving greater than 406 cm annual rainfall)") ) - setattr(cls, "swamp (permanent or semi-permanent water body dominated by woody plants)", - PermissibleValue(text="swamp (permanent or semi-permanent water body dominated by woody plants)") ) - setattr(cls, "crop trees (nuts,fruit,christmas trees,nursery trees)", - PermissibleValue(text="crop trees (nuts,fruit,christmas trees,nursery trees)") ) - -class DeposEnvEnum(EnumDefinitionImpl): - - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="DeposEnvEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "Continental - Alluvial", - PermissibleValue(text="Continental - Alluvial") ) - setattr(cls, "Continental - Aeolian", - PermissibleValue(text="Continental - Aeolian") ) - setattr(cls, "Continental - Fluvial", - PermissibleValue(text="Continental - Fluvial") ) - setattr(cls, "Continental - Lacustrine", - PermissibleValue(text="Continental - Lacustrine") ) - setattr(cls, "Transitional - Deltaic", - PermissibleValue(text="Transitional - Deltaic") ) - setattr(cls, "Transitional - Tidal", - PermissibleValue(text="Transitional - Tidal") ) - setattr(cls, "Transitional - Lagoonal", - PermissibleValue(text="Transitional - Lagoonal") ) - setattr(cls, "Transitional - Beach", - PermissibleValue(text="Transitional - Beach") ) - setattr(cls, "Transitional - Lake", - PermissibleValue(text="Transitional - Lake") ) - setattr(cls, "Marine - Shallow", - PermissibleValue(text="Marine - Shallow") ) - setattr(cls, "Marine - Deep", - PermissibleValue(text="Marine - Deep") ) - setattr(cls, "Marine - Reef", - PermissibleValue(text="Marine - Reef") ) - setattr(cls, "Other - Evaporite", - PermissibleValue(text="Other - Evaporite") ) - setattr(cls, "Other - Glacial", - PermissibleValue(text="Other - Glacial") ) - setattr(cls, "Other - Volcanic", - PermissibleValue(text="Other - Volcanic") ) - -class DoorCompTypeEnum(EnumDefinitionImpl): - - revolving = PermissibleValue(text="revolving") - sliding = PermissibleValue(text="sliding") - telescopic = PermissibleValue(text="telescopic") - - _defn = EnumDefinition( - name="DoorCompTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "metal covered", - PermissibleValue(text="metal covered") ) - -class DoorCondEnum(EnumDefinitionImpl): - - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="DoorCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair") ) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear") ) - -class DoorDirectEnum(EnumDefinitionImpl): - - inward = PermissibleValue(text="inward") - outward = PermissibleValue(text="outward") - sideways = PermissibleValue(text="sideways") - - _defn = EnumDefinition( - name="DoorDirectEnum", - ) - -class DoorLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="DoorLocEnum", - ) - -class DoorMatEnum(EnumDefinitionImpl): - - aluminum = PermissibleValue(text="aluminum") - fiberboard = PermissibleValue(text="fiberboard") - fiberglass = PermissibleValue(text="fiberglass") - metal = PermissibleValue(text="metal") - vinyl = PermissibleValue(text="vinyl") - wood = PermissibleValue(text="wood") - - _defn = EnumDefinition( - name="DoorMatEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "cellular PVC", - PermissibleValue(text="cellular PVC") ) - setattr(cls, "engineered plastic", - PermissibleValue(text="engineered plastic") ) - setattr(cls, "thermoplastic alloy", - PermissibleValue(text="thermoplastic alloy") ) - setattr(cls, "wood/plastic composite", - PermissibleValue(text="wood/plastic composite") ) - -class DoorMoveEnum(EnumDefinitionImpl): - - collapsible = PermissibleValue(text="collapsible") - folding = PermissibleValue(text="folding") - revolving = PermissibleValue(text="revolving") - sliding = PermissibleValue(text="sliding") - swinging = PermissibleValue(text="swinging") - - _defn = EnumDefinition( - name="DoorMoveEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "rolling shutter", - PermissibleValue(text="rolling shutter") ) - -class DoorTypeEnum(EnumDefinitionImpl): - - composite = PermissibleValue(text="composite") - metal = PermissibleValue(text="metal") - wooden = PermissibleValue(text="wooden") - - _defn = EnumDefinition( - name="DoorTypeEnum", - ) - -class DoorTypeMetalEnum(EnumDefinitionImpl): - - collapsible = PermissibleValue(text="collapsible") - hollow = PermissibleValue(text="hollow") - - _defn = EnumDefinition( - name="DoorTypeMetalEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "corrugated steel", - PermissibleValue(text="corrugated steel") ) - setattr(cls, "rolling shutters", - PermissibleValue(text="rolling shutters") ) - setattr(cls, "steel plate", - PermissibleValue(text="steel plate") ) - -class DoorTypeWoodEnum(EnumDefinitionImpl): - - battened = PermissibleValue(text="battened") - flush = PermissibleValue(text="flush") - louvered = PermissibleValue(text="louvered") - - _defn = EnumDefinition( - name="DoorTypeWoodEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "bettened and ledged", - PermissibleValue(text="bettened and ledged") ) - setattr(cls, "ledged and braced", - PermissibleValue(text="ledged and braced") ) - setattr(cls, "ledged and framed", - PermissibleValue(text="ledged and framed") ) - setattr(cls, "ledged, braced and frame", - PermissibleValue(text="ledged, braced and frame") ) - setattr(cls, "framed and paneled", - PermissibleValue(text="framed and paneled") ) - setattr(cls, "glashed or sash", - PermissibleValue(text="glashed or sash") ) - setattr(cls, "wire gauged", - PermissibleValue(text="wire gauged") ) - -class DrainageClassEnum(EnumDefinitionImpl): - - poorly = PermissibleValue(text="poorly") - well = PermissibleValue(text="well") - - _defn = EnumDefinition( - name="DrainageClassEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "very poorly", - PermissibleValue(text="very poorly") ) - setattr(cls, "somewhat poorly", - PermissibleValue(text="somewhat poorly") ) - setattr(cls, "moderately well", - PermissibleValue(text="moderately well") ) - setattr(cls, "excessively drained", - PermissibleValue(text="excessively drained") ) - -class DrawingsEnum(EnumDefinitionImpl): - - operation = PermissibleValue(text="operation") - construction = PermissibleValue(text="construction") - bid = PermissibleValue(text="bid") - design = PermissibleValue(text="design") - diagram = PermissibleValue(text="diagram") - sketch = PermissibleValue(text="sketch") - - _defn = EnumDefinition( - name="DrawingsEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "as built", - PermissibleValue(text="as built") ) - setattr(cls, "building navigation map", - PermissibleValue(text="building navigation map") ) - -class ExtWallOrientEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - northeast = PermissibleValue(text="northeast") - southeast = PermissibleValue(text="southeast") - southwest = PermissibleValue(text="southwest") - northwest = PermissibleValue(text="northwest") - - _defn = EnumDefinition( - name="ExtWallOrientEnum", - ) - -class ExtWindowOrientEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - northeast = PermissibleValue(text="northeast") - southeast = PermissibleValue(text="southeast") - southwest = PermissibleValue(text="southwest") - northwest = PermissibleValue(text="northwest") - - _defn = EnumDefinition( - name="ExtWindowOrientEnum", - ) - -class FaoClassEnum(EnumDefinitionImpl): - - Acrisols = PermissibleValue(text="Acrisols") - Andosols = PermissibleValue(text="Andosols") - Arenosols = PermissibleValue(text="Arenosols") - Cambisols = PermissibleValue(text="Cambisols") - Chernozems = PermissibleValue(text="Chernozems") - Ferralsols = PermissibleValue(text="Ferralsols") - Fluvisols = PermissibleValue(text="Fluvisols") - Gleysols = PermissibleValue(text="Gleysols") - Greyzems = PermissibleValue(text="Greyzems") - Gypsisols = PermissibleValue(text="Gypsisols") - Histosols = PermissibleValue(text="Histosols") - Kastanozems = PermissibleValue(text="Kastanozems") - Lithosols = PermissibleValue(text="Lithosols") - Luvisols = PermissibleValue(text="Luvisols") - Nitosols = PermissibleValue(text="Nitosols") - Phaeozems = PermissibleValue(text="Phaeozems") - Planosols = PermissibleValue(text="Planosols") - Podzols = PermissibleValue(text="Podzols") - Podzoluvisols = PermissibleValue(text="Podzoluvisols") - Rankers = PermissibleValue(text="Rankers") - Regosols = PermissibleValue(text="Regosols") - Rendzinas = PermissibleValue(text="Rendzinas") - Solonchaks = PermissibleValue(text="Solonchaks") - Solonetz = PermissibleValue(text="Solonetz") - Vertisols = PermissibleValue(text="Vertisols") - Yermosols = PermissibleValue(text="Yermosols") - - _defn = EnumDefinition( - name="FaoClassEnum", - ) - -class FilterTypeEnum(EnumDefinitionImpl): - - HEPA = PermissibleValue(text="HEPA") - electrostatic = PermissibleValue(text="electrostatic") - - _defn = EnumDefinition( - name="FilterTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "particulate air filter", - PermissibleValue(text="particulate air filter") ) - setattr(cls, "chemical air filter", - PermissibleValue(text="chemical air filter") ) - setattr(cls, "low-MERV pleated media", - PermissibleValue(text="low-MERV pleated media") ) - setattr(cls, "gas-phase or ultraviolet air treatments", - PermissibleValue(text="gas-phase or ultraviolet air treatments") ) - -class FloorCondEnum(EnumDefinitionImpl): - - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="FloorCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear") ) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair") ) - -class FloorFinishMatEnum(EnumDefinitionImpl): - - tile = PermissibleValue(text="tile") - carpet = PermissibleValue(text="carpet") - rug = PermissibleValue(text="rug") - lineoleum = PermissibleValue(text="lineoleum") - stone = PermissibleValue(text="stone") - bamboo = PermissibleValue(text="bamboo") - cork = PermissibleValue(text="cork") - terrazo = PermissibleValue(text="terrazo") - concrete = PermissibleValue(text="concrete") - none = PermissibleValue(text="none") - sealed = PermissibleValue(text="sealed") - paint = PermissibleValue(text="paint") - - _defn = EnumDefinition( - name="FloorFinishMatEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "wood strip or parquet", - PermissibleValue(text="wood strip or parquet") ) - setattr(cls, "laminate wood", - PermissibleValue(text="laminate wood") ) - setattr(cls, "vinyl composition tile", - PermissibleValue(text="vinyl composition tile") ) - setattr(cls, "sheet vinyl", - PermissibleValue(text="sheet vinyl") ) - setattr(cls, "clear finish", - PermissibleValue(text="clear finish") ) - setattr(cls, "none or unfinished", - PermissibleValue(text="none or unfinished") ) - -class FloorStrucEnum(EnumDefinitionImpl): - - balcony = PermissibleValue(text="balcony") - concrete = PermissibleValue(text="concrete") - - _defn = EnumDefinition( - name="FloorStrucEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "floating floor", - PermissibleValue(text="floating floor") ) - setattr(cls, "glass floor", - PermissibleValue(text="glass floor") ) - setattr(cls, "raised floor", - PermissibleValue(text="raised floor") ) - setattr(cls, "sprung floor", - PermissibleValue(text="sprung floor") ) - setattr(cls, "wood-framed", - PermissibleValue(text="wood-framed") ) - -class FloorWaterMoldEnum(EnumDefinitionImpl): - - condensation = PermissibleValue(text="condensation") - - _defn = EnumDefinition( - name="FloorWaterMoldEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "mold odor", - PermissibleValue(text="mold odor") ) - setattr(cls, "wet floor", - PermissibleValue(text="wet floor") ) - setattr(cls, "water stains", - PermissibleValue(text="water stains") ) - setattr(cls, "wall discoloration", - PermissibleValue(text="wall discoloration") ) - setattr(cls, "floor discoloration", - PermissibleValue(text="floor discoloration") ) - setattr(cls, "ceiling discoloration", - PermissibleValue(text="ceiling discoloration") ) - setattr(cls, "peeling paint or wallpaper", - PermissibleValue(text="peeling paint or wallpaper") ) - setattr(cls, "bulging walls", - PermissibleValue(text="bulging walls") ) - -class FreqCleanEnum(EnumDefinitionImpl): - - Daily = PermissibleValue(text="Daily") - Weekly = PermissibleValue(text="Weekly") - Monthly = PermissibleValue(text="Monthly") - Quarterly = PermissibleValue(text="Quarterly") - Annually = PermissibleValue(text="Annually") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="FreqCleanEnum", - ) - -class FurnitureEnum(EnumDefinitionImpl): - - cabinet = PermissibleValue(text="cabinet") - chair = PermissibleValue(text="chair") - desks = PermissibleValue(text="desks") - - _defn = EnumDefinition( - name="FurnitureEnum", - ) - -class GenderRestroomEnum(EnumDefinitionImpl): - - female = PermissibleValue(text="female") - male = PermissibleValue(text="male") - unisex = PermissibleValue(text="unisex") - - _defn = EnumDefinition( - name="GenderRestroomEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "all gender", - PermissibleValue(text="all gender") ) - setattr(cls, "gender neurtral", - PermissibleValue(text="gender neurtral") ) - setattr(cls, "male and female", - PermissibleValue(text="male and female") ) - -class GrowthHabitEnum(EnumDefinitionImpl): - - erect = PermissibleValue(text="erect") - spreading = PermissibleValue(text="spreading") - prostrate = PermissibleValue(text="prostrate") - - _defn = EnumDefinition( - name="GrowthHabitEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "semi-erect", - PermissibleValue(text="semi-erect") ) - -class HandidnessEnum(EnumDefinitionImpl): - - ambidexterity = PermissibleValue(text="ambidexterity") - - _defn = EnumDefinition( - name="HandidnessEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "left handedness", - PermissibleValue(text="left handedness") ) - setattr(cls, "mixed-handedness", - PermissibleValue(text="mixed-handedness") ) - setattr(cls, "right handedness", - PermissibleValue(text="right handedness") ) - -class HcProducedEnum(EnumDefinitionImpl): - - Oil = PermissibleValue(text="Oil") - Gas = PermissibleValue(text="Gas") - Bitumen = PermissibleValue(text="Bitumen") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="HcProducedEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "Gas-Condensate", - PermissibleValue(text="Gas-Condensate") ) - setattr(cls, "Coalbed Methane", - PermissibleValue(text="Coalbed Methane") ) - -class HcrEnum(EnumDefinitionImpl): - - Coalbed = PermissibleValue(text="Coalbed") - Shale = PermissibleValue(text="Shale") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="HcrEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "Oil Reservoir", - PermissibleValue(text="Oil Reservoir") ) - setattr(cls, "Gas Reservoir", - PermissibleValue(text="Gas Reservoir") ) - setattr(cls, "Oil Sand", - PermissibleValue(text="Oil Sand") ) - setattr(cls, "Tight Oil Reservoir", - PermissibleValue(text="Tight Oil Reservoir") ) - setattr(cls, "Tight Gas Reservoir", - PermissibleValue(text="Tight Gas Reservoir") ) - -class HcrGeolAgeEnum(EnumDefinitionImpl): - - Archean = PermissibleValue(text="Archean") - Cambrian = PermissibleValue(text="Cambrian") - Carboniferous = PermissibleValue(text="Carboniferous") - Cenozoic = PermissibleValue(text="Cenozoic") - Cretaceous = PermissibleValue(text="Cretaceous") - Devonian = PermissibleValue(text="Devonian") - Jurassic = PermissibleValue(text="Jurassic") - Mesozoic = PermissibleValue(text="Mesozoic") - Neogene = PermissibleValue(text="Neogene") - Ordovician = PermissibleValue(text="Ordovician") - Paleogene = PermissibleValue(text="Paleogene") - Paleozoic = PermissibleValue(text="Paleozoic") - Permian = PermissibleValue(text="Permian") - Precambrian = PermissibleValue(text="Precambrian") - Proterozoic = PermissibleValue(text="Proterozoic") - Silurian = PermissibleValue(text="Silurian") - Triassic = PermissibleValue(text="Triassic") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="HcrGeolAgeEnum", - ) - -class HeatCoolTypeEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="HeatCoolTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "radiant system", - PermissibleValue(text="radiant system") ) - setattr(cls, "heat pump", - PermissibleValue(text="heat pump") ) - setattr(cls, "forced air system", - PermissibleValue(text="forced air system") ) - setattr(cls, "steam forced heat", - PermissibleValue(text="steam forced heat") ) - setattr(cls, "wood stove", - PermissibleValue(text="wood stove") ) - -class HeatDelivLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="HeatDelivLocEnum", - ) - -class HorizonEnum(EnumDefinitionImpl): - - Permafrost = PermissibleValue(text="Permafrost") - - _defn = EnumDefinition( - name="HorizonEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "O horizon", - PermissibleValue(text="O horizon") ) - setattr(cls, "A horizon", - PermissibleValue(text="A horizon") ) - setattr(cls, "E horizon", - PermissibleValue(text="E horizon") ) - setattr(cls, "B horizon", - PermissibleValue(text="B horizon") ) - setattr(cls, "C horizon", - PermissibleValue(text="C horizon") ) - setattr(cls, "R layer", - PermissibleValue(text="R layer") ) - -class HostSexEnum(EnumDefinitionImpl): - - female = PermissibleValue(text="female") - hermaphrodite = PermissibleValue(text="hermaphrodite") - male = PermissibleValue(text="male") - neuter = PermissibleValue(text="neuter") - - _defn = EnumDefinition( - name="HostSexEnum", - ) - -class IndoorSpaceEnum(EnumDefinitionImpl): - - bedroom = PermissibleValue(text="bedroom") - office = PermissibleValue(text="office") - bathroom = PermissibleValue(text="bathroom") - foyer = PermissibleValue(text="foyer") - kitchen = PermissibleValue(text="kitchen") - hallway = PermissibleValue(text="hallway") - elevator = PermissibleValue(text="elevator") - - _defn = EnumDefinition( - name="IndoorSpaceEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "locker room", - PermissibleValue(text="locker room") ) - -class IndoorSurfEnum(EnumDefinitionImpl): - - cabinet = PermissibleValue(text="cabinet") - ceiling = PermissibleValue(text="ceiling") - door = PermissibleValue(text="door") - shelving = PermissibleValue(text="shelving") - window = PermissibleValue(text="window") - wall = PermissibleValue(text="wall") - - _defn = EnumDefinition( - name="IndoorSurfEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "counter top", - PermissibleValue(text="counter top") ) - setattr(cls, "vent cover", - PermissibleValue(text="vent cover") ) - -class IntWallCondEnum(EnumDefinitionImpl): - - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="IntWallCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear") ) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair") ) - -class LightTypeEnum(EnumDefinitionImpl): - - none = PermissibleValue(text="none") - - _defn = EnumDefinition( - name="LightTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "natural light", - PermissibleValue(text="natural light") ) - setattr(cls, "electric light", - PermissibleValue(text="electric light") ) - setattr(cls, "desk lamp", - PermissibleValue(text="desk lamp") ) - setattr(cls, "flourescent lights", - PermissibleValue(text="flourescent lights") ) - -class LithologyEnum(EnumDefinitionImpl): - - Basement = PermissibleValue(text="Basement") - Chalk = PermissibleValue(text="Chalk") - Chert = PermissibleValue(text="Chert") - Coal = PermissibleValue(text="Coal") - Conglomerate = PermissibleValue(text="Conglomerate") - Diatomite = PermissibleValue(text="Diatomite") - Dolomite = PermissibleValue(text="Dolomite") - Limestone = PermissibleValue(text="Limestone") - Sandstone = PermissibleValue(text="Sandstone") - Shale = PermissibleValue(text="Shale") - Siltstone = PermissibleValue(text="Siltstone") - Volcanic = PermissibleValue(text="Volcanic") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="LithologyEnum", - ) - -class MechStrucEnum(EnumDefinitionImpl): - - subway = PermissibleValue(text="subway") - coach = PermissibleValue(text="coach") - carriage = PermissibleValue(text="carriage") - elevator = PermissibleValue(text="elevator") - escalator = PermissibleValue(text="escalator") - boat = PermissibleValue(text="boat") - train = PermissibleValue(text="train") - car = PermissibleValue(text="car") - bus = PermissibleValue(text="bus") - - _defn = EnumDefinition( - name="MechStrucEnum", - ) - -class OccupDocumentEnum(EnumDefinitionImpl): - - estimate = PermissibleValue(text="estimate") - videos = PermissibleValue(text="videos") - - _defn = EnumDefinition( - name="OccupDocumentEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "automated count", - PermissibleValue(text="automated count") ) - setattr(cls, "manual count", - PermissibleValue(text="manual count") ) - -class OrganismCountEnum(EnumDefinitionImpl): - - ATP = PermissibleValue(text="ATP") - MPN = PermissibleValue(text="MPN") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="OrganismCountEnum", - ) - -class OxyStatSampEnum(EnumDefinitionImpl): - - aerobic = PermissibleValue(text="aerobic") - anaerobic = PermissibleValue(text="anaerobic") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="OxyStatSampEnum", - ) - -class PlantGrowthMedEnum(EnumDefinitionImpl): - - perlite = PermissibleValue(text="perlite") - pumice = PermissibleValue(text="pumice") - sand = PermissibleValue(text="sand") - soil = PermissibleValue(text="soil") - vermiculite = PermissibleValue(text="vermiculite") - water = PermissibleValue(text="water") - - _defn = EnumDefinition( - name="PlantGrowthMedEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "other artificial liquid medium", - PermissibleValue(text="other artificial liquid medium") ) - setattr(cls, "other artificial solid medium", - PermissibleValue(text="other artificial solid medium") ) - setattr(cls, "peat moss", - PermissibleValue(text="peat moss") ) - -class PlantSexEnum(EnumDefinitionImpl): - - Androdioecious = PermissibleValue(text="Androdioecious") - Androecious = PermissibleValue(text="Androecious") - Androgynous = PermissibleValue(text="Androgynous") - Androgynomonoecious = PermissibleValue(text="Androgynomonoecious") - Andromonoecious = PermissibleValue(text="Andromonoecious") - Bisexual = PermissibleValue(text="Bisexual") - Dichogamous = PermissibleValue(text="Dichogamous") - Diclinous = PermissibleValue(text="Diclinous") - Dioecious = PermissibleValue(text="Dioecious") - Gynodioecious = PermissibleValue(text="Gynodioecious") - Gynoecious = PermissibleValue(text="Gynoecious") - Gynomonoecious = PermissibleValue(text="Gynomonoecious") - Hermaphroditic = PermissibleValue(text="Hermaphroditic") - Imperfect = PermissibleValue(text="Imperfect") - Monoclinous = PermissibleValue(text="Monoclinous") - Monoecious = PermissibleValue(text="Monoecious") - Perfect = PermissibleValue(text="Perfect") - Polygamodioecious = PermissibleValue(text="Polygamodioecious") - Polygamomonoecious = PermissibleValue(text="Polygamomonoecious") - Polygamous = PermissibleValue(text="Polygamous") - Protandrous = PermissibleValue(text="Protandrous") - Protogynous = PermissibleValue(text="Protogynous") - Subandroecious = PermissibleValue(text="Subandroecious") - Subdioecious = PermissibleValue(text="Subdioecious") - Subgynoecious = PermissibleValue(text="Subgynoecious") - Synoecious = PermissibleValue(text="Synoecious") - Trimonoecious = PermissibleValue(text="Trimonoecious") - Trioecious = PermissibleValue(text="Trioecious") - Unisexual = PermissibleValue(text="Unisexual") - - _defn = EnumDefinition( - name="PlantSexEnum", - ) - -class ProfilePositionEnum(EnumDefinitionImpl): - - summit = PermissibleValue(text="summit") - shoulder = PermissibleValue(text="shoulder") - backslope = PermissibleValue(text="backslope") - footslope = PermissibleValue(text="footslope") - toeslope = PermissibleValue(text="toeslope") - - _defn = EnumDefinition( - name="ProfilePositionEnum", - ) - -class QuadPosEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="QuadPosEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "North side", - PermissibleValue(text="North side") ) - setattr(cls, "West side", - PermissibleValue(text="West side") ) - setattr(cls, "South side", - PermissibleValue(text="South side") ) - setattr(cls, "East side", - PermissibleValue(text="East side") ) - -class RelSampLocEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="RelSampLocEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "edge of car", - PermissibleValue(text="edge of car") ) - setattr(cls, "center of car", - PermissibleValue(text="center of car") ) - setattr(cls, "under a seat", - PermissibleValue(text="under a seat") ) - -class RelToOxygenEnum(EnumDefinitionImpl): - - aerobe = PermissibleValue(text="aerobe") - anaerobe = PermissibleValue(text="anaerobe") - facultative = PermissibleValue(text="facultative") - microaerophilic = PermissibleValue(text="microaerophilic") - microanaerobe = PermissibleValue(text="microanaerobe") - - _defn = EnumDefinition( - name="RelToOxygenEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "obligate aerobe", - PermissibleValue(text="obligate aerobe") ) - setattr(cls, "obligate anaerobe", - PermissibleValue(text="obligate anaerobe") ) - -class RoomCondtEnum(EnumDefinitionImpl): - - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="RoomCondtEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear") ) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair") ) - setattr(cls, "visible signs of mold/mildew", - PermissibleValue(text="visible signs of mold/mildew") ) - -class RoomConnectedEnum(EnumDefinitionImpl): - - attic = PermissibleValue(text="attic") - bathroom = PermissibleValue(text="bathroom") - closet = PermissibleValue(text="closet") - elevator = PermissibleValue(text="elevator") - hallway = PermissibleValue(text="hallway") - kitchen = PermissibleValue(text="kitchen") - office = PermissibleValue(text="office") - stairwell = PermissibleValue(text="stairwell") - - _defn = EnumDefinition( - name="RoomConnectedEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "conference room", - PermissibleValue(text="conference room") ) - setattr(cls, "examining room", - PermissibleValue(text="examining room") ) - setattr(cls, "mail room", - PermissibleValue(text="mail room") ) - -class RoomLocEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="RoomLocEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "corner room", - PermissibleValue(text="corner room") ) - setattr(cls, "interior room", - PermissibleValue(text="interior room") ) - setattr(cls, "exterior wall", - PermissibleValue(text="exterior wall") ) - -class RoomSampPosEnum(EnumDefinitionImpl): - - center = PermissibleValue(text="center") - - _defn = EnumDefinition( - name="RoomSampPosEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "north corner", - PermissibleValue(text="north corner") ) - setattr(cls, "south corner", - PermissibleValue(text="south corner") ) - setattr(cls, "west corner", - PermissibleValue(text="west corner") ) - setattr(cls, "east corner", - PermissibleValue(text="east corner") ) - setattr(cls, "northeast corner", - PermissibleValue(text="northeast corner") ) - setattr(cls, "northwest corner", - PermissibleValue(text="northwest corner") ) - setattr(cls, "southeast corner", - PermissibleValue(text="southeast corner") ) - setattr(cls, "southwest corner", - PermissibleValue(text="southwest corner") ) - -class RoomTypeEnum(EnumDefinitionImpl): - - attic = PermissibleValue(text="attic") - bathroom = PermissibleValue(text="bathroom") - closet = PermissibleValue(text="closet") - elevator = PermissibleValue(text="elevator") - hallway = PermissibleValue(text="hallway") - kitchen = PermissibleValue(text="kitchen") - stairwell = PermissibleValue(text="stairwell") - lobby = PermissibleValue(text="lobby") - vestibule = PermissibleValue(text="vestibule") - laboratory_wet = PermissibleValue(text="laboratory_wet") - laboratory_dry = PermissibleValue(text="laboratory_dry") - gymnasium = PermissibleValue(text="gymnasium") - natatorium = PermissibleValue(text="natatorium") - auditorium = PermissibleValue(text="auditorium") - lockers = PermissibleValue(text="lockers") - cafe = PermissibleValue(text="cafe") - warehouse = PermissibleValue(text="warehouse") - - _defn = EnumDefinition( - name="RoomTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "conference room", - PermissibleValue(text="conference room") ) - setattr(cls, "examining room", - PermissibleValue(text="examining room") ) - setattr(cls, "mail room", - PermissibleValue(text="mail room") ) - setattr(cls, "private office", - PermissibleValue(text="private office") ) - setattr(cls, "open office", - PermissibleValue(text="open office") ) - setattr(cls, ",restroom", - PermissibleValue(text=",restroom") ) - setattr(cls, "mechanical or electrical room", - PermissibleValue(text="mechanical or electrical room") ) - setattr(cls, "data center", - PermissibleValue(text="data center") ) - -class SampCaptStatusEnum(EnumDefinitionImpl): - - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SampCaptStatusEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "active surveillance in response to an outbreak", - PermissibleValue(text="active surveillance in response to an outbreak") ) - setattr(cls, "active surveillance not initiated by an outbreak", - PermissibleValue(text="active surveillance not initiated by an outbreak") ) - setattr(cls, "farm sample", - PermissibleValue(text="farm sample") ) - setattr(cls, "market sample", - PermissibleValue(text="market sample") ) - -class SampCollectPointEnum(EnumDefinitionImpl): - - well = PermissibleValue(text="well") - wellhead = PermissibleValue(text="wellhead") - separator = PermissibleValue(text="separator") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SampCollectPointEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "test well", - PermissibleValue(text="test well") ) - setattr(cls, "drilling rig", - PermissibleValue(text="drilling rig") ) - setattr(cls, "storage tank", - PermissibleValue(text="storage tank") ) - -class SampDisStageEnum(EnumDefinitionImpl): - - dissemination = PermissibleValue(text="dissemination") - infection = PermissibleValue(text="infection") - inoculation = PermissibleValue(text="inoculation") - penetration = PermissibleValue(text="penetration") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SampDisStageEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "growth and reproduction", - PermissibleValue(text="growth and reproduction") ) - -class SampFloorEnum(EnumDefinitionImpl): - - basement = PermissibleValue(text="basement") - lobby = PermissibleValue(text="lobby") - - _defn = EnumDefinition( - name="SampFloorEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "1st floor", - PermissibleValue(text="1st floor") ) - setattr(cls, "2nd floor", - PermissibleValue(text="2nd floor") ) - -class SampMdEnum(EnumDefinitionImpl): - - DF = PermissibleValue(text="DF") - RT = PermissibleValue(text="RT") - KB = PermissibleValue(text="KB") - MSL = PermissibleValue(text="MSL") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SampMdEnum", - ) - -class SampSubtypeEnum(EnumDefinitionImpl): - - biofilm = PermissibleValue(text="biofilm") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SampSubtypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "oil phase", - PermissibleValue(text="oil phase") ) - setattr(cls, "water phase", - PermissibleValue(text="water phase") ) - setattr(cls, "not applicable", - PermissibleValue(text="not applicable") ) - -class SampWeatherEnum(EnumDefinitionImpl): - - cloudy = PermissibleValue(text="cloudy") - foggy = PermissibleValue(text="foggy") - hail = PermissibleValue(text="hail") - rain = PermissibleValue(text="rain") - snow = PermissibleValue(text="snow") - sleet = PermissibleValue(text="sleet") - sunny = PermissibleValue(text="sunny") - windy = PermissibleValue(text="windy") - - _defn = EnumDefinition( - name="SampWeatherEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "clear sky", - PermissibleValue(text="clear sky") ) - -class SeasonUseEnum(EnumDefinitionImpl): - - Spring = PermissibleValue(text="Spring") - Summer = PermissibleValue(text="Summer") - Fall = PermissibleValue(text="Fall") - Winter = PermissibleValue(text="Winter") - - _defn = EnumDefinition( - name="SeasonUseEnum", - ) - -class SedimentTypeEnum(EnumDefinitionImpl): - - biogenous = PermissibleValue(text="biogenous") - cosmogenous = PermissibleValue(text="cosmogenous") - hydrogenous = PermissibleValue(text="hydrogenous") - lithogenous = PermissibleValue(text="lithogenous") - - _defn = EnumDefinition( - name="SedimentTypeEnum", - ) - -class ShadingDeviceCondEnum(EnumDefinitionImpl): - - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="ShadingDeviceCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair") ) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear") ) - -class ShadingDeviceTypeEnum(EnumDefinitionImpl): - - tree = PermissibleValue(text="tree") - trellis = PermissibleValue(text="trellis") - - _defn = EnumDefinition( - name="ShadingDeviceTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "bahama shutters", - PermissibleValue(text="bahama shutters") ) - setattr(cls, "exterior roll blind", - PermissibleValue(text="exterior roll blind") ) - setattr(cls, "gambrel awning", - PermissibleValue(text="gambrel awning") ) - setattr(cls, "hood awning", - PermissibleValue(text="hood awning") ) - setattr(cls, "porchroller awning", - PermissibleValue(text="porchroller awning") ) - setattr(cls, "sarasota shutters", - PermissibleValue(text="sarasota shutters") ) - setattr(cls, "slatted aluminum", - PermissibleValue(text="slatted aluminum") ) - setattr(cls, "solid aluminum awning", - PermissibleValue(text="solid aluminum awning") ) - setattr(cls, "sun screen", - PermissibleValue(text="sun screen") ) - setattr(cls, "venetian awning", - PermissibleValue(text="venetian awning") ) - -class SoilHorizonEnum(EnumDefinitionImpl): - - Permafrost = PermissibleValue(text="Permafrost") - - _defn = EnumDefinition( - name="SoilHorizonEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "O horizon", - PermissibleValue(text="O horizon") ) - setattr(cls, "A horizon", - PermissibleValue(text="A horizon") ) - setattr(cls, "E horizon", - PermissibleValue(text="E horizon") ) - setattr(cls, "B horizon", - PermissibleValue(text="B horizon") ) - setattr(cls, "C horizon", - PermissibleValue(text="C horizon") ) - setattr(cls, "R layer", - PermissibleValue(text="R layer") ) - -class SpecificEnum(EnumDefinitionImpl): - - operation = PermissibleValue(text="operation") - construction = PermissibleValue(text="construction") - bid = PermissibleValue(text="bid") - design = PermissibleValue(text="design") - photos = PermissibleValue(text="photos") - - _defn = EnumDefinition( - name="SpecificEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "as built", - PermissibleValue(text="as built") ) - -class SrDepEnvEnum(EnumDefinitionImpl): - - Lacustine = PermissibleValue(text="Lacustine") - Fluvioldeltaic = PermissibleValue(text="Fluvioldeltaic") - Fluviomarine = PermissibleValue(text="Fluviomarine") - Marine = PermissibleValue(text="Marine") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SrDepEnvEnum", - ) - -class SrGeolAgeEnum(EnumDefinitionImpl): - - Archean = PermissibleValue(text="Archean") - Cambrian = PermissibleValue(text="Cambrian") - Carboniferous = PermissibleValue(text="Carboniferous") - Cenozoic = PermissibleValue(text="Cenozoic") - Cretaceous = PermissibleValue(text="Cretaceous") - Devonian = PermissibleValue(text="Devonian") - Jurassic = PermissibleValue(text="Jurassic") - Mesozoic = PermissibleValue(text="Mesozoic") - Neogene = PermissibleValue(text="Neogene") - Ordovician = PermissibleValue(text="Ordovician") - Paleogene = PermissibleValue(text="Paleogene") - Paleozoic = PermissibleValue(text="Paleozoic") - Permian = PermissibleValue(text="Permian") - Precambrian = PermissibleValue(text="Precambrian") - Proterozoic = PermissibleValue(text="Proterozoic") - Silurian = PermissibleValue(text="Silurian") - Triassic = PermissibleValue(text="Triassic") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SrGeolAgeEnum", - ) - -class SrKerogTypeEnum(EnumDefinitionImpl): - - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SrKerogTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "Type I", - PermissibleValue(text="Type I") ) - setattr(cls, "Type II", - PermissibleValue(text="Type II") ) - setattr(cls, "Type III", - PermissibleValue(text="Type III") ) - setattr(cls, "Type IV", - PermissibleValue(text="Type IV") ) - -class SrLithologyEnum(EnumDefinitionImpl): - - Clastic = PermissibleValue(text="Clastic") - Carbonate = PermissibleValue(text="Carbonate") - Coal = PermissibleValue(text="Coal") - Biosilicieous = PermissibleValue(text="Biosilicieous") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SrLithologyEnum", - ) - -class SubstructureTypeEnum(EnumDefinitionImpl): - - crawlspace = PermissibleValue(text="crawlspace") - basement = PermissibleValue(text="basement") - - _defn = EnumDefinition( - name="SubstructureTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "slab on grade", - PermissibleValue(text="slab on grade") ) - -class SurfAirContEnum(EnumDefinitionImpl): - - dust = PermissibleValue(text="dust") - radon = PermissibleValue(text="radon") - nutrients = PermissibleValue(text="nutrients") - biocides = PermissibleValue(text="biocides") - - _defn = EnumDefinition( - name="SurfAirContEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "organic matter", - PermissibleValue(text="organic matter") ) - setattr(cls, "particulate matter", - PermissibleValue(text="particulate matter") ) - setattr(cls, "volatile organic compounds", - PermissibleValue(text="volatile organic compounds") ) - setattr(cls, "biological contaminants", - PermissibleValue(text="biological contaminants") ) - -class SurfMaterialEnum(EnumDefinitionImpl): - - adobe = PermissibleValue(text="adobe") - carpet = PermissibleValue(text="carpet") - concrete = PermissibleValue(text="concrete") - glass = PermissibleValue(text="glass") - metal = PermissibleValue(text="metal") - paint = PermissibleValue(text="paint") - plastic = PermissibleValue(text="plastic") - stone = PermissibleValue(text="stone") - stucco = PermissibleValue(text="stucco") - tile = PermissibleValue(text="tile") - vinyl = PermissibleValue(text="vinyl") - wood = PermissibleValue(text="wood") - - _defn = EnumDefinition( - name="SurfMaterialEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "cinder blocks", - PermissibleValue(text="cinder blocks") ) - setattr(cls, "hay bales", - PermissibleValue(text="hay bales") ) - setattr(cls, "stainless steel", - PermissibleValue(text="stainless steel") ) - -class TidalStageEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="TidalStageEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "low tide", - PermissibleValue(text="low tide") ) - setattr(cls, "ebb tide", - PermissibleValue(text="ebb tide") ) - setattr(cls, "flood tide", - PermissibleValue(text="flood tide") ) - setattr(cls, "high tide", - PermissibleValue(text="high tide") ) - -class TillageEnum(EnumDefinitionImpl): - - drill = PermissibleValue(text="drill") - chisel = PermissibleValue(text="chisel") - tined = PermissibleValue(text="tined") - mouldboard = PermissibleValue(text="mouldboard") - - _defn = EnumDefinition( - name="TillageEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "cutting disc", - PermissibleValue(text="cutting disc") ) - setattr(cls, "ridge till", - PermissibleValue(text="ridge till") ) - setattr(cls, "strip tillage", - PermissibleValue(text="strip tillage") ) - setattr(cls, "zonal tillage", - PermissibleValue(text="zonal tillage") ) - setattr(cls, "disc plough", - PermissibleValue(text="disc plough") ) - -class TrainLineEnum(EnumDefinitionImpl): - - red = PermissibleValue(text="red") - green = PermissibleValue(text="green") - orange = PermissibleValue(text="orange") - - _defn = EnumDefinition( - name="TrainLineEnum", - ) - -class TrainStatLocEnum(EnumDefinitionImpl): - - riverside = PermissibleValue(text="riverside") - - _defn = EnumDefinition( - name="TrainStatLocEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "south station above ground", - PermissibleValue(text="south station above ground") ) - setattr(cls, "south station underground", - PermissibleValue(text="south station underground") ) - setattr(cls, "south station amtrak", - PermissibleValue(text="south station amtrak") ) - setattr(cls, "forest hills", - PermissibleValue(text="forest hills") ) - -class TrainStopLocEnum(EnumDefinitionImpl): - - end = PermissibleValue(text="end") - mid = PermissibleValue(text="mid") - downtown = PermissibleValue(text="downtown") - - _defn = EnumDefinition( - name="TrainStopLocEnum", - ) - -class VisMediaEnum(EnumDefinitionImpl): - - photos = PermissibleValue(text="photos") - videos = PermissibleValue(text="videos") - interiors = PermissibleValue(text="interiors") - equipment = PermissibleValue(text="equipment") - - _defn = EnumDefinition( - name="VisMediaEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "commonly of the building", - PermissibleValue(text="commonly of the building") ) - setattr(cls, "site context (adjacent buildings, vegetation, terrain, streets)", - PermissibleValue(text="site context (adjacent buildings, vegetation, terrain, streets)") ) - setattr(cls, "3D scans", - PermissibleValue(text="3D scans") ) - -class WallConstTypeEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="WallConstTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "frame construction", - PermissibleValue(text="frame construction") ) - setattr(cls, "joisted masonry", - PermissibleValue(text="joisted masonry") ) - setattr(cls, "light noncombustible", - PermissibleValue(text="light noncombustible") ) - setattr(cls, "masonry noncombustible", - PermissibleValue(text="masonry noncombustible") ) - setattr(cls, "modified fire resistive", - PermissibleValue(text="modified fire resistive") ) - setattr(cls, "fire resistive", - PermissibleValue(text="fire resistive") ) - -class WallFinishMatEnum(EnumDefinitionImpl): - - plaster = PermissibleValue(text="plaster") - tile = PermissibleValue(text="tile") - terrazzo = PermissibleValue(text="terrazzo") - wood = PermissibleValue(text="wood") - metal = PermissibleValue(text="metal") - masonry = PermissibleValue(text="masonry") - - _defn = EnumDefinition( - name="WallFinishMatEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "gypsum plaster", - PermissibleValue(text="gypsum plaster") ) - setattr(cls, "veneer plaster", - PermissibleValue(text="veneer plaster") ) - setattr(cls, "gypsum board", - PermissibleValue(text="gypsum board") ) - setattr(cls, "stone facing", - PermissibleValue(text="stone facing") ) - setattr(cls, "acoustical treatment", - PermissibleValue(text="acoustical treatment") ) - -class WallLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="WallLocEnum", - ) - -class WallSurfTreatmentEnum(EnumDefinitionImpl): - - painted = PermissibleValue(text="painted") - paneling = PermissibleValue(text="paneling") - stucco = PermissibleValue(text="stucco") - fabric = PermissibleValue(text="fabric") - - _defn = EnumDefinition( - name="WallSurfTreatmentEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "wall paper", - PermissibleValue(text="wall paper") ) - setattr(cls, "no treatment", - PermissibleValue(text="no treatment") ) - -class WallTextureEnum(EnumDefinitionImpl): - - knockdown = PermissibleValue(text="knockdown") - popcorn = PermissibleValue(text="popcorn") - smooth = PermissibleValue(text="smooth") - swirl = PermissibleValue(text="swirl") - - _defn = EnumDefinition( - name="WallTextureEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "crows feet", - PermissibleValue(text="crows feet") ) - setattr(cls, "crows-foot stomp", - PermissibleValue(text="crows-foot stomp") ) - setattr(cls, "", - PermissibleValue(text="") ) - setattr(cls, "double skip", - PermissibleValue(text="double skip") ) - setattr(cls, "hawk and trowel", - PermissibleValue(text="hawk and trowel") ) - setattr(cls, "orange peel", - PermissibleValue(text="orange peel") ) - setattr(cls, "rosebud stomp", - PermissibleValue(text="rosebud stomp") ) - setattr(cls, "Santa-Fe texture", - PermissibleValue(text="Santa-Fe texture") ) - setattr(cls, "skip trowel", - PermissibleValue(text="skip trowel") ) - setattr(cls, "stomp knockdown", - PermissibleValue(text="stomp knockdown") ) - -class WaterFeatTypeEnum(EnumDefinitionImpl): - - fountain = PermissibleValue(text="fountain") - pool = PermissibleValue(text="pool") - stream = PermissibleValue(text="stream") - waterfall = PermissibleValue(text="waterfall") - - _defn = EnumDefinition( - name="WaterFeatTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "standing feature", - PermissibleValue(text="standing feature") ) - -class WeekdayEnum(EnumDefinitionImpl): - - Monday = PermissibleValue(text="Monday") - Tuesday = PermissibleValue(text="Tuesday") - Wednesday = PermissibleValue(text="Wednesday") - Thursday = PermissibleValue(text="Thursday") - Friday = PermissibleValue(text="Friday") - Saturday = PermissibleValue(text="Saturday") - Sunday = PermissibleValue(text="Sunday") - - _defn = EnumDefinition( - name="WeekdayEnum", - ) - -class WindowCondEnum(EnumDefinitionImpl): - - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="WindowCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair") ) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear") ) - -class WindowCoverEnum(EnumDefinitionImpl): - - blinds = PermissibleValue(text="blinds") - curtains = PermissibleValue(text="curtains") - none = PermissibleValue(text="none") - - _defn = EnumDefinition( - name="WindowCoverEnum", - ) - -class WindowHorizPosEnum(EnumDefinitionImpl): - - left = PermissibleValue(text="left") - middle = PermissibleValue(text="middle") - right = PermissibleValue(text="right") - - _defn = EnumDefinition( - name="WindowHorizPosEnum", - ) - -class WindowLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="WindowLocEnum", - ) - -class WindowMatEnum(EnumDefinitionImpl): - - clad = PermissibleValue(text="clad") - fiberglass = PermissibleValue(text="fiberglass") - metal = PermissibleValue(text="metal") - vinyl = PermissibleValue(text="vinyl") - wood = PermissibleValue(text="wood") - - _defn = EnumDefinition( - name="WindowMatEnum", - ) - -class WindowTypeEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="WindowTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "single-hung sash window", - PermissibleValue(text="single-hung sash window") ) - setattr(cls, "horizontal sash window", - PermissibleValue(text="horizontal sash window") ) - setattr(cls, "fixed window", - PermissibleValue(text="fixed window") ) - -class WindowVertPosEnum(EnumDefinitionImpl): - - bottom = PermissibleValue(text="bottom") - middle = PermissibleValue(text="middle") - top = PermissibleValue(text="top") - low = PermissibleValue(text="low") - high = PermissibleValue(text="high") - - _defn = EnumDefinition( - name="WindowVertPosEnum", - ) - -# Slots -class slots: - pass - -slots.abs_air_humidity = Slot(uri=MIXS['0000122'], name="abs_air_humidity", curie=MIXS.curie('0000122'), - model_uri=DEFAULT_.abs_air_humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.core_field = Slot(uri=DEFAULT_.core_field, name="core field", curie=DEFAULT_.curie('core_field'), - model_uri=DEFAULT_.core_field, domain=None, range=Optional[str]) - -slots.add_recov_method = Slot(uri=MIXS['0001009'], name="add_recov_method", curie=MIXS.curie('0001009'), - model_uri=DEFAULT_.add_recov_method, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.additional_info = Slot(uri=MIXS['0000300'], name="additional_info", curie=MIXS.curie('0000300'), - model_uri=DEFAULT_.additional_info, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.address = Slot(uri=MIXS['0000218'], name="address", curie=MIXS.curie('0000218'), - model_uri=DEFAULT_.address, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.adj_room = Slot(uri=MIXS['0000219'], name="adj_room", curie=MIXS.curie('0000219'), - model_uri=DEFAULT_.adj_room, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.aero_struc = Slot(uri=MIXS['0000773'], name="aero_struc", curie=MIXS.curie('0000773'), - model_uri=DEFAULT_.aero_struc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.agrochem_addition = Slot(uri=MIXS['0000639'], name="agrochem_addition", curie=MIXS.curie('0000639'), - model_uri=DEFAULT_.agrochem_addition, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.air_temp = Slot(uri=MIXS['0000124'], name="air_temp", curie=MIXS.curie('0000124'), - model_uri=DEFAULT_.air_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.air_temp_regm = Slot(uri=MIXS['0000551'], name="air_temp_regm", curie=MIXS.curie('0000551'), - model_uri=DEFAULT_.air_temp_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.al_sat = Slot(uri=MIXS['0000607'], name="al_sat", curie=MIXS.curie('0000607'), - model_uri=DEFAULT_.al_sat, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.al_sat_meth = Slot(uri=MIXS['0000324'], name="al_sat_meth", curie=MIXS.curie('0000324'), - model_uri=DEFAULT_.al_sat_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.alkalinity = Slot(uri=MIXS['0000421'], name="alkalinity", curie=MIXS.curie('0000421'), - model_uri=DEFAULT_.alkalinity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.alkalinity_method = Slot(uri=MIXS['0000298'], name="alkalinity_method", curie=MIXS.curie('0000298'), - model_uri=DEFAULT_.alkalinity_method, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.alkyl_diethers = Slot(uri=MIXS['0000490'], name="alkyl_diethers", curie=MIXS.curie('0000490'), - model_uri=DEFAULT_.alkyl_diethers, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.alt = Slot(uri=MIXS['0000094'], name="alt", curie=MIXS.curie('0000094'), - model_uri=DEFAULT_.alt, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.environment_field = Slot(uri=DEFAULT_.environment_field, name="environment field", curie=DEFAULT_.curie('environment_field'), - model_uri=DEFAULT_.environment_field, domain=None, range=Optional[str]) - -slots.aminopept_act = Slot(uri=MIXS['0000172'], name="aminopept_act", curie=MIXS.curie('0000172'), - model_uri=DEFAULT_.aminopept_act, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ammonium = Slot(uri=MIXS['0000427'], name="ammonium", curie=MIXS.curie('0000427'), - model_uri=DEFAULT_.ammonium, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.amount_light = Slot(uri=MIXS['0000140'], name="amount_light", curie=MIXS.curie('0000140'), - model_uri=DEFAULT_.amount_light, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ances_data = Slot(uri=MIXS['0000247'], name="ances_data", curie=MIXS.curie('0000247'), - model_uri=DEFAULT_.ances_data, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.annual_precpt = Slot(uri=MIXS['0000644'], name="annual_precpt", curie=MIXS.curie('0000644'), - model_uri=DEFAULT_.annual_precpt, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.annual_temp = Slot(uri=MIXS['0000642'], name="annual_temp", curie=MIXS.curie('0000642'), - model_uri=DEFAULT_.annual_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.antibiotic_regm = Slot(uri=MIXS['0000553'], name="antibiotic_regm", curie=MIXS.curie('0000553'), - model_uri=DEFAULT_.antibiotic_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.api = Slot(uri=MIXS['0000157'], name="api", curie=MIXS.curie('0000157'), - model_uri=DEFAULT_.api, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.arch_struc = Slot(uri=MIXS['0000774'], name="arch_struc", curie=MIXS.curie('0000774'), - model_uri=DEFAULT_.arch_struc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.aromatics_pc = Slot(uri=MIXS['0000133'], name="aromatics_pc", curie=MIXS.curie('0000133'), - model_uri=DEFAULT_.aromatics_pc, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.asphaltenes_pc = Slot(uri=MIXS['0000135'], name="asphaltenes_pc", curie=MIXS.curie('0000135'), - model_uri=DEFAULT_.asphaltenes_pc, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.atmospheric_data = Slot(uri=MIXS['0001097'], name="atmospheric_data", curie=MIXS.curie('0001097'), - model_uri=DEFAULT_.atmospheric_data, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.avg_dew_point = Slot(uri=MIXS['0000141'], name="avg_dew_point", curie=MIXS.curie('0000141'), - model_uri=DEFAULT_.avg_dew_point, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.avg_occup = Slot(uri=MIXS['0000775'], name="avg_occup", curie=MIXS.curie('0000775'), - model_uri=DEFAULT_.avg_occup, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.avg_temp = Slot(uri=MIXS['0000142'], name="avg_temp", curie=MIXS.curie('0000142'), - model_uri=DEFAULT_.avg_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.bac_prod = Slot(uri=MIXS['0000683'], name="bac_prod", curie=MIXS.curie('0000683'), - model_uri=DEFAULT_.bac_prod, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.bac_resp = Slot(uri=MIXS['0000684'], name="bac_resp", curie=MIXS.curie('0000684'), - model_uri=DEFAULT_.bac_resp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.bacteria_carb_prod = Slot(uri=MIXS['0000173'], name="bacteria_carb_prod", curie=MIXS.curie('0000173'), - model_uri=DEFAULT_.bacteria_carb_prod, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.barometric_press = Slot(uri=MIXS['0000096'], name="barometric_press", curie=MIXS.curie('0000096'), - model_uri=DEFAULT_.barometric_press, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.basin = Slot(uri=MIXS['0000290'], name="basin", curie=MIXS.curie('0000290'), - model_uri=DEFAULT_.basin, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.bathroom_count = Slot(uri=MIXS['0000776'], name="bathroom_count", curie=MIXS.curie('0000776'), - model_uri=DEFAULT_.bathroom_count, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.bedroom_count = Slot(uri=MIXS['0000777'], name="bedroom_count", curie=MIXS.curie('0000777'), - model_uri=DEFAULT_.bedroom_count, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.benzene = Slot(uri=MIXS['0000153'], name="benzene", curie=MIXS.curie('0000153'), - model_uri=DEFAULT_.benzene, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.biochem_oxygen_dem = Slot(uri=MIXS['0000653'], name="biochem_oxygen_dem", curie=MIXS.curie('0000653'), - model_uri=DEFAULT_.biochem_oxygen_dem, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.biocide = Slot(uri=MIXS['0001011'], name="biocide", curie=MIXS.curie('0001011'), - model_uri=DEFAULT_.biocide, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.biocide_admin_method = Slot(uri=MIXS['0000456'], name="biocide_admin_method", curie=MIXS.curie('0000456'), - model_uri=DEFAULT_.biocide_admin_method, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.biol_stat = Slot(uri=MIXS['0000858'], name="biol_stat", curie=MIXS.curie('0000858'), - model_uri=DEFAULT_.biol_stat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.biomass = Slot(uri=MIXS['0000174'], name="biomass", curie=MIXS.curie('0000174'), - model_uri=DEFAULT_.biomass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.biotic_regm = Slot(uri=MIXS['0001038'], name="biotic_regm", curie=MIXS.curie('0001038'), - model_uri=DEFAULT_.biotic_regm, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.biotic_relationship = Slot(uri=MIXS['0000028'], name="biotic_relationship", curie=MIXS.curie('0000028'), - model_uri=DEFAULT_.biotic_relationship, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.nucleic_acid_sequence_source_field = Slot(uri=DEFAULT_.nucleic_acid_sequence_source_field, name="nucleic acid sequence source field", curie=DEFAULT_.curie('nucleic_acid_sequence_source_field'), - model_uri=DEFAULT_.nucleic_acid_sequence_source_field, domain=None, range=Optional[str]) - -slots.bishomohopanol = Slot(uri=MIXS['0000175'], name="bishomohopanol", curie=MIXS.curie('0000175'), - model_uri=DEFAULT_.bishomohopanol, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.blood_press_diast = Slot(uri=MIXS['0000258'], name="blood_press_diast", curie=MIXS.curie('0000258'), - model_uri=DEFAULT_.blood_press_diast, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.blood_press_syst = Slot(uri=MIXS['0000259'], name="blood_press_syst", curie=MIXS.curie('0000259'), - model_uri=DEFAULT_.blood_press_syst, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.bromide = Slot(uri=MIXS['0000176'], name="bromide", curie=MIXS.curie('0000176'), - model_uri=DEFAULT_.bromide, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.build_docs = Slot(uri=MIXS['0000787'], name="build_docs", curie=MIXS.curie('0000787'), - model_uri=DEFAULT_.build_docs, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.build_occup_type = Slot(uri=MIXS['0000761'], name="build_occup_type", curie=MIXS.curie('0000761'), - model_uri=DEFAULT_.build_occup_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.building_setting = Slot(uri=MIXS['0000768'], name="building_setting", curie=MIXS.curie('0000768'), - model_uri=DEFAULT_.building_setting, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.built_struc_age = Slot(uri=MIXS['0000145'], name="built_struc_age", curie=MIXS.curie('0000145'), - model_uri=DEFAULT_.built_struc_age, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.built_struc_set = Slot(uri=MIXS['0000778'], name="built_struc_set", curie=MIXS.curie('0000778'), - model_uri=DEFAULT_.built_struc_set, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.built_struc_type = Slot(uri=MIXS['0000721'], name="built_struc_type", curie=MIXS.curie('0000721'), - model_uri=DEFAULT_.built_struc_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.calcium = Slot(uri=MIXS['0000432'], name="calcium", curie=MIXS.curie('0000432'), - model_uri=DEFAULT_.calcium, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.carb_dioxide = Slot(uri=MIXS['0000097'], name="carb_dioxide", curie=MIXS.curie('0000097'), - model_uri=DEFAULT_.carb_dioxide, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.carb_monoxide = Slot(uri=MIXS['0000098'], name="carb_monoxide", curie=MIXS.curie('0000098'), - model_uri=DEFAULT_.carb_monoxide, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.carb_nitro_ratio = Slot(uri=MIXS['0000310'], name="carb_nitro_ratio", curie=MIXS.curie('0000310'), - model_uri=DEFAULT_.carb_nitro_ratio, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ceil_area = Slot(uri=MIXS['0000148'], name="ceil_area", curie=MIXS.curie('0000148'), - model_uri=DEFAULT_.ceil_area, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ceil_cond = Slot(uri=MIXS['0000779'], name="ceil_cond", curie=MIXS.curie('0000779'), - model_uri=DEFAULT_.ceil_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ceil_finish_mat = Slot(uri=MIXS['0000780'], name="ceil_finish_mat", curie=MIXS.curie('0000780'), - model_uri=DEFAULT_.ceil_finish_mat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ceil_struc = Slot(uri=MIXS['0000782'], name="ceil_struc", curie=MIXS.curie('0000782'), - model_uri=DEFAULT_.ceil_struc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ceil_texture = Slot(uri=MIXS['0000783'], name="ceil_texture", curie=MIXS.curie('0000783'), - model_uri=DEFAULT_.ceil_texture, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ceil_thermal_mass = Slot(uri=MIXS['0000143'], name="ceil_thermal_mass", curie=MIXS.curie('0000143'), - model_uri=DEFAULT_.ceil_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ceil_type = Slot(uri=MIXS['0000784'], name="ceil_type", curie=MIXS.curie('0000784'), - model_uri=DEFAULT_.ceil_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ceil_water_mold = Slot(uri=MIXS['0000781'], name="ceil_water_mold", curie=MIXS.curie('0000781'), - model_uri=DEFAULT_.ceil_water_mold, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.chem_administration = Slot(uri=MIXS['0000751'], name="chem_administration", curie=MIXS.curie('0000751'), - model_uri=DEFAULT_.chem_administration, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.chem_mutagen = Slot(uri=MIXS['0000555'], name="chem_mutagen", curie=MIXS.curie('0000555'), - model_uri=DEFAULT_.chem_mutagen, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.chem_oxygen_dem = Slot(uri=MIXS['0000656'], name="chem_oxygen_dem", curie=MIXS.curie('0000656'), - model_uri=DEFAULT_.chem_oxygen_dem, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.chem_treat_method = Slot(uri=MIXS['0000457'], name="chem_treat_method", curie=MIXS.curie('0000457'), - model_uri=DEFAULT_.chem_treat_method, domain=None, range=Optional[str]) - -slots.chem_treatment = Slot(uri=MIXS['0001012'], name="chem_treatment", curie=MIXS.curie('0001012'), - model_uri=DEFAULT_.chem_treatment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.chimera_check = Slot(uri=MIXS['0000052'], name="chimera_check", curie=MIXS.curie('0000052'), - model_uri=DEFAULT_.chimera_check, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sequencing_field = Slot(uri=DEFAULT_.sequencing_field, name="sequencing field", curie=DEFAULT_.curie('sequencing_field'), - model_uri=DEFAULT_.sequencing_field, domain=None, range=Optional[str]) - -slots.chloride = Slot(uri=MIXS['0000429'], name="chloride", curie=MIXS.curie('0000429'), - model_uri=DEFAULT_.chloride, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.chlorophyll = Slot(uri=MIXS['0000177'], name="chlorophyll", curie=MIXS.curie('0000177'), - model_uri=DEFAULT_.chlorophyll, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.climate_environment = Slot(uri=MIXS['0001040'], name="climate_environment", curie=MIXS.curie('0001040'), - model_uri=DEFAULT_.climate_environment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.collection_date = Slot(uri=MIXS['0000011'], name="collection_date", curie=MIXS.curie('0000011'), - model_uri=DEFAULT_.collection_date, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.conduc = Slot(uri=MIXS['0000692'], name="conduc", curie=MIXS.curie('0000692'), - model_uri=DEFAULT_.conduc, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.cool_syst_id = Slot(uri=MIXS['0000785'], name="cool_syst_id", curie=MIXS.curie('0000785'), - model_uri=DEFAULT_.cool_syst_id, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.crop_rotation = Slot(uri=MIXS['0000318'], name="crop_rotation", curie=MIXS.curie('0000318'), - model_uri=DEFAULT_.crop_rotation, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.cult_root_med = Slot(uri=MIXS['0001041'], name="cult_root_med", curie=MIXS.curie('0001041'), - model_uri=DEFAULT_.cult_root_med, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.cur_land_use = Slot(uri=MIXS['0001080'], name="cur_land_use", curie=MIXS.curie('0001080'), - model_uri=DEFAULT_.cur_land_use, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.cur_vegetation = Slot(uri=MIXS['0000312'], name="cur_vegetation", curie=MIXS.curie('0000312'), - model_uri=DEFAULT_.cur_vegetation, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.cur_vegetation_meth = Slot(uri=MIXS['0000314'], name="cur_vegetation_meth", curie=MIXS.curie('0000314'), - model_uri=DEFAULT_.cur_vegetation_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.date_last_rain = Slot(uri=MIXS['0000786'], name="date_last_rain", curie=MIXS.curie('0000786'), - model_uri=DEFAULT_.date_last_rain, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.density = Slot(uri=MIXS['0000435'], name="density", curie=MIXS.curie('0000435'), - model_uri=DEFAULT_.density, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.depos_env = Slot(uri=MIXS['0000992'], name="depos_env", curie=MIXS.curie('0000992'), - model_uri=DEFAULT_.depos_env, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.depth = Slot(uri=MIXS['0000018'], name="depth", curie=MIXS.curie('0000018'), - model_uri=DEFAULT_.depth, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.dew_point = Slot(uri=MIXS['0000129'], name="dew_point", curie=MIXS.curie('0000129'), - model_uri=DEFAULT_.dew_point, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diether_lipids = Slot(uri=MIXS['0000178'], name="diether_lipids", curie=MIXS.curie('0000178'), - model_uri=DEFAULT_.diether_lipids, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_carb_dioxide = Slot(uri=MIXS['0000436'], name="diss_carb_dioxide", curie=MIXS.curie('0000436'), - model_uri=DEFAULT_.diss_carb_dioxide, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_hydrogen = Slot(uri=MIXS['0000179'], name="diss_hydrogen", curie=MIXS.curie('0000179'), - model_uri=DEFAULT_.diss_hydrogen, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_inorg_carb = Slot(uri=MIXS['0000434'], name="diss_inorg_carb", curie=MIXS.curie('0000434'), - model_uri=DEFAULT_.diss_inorg_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_inorg_nitro = Slot(uri=MIXS['0000698'], name="diss_inorg_nitro", curie=MIXS.curie('0000698'), - model_uri=DEFAULT_.diss_inorg_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_inorg_phosp = Slot(uri=MIXS['0000106'], name="diss_inorg_phosp", curie=MIXS.curie('0000106'), - model_uri=DEFAULT_.diss_inorg_phosp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_iron = Slot(uri=MIXS['0000139'], name="diss_iron", curie=MIXS.curie('0000139'), - model_uri=DEFAULT_.diss_iron, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_org_carb = Slot(uri=MIXS['0000433'], name="diss_org_carb", curie=MIXS.curie('0000433'), - model_uri=DEFAULT_.diss_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_org_nitro = Slot(uri=MIXS['0000162'], name="diss_org_nitro", curie=MIXS.curie('0000162'), - model_uri=DEFAULT_.diss_org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_oxygen = Slot(uri=MIXS['0000119'], name="diss_oxygen", curie=MIXS.curie('0000119'), - model_uri=DEFAULT_.diss_oxygen, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_oxygen_fluid = Slot(uri=MIXS['0000438'], name="diss_oxygen_fluid", curie=MIXS.curie('0000438'), - model_uri=DEFAULT_.diss_oxygen_fluid, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.door_comp_type = Slot(uri=MIXS['0000795'], name="door_comp_type", curie=MIXS.curie('0000795'), - model_uri=DEFAULT_.door_comp_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_cond = Slot(uri=MIXS['0000788'], name="door_cond", curie=MIXS.curie('0000788'), - model_uri=DEFAULT_.door_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_direct = Slot(uri=MIXS['0000789'], name="door_direct", curie=MIXS.curie('0000789'), - model_uri=DEFAULT_.door_direct, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_loc = Slot(uri=MIXS['0000790'], name="door_loc", curie=MIXS.curie('0000790'), - model_uri=DEFAULT_.door_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_mat = Slot(uri=MIXS['0000791'], name="door_mat", curie=MIXS.curie('0000791'), - model_uri=DEFAULT_.door_mat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_move = Slot(uri=MIXS['0000792'], name="door_move", curie=MIXS.curie('0000792'), - model_uri=DEFAULT_.door_move, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_size = Slot(uri=MIXS['0000158'], name="door_size", curie=MIXS.curie('0000158'), - model_uri=DEFAULT_.door_size, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.door_type = Slot(uri=MIXS['0000794'], name="door_type", curie=MIXS.curie('0000794'), - model_uri=DEFAULT_.door_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_type_metal = Slot(uri=MIXS['0000796'], name="door_type_metal", curie=MIXS.curie('0000796'), - model_uri=DEFAULT_.door_type_metal, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_type_wood = Slot(uri=MIXS['0000797'], name="door_type_wood", curie=MIXS.curie('0000797'), - model_uri=DEFAULT_.door_type_wood, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_water_mold = Slot(uri=MIXS['0000793'], name="door_water_mold", curie=MIXS.curie('0000793'), - model_uri=DEFAULT_.door_water_mold, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.down_par = Slot(uri=MIXS['0000703'], name="down_par", curie=MIXS.curie('0000703'), - model_uri=DEFAULT_.down_par, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.drainage_class = Slot(uri=MIXS['0001085'], name="drainage_class", curie=MIXS.curie('0001085'), - model_uri=DEFAULT_.drainage_class, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.drawings = Slot(uri=MIXS['0000798'], name="drawings", curie=MIXS.curie('0000798'), - model_uri=DEFAULT_.drawings, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.efficiency_percent = Slot(uri=MIXS['0000657'], name="efficiency_percent", curie=MIXS.curie('0000657'), - model_uri=DEFAULT_.efficiency_percent, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.elev = Slot(uri=MIXS['0000093'], name="elev", curie=MIXS.curie('0000093'), - model_uri=DEFAULT_.elev, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.elevator = Slot(uri=MIXS['0000799'], name="elevator", curie=MIXS.curie('0000799'), - model_uri=DEFAULT_.elevator, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.emulsions = Slot(uri=MIXS['0000660'], name="emulsions", curie=MIXS.curie('0000660'), - model_uri=DEFAULT_.emulsions, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.env_broad_scale = Slot(uri=MIXS['0000012'], name="env_broad_scale", curie=MIXS.curie('0000012'), - model_uri=DEFAULT_.env_broad_scale, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.env_local_scale = Slot(uri=MIXS['0000013'], name="env_local_scale", curie=MIXS.curie('0000013'), - model_uri=DEFAULT_.env_local_scale, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.env_medium = Slot(uri=MIXS['0000014'], name="env_medium", curie=MIXS.curie('0000014'), - model_uri=DEFAULT_.env_medium, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.escalator = Slot(uri=MIXS['0000800'], name="escalator", curie=MIXS.curie('0000800'), - model_uri=DEFAULT_.escalator, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ethylbenzene = Slot(uri=MIXS['0000155'], name="ethylbenzene", curie=MIXS.curie('0000155'), - model_uri=DEFAULT_.ethylbenzene, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.exp_duct = Slot(uri=MIXS['0000144'], name="exp_duct", curie=MIXS.curie('0000144'), - model_uri=DEFAULT_.exp_duct, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.exp_pipe = Slot(uri=MIXS['0000220'], name="exp_pipe", curie=MIXS.curie('0000220'), - model_uri=DEFAULT_.exp_pipe, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.experimental_factor = Slot(uri=MIXS['0000008'], name="experimental_factor", curie=MIXS.curie('0000008'), - model_uri=DEFAULT_.experimental_factor, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.investigation_field = Slot(uri=DEFAULT_.investigation_field, name="investigation field", curie=DEFAULT_.curie('investigation_field'), - model_uri=DEFAULT_.investigation_field, domain=None, range=Optional[str]) - -slots.ext_door = Slot(uri=MIXS['0000170'], name="ext_door", curie=MIXS.curie('0000170'), - model_uri=DEFAULT_.ext_door, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ext_wall_orient = Slot(uri=MIXS['0000817'], name="ext_wall_orient", curie=MIXS.curie('0000817'), - model_uri=DEFAULT_.ext_wall_orient, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ext_window_orient = Slot(uri=MIXS['0000818'], name="ext_window_orient", curie=MIXS.curie('0000818'), - model_uri=DEFAULT_.ext_window_orient, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.extreme_event = Slot(uri=MIXS['0000320'], name="extreme_event", curie=MIXS.curie('0000320'), - model_uri=DEFAULT_.extreme_event, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.fao_class = Slot(uri=MIXS['0001083'], name="fao_class", curie=MIXS.curie('0001083'), - model_uri=DEFAULT_.fao_class, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.fertilizer_regm = Slot(uri=MIXS['0000556'], name="fertilizer_regm", curie=MIXS.curie('0000556'), - model_uri=DEFAULT_.fertilizer_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.field = Slot(uri=MIXS['0000291'], name="field", curie=MIXS.curie('0000291'), - model_uri=DEFAULT_.field, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.filter_type = Slot(uri=MIXS['0000765'], name="filter_type", curie=MIXS.curie('0000765'), - model_uri=DEFAULT_.filter_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.fire = Slot(uri=MIXS['0001086'], name="fire", curie=MIXS.curie('0001086'), - model_uri=DEFAULT_.fire, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.fireplace_type = Slot(uri=MIXS['0000802'], name="fireplace_type", curie=MIXS.curie('0000802'), - model_uri=DEFAULT_.fireplace_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.flooding = Slot(uri=MIXS['0000319'], name="flooding", curie=MIXS.curie('0000319'), - model_uri=DEFAULT_.flooding, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.floor_age = Slot(uri=MIXS['0000164'], name="floor_age", curie=MIXS.curie('0000164'), - model_uri=DEFAULT_.floor_age, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.floor_area = Slot(uri=MIXS['0000165'], name="floor_area", curie=MIXS.curie('0000165'), - model_uri=DEFAULT_.floor_area, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.floor_cond = Slot(uri=MIXS['0000803'], name="floor_cond", curie=MIXS.curie('0000803'), - model_uri=DEFAULT_.floor_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.floor_count = Slot(uri=MIXS['0000225'], name="floor_count", curie=MIXS.curie('0000225'), - model_uri=DEFAULT_.floor_count, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.floor_finish_mat = Slot(uri=MIXS['0000804'], name="floor_finish_mat", curie=MIXS.curie('0000804'), - model_uri=DEFAULT_.floor_finish_mat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.floor_struc = Slot(uri=MIXS['0000806'], name="floor_struc", curie=MIXS.curie('0000806'), - model_uri=DEFAULT_.floor_struc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.floor_thermal_mass = Slot(uri=MIXS['0000166'], name="floor_thermal_mass", curie=MIXS.curie('0000166'), - model_uri=DEFAULT_.floor_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.floor_water_mold = Slot(uri=MIXS['0000805'], name="floor_water_mold", curie=MIXS.curie('0000805'), - model_uri=DEFAULT_.floor_water_mold, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.fluor = Slot(uri=MIXS['0000704'], name="fluor", curie=MIXS.curie('0000704'), - model_uri=DEFAULT_.fluor, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.freq_clean = Slot(uri=MIXS['0000226'], name="freq_clean", curie=MIXS.curie('0000226'), - model_uri=DEFAULT_.freq_clean, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.freq_cook = Slot(uri=MIXS['0000227'], name="freq_cook", curie=MIXS.curie('0000227'), - model_uri=DEFAULT_.freq_cook, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.fungicide_regm = Slot(uri=MIXS['0000557'], name="fungicide_regm", curie=MIXS.curie('0000557'), - model_uri=DEFAULT_.fungicide_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.furniture = Slot(uri=MIXS['0000807'], name="furniture", curie=MIXS.curie('0000807'), - model_uri=DEFAULT_.furniture, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.gaseous_environment = Slot(uri=MIXS['0000558'], name="gaseous_environment", curie=MIXS.curie('0000558'), - model_uri=DEFAULT_.gaseous_environment, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.gaseous_substances = Slot(uri=MIXS['0000661'], name="gaseous_substances", curie=MIXS.curie('0000661'), - model_uri=DEFAULT_.gaseous_substances, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.gender_restroom = Slot(uri=MIXS['0000808'], name="gender_restroom", curie=MIXS.curie('0000808'), - model_uri=DEFAULT_.gender_restroom, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.genetic_mod = Slot(uri=MIXS['0000859'], name="genetic_mod", curie=MIXS.curie('0000859'), - model_uri=DEFAULT_.genetic_mod, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.geo_loc_name = Slot(uri=MIXS['0000010'], name="geo_loc_name", curie=MIXS.curie('0000010'), - model_uri=DEFAULT_.geo_loc_name, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.glucosidase_act = Slot(uri=MIXS['0000137'], name="glucosidase_act", curie=MIXS.curie('0000137'), - model_uri=DEFAULT_.glucosidase_act, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.gravidity = Slot(uri=MIXS['0000875'], name="gravidity", curie=MIXS.curie('0000875'), - model_uri=DEFAULT_.gravidity, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.gravity = Slot(uri=MIXS['0000559'], name="gravity", curie=MIXS.curie('0000559'), - model_uri=DEFAULT_.gravity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.growth_facil = Slot(uri=MIXS['0001043'], name="growth_facil", curie=MIXS.curie('0001043'), - model_uri=DEFAULT_.growth_facil, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.growth_habit = Slot(uri=MIXS['0001044'], name="growth_habit", curie=MIXS.curie('0001044'), - model_uri=DEFAULT_.growth_habit, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.growth_hormone_regm = Slot(uri=MIXS['0000560'], name="growth_hormone_regm", curie=MIXS.curie('0000560'), - model_uri=DEFAULT_.growth_hormone_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.hall_count = Slot(uri=MIXS['0000228'], name="hall_count", curie=MIXS.curie('0000228'), - model_uri=DEFAULT_.hall_count, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.handidness = Slot(uri=MIXS['0000809'], name="handidness", curie=MIXS.curie('0000809'), - model_uri=DEFAULT_.handidness, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.hc_produced = Slot(uri=MIXS['0000989'], name="hc_produced", curie=MIXS.curie('0000989'), - model_uri=DEFAULT_.hc_produced, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.hcr = Slot(uri=MIXS['0000988'], name="hcr", curie=MIXS.curie('0000988'), - model_uri=DEFAULT_.hcr, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.hcr_fw_salinity = Slot(uri=MIXS['0000406'], name="hcr_fw_salinity", curie=MIXS.curie('0000406'), - model_uri=DEFAULT_.hcr_fw_salinity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.hcr_geol_age = Slot(uri=MIXS['0000993'], name="hcr_geol_age", curie=MIXS.curie('0000993'), - model_uri=DEFAULT_.hcr_geol_age, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.hcr_pressure = Slot(uri=MIXS['0000395'], name="hcr_pressure", curie=MIXS.curie('0000395'), - model_uri=DEFAULT_.hcr_pressure, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.hcr_temp = Slot(uri=MIXS['0000393'], name="hcr_temp", curie=MIXS.curie('0000393'), - model_uri=DEFAULT_.hcr_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.heat_cool_type = Slot(uri=MIXS['0000766'], name="heat_cool_type", curie=MIXS.curie('0000766'), - model_uri=DEFAULT_.heat_cool_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.heat_deliv_loc = Slot(uri=MIXS['0000810'], name="heat_deliv_loc", curie=MIXS.curie('0000810'), - model_uri=DEFAULT_.heat_deliv_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.heat_sys_deliv_meth = Slot(uri=MIXS['0000812'], name="heat_sys_deliv_meth", curie=MIXS.curie('0000812'), - model_uri=DEFAULT_.heat_sys_deliv_meth, domain=None, range=Optional[str]) - -slots.heat_system_id = Slot(uri=MIXS['0000833'], name="heat_system_id", curie=MIXS.curie('0000833'), - model_uri=DEFAULT_.heat_system_id, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.heavy_metals = Slot(uri=MIXS['0000652'], name="heavy_metals", curie=MIXS.curie('0000652'), - model_uri=DEFAULT_.heavy_metals, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.heavy_metals_meth = Slot(uri=MIXS['0000343'], name="heavy_metals_meth", curie=MIXS.curie('0000343'), - model_uri=DEFAULT_.heavy_metals_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.height_carper_fiber = Slot(uri=MIXS['0000167'], name="height_carper_fiber", curie=MIXS.curie('0000167'), - model_uri=DEFAULT_.height_carper_fiber, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.herbicide_regm = Slot(uri=MIXS['0000561'], name="herbicide_regm", curie=MIXS.curie('0000561'), - model_uri=DEFAULT_.herbicide_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.horizon = Slot(uri=MIXS['0001082'], name="horizon", curie=MIXS.curie('0001082'), - model_uri=DEFAULT_.horizon, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.horizon_meth = Slot(uri=MIXS['0000321'], name="horizon_meth", curie=MIXS.curie('0000321'), - model_uri=DEFAULT_.horizon_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_age = Slot(uri=MIXS['0000255'], name="host_age", curie=MIXS.curie('0000255'), - model_uri=DEFAULT_.host_age, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.host_body_habitat = Slot(uri=MIXS['0000866'], name="host_body_habitat", curie=MIXS.curie('0000866'), - model_uri=DEFAULT_.host_body_habitat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_body_product = Slot(uri=MIXS['0000888'], name="host_body_product", curie=MIXS.curie('0000888'), - model_uri=DEFAULT_.host_body_product, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.host_body_site = Slot(uri=MIXS['0000867'], name="host_body_site", curie=MIXS.curie('0000867'), - model_uri=DEFAULT_.host_body_site, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.host_body_temp = Slot(uri=MIXS['0000274'], name="host_body_temp", curie=MIXS.curie('0000274'), - model_uri=DEFAULT_.host_body_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.host_color = Slot(uri=MIXS['0000260'], name="host_color", curie=MIXS.curie('0000260'), - model_uri=DEFAULT_.host_color, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_common_name = Slot(uri=MIXS['0000248'], name="host_common_name", curie=MIXS.curie('0000248'), - model_uri=DEFAULT_.host_common_name, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_diet = Slot(uri=MIXS['0000869'], name="host_diet", curie=MIXS.curie('0000869'), - model_uri=DEFAULT_.host_diet, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_dry_mass = Slot(uri=MIXS['0000257'], name="host_dry_mass", curie=MIXS.curie('0000257'), - model_uri=DEFAULT_.host_dry_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.host_family_relation = Slot(uri=MIXS['0000872'], name="host_family_relation", curie=MIXS.curie('0000872'), - model_uri=DEFAULT_.host_family_relation, domain=None, range=Optional[Union[str, List[str]]]) - -slots.host_genotype = Slot(uri=MIXS['0000365'], name="host_genotype", curie=MIXS.curie('0000365'), - model_uri=DEFAULT_.host_genotype, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_growth_cond = Slot(uri=MIXS['0000871'], name="host_growth_cond", curie=MIXS.curie('0000871'), - model_uri=DEFAULT_.host_growth_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_height = Slot(uri=MIXS['0000264'], name="host_height", curie=MIXS.curie('0000264'), - model_uri=DEFAULT_.host_height, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.host_last_meal = Slot(uri=MIXS['0000870'], name="host_last_meal", curie=MIXS.curie('0000870'), - model_uri=DEFAULT_.host_last_meal, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_length = Slot(uri=MIXS['0000256'], name="host_length", curie=MIXS.curie('0000256'), - model_uri=DEFAULT_.host_length, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.host_life_stage = Slot(uri=MIXS['0000251'], name="host_life_stage", curie=MIXS.curie('0000251'), - model_uri=DEFAULT_.host_life_stage, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_phenotype = Slot(uri=MIXS['0000874'], name="host_phenotype", curie=MIXS.curie('0000874'), - model_uri=DEFAULT_.host_phenotype, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.host_sex = Slot(uri=MIXS['0000811'], name="host_sex", curie=MIXS.curie('0000811'), - model_uri=DEFAULT_.host_sex, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_shape = Slot(uri=MIXS['0000261'], name="host_shape", curie=MIXS.curie('0000261'), - model_uri=DEFAULT_.host_shape, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_subject_id = Slot(uri=MIXS['0000861'], name="host_subject_id", curie=MIXS.curie('0000861'), - model_uri=DEFAULT_.host_subject_id, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_subspecf_genlin = Slot(uri=MIXS['0001318'], name="host_subspecf_genlin", curie=MIXS.curie('0001318'), - model_uri=DEFAULT_.host_subspecf_genlin, domain=None, range=Optional[Union[str, List[str]]]) - -slots.host_substrate = Slot(uri=MIXS['0000252'], name="host_substrate", curie=MIXS.curie('0000252'), - model_uri=DEFAULT_.host_substrate, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_symbiont = Slot(uri=MIXS['0001298'], name="host_symbiont", curie=MIXS.curie('0001298'), - model_uri=DEFAULT_.host_symbiont, domain=None, range=Optional[Union[str, List[str]]]) - -slots.host_taxid = Slot(uri=MIXS['0000250'], name="host_taxid", curie=MIXS.curie('0000250'), - model_uri=DEFAULT_.host_taxid, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_tot_mass = Slot(uri=MIXS['0000263'], name="host_tot_mass", curie=MIXS.curie('0000263'), - model_uri=DEFAULT_.host_tot_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.host_wet_mass = Slot(uri=MIXS['0000567'], name="host_wet_mass", curie=MIXS.curie('0000567'), - model_uri=DEFAULT_.host_wet_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.humidity = Slot(uri=MIXS['0000100'], name="humidity", curie=MIXS.curie('0000100'), - model_uri=DEFAULT_.humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.humidity_regm = Slot(uri=MIXS['0000568'], name="humidity_regm", curie=MIXS.curie('0000568'), - model_uri=DEFAULT_.humidity_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.indoor_space = Slot(uri=MIXS['0000763'], name="indoor_space", curie=MIXS.curie('0000763'), - model_uri=DEFAULT_.indoor_space, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.indoor_surf = Slot(uri=MIXS['0000764'], name="indoor_surf", curie=MIXS.curie('0000764'), - model_uri=DEFAULT_.indoor_surf, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.indust_eff_percent = Slot(uri=MIXS['0000662'], name="indust_eff_percent", curie=MIXS.curie('0000662'), - model_uri=DEFAULT_.indust_eff_percent, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.inorg_particles = Slot(uri=MIXS['0000664'], name="inorg_particles", curie=MIXS.curie('0000664'), - model_uri=DEFAULT_.inorg_particles, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.inside_lux = Slot(uri=MIXS['0000168'], name="inside_lux", curie=MIXS.curie('0000168'), - model_uri=DEFAULT_.inside_lux, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.int_wall_cond = Slot(uri=MIXS['0000813'], name="int_wall_cond", curie=MIXS.curie('0000813'), - model_uri=DEFAULT_.int_wall_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.iw_bt_date_well = Slot(uri=MIXS['0001010'], name="iw_bt_date_well", curie=MIXS.curie('0001010'), - model_uri=DEFAULT_.iw_bt_date_well, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.iwf = Slot(uri=MIXS['0000455'], name="iwf", curie=MIXS.curie('0000455'), - model_uri=DEFAULT_.iwf, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.last_clean = Slot(uri=MIXS['0000814'], name="last_clean", curie=MIXS.curie('0000814'), - model_uri=DEFAULT_.last_clean, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.lat_lon = Slot(uri=MIXS['0000009'], name="lat_lon", curie=MIXS.curie('0000009'), - model_uri=DEFAULT_.lat_lon, domain=None, range=Optional[Union[dict, GeolocationValue]]) - -slots.light_intensity = Slot(uri=MIXS['0000706'], name="light_intensity", curie=MIXS.curie('0000706'), - model_uri=DEFAULT_.light_intensity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.light_regm = Slot(uri=MIXS['0000569'], name="light_regm", curie=MIXS.curie('0000569'), - model_uri=DEFAULT_.light_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.light_type = Slot(uri=MIXS['0000769'], name="light_type", curie=MIXS.curie('0000769'), - model_uri=DEFAULT_.light_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.link_addit_analys = Slot(uri=MIXS['0000340'], name="link_addit_analys", curie=MIXS.curie('0000340'), - model_uri=DEFAULT_.link_addit_analys, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.link_class_info = Slot(uri=MIXS['0000329'], name="link_class_info", curie=MIXS.curie('0000329'), - model_uri=DEFAULT_.link_class_info, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.link_climate_info = Slot(uri=MIXS['0000328'], name="link_climate_info", curie=MIXS.curie('0000328'), - model_uri=DEFAULT_.link_climate_info, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.lithology = Slot(uri=MIXS['0000990'], name="lithology", curie=MIXS.curie('0000990'), - model_uri=DEFAULT_.lithology, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.local_class = Slot(uri=MIXS['0000330'], name="local_class", curie=MIXS.curie('0000330'), - model_uri=DEFAULT_.local_class, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.local_class_meth = Slot(uri=MIXS['0000331'], name="local_class_meth", curie=MIXS.curie('0000331'), - model_uri=DEFAULT_.local_class_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.magnesium = Slot(uri=MIXS['0000431'], name="magnesium", curie=MIXS.curie('0000431'), - model_uri=DEFAULT_.magnesium, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.max_occup = Slot(uri=MIXS['0000229'], name="max_occup", curie=MIXS.curie('0000229'), - model_uri=DEFAULT_.max_occup, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.mean_frict_vel = Slot(uri=MIXS['0000498'], name="mean_frict_vel", curie=MIXS.curie('0000498'), - model_uri=DEFAULT_.mean_frict_vel, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.mean_peak_frict_vel = Slot(uri=MIXS['0000502'], name="mean_peak_frict_vel", curie=MIXS.curie('0000502'), - model_uri=DEFAULT_.mean_peak_frict_vel, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.mech_struc = Slot(uri=MIXS['0000815'], name="mech_struc", curie=MIXS.curie('0000815'), - model_uri=DEFAULT_.mech_struc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.mechanical_damage = Slot(uri=MIXS['0001052'], name="mechanical_damage", curie=MIXS.curie('0001052'), - model_uri=DEFAULT_.mechanical_damage, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.methane = Slot(uri=MIXS['0000101'], name="methane", curie=MIXS.curie('0000101'), - model_uri=DEFAULT_.methane, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.micro_biomass_meth = Slot(uri=MIXS['0000339'], name="micro_biomass_meth", curie=MIXS.curie('0000339'), - model_uri=DEFAULT_.micro_biomass_meth, domain=None, range=Optional[str]) - -slots.microbial_biomass = Slot(uri=MIXS['0000650'], name="microbial_biomass", curie=MIXS.curie('0000650'), - model_uri=DEFAULT_.microbial_biomass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.microbial_biomass_meth = Slot(uri=MIXS['0000339'], name="microbial_biomass_meth", curie=MIXS.curie('0000339'), - model_uri=DEFAULT_.microbial_biomass_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.mineral_nutr_regm = Slot(uri=MIXS['0000570'], name="mineral_nutr_regm", curie=MIXS.curie('0000570'), - model_uri=DEFAULT_.mineral_nutr_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.misc_param = Slot(uri=MIXS['0000752'], name="misc_param", curie=MIXS.curie('0000752'), - model_uri=DEFAULT_.misc_param, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.n_alkanes = Slot(uri=MIXS['0000503'], name="n_alkanes", curie=MIXS.curie('0000503'), - model_uri=DEFAULT_.n_alkanes, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.nitrate = Slot(uri=MIXS['0000425'], name="nitrate", curie=MIXS.curie('0000425'), - model_uri=DEFAULT_.nitrate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.nitrite = Slot(uri=MIXS['0000426'], name="nitrite", curie=MIXS.curie('0000426'), - model_uri=DEFAULT_.nitrite, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.nitro = Slot(uri=MIXS['0000504'], name="nitro", curie=MIXS.curie('0000504'), - model_uri=DEFAULT_.nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.non_min_nutr_regm = Slot(uri=MIXS['0000571'], name="non_min_nutr_regm", curie=MIXS.curie('0000571'), - model_uri=DEFAULT_.non_min_nutr_regm, domain=None, range=Optional[Union[str, List[str]]]) - -slots.nucl_acid_amp = Slot(uri=MIXS['0000038'], name="nucl_acid_amp", curie=MIXS.curie('0000038'), - model_uri=DEFAULT_.nucl_acid_amp, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.nucl_acid_ext = Slot(uri=MIXS['0000037'], name="nucl_acid_ext", curie=MIXS.curie('0000037'), - model_uri=DEFAULT_.nucl_acid_ext, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.number_pets = Slot(uri=MIXS['0000231'], name="number_pets", curie=MIXS.curie('0000231'), - model_uri=DEFAULT_.number_pets, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.number_plants = Slot(uri=MIXS['0000230'], name="number_plants", curie=MIXS.curie('0000230'), - model_uri=DEFAULT_.number_plants, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.number_resident = Slot(uri=MIXS['0000232'], name="number_resident", curie=MIXS.curie('0000232'), - model_uri=DEFAULT_.number_resident, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.occup_density_samp = Slot(uri=MIXS['0000217'], name="occup_density_samp", curie=MIXS.curie('0000217'), - model_uri=DEFAULT_.occup_density_samp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.occup_document = Slot(uri=MIXS['0000816'], name="occup_document", curie=MIXS.curie('0000816'), - model_uri=DEFAULT_.occup_document, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.occup_samp = Slot(uri=MIXS['0000772'], name="occup_samp", curie=MIXS.curie('0000772'), - model_uri=DEFAULT_.occup_samp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.org_carb = Slot(uri=MIXS['0000508'], name="org_carb", curie=MIXS.curie('0000508'), - model_uri=DEFAULT_.org_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.org_count_qpcr_info = Slot(uri=MIXS['0000099'], name="org_count_qpcr_info", curie=MIXS.curie('0000099'), - model_uri=DEFAULT_.org_count_qpcr_info, domain=None, range=Optional[str]) - -slots.org_matter = Slot(uri=MIXS['0000204'], name="org_matter", curie=MIXS.curie('0000204'), - model_uri=DEFAULT_.org_matter, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.org_nitro = Slot(uri=MIXS['0000205'], name="org_nitro", curie=MIXS.curie('0000205'), - model_uri=DEFAULT_.org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.org_particles = Slot(uri=MIXS['0000665'], name="org_particles", curie=MIXS.curie('0000665'), - model_uri=DEFAULT_.org_particles, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.organism_count = Slot(uri=MIXS['0000103'], name="organism_count", curie=MIXS.curie('0000103'), - model_uri=DEFAULT_.organism_count, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.owc_tvdss = Slot(uri=MIXS['0000405'], name="owc_tvdss", curie=MIXS.curie('0000405'), - model_uri=DEFAULT_.owc_tvdss, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.oxy_stat_samp = Slot(uri=MIXS['0000753'], name="oxy_stat_samp", curie=MIXS.curie('0000753'), - model_uri=DEFAULT_.oxy_stat_samp, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.oxygen = Slot(uri=MIXS['0000104'], name="oxygen", curie=MIXS.curie('0000104'), - model_uri=DEFAULT_.oxygen, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.part_org_carb = Slot(uri=MIXS['0000515'], name="part_org_carb", curie=MIXS.curie('0000515'), - model_uri=DEFAULT_.part_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.part_org_nitro = Slot(uri=MIXS['0000719'], name="part_org_nitro", curie=MIXS.curie('0000719'), - model_uri=DEFAULT_.part_org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.particle_class = Slot(uri=MIXS['0000206'], name="particle_class", curie=MIXS.curie('0000206'), - model_uri=DEFAULT_.particle_class, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.pcr_cond = Slot(uri=MIXS['0000049'], name="pcr_cond", curie=MIXS.curie('0000049'), - model_uri=DEFAULT_.pcr_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.pcr_primers = Slot(uri=MIXS['0000046'], name="pcr_primers", curie=MIXS.curie('0000046'), - model_uri=DEFAULT_.pcr_primers, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.permeability = Slot(uri=MIXS['0000404'], name="permeability", curie=MIXS.curie('0000404'), - model_uri=DEFAULT_.permeability, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.perturbation = Slot(uri=MIXS['0000754'], name="perturbation", curie=MIXS.curie('0000754'), - model_uri=DEFAULT_.perturbation, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.pesticide_regm = Slot(uri=MIXS['0000573'], name="pesticide_regm", curie=MIXS.curie('0000573'), - model_uri=DEFAULT_.pesticide_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.petroleum_hydrocarb = Slot(uri=MIXS['0000516'], name="petroleum_hydrocarb", curie=MIXS.curie('0000516'), - model_uri=DEFAULT_.petroleum_hydrocarb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ph = Slot(uri=MIXS['0001001'], name="ph", curie=MIXS.curie('0001001'), - model_uri=DEFAULT_.ph, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ph_meth = Slot(uri=MIXS['0001106'], name="ph_meth", curie=MIXS.curie('0001106'), - model_uri=DEFAULT_.ph_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ph_regm = Slot(uri=MIXS['0001056'], name="ph_regm", curie=MIXS.curie('0001056'), - model_uri=DEFAULT_.ph_regm, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.phaeopigments = Slot(uri=MIXS['0000180'], name="phaeopigments", curie=MIXS.curie('0000180'), - model_uri=DEFAULT_.phaeopigments, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.phosphate = Slot(uri=MIXS['0000505'], name="phosphate", curie=MIXS.curie('0000505'), - model_uri=DEFAULT_.phosphate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.phosplipid_fatt_acid = Slot(uri=MIXS['0000181'], name="phosplipid_fatt_acid", curie=MIXS.curie('0000181'), - model_uri=DEFAULT_.phosplipid_fatt_acid, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.photon_flux = Slot(uri=MIXS['0000725'], name="photon_flux", curie=MIXS.curie('0000725'), - model_uri=DEFAULT_.photon_flux, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.plant_growth_med = Slot(uri=MIXS['0001057'], name="plant_growth_med", curie=MIXS.curie('0001057'), - model_uri=DEFAULT_.plant_growth_med, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.plant_product = Slot(uri=MIXS['0001058'], name="plant_product", curie=MIXS.curie('0001058'), - model_uri=DEFAULT_.plant_product, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.plant_sex = Slot(uri=MIXS['0001059'], name="plant_sex", curie=MIXS.curie('0001059'), - model_uri=DEFAULT_.plant_sex, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.plant_struc = Slot(uri=MIXS['0001060'], name="plant_struc", curie=MIXS.curie('0001060'), - model_uri=DEFAULT_.plant_struc, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.pollutants = Slot(uri=MIXS['0000107'], name="pollutants", curie=MIXS.curie('0000107'), - model_uri=DEFAULT_.pollutants, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.pool_dna_extracts = Slot(uri=MIXS['0000325'], name="pool_dna_extracts", curie=MIXS.curie('0000325'), - model_uri=DEFAULT_.pool_dna_extracts, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.porosity = Slot(uri=MIXS['0000211'], name="porosity", curie=MIXS.curie('0000211'), - model_uri=DEFAULT_.porosity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.potassium = Slot(uri=MIXS['0000430'], name="potassium", curie=MIXS.curie('0000430'), - model_uri=DEFAULT_.potassium, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.pour_point = Slot(uri=MIXS['0000127'], name="pour_point", curie=MIXS.curie('0000127'), - model_uri=DEFAULT_.pour_point, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.pre_treatment = Slot(uri=MIXS['0000348'], name="pre_treatment", curie=MIXS.curie('0000348'), - model_uri=DEFAULT_.pre_treatment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.pres_animal_insect = Slot(uri=MIXS['0000819'], name="pres_animal_insect", curie=MIXS.curie('0000819'), - model_uri=DEFAULT_.pres_animal_insect, domain=None, range=Optional[str], - pattern=re.compile(r'^(cat|dog|rodent|snake|other);\d+$')) - -slots.pressure = Slot(uri=MIXS['0000412'], name="pressure", curie=MIXS.curie('0000412'), - model_uri=DEFAULT_.pressure, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.prev_land_use_meth = Slot(uri=MIXS['0000316'], name="prev_land_use_meth", curie=MIXS.curie('0000316'), - model_uri=DEFAULT_.prev_land_use_meth, domain=None, range=Optional[str]) - -slots.previous_land_use = Slot(uri=MIXS['0000315'], name="previous_land_use", curie=MIXS.curie('0000315'), - model_uri=DEFAULT_.previous_land_use, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.previous_land_use_meth = Slot(uri=MIXS['0000316'], name="previous_land_use_meth", curie=MIXS.curie('0000316'), - model_uri=DEFAULT_.previous_land_use_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.primary_prod = Slot(uri=MIXS['0000728'], name="primary_prod", curie=MIXS.curie('0000728'), - model_uri=DEFAULT_.primary_prod, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.primary_treatment = Slot(uri=MIXS['0000349'], name="primary_treatment", curie=MIXS.curie('0000349'), - model_uri=DEFAULT_.primary_treatment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.prod_rate = Slot(uri=MIXS['0000452'], name="prod_rate", curie=MIXS.curie('0000452'), - model_uri=DEFAULT_.prod_rate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.prod_start_date = Slot(uri=MIXS['0001008'], name="prod_start_date", curie=MIXS.curie('0001008'), - model_uri=DEFAULT_.prod_start_date, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.profile_position = Slot(uri=MIXS['0001084'], name="profile_position", curie=MIXS.curie('0001084'), - model_uri=DEFAULT_.profile_position, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.quad_pos = Slot(uri=MIXS['0000820'], name="quad_pos", curie=MIXS.curie('0000820'), - model_uri=DEFAULT_.quad_pos, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.radiation_regm = Slot(uri=MIXS['0000575'], name="radiation_regm", curie=MIXS.curie('0000575'), - model_uri=DEFAULT_.radiation_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.rainfall_regm = Slot(uri=MIXS['0000576'], name="rainfall_regm", curie=MIXS.curie('0000576'), - model_uri=DEFAULT_.rainfall_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.reactor_type = Slot(uri=MIXS['0000350'], name="reactor_type", curie=MIXS.curie('0000350'), - model_uri=DEFAULT_.reactor_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.redox_potential = Slot(uri=MIXS['0000182'], name="redox_potential", curie=MIXS.curie('0000182'), - model_uri=DEFAULT_.redox_potential, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.rel_air_humidity = Slot(uri=MIXS['0000121'], name="rel_air_humidity", curie=MIXS.curie('0000121'), - model_uri=DEFAULT_.rel_air_humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.rel_humidity_out = Slot(uri=MIXS['0000188'], name="rel_humidity_out", curie=MIXS.curie('0000188'), - model_uri=DEFAULT_.rel_humidity_out, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.rel_samp_loc = Slot(uri=MIXS['0000821'], name="rel_samp_loc", curie=MIXS.curie('0000821'), - model_uri=DEFAULT_.rel_samp_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.rel_to_oxygen = Slot(uri=MIXS['0000015'], name="rel_to_oxygen", curie=MIXS.curie('0000015'), - model_uri=DEFAULT_.rel_to_oxygen, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.reservoir = Slot(uri=MIXS['0000303'], name="reservoir", curie=MIXS.curie('0000303'), - model_uri=DEFAULT_.reservoir, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.resins_pc = Slot(uri=MIXS['0000134'], name="resins_pc", curie=MIXS.curie('0000134'), - model_uri=DEFAULT_.resins_pc, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.room_air_exch_rate = Slot(uri=MIXS['0000169'], name="room_air_exch_rate", curie=MIXS.curie('0000169'), - model_uri=DEFAULT_.room_air_exch_rate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.room_architec_elem = Slot(uri=MIXS['0000233'], name="room_architec_elem", curie=MIXS.curie('0000233'), - model_uri=DEFAULT_.room_architec_elem, domain=None, range=Optional[str]) - -slots.room_condt = Slot(uri=MIXS['0000822'], name="room_condt", curie=MIXS.curie('0000822'), - model_uri=DEFAULT_.room_condt, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_connected = Slot(uri=MIXS['0000826'], name="room_connected", curie=MIXS.curie('0000826'), - model_uri=DEFAULT_.room_connected, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_count = Slot(uri=MIXS['0000234'], name="room_count", curie=MIXS.curie('0000234'), - model_uri=DEFAULT_.room_count, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_dim = Slot(uri=MIXS['0000192'], name="room_dim", curie=MIXS.curie('0000192'), - model_uri=DEFAULT_.room_dim, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.room_door_dist = Slot(uri=MIXS['0000193'], name="room_door_dist", curie=MIXS.curie('0000193'), - model_uri=DEFAULT_.room_door_dist, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.room_door_share = Slot(uri=MIXS['0000242'], name="room_door_share", curie=MIXS.curie('0000242'), - model_uri=DEFAULT_.room_door_share, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_hallway = Slot(uri=MIXS['0000238'], name="room_hallway", curie=MIXS.curie('0000238'), - model_uri=DEFAULT_.room_hallway, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_loc = Slot(uri=MIXS['0000823'], name="room_loc", curie=MIXS.curie('0000823'), - model_uri=DEFAULT_.room_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_moist_dam_hist = Slot(uri=MIXS['0000235'], name="room_moist_dam_hist", curie=MIXS.curie('0000235'), - model_uri=DEFAULT_.room_moist_dam_hist, domain=None, range=Optional[int]) - -slots.room_net_area = Slot(uri=MIXS['0000194'], name="room_net_area", curie=MIXS.curie('0000194'), - model_uri=DEFAULT_.room_net_area, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.room_occup = Slot(uri=MIXS['0000236'], name="room_occup", curie=MIXS.curie('0000236'), - model_uri=DEFAULT_.room_occup, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.room_samp_pos = Slot(uri=MIXS['0000824'], name="room_samp_pos", curie=MIXS.curie('0000824'), - model_uri=DEFAULT_.room_samp_pos, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_type = Slot(uri=MIXS['0000825'], name="room_type", curie=MIXS.curie('0000825'), - model_uri=DEFAULT_.room_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_vol = Slot(uri=MIXS['0000195'], name="room_vol", curie=MIXS.curie('0000195'), - model_uri=DEFAULT_.room_vol, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.room_wall_share = Slot(uri=MIXS['0000243'], name="room_wall_share", curie=MIXS.curie('0000243'), - model_uri=DEFAULT_.room_wall_share, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_window_count = Slot(uri=MIXS['0000237'], name="room_window_count", curie=MIXS.curie('0000237'), - model_uri=DEFAULT_.room_window_count, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.root_cond = Slot(uri=MIXS['0001061'], name="root_cond", curie=MIXS.curie('0001061'), - model_uri=DEFAULT_.root_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.root_med_carbon = Slot(uri=MIXS['0000577'], name="root_med_carbon", curie=MIXS.curie('0000577'), - model_uri=DEFAULT_.root_med_carbon, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.root_med_macronutr = Slot(uri=MIXS['0000578'], name="root_med_macronutr", curie=MIXS.curie('0000578'), - model_uri=DEFAULT_.root_med_macronutr, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.root_med_micronutr = Slot(uri=MIXS['0000579'], name="root_med_micronutr", curie=MIXS.curie('0000579'), - model_uri=DEFAULT_.root_med_micronutr, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.root_med_ph = Slot(uri=MIXS['0001062'], name="root_med_ph", curie=MIXS.curie('0001062'), - model_uri=DEFAULT_.root_med_ph, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.root_med_regl = Slot(uri=MIXS['0000581'], name="root_med_regl", curie=MIXS.curie('0000581'), - model_uri=DEFAULT_.root_med_regl, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.root_med_solid = Slot(uri=MIXS['0001063'], name="root_med_solid", curie=MIXS.curie('0001063'), - model_uri=DEFAULT_.root_med_solid, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.root_med_suppl = Slot(uri=MIXS['0000580'], name="root_med_suppl", curie=MIXS.curie('0000580'), - model_uri=DEFAULT_.root_med_suppl, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.salinity = Slot(uri=MIXS['0000183'], name="salinity", curie=MIXS.curie('0000183'), - model_uri=DEFAULT_.salinity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.salinity_meth = Slot(uri=MIXS['0000341'], name="salinity_meth", curie=MIXS.curie('0000341'), - model_uri=DEFAULT_.salinity_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.salt_regm = Slot(uri=MIXS['0000582'], name="salt_regm", curie=MIXS.curie('0000582'), - model_uri=DEFAULT_.salt_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_capt_status = Slot(uri=MIXS['0000860'], name="samp_capt_status", curie=MIXS.curie('0000860'), - model_uri=DEFAULT_.samp_capt_status, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_collec_device = Slot(uri=MIXS['0000002'], name="samp_collec_device", curie=MIXS.curie('0000002'), - model_uri=DEFAULT_.samp_collec_device, domain=None, range=Optional[str]) - -slots.samp_collec_method = Slot(uri=MIXS['0001225'], name="samp_collec_method", curie=MIXS.curie('0001225'), - model_uri=DEFAULT_.samp_collec_method, domain=None, range=Optional[str]) - -slots.samp_collect_device = Slot(uri=MIXS['0000002'], name="samp_collect_device", curie=MIXS.curie('0000002'), - model_uri=DEFAULT_.samp_collect_device, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_collect_point = Slot(uri=MIXS['0001015'], name="samp_collect_point", curie=MIXS.curie('0001015'), - model_uri=DEFAULT_.samp_collect_point, domain=None, range=Optional[Union[str, "SampCollectPointEnum"]]) - -slots.samp_dis_stage = Slot(uri=MIXS['0000249'], name="samp_dis_stage", curie=MIXS.curie('0000249'), - model_uri=DEFAULT_.samp_dis_stage, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_floor = Slot(uri=MIXS['0000828'], name="samp_floor", curie=MIXS.curie('0000828'), - model_uri=DEFAULT_.samp_floor, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_loc_corr_rate = Slot(uri=MIXS['0000136'], name="samp_loc_corr_rate", curie=MIXS.curie('0000136'), - model_uri=DEFAULT_.samp_loc_corr_rate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_mat_process = Slot(uri=MIXS['0000016'], name="samp_mat_process", curie=MIXS.curie('0000016'), - model_uri=DEFAULT_.samp_mat_process, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.samp_md = Slot(uri=MIXS['0000413'], name="samp_md", curie=MIXS.curie('0000413'), - model_uri=DEFAULT_.samp_md, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_name = Slot(uri=MIXS['0001107'], name="samp_name", curie=MIXS.curie('0001107'), - model_uri=DEFAULT_.samp_name, domain=None, range=Optional[str]) - -slots.samp_preserv = Slot(uri=MIXS['0000463'], name="samp_preserv", curie=MIXS.curie('0000463'), - model_uri=DEFAULT_.samp_preserv, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_room_id = Slot(uri=MIXS['0000244'], name="samp_room_id", curie=MIXS.curie('0000244'), - model_uri=DEFAULT_.samp_room_id, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_size = Slot(uri=MIXS['0000001'], name="samp_size", curie=MIXS.curie('0000001'), - model_uri=DEFAULT_.samp_size, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_sort_meth = Slot(uri=MIXS['0000216'], name="samp_sort_meth", curie=MIXS.curie('0000216'), - model_uri=DEFAULT_.samp_sort_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_store_dur = Slot(uri=MIXS['0000116'], name="samp_store_dur", curie=MIXS.curie('0000116'), - model_uri=DEFAULT_.samp_store_dur, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_store_loc = Slot(uri=MIXS['0000755'], name="samp_store_loc", curie=MIXS.curie('0000755'), - model_uri=DEFAULT_.samp_store_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_store_temp = Slot(uri=MIXS['0000110'], name="samp_store_temp", curie=MIXS.curie('0000110'), - model_uri=DEFAULT_.samp_store_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_subtype = Slot(uri=MIXS['0000999'], name="samp_subtype", curie=MIXS.curie('0000999'), - model_uri=DEFAULT_.samp_subtype, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_time_out = Slot(uri=MIXS['0000196'], name="samp_time_out", curie=MIXS.curie('0000196'), - model_uri=DEFAULT_.samp_time_out, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_transport_cond = Slot(uri=MIXS['0000410'], name="samp_transport_cond", curie=MIXS.curie('0000410'), - model_uri=DEFAULT_.samp_transport_cond, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_tvdss = Slot(uri=MIXS['0000409'], name="samp_tvdss", curie=MIXS.curie('0000409'), - model_uri=DEFAULT_.samp_tvdss, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_type = Slot(uri=MIXS['0000998'], name="samp_type", curie=MIXS.curie('0000998'), - model_uri=DEFAULT_.samp_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_vol_we_dna_ext = Slot(uri=MIXS['0000111'], name="samp_vol_we_dna_ext", curie=MIXS.curie('0000111'), - model_uri=DEFAULT_.samp_vol_we_dna_ext, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_weather = Slot(uri=MIXS['0000827'], name="samp_weather", curie=MIXS.curie('0000827'), - model_uri=DEFAULT_.samp_weather, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_well_name = Slot(uri=MIXS['0000296'], name="samp_well_name", curie=MIXS.curie('0000296'), - model_uri=DEFAULT_.samp_well_name, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.saturates_pc = Slot(uri=MIXS['0000131'], name="saturates_pc", curie=MIXS.curie('0000131'), - model_uri=DEFAULT_.saturates_pc, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.season = Slot(uri=MIXS['0000829'], name="season", curie=MIXS.curie('0000829'), - model_uri=DEFAULT_.season, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.season_environment = Slot(uri=MIXS['0001068'], name="season_environment", curie=MIXS.curie('0001068'), - model_uri=DEFAULT_.season_environment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.season_precpt = Slot(uri=MIXS['0000645'], name="season_precpt", curie=MIXS.curie('0000645'), - model_uri=DEFAULT_.season_precpt, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.season_temp = Slot(uri=MIXS['0000643'], name="season_temp", curie=MIXS.curie('0000643'), - model_uri=DEFAULT_.season_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.season_use = Slot(uri=MIXS['0000830'], name="season_use", curie=MIXS.curie('0000830'), - model_uri=DEFAULT_.season_use, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.secondary_treatment = Slot(uri=MIXS['0000351'], name="secondary_treatment", curie=MIXS.curie('0000351'), - model_uri=DEFAULT_.secondary_treatment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sediment_type = Slot(uri=MIXS['0001078'], name="sediment_type", curie=MIXS.curie('0001078'), - model_uri=DEFAULT_.sediment_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.seq_meth = Slot(uri=MIXS['0000050'], name="seq_meth", curie=MIXS.curie('0000050'), - model_uri=DEFAULT_.seq_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.seq_quality_check = Slot(uri=MIXS['0000051'], name="seq_quality_check", curie=MIXS.curie('0000051'), - model_uri=DEFAULT_.seq_quality_check, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sewage_type = Slot(uri=MIXS['0000215'], name="sewage_type", curie=MIXS.curie('0000215'), - model_uri=DEFAULT_.sewage_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.shad_dev_water_mold = Slot(uri=MIXS['0000834'], name="shad_dev_water_mold", curie=MIXS.curie('0000834'), - model_uri=DEFAULT_.shad_dev_water_mold, domain=None, range=Optional[str]) - -slots.shading_device_cond = Slot(uri=MIXS['0000831'], name="shading_device_cond", curie=MIXS.curie('0000831'), - model_uri=DEFAULT_.shading_device_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.shading_device_loc = Slot(uri=MIXS['0000832'], name="shading_device_loc", curie=MIXS.curie('0000832'), - model_uri=DEFAULT_.shading_device_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.shading_device_mat = Slot(uri=MIXS['0000245'], name="shading_device_mat", curie=MIXS.curie('0000245'), - model_uri=DEFAULT_.shading_device_mat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.shading_device_type = Slot(uri=MIXS['0000835'], name="shading_device_type", curie=MIXS.curie('0000835'), - model_uri=DEFAULT_.shading_device_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sieving = Slot(uri=MIXS['0000322'], name="sieving", curie=MIXS.curie('0000322'), - model_uri=DEFAULT_.sieving, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.silicate = Slot(uri=MIXS['0000184'], name="silicate", curie=MIXS.curie('0000184'), - model_uri=DEFAULT_.silicate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.size_frac = Slot(uri=MIXS['0000017'], name="size_frac", curie=MIXS.curie('0000017'), - model_uri=DEFAULT_.size_frac, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.size_frac_low = Slot(uri=MIXS['0000735'], name="size_frac_low", curie=MIXS.curie('0000735'), - model_uri=DEFAULT_.size_frac_low, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.size_frac_up = Slot(uri=MIXS['0000736'], name="size_frac_up", curie=MIXS.curie('0000736'), - model_uri=DEFAULT_.size_frac_up, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.slope_aspect = Slot(uri=MIXS['0000647'], name="slope_aspect", curie=MIXS.curie('0000647'), - model_uri=DEFAULT_.slope_aspect, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.slope_gradient = Slot(uri=MIXS['0000646'], name="slope_gradient", curie=MIXS.curie('0000646'), - model_uri=DEFAULT_.slope_gradient, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.sludge_retent_time = Slot(uri=MIXS['0000669'], name="sludge_retent_time", curie=MIXS.curie('0000669'), - model_uri=DEFAULT_.sludge_retent_time, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.sodium = Slot(uri=MIXS['0000428'], name="sodium", curie=MIXS.curie('0000428'), - model_uri=DEFAULT_.sodium, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.soil_horizon = Slot(uri=MIXS['0001082'], name="soil_horizon", curie=MIXS.curie('0001082'), - model_uri=DEFAULT_.soil_horizon, domain=None, range=Optional[Union[str, "SoilHorizonEnum"]]) - -slots.soil_text_measure = Slot(uri=MIXS['0000335'], name="soil_text_measure", curie=MIXS.curie('0000335'), - model_uri=DEFAULT_.soil_text_measure, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.soil_texture_meth = Slot(uri=MIXS['0000336'], name="soil_texture_meth", curie=MIXS.curie('0000336'), - model_uri=DEFAULT_.soil_texture_meth, domain=None, range=Optional[str]) - -slots.soil_type = Slot(uri=MIXS['0000332'], name="soil_type", curie=MIXS.curie('0000332'), - model_uri=DEFAULT_.soil_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.soil_type_meth = Slot(uri=MIXS['0000334'], name="soil_type_meth", curie=MIXS.curie('0000334'), - model_uri=DEFAULT_.soil_type_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.solar_irradiance = Slot(uri=MIXS['0000112'], name="solar_irradiance", curie=MIXS.curie('0000112'), - model_uri=DEFAULT_.solar_irradiance, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.soluble_inorg_mat = Slot(uri=MIXS['0000672'], name="soluble_inorg_mat", curie=MIXS.curie('0000672'), - model_uri=DEFAULT_.soluble_inorg_mat, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.soluble_org_mat = Slot(uri=MIXS['0000673'], name="soluble_org_mat", curie=MIXS.curie('0000673'), - model_uri=DEFAULT_.soluble_org_mat, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.soluble_react_phosp = Slot(uri=MIXS['0000738'], name="soluble_react_phosp", curie=MIXS.curie('0000738'), - model_uri=DEFAULT_.soluble_react_phosp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.source_mat_id = Slot(uri=MIXS['0000026'], name="source_mat_id", curie=MIXS.curie('0000026'), - model_uri=DEFAULT_.source_mat_id, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.space_typ_state = Slot(uri=MIXS['0000770'], name="space_typ_state", curie=MIXS.curie('0000770'), - model_uri=DEFAULT_.space_typ_state, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.specific = Slot(uri=MIXS['0000836'], name="specific", curie=MIXS.curie('0000836'), - model_uri=DEFAULT_.specific, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.specific_humidity = Slot(uri=MIXS['0000214'], name="specific_humidity", curie=MIXS.curie('0000214'), - model_uri=DEFAULT_.specific_humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.sr_dep_env = Slot(uri=MIXS['0000996'], name="sr_dep_env", curie=MIXS.curie('0000996'), - model_uri=DEFAULT_.sr_dep_env, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sr_geol_age = Slot(uri=MIXS['0000997'], name="sr_geol_age", curie=MIXS.curie('0000997'), - model_uri=DEFAULT_.sr_geol_age, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sr_kerog_type = Slot(uri=MIXS['0000994'], name="sr_kerog_type", curie=MIXS.curie('0000994'), - model_uri=DEFAULT_.sr_kerog_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sr_lithology = Slot(uri=MIXS['0000995'], name="sr_lithology", curie=MIXS.curie('0000995'), - model_uri=DEFAULT_.sr_lithology, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.standing_water_regm = Slot(uri=MIXS['0001069'], name="standing_water_regm", curie=MIXS.curie('0001069'), - model_uri=DEFAULT_.standing_water_regm, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.store_cond = Slot(uri=MIXS['0000327'], name="store_cond", curie=MIXS.curie('0000327'), - model_uri=DEFAULT_.store_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.substructure_type = Slot(uri=MIXS['0000767'], name="substructure_type", curie=MIXS.curie('0000767'), - model_uri=DEFAULT_.substructure_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sulfate = Slot(uri=MIXS['0000423'], name="sulfate", curie=MIXS.curie('0000423'), - model_uri=DEFAULT_.sulfate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.sulfate_fw = Slot(uri=MIXS['0000407'], name="sulfate_fw", curie=MIXS.curie('0000407'), - model_uri=DEFAULT_.sulfate_fw, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.sulfide = Slot(uri=MIXS['0000424'], name="sulfide", curie=MIXS.curie('0000424'), - model_uri=DEFAULT_.sulfide, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.surf_air_cont = Slot(uri=MIXS['0000759'], name="surf_air_cont", curie=MIXS.curie('0000759'), - model_uri=DEFAULT_.surf_air_cont, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.surf_humidity = Slot(uri=MIXS['0000123'], name="surf_humidity", curie=MIXS.curie('0000123'), - model_uri=DEFAULT_.surf_humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.surf_material = Slot(uri=MIXS['0000758'], name="surf_material", curie=MIXS.curie('0000758'), - model_uri=DEFAULT_.surf_material, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.surf_moisture = Slot(uri=MIXS['0000128'], name="surf_moisture", curie=MIXS.curie('0000128'), - model_uri=DEFAULT_.surf_moisture, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.surf_moisture_ph = Slot(uri=MIXS['0000760'], name="surf_moisture_ph", curie=MIXS.curie('0000760'), - model_uri=DEFAULT_.surf_moisture_ph, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.surf_temp = Slot(uri=MIXS['0000125'], name="surf_temp", curie=MIXS.curie('0000125'), - model_uri=DEFAULT_.surf_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.suspend_part_matter = Slot(uri=MIXS['0000741'], name="suspend_part_matter", curie=MIXS.curie('0000741'), - model_uri=DEFAULT_.suspend_part_matter, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.suspend_solids = Slot(uri=MIXS['0000150'], name="suspend_solids", curie=MIXS.curie('0000150'), - model_uri=DEFAULT_.suspend_solids, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tan = Slot(uri=MIXS['0000120'], name="tan", curie=MIXS.curie('0000120'), - model_uri=DEFAULT_.tan, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.target_gene = Slot(uri=MIXS['0000044'], name="target_gene", curie=MIXS.curie('0000044'), - model_uri=DEFAULT_.target_gene, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.target_subfragment = Slot(uri=MIXS['0000045'], name="target_subfragment", curie=MIXS.curie('0000045'), - model_uri=DEFAULT_.target_subfragment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.temp = Slot(uri=MIXS['0000113'], name="temp", curie=MIXS.curie('0000113'), - model_uri=DEFAULT_.temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.temp_out = Slot(uri=MIXS['0000197'], name="temp_out", curie=MIXS.curie('0000197'), - model_uri=DEFAULT_.temp_out, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tertiary_treatment = Slot(uri=MIXS['0000352'], name="tertiary_treatment", curie=MIXS.curie('0000352'), - model_uri=DEFAULT_.tertiary_treatment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.texture = Slot(uri=MIXS['0000335'], name="texture", curie=MIXS.curie('0000335'), - model_uri=DEFAULT_.texture, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.texture_meth = Slot(uri=MIXS['0000336'], name="texture_meth", curie=MIXS.curie('0000336'), - model_uri=DEFAULT_.texture_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.tidal_stage = Slot(uri=MIXS['0000750'], name="tidal_stage", curie=MIXS.curie('0000750'), - model_uri=DEFAULT_.tidal_stage, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.tillage = Slot(uri=MIXS['0001081'], name="tillage", curie=MIXS.curie('0001081'), - model_uri=DEFAULT_.tillage, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.tiss_cult_growth_med = Slot(uri=MIXS['0001070'], name="tiss_cult_growth_med", curie=MIXS.curie('0001070'), - model_uri=DEFAULT_.tiss_cult_growth_med, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.toluene = Slot(uri=MIXS['0000154'], name="toluene", curie=MIXS.curie('0000154'), - model_uri=DEFAULT_.toluene, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_carb = Slot(uri=MIXS['0000525'], name="tot_carb", curie=MIXS.curie('0000525'), - model_uri=DEFAULT_.tot_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_depth_water_col = Slot(uri=MIXS['0000634'], name="tot_depth_water_col", curie=MIXS.curie('0000634'), - model_uri=DEFAULT_.tot_depth_water_col, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_diss_nitro = Slot(uri=MIXS['0000744'], name="tot_diss_nitro", curie=MIXS.curie('0000744'), - model_uri=DEFAULT_.tot_diss_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_inorg_nitro = Slot(uri=MIXS['0000745'], name="tot_inorg_nitro", curie=MIXS.curie('0000745'), - model_uri=DEFAULT_.tot_inorg_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_iron = Slot(uri=MIXS['0000105'], name="tot_iron", curie=MIXS.curie('0000105'), - model_uri=DEFAULT_.tot_iron, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_nitro = Slot(uri=MIXS['0000102'], name="tot_nitro", curie=MIXS.curie('0000102'), - model_uri=DEFAULT_.tot_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_nitro_cont_meth = Slot(uri=MIXS['0000338'], name="tot_nitro_cont_meth", curie=MIXS.curie('0000338'), - model_uri=DEFAULT_.tot_nitro_cont_meth, domain=None, range=Optional[str]) - -slots.tot_nitro_content = Slot(uri=MIXS['0000530'], name="tot_nitro_content", curie=MIXS.curie('0000530'), - model_uri=DEFAULT_.tot_nitro_content, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_org_c_meth = Slot(uri=MIXS['0000337'], name="tot_org_c_meth", curie=MIXS.curie('0000337'), - model_uri=DEFAULT_.tot_org_c_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.tot_org_carb = Slot(uri=MIXS['0000533'], name="tot_org_carb", curie=MIXS.curie('0000533'), - model_uri=DEFAULT_.tot_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_part_carb = Slot(uri=MIXS['0000747'], name="tot_part_carb", curie=MIXS.curie('0000747'), - model_uri=DEFAULT_.tot_part_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_phosp = Slot(uri=MIXS['0000117'], name="tot_phosp", curie=MIXS.curie('0000117'), - model_uri=DEFAULT_.tot_phosp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_phosphate = Slot(uri=MIXS['0000689'], name="tot_phosphate", curie=MIXS.curie('0000689'), - model_uri=DEFAULT_.tot_phosphate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_sulfur = Slot(uri=MIXS['0000419'], name="tot_sulfur", curie=MIXS.curie('0000419'), - model_uri=DEFAULT_.tot_sulfur, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.train_line = Slot(uri=MIXS['0000837'], name="train_line", curie=MIXS.curie('0000837'), - model_uri=DEFAULT_.train_line, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.train_stat_loc = Slot(uri=MIXS['0000838'], name="train_stat_loc", curie=MIXS.curie('0000838'), - model_uri=DEFAULT_.train_stat_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.train_stop_loc = Slot(uri=MIXS['0000839'], name="train_stop_loc", curie=MIXS.curie('0000839'), - model_uri=DEFAULT_.train_stop_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.turbidity = Slot(uri=MIXS['0000191'], name="turbidity", curie=MIXS.curie('0000191'), - model_uri=DEFAULT_.turbidity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tvdss_of_hcr_press = Slot(uri=MIXS['0000397'], name="tvdss_of_hcr_press", curie=MIXS.curie('0000397'), - model_uri=DEFAULT_.tvdss_of_hcr_press, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tvdss_of_hcr_temp = Slot(uri=MIXS['0000394'], name="tvdss_of_hcr_temp", curie=MIXS.curie('0000394'), - model_uri=DEFAULT_.tvdss_of_hcr_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.typ_occup_density = Slot(uri=MIXS['0000771'], name="typ_occup_density", curie=MIXS.curie('0000771'), - model_uri=DEFAULT_.typ_occup_density, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ventilation_rate = Slot(uri=MIXS['0000114'], name="ventilation_rate", curie=MIXS.curie('0000114'), - model_uri=DEFAULT_.ventilation_rate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ventilation_type = Slot(uri=MIXS['0000756'], name="ventilation_type", curie=MIXS.curie('0000756'), - model_uri=DEFAULT_.ventilation_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.vfa = Slot(uri=MIXS['0000152'], name="vfa", curie=MIXS.curie('0000152'), - model_uri=DEFAULT_.vfa, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.vfa_fw = Slot(uri=MIXS['0000408'], name="vfa_fw", curie=MIXS.curie('0000408'), - model_uri=DEFAULT_.vfa_fw, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.vis_media = Slot(uri=MIXS['0000840'], name="vis_media", curie=MIXS.curie('0000840'), - model_uri=DEFAULT_.vis_media, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.viscosity = Slot(uri=MIXS['0000126'], name="viscosity", curie=MIXS.curie('0000126'), - model_uri=DEFAULT_.viscosity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.volatile_org_comp = Slot(uri=MIXS['0000115'], name="volatile_org_comp", curie=MIXS.curie('0000115'), - model_uri=DEFAULT_.volatile_org_comp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.wall_area = Slot(uri=MIXS['0000198'], name="wall_area", curie=MIXS.curie('0000198'), - model_uri=DEFAULT_.wall_area, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.wall_const_type = Slot(uri=MIXS['0000841'], name="wall_const_type", curie=MIXS.curie('0000841'), - model_uri=DEFAULT_.wall_const_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wall_finish_mat = Slot(uri=MIXS['0000842'], name="wall_finish_mat", curie=MIXS.curie('0000842'), - model_uri=DEFAULT_.wall_finish_mat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wall_height = Slot(uri=MIXS['0000221'], name="wall_height", curie=MIXS.curie('0000221'), - model_uri=DEFAULT_.wall_height, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.wall_loc = Slot(uri=MIXS['0000843'], name="wall_loc", curie=MIXS.curie('0000843'), - model_uri=DEFAULT_.wall_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wall_surf_treatment = Slot(uri=MIXS['0000845'], name="wall_surf_treatment", curie=MIXS.curie('0000845'), - model_uri=DEFAULT_.wall_surf_treatment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wall_texture = Slot(uri=MIXS['0000846'], name="wall_texture", curie=MIXS.curie('0000846'), - model_uri=DEFAULT_.wall_texture, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wall_thermal_mass = Slot(uri=MIXS['0000222'], name="wall_thermal_mass", curie=MIXS.curie('0000222'), - model_uri=DEFAULT_.wall_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.wall_water_mold = Slot(uri=MIXS['0000844'], name="wall_water_mold", curie=MIXS.curie('0000844'), - model_uri=DEFAULT_.wall_water_mold, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wastewater_type = Slot(uri=MIXS['0000353'], name="wastewater_type", curie=MIXS.curie('0000353'), - model_uri=DEFAULT_.wastewater_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.water_cont_soil_meth = Slot(uri=MIXS['0000323'], name="water_cont_soil_meth", curie=MIXS.curie('0000323'), - model_uri=DEFAULT_.water_cont_soil_meth, domain=None, range=Optional[str]) - -slots.water_content = Slot(uri=MIXS['0000185'], name="water_content", curie=MIXS.curie('0000185'), - model_uri=DEFAULT_.water_content, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.water_current = Slot(uri=MIXS['0000203'], name="water_current", curie=MIXS.curie('0000203'), - model_uri=DEFAULT_.water_current, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.water_cut = Slot(uri=MIXS['0000454'], name="water_cut", curie=MIXS.curie('0000454'), - model_uri=DEFAULT_.water_cut, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.water_feat_size = Slot(uri=MIXS['0000223'], name="water_feat_size", curie=MIXS.curie('0000223'), - model_uri=DEFAULT_.water_feat_size, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.water_feat_type = Slot(uri=MIXS['0000847'], name="water_feat_type", curie=MIXS.curie('0000847'), - model_uri=DEFAULT_.water_feat_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.water_prod_rate = Slot(uri=MIXS['0000453'], name="water_prod_rate", curie=MIXS.curie('0000453'), - model_uri=DEFAULT_.water_prod_rate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.water_temp_regm = Slot(uri=MIXS['0000590'], name="water_temp_regm", curie=MIXS.curie('0000590'), - model_uri=DEFAULT_.water_temp_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.watering_regm = Slot(uri=MIXS['0000591'], name="watering_regm", curie=MIXS.curie('0000591'), - model_uri=DEFAULT_.watering_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.weekday = Slot(uri=MIXS['0000848'], name="weekday", curie=MIXS.curie('0000848'), - model_uri=DEFAULT_.weekday, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.win = Slot(uri=MIXS['0000297'], name="win", curie=MIXS.curie('0000297'), - model_uri=DEFAULT_.win, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wind_direction = Slot(uri=MIXS['0000757'], name="wind_direction", curie=MIXS.curie('0000757'), - model_uri=DEFAULT_.wind_direction, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wind_speed = Slot(uri=MIXS['0000118'], name="wind_speed", curie=MIXS.curie('0000118'), - model_uri=DEFAULT_.wind_speed, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.window_cond = Slot(uri=MIXS['0000849'], name="window_cond", curie=MIXS.curie('0000849'), - model_uri=DEFAULT_.window_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_cover = Slot(uri=MIXS['0000850'], name="window_cover", curie=MIXS.curie('0000850'), - model_uri=DEFAULT_.window_cover, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_horiz_pos = Slot(uri=MIXS['0000851'], name="window_horiz_pos", curie=MIXS.curie('0000851'), - model_uri=DEFAULT_.window_horiz_pos, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_loc = Slot(uri=MIXS['0000852'], name="window_loc", curie=MIXS.curie('0000852'), - model_uri=DEFAULT_.window_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_mat = Slot(uri=MIXS['0000853'], name="window_mat", curie=MIXS.curie('0000853'), - model_uri=DEFAULT_.window_mat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_open_freq = Slot(uri=MIXS['0000246'], name="window_open_freq", curie=MIXS.curie('0000246'), - model_uri=DEFAULT_.window_open_freq, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_size = Slot(uri=MIXS['0000224'], name="window_size", curie=MIXS.curie('0000224'), - model_uri=DEFAULT_.window_size, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.window_status = Slot(uri=MIXS['0000855'], name="window_status", curie=MIXS.curie('0000855'), - model_uri=DEFAULT_.window_status, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_type = Slot(uri=MIXS['0000856'], name="window_type", curie=MIXS.curie('0000856'), - model_uri=DEFAULT_.window_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_vert_pos = Slot(uri=MIXS['0000857'], name="window_vert_pos", curie=MIXS.curie('0000857'), - model_uri=DEFAULT_.window_vert_pos, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_water_mold = Slot(uri=MIXS['0000854'], name="window_water_mold", curie=MIXS.curie('0000854'), - model_uri=DEFAULT_.window_water_mold, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.xylene = Slot(uri=MIXS['0000156'], name="xylene", curie=MIXS.curie('0000156'), - model_uri=DEFAULT_.xylene, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.env_package = Slot(uri=DEFAULT_.env_package, name="env_package", curie=DEFAULT_.curie('env_package'), - model_uri=DEFAULT_.env_package, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.env_package], - pattern=re.compile(r'[air|built environment|host\-associated|human\-associated|human\-skin|human\-oral|human\-gut|human\-vaginal|hydrocarbon resources\-cores|hydrocarbon resources\-fluids\/swabs|microbial mat\/biofilm|misc environment|plant\-associated|sediment|soil|wastewater\/sludge|water]')) - -slots.language = Slot(uri=NMDC.language, name="language", curie=NMDC.curie('language'), - model_uri=DEFAULT_.language, domain=None, range=Optional[str]) - -slots.attribute = Slot(uri=NMDC.attribute, name="attribute", curie=NMDC.curie('attribute'), - model_uri=DEFAULT_.attribute, domain=None, range=Optional[str]) - -slots.has_raw_value = Slot(uri=NMDC.has_raw_value, name="has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.has_raw_value, domain=AttributeValue, range=Optional[str]) - -slots.has_unit = Slot(uri=NMDC.has_unit, name="has unit", curie=NMDC.curie('has_unit'), - model_uri=DEFAULT_.has_unit, domain=None, range=Optional[str], mappings = [QUD.unit, SCHEMA.unitCode]) - -slots.has_numeric_value = Slot(uri=NMDC.has_numeric_value, name="has numeric value", curie=NMDC.curie('has_numeric_value'), - model_uri=DEFAULT_.has_numeric_value, domain=None, range=Optional[float], mappings = [QUD.quantityValue, SCHEMA.value]) - -slots.has_minimum_numeric_value = Slot(uri=NMDC.has_minimum_numeric_value, name="has minimum numeric value", curie=NMDC.curie('has_minimum_numeric_value'), - model_uri=DEFAULT_.has_minimum_numeric_value, domain=None, range=Optional[float]) - -slots.has_maximum_numeric_value = Slot(uri=NMDC.has_maximum_numeric_value, name="has maximum numeric value", curie=NMDC.curie('has_maximum_numeric_value'), - model_uri=DEFAULT_.has_maximum_numeric_value, domain=None, range=Optional[float]) - -slots.has_boolean_value = Slot(uri=NMDC.has_boolean_value, name="has boolean value", curie=NMDC.curie('has_boolean_value'), - model_uri=DEFAULT_.has_boolean_value, domain=None, range=Optional[Union[bool, Bool]]) - -slots.latitude = Slot(uri=WGS.lat, name="latitude", curie=WGS.curie('lat'), - model_uri=DEFAULT_.latitude, domain=GeolocationValue, range=Optional[float], mappings = [SCHEMA.latitude]) - -slots.longitude = Slot(uri=WGS.long, name="longitude", curie=WGS.curie('long'), - model_uri=DEFAULT_.longitude, domain=GeolocationValue, range=Optional[float], mappings = [SCHEMA.longitude]) - -slots.term = Slot(uri=RDF.type, name="term", curie=RDF.curie('type'), - model_uri=DEFAULT_.term, domain=ControlledTermValue, range=Optional[Union[dict, OntologyClass]]) - -slots.orcid = Slot(uri=NMDC.orcid, name="orcid", curie=NMDC.curie('orcid'), - model_uri=DEFAULT_.orcid, domain=PersonValue, range=Optional[str]) - -slots.email = Slot(uri=SCHEMA.email, name="email", curie=SCHEMA.curie('email'), - model_uri=DEFAULT_.email, domain=None, range=Optional[str]) - -slots.alternate_emails = Slot(uri=NMDC.alternate_emails, name="alternate emails", curie=NMDC.curie('alternate_emails'), - model_uri=DEFAULT_.alternate_emails, domain=None, range=Optional[str]) - -slots.profile_image_url = Slot(uri=NMDC.profile_image_url, name="profile image url", curie=NMDC.curie('profile_image_url'), - model_uri=DEFAULT_.profile_image_url, domain=PersonValue, range=Optional[str]) - -slots.has_input = Slot(uri=NMDC.has_input, name="has input", curie=NMDC.curie('has_input'), - model_uri=DEFAULT_.has_input, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) - -slots.has_output = Slot(uri=NMDC.has_output, name="has output", curie=NMDC.curie('has_output'), - model_uri=DEFAULT_.has_output, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) - -slots.part_of = Slot(uri=DCTERMS.isPartOf, name="part of", curie=DCTERMS.curie('isPartOf'), - model_uri=DEFAULT_.part_of, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) - -slots.execution_resource = Slot(uri=NMDC.execution_resource, name="execution resource", curie=NMDC.curie('execution_resource'), - model_uri=DEFAULT_.execution_resource, domain=None, range=Optional[str]) - -slots.url = Slot(uri=NMDC.url, name="url", curie=NMDC.curie('url'), - model_uri=DEFAULT_.url, domain=None, range=Optional[str]) - -slots.display_order = Slot(uri=NMDC.display_order, name="display order", curie=NMDC.curie('display_order'), - model_uri=DEFAULT_.display_order, domain=None, range=Optional[str]) - -slots.git_url = Slot(uri=NMDC.git_url, name="git url", curie=NMDC.curie('git_url'), - model_uri=DEFAULT_.git_url, domain=None, range=Optional[str]) - -slots.file_size_bytes = Slot(uri=NMDC.file_size_bytes, name="file size bytes", curie=NMDC.curie('file_size_bytes'), - model_uri=DEFAULT_.file_size_bytes, domain=None, range=Optional[int]) - -slots.md5_checksum = Slot(uri=NMDC.md5_checksum, name="md5 checksum", curie=NMDC.curie('md5_checksum'), - model_uri=DEFAULT_.md5_checksum, domain=None, range=Optional[str]) - -slots.abstract = Slot(uri=NMDC.abstract, name="abstract", curie=NMDC.curie('abstract'), - model_uri=DEFAULT_.abstract, domain=None, range=Optional[str]) - -slots.keywords = Slot(uri=NMDC.keywords, name="keywords", curie=NMDC.curie('keywords'), - model_uri=DEFAULT_.keywords, domain=None, range=Optional[Union[str, List[str]]], mappings = [DCTERMS.subject]) - -slots.objective = Slot(uri=NMDC.objective, name="objective", curie=NMDC.curie('objective'), - model_uri=DEFAULT_.objective, domain=None, range=Optional[str], mappings = [SIO["000337"]]) - -slots.websites = Slot(uri=NMDC.websites, name="websites", curie=NMDC.curie('websites'), - model_uri=DEFAULT_.websites, domain=None, range=Optional[Union[str, List[str]]]) - -slots.publications = Slot(uri=NMDC.publications, name="publications", curie=NMDC.curie('publications'), - model_uri=DEFAULT_.publications, domain=None, range=Optional[Union[str, List[str]]]) - -slots.id = Slot(uri=NMDC.id, name="id", curie=NMDC.curie('id'), - model_uri=DEFAULT_.id, domain=None, range=URIRef) - -slots.name = Slot(uri=NMDC.name, name="name", curie=NMDC.curie('name'), - model_uri=DEFAULT_.name, domain=None, range=Optional[str]) - -slots.description = Slot(uri=DCTERMS.description, name="description", curie=DCTERMS.curie('description'), - model_uri=DEFAULT_.description, domain=None, range=Optional[str]) - -slots.type = Slot(uri=NMDC.type, name="type", curie=NMDC.curie('type'), - model_uri=DEFAULT_.type, domain=None, range=Optional[str]) - -slots.title = Slot(uri=NMDC.title, name="title", curie=NMDC.curie('title'), - model_uri=DEFAULT_.title, domain=None, range=Optional[str]) - -slots.alternative_titles = Slot(uri=NMDC.alternative_titles, name="alternative titles", curie=NMDC.curie('alternative_titles'), - model_uri=DEFAULT_.alternative_titles, domain=None, range=Optional[Union[str, List[str]]]) - -slots.alternative_names = Slot(uri=NMDC.alternative_names, name="alternative names", curie=NMDC.curie('alternative_names'), - model_uri=DEFAULT_.alternative_names, domain=None, range=Optional[Union[str, List[str]]]) - -slots.alternative_descriptions = Slot(uri=NMDC.alternative_descriptions, name="alternative descriptions", curie=NMDC.curie('alternative_descriptions'), - model_uri=DEFAULT_.alternative_descriptions, domain=None, range=Optional[Union[str, List[str]]]) - -slots.alternative_identifiers = Slot(uri=NMDC.alternative_identifiers, name="alternative identifiers", curie=NMDC.curie('alternative_identifiers'), - model_uri=DEFAULT_.alternative_identifiers, domain=None, range=Optional[Union[str, List[str]]]) - -slots.started_at_time = Slot(uri=NMDC.started_at_time, name="started at time", curie=NMDC.curie('started_at_time'), - model_uri=DEFAULT_.started_at_time, domain=None, range=Optional[Union[str, XSDDateTime]], mappings = [PROV.startedAtTime], - pattern=re.compile(r'^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$')) - -slots.ended_at_time = Slot(uri=NMDC.ended_at_time, name="ended at time", curie=NMDC.curie('ended_at_time'), - model_uri=DEFAULT_.ended_at_time, domain=None, range=Optional[Union[str, XSDDateTime]], mappings = [PROV.endedAtTime], - pattern=re.compile(r'^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$')) - -slots.was_informed_by = Slot(uri=NMDC.was_informed_by, name="was informed by", curie=NMDC.curie('was_informed_by'), - model_uri=DEFAULT_.was_informed_by, domain=None, range=Optional[Union[str, ActivityId]], mappings = [PROV.wasInformedBy]) - -slots.was_associated_with = Slot(uri=NMDC.was_associated_with, name="was associated with", curie=NMDC.curie('was_associated_with'), - model_uri=DEFAULT_.was_associated_with, domain=None, range=Optional[Union[dict, Agent]], mappings = [PROV.wasAssociatedWith]) - -slots.acted_on_behalf_of = Slot(uri=NMDC.acted_on_behalf_of, name="acted on behalf of", curie=NMDC.curie('acted_on_behalf_of'), - model_uri=DEFAULT_.acted_on_behalf_of, domain=None, range=Optional[Union[dict, Agent]], mappings = [PROV.actedOnBehalfOf]) - -slots.was_generated_by = Slot(uri=NMDC.was_generated_by, name="was generated by", curie=NMDC.curie('was_generated_by'), - model_uri=DEFAULT_.was_generated_by, domain=None, range=Optional[Union[str, ActivityId]], mappings = [PROV.wasGeneratedBy]) - -slots.used = Slot(uri=NMDC.used, name="used", curie=NMDC.curie('used'), - model_uri=DEFAULT_.used, domain=Activity, range=Optional[str], mappings = [PROV.used]) - -slots.mAGBin__bin_name = Slot(uri=DEFAULT_.bin_name, name="mAGBin__bin_name", curie=DEFAULT_.curie('bin_name'), - model_uri=DEFAULT_.mAGBin__bin_name, domain=None, range=Optional[str]) - -slots.mAGBin__number_of_contig = Slot(uri=DEFAULT_.number_of_contig, name="mAGBin__number_of_contig", curie=DEFAULT_.curie('number_of_contig'), - model_uri=DEFAULT_.mAGBin__number_of_contig, domain=None, range=Optional[int]) - -slots.mAGBin__completeness = Slot(uri=DEFAULT_.completeness, name="mAGBin__completeness", curie=DEFAULT_.curie('completeness'), - model_uri=DEFAULT_.mAGBin__completeness, domain=None, range=Optional[float]) - -slots.mAGBin__contamination = Slot(uri=DEFAULT_.contamination, name="mAGBin__contamination", curie=DEFAULT_.curie('contamination'), - model_uri=DEFAULT_.mAGBin__contamination, domain=None, range=Optional[float]) - -slots.mAGBin__gene_count = Slot(uri=DEFAULT_.gene_count, name="mAGBin__gene_count", curie=DEFAULT_.curie('gene_count'), - model_uri=DEFAULT_.mAGBin__gene_count, domain=None, range=Optional[int]) - -slots.mAGBin__bin_quality = Slot(uri=DEFAULT_.bin_quality, name="mAGBin__bin_quality", curie=DEFAULT_.curie('bin_quality'), - model_uri=DEFAULT_.mAGBin__bin_quality, domain=None, range=Optional[str]) - -slots.mAGBin__num_16s = Slot(uri=DEFAULT_.num_16s, name="mAGBin__num_16s", curie=DEFAULT_.curie('num_16s'), - model_uri=DEFAULT_.mAGBin__num_16s, domain=None, range=Optional[int]) - -slots.mAGBin__num_5s = Slot(uri=DEFAULT_.num_5s, name="mAGBin__num_5s", curie=DEFAULT_.curie('num_5s'), - model_uri=DEFAULT_.mAGBin__num_5s, domain=None, range=Optional[int]) - -slots.mAGBin__num_23s = Slot(uri=DEFAULT_.num_23s, name="mAGBin__num_23s", curie=DEFAULT_.curie('num_23s'), - model_uri=DEFAULT_.mAGBin__num_23s, domain=None, range=Optional[int]) - -slots.mAGBin__num_tRNA = Slot(uri=DEFAULT_.num_tRNA, name="mAGBin__num_tRNA", curie=DEFAULT_.curie('num_tRNA'), - model_uri=DEFAULT_.mAGBin__num_tRNA, domain=None, range=Optional[int]) - -slots.mAGBin__gtdbtk_domain = Slot(uri=DEFAULT_.gtdbtk_domain, name="mAGBin__gtdbtk_domain", curie=DEFAULT_.curie('gtdbtk_domain'), - model_uri=DEFAULT_.mAGBin__gtdbtk_domain, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_phylum = Slot(uri=DEFAULT_.gtdbtk_phylum, name="mAGBin__gtdbtk_phylum", curie=DEFAULT_.curie('gtdbtk_phylum'), - model_uri=DEFAULT_.mAGBin__gtdbtk_phylum, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_class = Slot(uri=DEFAULT_.gtdbtk_class, name="mAGBin__gtdbtk_class", curie=DEFAULT_.curie('gtdbtk_class'), - model_uri=DEFAULT_.mAGBin__gtdbtk_class, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_order = Slot(uri=DEFAULT_.gtdbtk_order, name="mAGBin__gtdbtk_order", curie=DEFAULT_.curie('gtdbtk_order'), - model_uri=DEFAULT_.mAGBin__gtdbtk_order, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_family = Slot(uri=DEFAULT_.gtdbtk_family, name="mAGBin__gtdbtk_family", curie=DEFAULT_.curie('gtdbtk_family'), - model_uri=DEFAULT_.mAGBin__gtdbtk_family, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_genus = Slot(uri=DEFAULT_.gtdbtk_genus, name="mAGBin__gtdbtk_genus", curie=DEFAULT_.curie('gtdbtk_genus'), - model_uri=DEFAULT_.mAGBin__gtdbtk_genus, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_species = Slot(uri=DEFAULT_.gtdbtk_species, name="mAGBin__gtdbtk_species", curie=DEFAULT_.curie('gtdbtk_species'), - model_uri=DEFAULT_.mAGBin__gtdbtk_species, domain=None, range=Optional[str]) - -slots.metabolite_quantified = Slot(uri=DEFAULT_.metabolite_quantified, name="metabolite quantified", curie=DEFAULT_.curie('metabolite_quantified'), - model_uri=DEFAULT_.metabolite_quantified, domain=None, range=Optional[Union[str, ChemicalEntityId]]) - -slots.highest_similarity_score = Slot(uri=DEFAULT_.highest_similarity_score, name="highest similarity score", curie=DEFAULT_.curie('highest_similarity_score'), - model_uri=DEFAULT_.highest_similarity_score, domain=None, range=Optional[float]) - -slots.peptide_sequence = Slot(uri=DEFAULT_.peptide_sequence, name="peptide sequence", curie=DEFAULT_.curie('peptide_sequence'), - model_uri=DEFAULT_.peptide_sequence, domain=None, range=Optional[str]) - -slots.best_protein = Slot(uri=DEFAULT_.best_protein, name="best protein", curie=DEFAULT_.curie('best_protein'), - model_uri=DEFAULT_.best_protein, domain=None, range=Optional[Union[str, GeneProductId]]) - -slots.all_proteins = Slot(uri=DEFAULT_.all_proteins, name="all proteins", curie=DEFAULT_.curie('all_proteins'), - model_uri=DEFAULT_.all_proteins, domain=None, range=Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]]) - -slots.min_q_value = Slot(uri=DEFAULT_.min_q_value, name="min_q_value", curie=DEFAULT_.curie('min_q_value'), - model_uri=DEFAULT_.min_q_value, domain=None, range=Optional[float]) - -slots.peptide_spectral_count = Slot(uri=DEFAULT_.peptide_spectral_count, name="peptide_spectral_count", curie=DEFAULT_.curie('peptide_spectral_count'), - model_uri=DEFAULT_.peptide_spectral_count, domain=None, range=Optional[int]) - -slots.peptide_sum_masic_abundance = Slot(uri=DEFAULT_.peptide_sum_masic_abundance, name="peptide_sum_masic_abundance", curie=DEFAULT_.curie('peptide_sum_masic_abundance'), - model_uri=DEFAULT_.peptide_sum_masic_abundance, domain=None, range=Optional[int]) - -slots.peptide_sequence_count = Slot(uri=DEFAULT_.peptide_sequence_count, name="peptide_sequence_count", curie=DEFAULT_.curie('peptide_sequence_count'), - model_uri=DEFAULT_.peptide_sequence_count, domain=None, range=Optional[int]) - -slots.protein_spectral_count = Slot(uri=DEFAULT_.protein_spectral_count, name="protein_spectral_count", curie=DEFAULT_.curie('protein_spectral_count'), - model_uri=DEFAULT_.protein_spectral_count, domain=None, range=Optional[int]) - -slots.protein_sum_masic_abundance = Slot(uri=DEFAULT_.protein_sum_masic_abundance, name="protein_sum_masic_abundance", curie=DEFAULT_.curie('protein_sum_masic_abundance'), - model_uri=DEFAULT_.protein_sum_masic_abundance, domain=None, range=Optional[int]) - -slots.inchi = Slot(uri=DEFAULT_.inchi, name="inchi", curie=DEFAULT_.curie('inchi'), - model_uri=DEFAULT_.inchi, domain=None, range=Optional[str]) - -slots.inchi_key = Slot(uri=DEFAULT_.inchi_key, name="inchi key", curie=DEFAULT_.curie('inchi_key'), - model_uri=DEFAULT_.inchi_key, domain=None, range=Optional[str]) - -slots.smiles = Slot(uri=DEFAULT_.smiles, name="smiles", curie=DEFAULT_.curie('smiles'), - model_uri=DEFAULT_.smiles, domain=None, range=Optional[Union[str, List[str]]]) - -slots.chemical_formula = Slot(uri=DEFAULT_.chemical_formula, name="chemical formula", curie=DEFAULT_.curie('chemical_formula'), - model_uri=DEFAULT_.chemical_formula, domain=None, range=Optional[str]) - -slots.attribute_value_type = Slot(uri=NMDC.type, name="attribute value_type", curie=NMDC.curie('type'), - model_uri=DEFAULT_.attribute_value_type, domain=AttributeValue, range=Optional[str]) - -slots.quantity_value_has_raw_value = Slot(uri=NMDC.has_raw_value, name="quantity value_has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.quantity_value_has_raw_value, domain=QuantityValue, range=Optional[str]) - -slots.quantity_value_has_unit = Slot(uri=NMDC.has_unit, name="quantity value_has unit", curie=NMDC.curie('has_unit'), - model_uri=DEFAULT_.quantity_value_has_unit, domain=QuantityValue, range=Optional[str], mappings = [QUD.unit, SCHEMA.unitCode]) - -slots.quantity_value_has_numeric_value = Slot(uri=NMDC.has_numeric_value, name="quantity value_has numeric value", curie=NMDC.curie('has_numeric_value'), - model_uri=DEFAULT_.quantity_value_has_numeric_value, domain=QuantityValue, range=Optional[float], mappings = [QUD.quantityValue, SCHEMA.value]) - -slots.person_value_orcid = Slot(uri=NMDC.orcid, name="person value_orcid", curie=NMDC.curie('orcid'), - model_uri=DEFAULT_.person_value_orcid, domain=PersonValue, range=Optional[str]) - -slots.person_value_email = Slot(uri=SCHEMA.email, name="person value_email", curie=SCHEMA.curie('email'), - model_uri=DEFAULT_.person_value_email, domain=PersonValue, range=Optional[str]) - -slots.person_value_has_raw_value = Slot(uri=NMDC.has_raw_value, name="person value_has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.person_value_has_raw_value, domain=PersonValue, range=Optional[str]) - -slots.person_value_name = Slot(uri=NMDC.name, name="person value_name", curie=NMDC.curie('name'), - model_uri=DEFAULT_.person_value_name, domain=PersonValue, range=Optional[str]) - -slots.person_id = Slot(uri=NMDC.id, name="person_id", curie=NMDC.curie('id'), - model_uri=DEFAULT_.person_id, domain=Person, range=Union[str, PersonId]) - -slots.metabolite_quantification_metabolite_quantified = Slot(uri=DEFAULT_.metabolite_quantified, name="metabolite quantification_metabolite quantified", curie=DEFAULT_.curie('metabolite_quantified'), - model_uri=DEFAULT_.metabolite_quantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) - -slots.metabolite_quantification_highest_similarity_score = Slot(uri=DEFAULT_.highest_similarity_score, name="metabolite quantification_highest similarity score", curie=DEFAULT_.curie('highest_similarity_score'), - model_uri=DEFAULT_.metabolite_quantification_highest_similarity_score, domain=MetaboliteQuantification, range=Optional[float]) - -slots.peptide_quantification_peptide_sequence = Slot(uri=DEFAULT_.peptide_sequence, name="peptide quantification_peptide sequence", curie=DEFAULT_.curie('peptide_sequence'), - model_uri=DEFAULT_.peptide_quantification_peptide_sequence, domain=PeptideQuantification, range=Optional[str]) - -slots.peptide_quantification_best_protein = Slot(uri=DEFAULT_.best_protein, name="peptide quantification_best protein", curie=DEFAULT_.curie('best_protein'), - model_uri=DEFAULT_.peptide_quantification_best_protein, domain=PeptideQuantification, range=Optional[Union[str, GeneProductId]]) - -slots.peptide_quantification_all_proteins = Slot(uri=DEFAULT_.all_proteins, name="peptide quantification_all proteins", curie=DEFAULT_.curie('all_proteins'), - model_uri=DEFAULT_.peptide_quantification_all_proteins, domain=PeptideQuantification, range=Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]]) - -slots.peptide_quantification_min_q_value = Slot(uri=DEFAULT_.min_q_value, name="peptide quantification_min_q_value", curie=DEFAULT_.curie('min_q_value'), - model_uri=DEFAULT_.peptide_quantification_min_q_value, domain=PeptideQuantification, range=Optional[float]) - -slots.peptide_quantification_peptide_spectral_count = Slot(uri=DEFAULT_.peptide_spectral_count, name="peptide quantification_peptide_spectral_count", curie=DEFAULT_.curie('peptide_spectral_count'), - model_uri=DEFAULT_.peptide_quantification_peptide_spectral_count, domain=PeptideQuantification, range=Optional[int]) - -slots.peptide_quantification_peptide_sum_masic_abundance = Slot(uri=DEFAULT_.peptide_sum_masic_abundance, name="peptide quantification_peptide_sum_masic_abundance", curie=DEFAULT_.curie('peptide_sum_masic_abundance'), - model_uri=DEFAULT_.peptide_quantification_peptide_sum_masic_abundance, domain=PeptideQuantification, range=Optional[int]) - -slots.protein_quantification_best_protein = Slot(uri=DEFAULT_.best_protein, name="protein quantification_best protein", curie=DEFAULT_.curie('best_protein'), - model_uri=DEFAULT_.protein_quantification_best_protein, domain=ProteinQuantification, range=Optional[Union[str, GeneProductId]]) - -slots.protein_quantification_all_proteins = Slot(uri=DEFAULT_.all_proteins, name="protein quantification_all proteins", curie=DEFAULT_.curie('all_proteins'), - model_uri=DEFAULT_.protein_quantification_all_proteins, domain=ProteinQuantification, range=Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]]) - -slots.protein_quantification_peptide_sequence_count = Slot(uri=DEFAULT_.peptide_sequence_count, name="protein quantification_peptide_sequence_count", curie=DEFAULT_.curie('peptide_sequence_count'), - model_uri=DEFAULT_.protein_quantification_peptide_sequence_count, domain=ProteinQuantification, range=Optional[int]) - -slots.protein_quantification_protein_spectral_count = Slot(uri=DEFAULT_.protein_spectral_count, name="protein quantification_protein_spectral_count", curie=DEFAULT_.curie('protein_spectral_count'), - model_uri=DEFAULT_.protein_quantification_protein_spectral_count, domain=ProteinQuantification, range=Optional[int]) - -slots.protein_quantification_protein_sum_masic_abundance = Slot(uri=DEFAULT_.protein_sum_masic_abundance, name="protein quantification_protein_sum_masic_abundance", curie=DEFAULT_.curie('protein_sum_masic_abundance'), - model_uri=DEFAULT_.protein_quantification_protein_sum_masic_abundance, domain=ProteinQuantification, range=Optional[int]) - -slots.chemical_entity_inchi = Slot(uri=DEFAULT_.inchi, name="chemical entity_inchi", curie=DEFAULT_.curie('inchi'), - model_uri=DEFAULT_.chemical_entity_inchi, domain=ChemicalEntity, range=Optional[str]) - -slots.chemical_entity_inchi_key = Slot(uri=DEFAULT_.inchi_key, name="chemical entity_inchi key", curie=DEFAULT_.curie('inchi_key'), - model_uri=DEFAULT_.chemical_entity_inchi_key, domain=ChemicalEntity, range=Optional[str]) - -slots.chemical_entity_smiles = Slot(uri=DEFAULT_.smiles, name="chemical entity_smiles", curie=DEFAULT_.curie('smiles'), - model_uri=DEFAULT_.chemical_entity_smiles, domain=ChemicalEntity, range=Optional[Union[str, List[str]]]) - -slots.chemical_entity_chemical_formula = Slot(uri=DEFAULT_.chemical_formula, name="chemical entity_chemical formula", curie=DEFAULT_.curie('chemical_formula'), - model_uri=DEFAULT_.chemical_entity_chemical_formula, domain=ChemicalEntity, range=Optional[str]) - -slots.geolocation_value_has_raw_value = Slot(uri=NMDC.has_raw_value, name="geolocation value_has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.geolocation_value_has_raw_value, domain=GeolocationValue, range=Optional[str]) diff --git a/nmdc_schema/nmdc.py b/nmdc_schema/nmdc.py index 6f80137795..85464f8111 100644 --- a/nmdc_schema/nmdc.py +++ b/nmdc_schema/nmdc.py @@ -1,5 +1,5 @@ # Auto generated from nmdc.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:11 +# Generation date: 2023-01-20T13:17:08 # Schema: NMDC # # id: https://microbiomedata/schema @@ -971,15 +971,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class Biosample(MaterialEntity): """ @@ -1982,11 +1973,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -8266,7 +8252,8 @@ class slots: model_uri=NMDC.dna_cont_type, domain=None, range=Optional[Union[str, "DnaContTypeEnum"]]) slots.dna_cont_well = Slot(uri=NMDC.dna_cont_well, name="dna_cont_well", curie=NMDC.curie('dna_cont_well'), - model_uri=NMDC.dna_cont_well, domain=None, range=Optional[str]) + model_uri=NMDC.dna_cont_well, domain=None, range=Optional[str], + pattern=re.compile(r'^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$')) slots.dna_container_id = Slot(uri=NMDC.dna_container_id, name="dna_container_id", curie=NMDC.curie('dna_container_id'), model_uri=NMDC.dna_container_id, domain=None, range=Optional[str]) @@ -8329,7 +8316,8 @@ class slots: model_uri=NMDC.rna_cont_type, domain=None, range=Optional[Union[str, "RnaContTypeEnum"]]) slots.rna_cont_well = Slot(uri=NMDC.rna_cont_well, name="rna_cont_well", curie=NMDC.curie('rna_cont_well'), - model_uri=NMDC.rna_cont_well, domain=None, range=Optional[str]) + model_uri=NMDC.rna_cont_well, domain=None, range=Optional[str], + pattern=re.compile(r'^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$')) slots.rna_container_id = Slot(uri=NMDC.rna_container_id, name="rna_container_id", curie=NMDC.curie('rna_container_id'), model_uri=NMDC.rna_container_id, domain=None, range=Optional[str]) @@ -8702,21 +8690,33 @@ class slots: slots.Database_metatranscriptome_activity_set = Slot(uri=NMDC.metatranscriptome_activity_set, name="Database_metatranscriptome_activity_set", curie=NMDC.curie('metatranscriptome_activity_set'), model_uri=NMDC.Database_metatranscriptome_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]]) +slots.FieldResearchSite_id = Slot(uri=NMDC.id, name="FieldResearchSite_id", curie=NMDC.curie('id'), + model_uri=NMDC.FieldResearchSite_id, domain=FieldResearchSite, range=Union[str, FieldResearchSiteId], + pattern=re.compile(r'^nmdc:frsite')) + slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) slots.CollectingBiosamplesFromSite_has_outputs = Slot(uri=NMDC.has_outputs, name="CollectingBiosamplesFromSite_has_outputs", curie=NMDC.curie('has_outputs'), model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) +slots.CollectingBiosamplesFromSite_id = Slot(uri=NMDC.id, name="CollectingBiosamplesFromSite_id", curie=NMDC.curie('id'), + model_uri=NMDC.CollectingBiosamplesFromSite_id, domain=CollectingBiosamplesFromSite, range=Union[str, CollectingBiosamplesFromSiteId], + pattern=re.compile(r'^nmdc:clsite')) + slots.DataObject_name = Slot(uri=NMDC.name, name="DataObject_name", curie=NMDC.curie('name'), model_uri=NMDC.DataObject_name, domain=DataObject, range=str) slots.DataObject_description = Slot(uri=DCTERMS.description, name="DataObject_description", curie=DCTERMS.curie('description'), model_uri=NMDC.DataObject_description, domain=DataObject, range=str) +slots.DataObject_id = Slot(uri=NMDC.id, name="DataObject_id", curie=NMDC.curie('id'), + model_uri=NMDC.DataObject_id, domain=DataObject, range=Union[str, DataObjectId], + pattern=re.compile(r'^nmdc:dobj')) + slots.Biosample_id = Slot(uri=NMDC.id, name="Biosample_id", curie=NMDC.curie('id'), model_uri=NMDC.Biosample_id, domain=Biosample, range=Union[str, BiosampleId], - pattern=re.compile(r'^nmdc:')) + pattern=re.compile(r'^nmdc:bsm')) slots.Biosample_gold_biosample_identifiers = Slot(uri=NMDC.gold_biosample_identifiers, name="Biosample_gold_biosample_identifiers", curie=NMDC.curie('gold_biosample_identifiers'), model_uri=NMDC.Biosample_gold_biosample_identifiers, domain=Biosample, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]], @@ -8747,7 +8747,8 @@ class slots: model_uri=NMDC.Biosample_extreme_event, domain=Biosample, range=Optional[str]) slots.Study_id = Slot(uri=NMDC.id, name="Study_id", curie=NMDC.curie('id'), - model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId]) + model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId], + pattern=re.compile(r'^nmdc:sty')) slots.Study_doi = Slot(uri=NMDC.doi, name="Study_doi", curie=NMDC.curie('doi'), model_uri=NMDC.Study_doi, domain=Study, range=Optional[Union[dict, "AttributeValue"]]) @@ -8784,13 +8785,15 @@ class slots: model_uri=NMDC.Study_emsl_proposal_doi, domain=Study, range=Optional[str]) slots.BiosampleProcessing_id = Slot(uri=NMDC.id, name="BiosampleProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId]) + model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId], + pattern=re.compile(r'^nmdc:bsmprc')) slots.BiosampleProcessing_has_input = Slot(uri=NMDC.has_input, name="BiosampleProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.BiosampleProcessing_has_input, domain=BiosampleProcessing, range=Optional[Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]]) slots.OmicsProcessing_id = Slot(uri=NMDC.id, name="OmicsProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId]) + model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId], + pattern=re.compile(r'^nmdc:omprc')) slots.OmicsProcessing_has_input = Slot(uri=NMDC.has_input, name="OmicsProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.OmicsProcessing_has_input, domain=OmicsProcessing, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) @@ -8865,6 +8868,14 @@ class slots: slots.FunctionalAnnotation_was_generated_by = Slot(uri=NMDC.was_generated_by, name="FunctionalAnnotation_was_generated_by", curie=NMDC.curie('was_generated_by'), model_uri=NMDC.FunctionalAnnotation_was_generated_by, domain=FunctionalAnnotation, range=Optional[Union[str, MetagenomeAnnotationActivityId]], mappings = [PROV.wasGeneratedBy]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -8892,6 +8903,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -8949,12 +8964,20 @@ class slots: slots.GeolocationValue_has_raw_value = Slot(uri=NMDC.has_raw_value, name="GeolocationValue_has_raw_value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) + slots.DissolvingActivity_material_input = Slot(uri=NMDC.material_input, name="DissolvingActivity_material_input", curie=NMDC.curie('material_input'), model_uri=NMDC.DissolvingActivity_material_input, domain=DissolvingActivity, range=Optional[Union[str, MaterialSampleId]]) slots.DissolvingActivity_material_output = Slot(uri=NMDC.material_output, name="DissolvingActivity_material_output", curie=NMDC.curie('material_output'), model_uri=NMDC.DissolvingActivity_material_output, domain=DissolvingActivity, range=Optional[Union[str, MaterialSampleId]]) +slots.MaterialSample_id = Slot(uri=NMDC.id, name="MaterialSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.MaterialSample_id, domain=MaterialSample, range=Union[str, MaterialSampleId], + pattern=re.compile(r'^nmdc:matsm')) + slots.MaterialSamplingActivity_amount_collected = Slot(uri=NMDC.amount_collected, name="MaterialSamplingActivity_amount_collected", curie=NMDC.curie('amount_collected'), model_uri=NMDC.MaterialSamplingActivity_amount_collected, domain=MaterialSamplingActivity, range=Optional[Union[dict, QuantityValue]]) @@ -9008,6 +9031,34 @@ class slots: slots.WorkflowExecutionActivity_type = Slot(uri=NMDC.type, name="WorkflowExecutionActivity_type", curie=NMDC.curie('type'), model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) +slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], + pattern=re.compile(r'^nmdc:wf')) + +slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmgas')) + +slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmtas')) + +slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmgan')) + +slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmtan')) + +slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], + pattern=re.compile(r'^nmdc:wfmt')) + +slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmag')) + slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -9020,6 +9071,14 @@ class slots: slots.ReadQcAnalysisActivity_has_output = Slot(uri=NMDC.has_output, name="ReadQcAnalysisActivity_has_output", curie=NMDC.curie('has_output'), model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) +slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrqc')) + +slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrbt')) + slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9029,14 +9088,26 @@ class slots: slots.MetabolomicsAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="MetabolomicsAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) +slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmb')) + slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.MetaproteomicsAnalysisActivity_has_peptide_quantifications = Slot(uri=NMDC.has_peptide_quantifications, name="MetaproteomicsAnalysisActivity_has_peptide_quantifications", curie=NMDC.curie('has_peptide_quantifications'), model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, PeptideQuantification], List[Union[dict, PeptideQuantification]]]]) +slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmp')) + slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.NomAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="NomAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) + +slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfnom')) diff --git a/nmdc_schema/nmdc.schema.json b/nmdc_schema/nmdc.schema.json index 25ae6de4fc..71442f7add 100644 --- a/nmdc_schema/nmdc.schema.json +++ b/nmdc_schema/nmdc.schema.json @@ -1 +1,5573 @@ -{"$defs": {"Activity": {"additionalProperties": false, "description": "a provence-generating activity", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"$ref": "#/$defs/Agent"}, "was_informed_by": {"type": "string"}}, "required": ["id"], "title": "Activity", "type": "object"}, "Agent": {"additionalProperties": false, "description": "a provence-generating agent", "properties": {"acted_on_behalf_of": {"$ref": "#/$defs/Agent"}, "was_informed_by": {"type": "string"}}, "title": "Agent", "type": "object"}, "AnalysisTypeEnum": {"description": "", "enum": ["metabolomics", "metagenomics", "metaproteomics", "metatranscriptomics", "natural organic matter"], "title": "AnalysisTypeEnum", "type": "string"}, "AnalyticalSample": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "AnalyticalSample", "type": "object"}, "ArchStrucEnum": {"description": "", "enum": ["building", "shed", "home"], "title": "ArchStrucEnum", "type": "string"}, "AttributeValue": {"additionalProperties": false, "description": "The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "AttributeValue", "type": "object"}, "BiolStatEnum": {"description": "", "enum": ["wild", "natural", "semi-natural", "inbred line", "breeder's line", "hybrid", "clonal selection", "mutant"], "title": "BiolStatEnum", "type": "string"}, "Biosample": {"additionalProperties": false, "description": "Biological source material which can be characterized by an experiment.", "properties": {"add_date": {"description": "The date on which the information was added to the database.", "type": "string"}, "agrochem_addition": {"$ref": "#/$defs/QuantityValue", "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications"}, "air_temp_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens"}, "al_sat": {"$ref": "#/$defs/QuantityValue", "description": "Aluminum saturation (esp. For tropical soils)"}, "al_sat_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining Al saturation"}, "alkalinity": {"$ref": "#/$defs/QuantityValue", "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate"}, "alkalinity_method": {"$ref": "#/$defs/TextValue", "description": "Method used for alkalinity measurement"}, "alkyl_diethers": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of alkyl diethers"}, "alt": {"$ref": "#/$defs/QuantityValue", "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air"}, "alternative_identifiers": {"description": "Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC", "items": {"type": "string"}, "type": "array"}, "aminopept_act": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of aminopeptidase activity"}, "ammonium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of ammonium in the sample"}, "ammonium_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of ammonium nitrogen in the sample"}, "analysis_type": {"description": "Select all the data types associated or available for this biosample", "items": {"$ref": "#/$defs/AnalysisTypeEnum"}, "type": "array"}, "annual_precpt": {"$ref": "#/$defs/QuantityValue", "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps."}, "annual_temp": {"$ref": "#/$defs/QuantityValue", "description": "Mean annual temperature"}, "bacteria_carb_prod": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of bacterial carbon production"}, "biosample_categories": {"items": {"$ref": "#/$defs/BiosampleCategoryEnum"}, "type": "array"}, "biotic_regm": {"$ref": "#/$defs/TextValue", "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi."}, "biotic_relationship": {"$ref": "#/$defs/TextValue", "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object"}, "bishomohopanol": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of bishomohopanol"}, "bromide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of bromide"}, "calcium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of calcium in the sample"}, "carb_nitro_ratio": {"$ref": "#/$defs/QuantityValue", "description": "Ratio of amount or concentrations of carbon to nitrogen"}, "chem_administration": {"$ref": "#/$defs/ControlledTermValue", "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi"}, "chloride": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of chloride in the sample"}, "chlorophyll": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of chlorophyll"}, "climate_environment": {"$ref": "#/$defs/TextValue", "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates"}, "collected_from": {"description": "The Site from which a Biosample was collected", "type": "string"}, "collection_date": {"$ref": "#/$defs/TimestampValue", "description": "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant"}, "collection_date_inc": {"description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", "type": "string"}, "collection_time": {"description": "The time of sampling, either as an instance (single point) or interval.", "type": "string"}, "collection_time_inc": {"description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", "type": "string"}, "community": {"type": "string"}, "crop_rotation": {"$ref": "#/$defs/TextValue", "description": "Whether or not crop is rotated, and if yes, rotation schedule"}, "cur_land_use": {"$ref": "#/$defs/TextValue", "description": "Present state of sample site"}, "cur_vegetation": {"$ref": "#/$defs/TextValue", "description": "Vegetation classification from one or more standard classification systems, or agricultural crop"}, "cur_vegetation_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in vegetation classification"}, "density": {"$ref": "#/$defs/QuantityValue", "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)"}, "depth": {"$ref": "#/$defs/QuantityValue", "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "diss_carb_dioxide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample"}, "diss_hydrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved hydrogen"}, "diss_inorg_carb": {"$ref": "#/$defs/QuantityValue", "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter"}, "diss_inorg_phosp": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved inorganic phosphorus in the sample"}, "diss_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid"}, "diss_org_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2"}, "diss_oxygen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of dissolved oxygen"}, "dna_absorb1": {"description": "260/280 measurement of DNA sample purity", "type": "string"}, "dna_absorb2": {"description": "260/230 measurement of DNA sample purity", "type": "string"}, "dna_collect_site": {"description": "Provide information on the site your DNA sample was collected from", "type": "string"}, "dna_concentration": {"maximum": 2000, "minimum": 0, "type": "string"}, "dna_cont_type": {"$ref": "#/$defs/DnaContTypeEnum", "description": "Tube or plate (96-well)"}, "dna_cont_well": {"type": "string"}, "dna_container_id": {"type": "string"}, "dna_dnase": {"$ref": "#/$defs/DnaDnaseEnum"}, "dna_isolate_meth": {"description": "Describe the method/protocol/kit used to extract DNA/RNA.", "type": "string"}, "dna_organisms": {"description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", "type": "string"}, "dna_project_contact": {"type": "string"}, "dna_samp_id": {"type": "string"}, "dna_sample_format": {"$ref": "#/$defs/DnaSampleFormatEnum", "description": "Solution in which the DNA sample has been suspended"}, "dna_sample_name": {"description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", "type": "string"}, "dna_seq_project": {"type": "string"}, "dna_seq_project_name": {"type": "string"}, "dna_seq_project_pi": {"type": "string"}, "dna_volume": {"maximum": 1000, "minimum": 0, "type": "string"}, "dnase_rna": {"$ref": "#/$defs/DnaseRnaEnum"}, "drainage_class": {"$ref": "#/$defs/TextValue", "description": "Drainage classification from a standard system such as the USDA system"}, "ecosystem": {"description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", "type": "string"}, "ecosystem_category": {"description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", "type": "string"}, "ecosystem_subtype": {"description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", "type": "string"}, "ecosystem_type": {"description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", "type": "string"}, "elev": {"$ref": "#/$defs/QuantityValue", "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit."}, "emsl_biosample_identifiers": {"description": "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.", "items": {"type": "string"}, "type": "array"}, "env_broad_scale": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS"}, "env_local_scale": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS."}, "env_medium": {"$ref": "#/$defs/ControlledIdentifiedTermValue", "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top)."}, "env_package": {"$ref": "#/$defs/TextValue", "description": "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported", "pattern": "[air|built environment|host\\-associated|human\\-associated|human\\-skin|human\\-oral|human\\-gut|human\\-vaginal|hydrocarbon resources\\-cores|hydrocarbon resources\\-fluids\\/swabs|microbial mat\\/biofilm|misc environment|plant\\-associated|sediment|soil|wastewater\\/sludge|water]"}, "experimental_factor": {"$ref": "#/$defs/ControlledTermValue", "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI"}, "experimental_factor_other": {"description": "Other details about your sample that you feel can't be accurately represented in the available columns.", "type": "string"}, "extreme_event": {"description": "Unusual physical events that may have affected microbial populations", "type": "string"}, "fao_class": {"$ref": "#/$defs/TextValue", "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups"}, "filter_method": {"description": "Type of filter used or how the sample was filtered", "type": "string"}, "fire": {"$ref": "#/$defs/TimestampValue", "description": "Historical and/or physical evidence of fire"}, "flooding": {"$ref": "#/$defs/TimestampValue", "description": "Historical and/or physical evidence of flooding"}, "gaseous_environment": {"$ref": "#/$defs/QuantityValue", "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens"}, "geo_loc_name": {"$ref": "#/$defs/TextValue", "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)"}, "glucosidase_act": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of glucosidase activity"}, "gold_biosample_identifiers": {"description": "Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample", "items": {"type": "string"}, "pattern": "^GOLD:Gb[0-9]+$", "type": "array"}, "growth_facil": {"$ref": "#/$defs/ControlledTermValue", "description": "Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research"}, "habitat": {"type": "string"}, "heavy_metals": {"$ref": "#/$defs/QuantityValue", "description": "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field."}, "heavy_metals_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining heavy metals"}, "host_name": {"type": "string"}, "humidity_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens"}, "id": {"description": "An NMDC assigned unique identifier for a biosample submitted to NMDC.", "pattern": "^nmdc:", "type": "string"}, "igsn_biosample_identifiers": {"description": "A list of identifiers for the biosample from the IGSN database.", "items": {"type": "string"}, "type": "array"}, "img_identifiers": {"description": "A list of identifiers that relate the biosample to records in the IMG database.", "items": {"type": "string"}, "type": "array"}, "insdc_biosample_identifiers": {"description": "identifiers for corresponding sample in INSDC", "items": {"type": "string"}, "pattern": "^biosample:SAM[NED]([A-Z])?[0-9]+$", "type": "array"}, "isotope_exposure": {"description": "List isotope exposure or addition applied to your sample.", "type": "string"}, "lat_lon": {"$ref": "#/$defs/GeolocationValue", "description": "This is currently a required field but it's not clear if this should be required for human hosts"}, "lbc_thirty": {"$ref": "#/$defs/QuantityValue", "description": "lime buffer capacity, determined after 30 minute incubation"}, "lbceq": {"$ref": "#/$defs/QuantityValue", "description": "lime buffer capacity, determined at equilibrium after 5 day incubation"}, "light_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality."}, "link_addit_analys": {"$ref": "#/$defs/TextValue", "description": "Link to additional analysis results performed on the sample"}, "link_class_info": {"$ref": "#/$defs/TextValue", "description": "Link to digitized soil maps or other soil classification information"}, "link_climate_info": {"$ref": "#/$defs/TextValue", "description": "Link to climate resource"}, "local_class": {"$ref": "#/$defs/TextValue", "description": "Soil classification based on local soil classification system"}, "local_class_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining the local soil classification"}, "location": {"type": "string"}, "magnesium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of magnesium in the sample"}, "manganese": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of manganese in the sample"}, "mean_frict_vel": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of mean friction velocity"}, "mean_peak_frict_vel": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of mean peak friction velocity"}, "micro_biomass_c_meth": {"description": "Reference or method used in determining microbial biomass", "type": "string"}, "micro_biomass_n_meth": {"description": "Reference or method used in determining microbial biomass nitrogen", "type": "string"}, "microbial_biomass_c": {"description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", "type": "string"}, "microbial_biomass_n": {"description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", "type": "string"}, "misc_param": {"$ref": "#/$defs/QuantityValue", "description": "Any other measurement performed or parameter collected, that is not listed here"}, "mod_date": {"description": "The last date on which the database information was modified.", "type": "string"}, "n_alkanes": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of n-alkanes; can include multiple n-alkanes"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "ncbi_taxonomy_name": {"type": "string"}, "nitrate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrate in the sample"}, "nitrate_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrate nitrogen in the sample"}, "nitrite": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrite in the sample"}, "nitrite_nitrogen": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of nitrite nitrogen in the sample"}, "non_microb_biomass": {"description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", "type": "string"}, "non_microb_biomass_method": {"description": "Reference or method used in determining biomass", "type": "string"}, "org_matter": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of organic matter"}, "org_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of organic nitrogen"}, "org_nitro_method": {"description": "Method used for obtaining organic nitrogen", "type": "string"}, "organism_count": {"$ref": "#/$defs/QuantityValue", "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)"}, "other_treatment": {"description": "Other treatments applied to your samples that are not applicable to the provided fields", "type": "string"}, "oxy_stat_samp": {"$ref": "#/$defs/TextValue", "description": "Oxygenation status of sample"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "part_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of particulate organic carbon"}, "perturbation": {"$ref": "#/$defs/TextValue", "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types"}, "petroleum_hydrocarb": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of petroleum hydrocarbon"}, "ph": {"$ref": "#/$defs/QuantityValue", "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid"}, "ph_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining ph"}, "phaeopigments": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phaeopigments; can include multiple phaeopigments"}, "phosphate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phosphate"}, "phosplipid_fatt_acid": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of phospholipid fatty acids; can include multiple values"}, "pool_dna_extracts": {"$ref": "#/$defs/TextValue", "description": "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given"}, "potassium": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of potassium in the sample"}, "pressure": {"$ref": "#/$defs/QuantityValue", "description": "Pressure to which the sample is subject to, in atmospheres"}, "profile_position": {"$ref": "#/$defs/TextValue", "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas"}, "project_id": {"description": "Proposal IDs or names associated with dataset", "type": "string"}, "proport_woa_temperature": {"type": "string"}, "proposal_dna": {"type": "string"}, "proposal_rna": {"type": "string"}, "redox_potential": {"$ref": "#/$defs/QuantityValue", "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential"}, "rel_to_oxygen": {"$ref": "#/$defs/TextValue", "description": "Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments"}, "replicate_number": {"description": "If sending biological replicates, indicate the rep number here.", "type": "string"}, "rna_absorb1": {"description": "260/280 measurement of RNA sample purity", "type": "string"}, "rna_absorb2": {"description": "260/230 measurement of RNA sample purity", "type": "string"}, "rna_collect_site": {"description": "Provide information on the site your RNA sample was collected from", "type": "string"}, "rna_concentration": {"maximum": 1000, "minimum": 0, "type": "string"}, "rna_cont_type": {"$ref": "#/$defs/RnaContTypeEnum", "description": "Tube or plate (96-well)"}, "rna_cont_well": {"type": "string"}, "rna_container_id": {"type": "string"}, "rna_isolate_meth": {"description": "Describe the method/protocol/kit used to extract DNA/RNA.", "type": "string"}, "rna_organisms": {"description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", "type": "string"}, "rna_project_contact": {"type": "string"}, "rna_samp_id": {"type": "string"}, "rna_sample_format": {"$ref": "#/$defs/RnaSampleFormatEnum", "description": "Solution in which the RNA sample has been suspended"}, "rna_sample_name": {"description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", "maximum": 2000, "minimum": 0, "type": "string"}, "rna_seq_project": {"type": "string"}, "rna_seq_project_name": {"type": "string"}, "rna_seq_project_pi": {"type": "string"}, "rna_volume": {"type": "string"}, "salinity": {"$ref": "#/$defs/QuantityValue", "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater."}, "salinity_category": {"description": "Categorcial description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline", "type": "string"}, "salinity_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining salinity"}, "samp_collec_method": {"description": "The method employed for collecting the sample.", "type": "string"}, "samp_mat_process": {"$ref": "#/$defs/ControlledTermValue", "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed."}, "samp_name": {"description": "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.", "type": "string"}, "samp_size": {"$ref": "#/$defs/QuantityValue", "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected."}, "samp_store_dur": {"$ref": "#/$defs/TextValue", "description": "Duration for which the sample was stored"}, "samp_store_loc": {"$ref": "#/$defs/TextValue", "description": "Location at which sample was stored, usually name of a specific freezer/room"}, "samp_store_temp": {"$ref": "#/$defs/QuantityValue", "description": "Temperature at which sample was stored, e.g. -80 degree Celsius"}, "samp_vol_we_dna_ext": {"$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)."}, "sample_collection_site": {"type": "string"}, "sample_link": {"description": "JsonObj()", "items": {"type": "string"}, "type": "array"}, "sample_shipped": {"description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL", "type": "string"}, "sample_type": {"$ref": "#/$defs/SampleTypeEnum", "description": "Type of sample being submitted"}, "season_precpt": {"$ref": "#/$defs/QuantityValue", "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps."}, "season_temp": {"$ref": "#/$defs/QuantityValue", "description": "Mean seasonal temperature"}, "sieving": {"$ref": "#/$defs/QuantityValue", "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved"}, "size_frac_low": {"$ref": "#/$defs/QuantityValue", "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample"}, "size_frac_up": {"$ref": "#/$defs/QuantityValue", "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample"}, "slope_aspect": {"$ref": "#/$defs/QuantityValue", "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration."}, "slope_gradient": {"$ref": "#/$defs/QuantityValue", "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer"}, "sodium": {"$ref": "#/$defs/QuantityValue", "description": "Sodium concentration in the sample"}, "soil_type": {"$ref": "#/$defs/TextValue", "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes."}, "soil_type_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining soil series name or other lower-level classification"}, "soluble_iron_micromol": {"type": "string"}, "source_mat_id": {"$ref": "#/$defs/TextValue", "description": "A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2)."}, "specific_ecosystem": {"description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", "type": "string"}, "start_date_inc": {"description": "Date the incubation was started. Only relevant for incubation samples.", "type": "string"}, "start_time_inc": {"description": "Time the incubation was started. Only relevant for incubation samples.", "type": "string"}, "store_cond": {"$ref": "#/$defs/TextValue", "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)."}, "subsurface_depth": {"$ref": "#/$defs/QuantityValue"}, "sulfate": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of sulfate in the sample"}, "sulfide": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of sulfide in the sample"}, "technical_reps": {"description": "If sending multiple technical replicates of the same sample, indicate how many replicates are being sent", "type": "string"}, "temp": {"$ref": "#/$defs/QuantityValue", "description": "Temperature of the sample at the time of sampling."}, "tidal_stage": {"$ref": "#/$defs/TextValue", "description": "Stage of tide"}, "tillage": {"$ref": "#/$defs/TextValue", "description": "Note method(s) used for tilling"}, "tot_carb": {"$ref": "#/$defs/QuantityValue", "description": "Total carbon content"}, "tot_depth_water_col": {"$ref": "#/$defs/QuantityValue", "description": "Measurement of total depth of water column"}, "tot_diss_nitro": {"$ref": "#/$defs/QuantityValue", "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen"}, "tot_nitro_cont_meth": {"description": "Reference or method used in determining the total nitrogen", "type": "string"}, "tot_nitro_content": {"$ref": "#/$defs/QuantityValue", "description": "Total nitrogen content of the sample"}, "tot_org_c_meth": {"$ref": "#/$defs/TextValue", "description": "Reference or method used in determining total organic carbon"}, "tot_org_carb": {"$ref": "#/$defs/QuantityValue", "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content"}, "tot_phosp": {"$ref": "#/$defs/QuantityValue", "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "water_cont_soil_meth": {"description": "Reference or method used in determining the water content of soil", "type": "string"}, "water_content": {"$ref": "#/$defs/QuantityValue", "description": "Water content measurement"}, "watering_regm": {"$ref": "#/$defs/QuantityValue", "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens"}, "zinc": {"$ref": "#/$defs/QuantityValue", "description": "Concentration of zinc in the sample"}}, "required": ["part_of", "id", "env_broad_scale", "env_local_scale", "env_medium"], "title": "Biosample", "type": "object"}, "BiosampleCategoryEnum": {"description": "Funding-based, sample location-based, or experimental method-based defined categories", "enum": ["LTER", "SIP", "SFA", "FICUS", "NEON"], "title": "BiosampleCategoryEnum", "type": "string"}, "BiosampleProcessing": {"additionalProperties": false, "description": "A process that takes one or more biosamples as inputs and generates one or as outputs. Examples of outputs include samples cultivated from another sample or data objects created by instruments runs.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "BiosampleProcessing", "type": "object"}, "BioticRelationshipEnum": {"description": "", "enum": ["free living", "parasite", "commensal", "symbiont"], "title": "BioticRelationshipEnum", "type": "string"}, "BooleanValue": {"additionalProperties": false, "description": "A value that is a boolean", "properties": {"has_boolean_value": {"description": "Links a quantity value to a boolean", "type": "boolean"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "BooleanValue", "type": "object"}, "BuildDocsEnum": {"description": "", "enum": ["building information model", "commissioning report", "complaint logs", "contract administration", "cost estimate", "janitorial schedules or logs", "maintenance plans", "schedule", "sections", "shop drawings", "submittals", "ventilation system", "windows"], "title": "BuildDocsEnum", "type": "string"}, "BuildOccupTypeEnum": {"description": "", "enum": ["office", "market", "restaurant", "residence", "school", "residential", "commercial", "low rise", "high rise", "wood framed", "health care", "airport", "sports complex"], "title": "BuildOccupTypeEnum", "type": "string"}, "BuildingSettingEnum": {"description": "", "enum": ["urban", "suburban", "exurban", "rural"], "title": "BuildingSettingEnum", "type": "string"}, "CeilCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "CeilCondEnum", "type": "string"}, "CeilFinishMatEnum": {"description": "", "enum": ["drywall", "mineral fibre", "tiles", "PVC", "plasterboard", "metal", "fiberglass", "stucco", "mineral wool/calcium silicate", "wood"], "title": "CeilFinishMatEnum", "type": "string"}, "CeilTextureEnum": {"description": "", "enum": ["crows feet", "crows-foot stomp", "double skip", "hawk and trowel", "knockdown", "popcorn", "orange peel", "rosebud stomp", "Santa-Fe texture", "skip trowel", "smooth", "stomp knockdown", "swirl"], "title": "CeilTextureEnum", "type": "string"}, "CeilTypeEnum": {"description": "", "enum": ["cathedral", "dropped", "concave", "barrel-shaped", "coffered", "cove", "stretched"], "title": "CeilTypeEnum", "type": "string"}, "ChemicalEntity": {"additionalProperties": false, "description": "An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "ChemicalEntity", "type": "object"}, "CollectingBiosamplesFromSite": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_inputs": {"items": {"type": "string"}, "type": "array"}, "has_outputs": {"items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "participating_agent": {"$ref": "#/$defs/Agent"}}, "required": ["has_inputs", "has_outputs", "id"], "title": "CollectingBiosamplesFromSite", "type": "object"}, "ContainerTypeEnum": {"description": "", "enum": ["screw_top_conical"], "title": "ContainerTypeEnum", "type": "string"}, "ControlledIdentifiedTermValue": {"additionalProperties": false, "description": "A controlled term or class from an ontology, requiring the presence of term with an id", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "term": {"$ref": "#/$defs/OntologyClass", "description": "pointer to an ontology class"}, "was_generated_by": {"type": "string"}}, "required": ["term"], "title": "ControlledIdentifiedTermValue", "type": "object"}, "ControlledTermValue": {"additionalProperties": false, "description": "A controlled term or class from an ontology", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "term": {"$ref": "#/$defs/OntologyClass", "description": "pointer to an ontology class"}, "was_generated_by": {"type": "string"}}, "title": "ControlledTermValue", "type": "object"}, "CreditAssociation": {"additionalProperties": false, "description": "This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0", "properties": {"applied_role": {"$ref": "#/$defs/CreditEnum"}, "applied_roles": {"items": {"$ref": "#/$defs/CreditEnum"}, "type": "array"}, "applies_to_person": {"$ref": "#/$defs/PersonValue"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "required": ["applies_to_person", "applied_roles"], "title": "CreditAssociation", "type": "object"}, "CreditEnum": {"description": "", "enum": ["Conceptualization", "Data curation", "Formal Analysis", "Funding acquisition", "Investigation", "Methodology", "Project administration", "Resources", "Software", "Supervision", "Validation", "Visualization", "Writing original draft", "Writing review and editing", "Principal Investigator", "Submitter"], "title": "CreditEnum", "type": "string"}, "CurLandUseEnum": {"description": "", "enum": ["cities", "farmstead", "industrial areas", "roads/railroads", "rock", "sand", "gravel", "mudflats", "salt flats", "badlands", "permanent snow or ice", "saline seeps", "mines/quarries", "oil waste areas", "small grains", "row crops", "vegetable crops", "horticultural plants (e.g. tulips)", "marshlands (grass,sedges,rushes)", "tundra (mosses,lichens)", "rangeland", "pastureland (grasslands used for livestock grazing)", "hayland", "meadows (grasses,alfalfa,fescue,bromegrass,timothy)", "shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)", "successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)", "shrub crops (blueberries,nursery ornamentals,filberts)", "vine crops (grapes)", "conifers (e.g. pine,spruce,fir,cypress)", "hardwoods (e.g. oak,hickory,elm,aspen)", "intermixed hardwood and conifers", "tropical (e.g. mangrove,palms)", "rainforest (evergreen forest receiving greater than 406 cm annual rainfall)", "swamp (permanent or semi-permanent water body dominated by woody plants)", "crop trees (nuts,fruit,christmas trees,nursery trees)"], "title": "CurLandUseEnum", "type": "string"}, "DataObject": {"additionalProperties": false, "description": "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "compression_type": {"description": "If provided, specifies the compression type", "type": "string"}, "data_object_type": {"$ref": "#/$defs/FileTypeEnum", "description": "The type of file represented by the data object."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "file_size_bytes": {"description": "Size of the file in bytes", "type": "integer"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "md5_checksum": {"description": "MD5 checksum of file (pre-compressed)", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "url": {"type": "string"}, "was_generated_by": {"type": "string"}}, "required": ["id", "name", "description"], "title": "DataObject", "type": "object"}, "Database": {"additionalProperties": false, "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest", "properties": {"activity_set": {"description": "This property links a database object to the set of workflow activities.", "items": {"$ref": "#/$defs/WorkflowExecutionActivity"}, "type": "array"}, "biosample_set": {"description": "This property links a database object to the set of samples within it.", "items": {"$ref": "#/$defs/Biosample"}, "type": "array"}, "collecting_biosamples_from_site_set": {"items": {"$ref": "#/$defs/CollectingBiosamplesFromSite"}, "type": "array"}, "data_object_set": {"description": "This property links a database object to the set of data objects within it.", "items": {"$ref": "#/$defs/DataObject"}, "type": "array"}, "dissolving_activity_set": {"items": {"$ref": "#/$defs/DissolvingActivity"}, "type": "array"}, "field_research_site_set": {"items": {"$ref": "#/$defs/FieldResearchSite"}, "type": "array"}, "functional_annotation_set": {"description": "This property links a database object to the set of all functional annotations", "items": {"$ref": "#/$defs/FunctionalAnnotation"}, "type": "array"}, "genome_feature_set": {"description": "This property links a database object to the set of all features", "items": {"$ref": "#/$defs/GenomeFeature"}, "type": "array"}, "mags_activity_set": {"description": "This property links a database object to the set of MAGs analysis activities.", "items": {"$ref": "#/$defs/MagsAnalysisActivity"}, "type": "array"}, "material_sample_set": {"items": {"$ref": "#/$defs/MaterialSample"}, "type": "array"}, "material_sampling_activity_set": {"items": {"$ref": "#/$defs/MaterialSamplingActivity"}, "type": "array"}, "metabolomics_analysis_activity_set": {"description": "This property links a database object to the set of metabolomics analysis activities.", "items": {"$ref": "#/$defs/MetabolomicsAnalysisActivity"}, "type": "array"}, "metagenome_annotation_activity_set": {"description": "This property links a database object to the set of metagenome annotation activities.", "items": {"$ref": "#/$defs/MetagenomeAnnotationActivity"}, "type": "array"}, "metagenome_assembly_set": {"description": "This property links a database object to the set of metagenome assembly activities.", "items": {"$ref": "#/$defs/MetagenomeAssembly"}, "type": "array"}, "metaproteomics_analysis_activity_set": {"description": "This property links a database object to the set of metaproteomics analysis activities.", "items": {"$ref": "#/$defs/MetaproteomicsAnalysisActivity"}, "type": "array"}, "metatranscriptome_activity_set": {"description": "TODO", "items": {"$ref": "#/$defs/MetatranscriptomeActivity"}, "type": "array"}, "nom_analysis_activity_set": {"description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", "items": {"$ref": "#/$defs/NomAnalysisActivity"}, "type": "array"}, "omics_processing_set": {"description": "This property links a database object to the set of omics processings within it.", "items": {"$ref": "#/$defs/OmicsProcessing"}, "type": "array"}, "reaction_activity_set": {"items": {"$ref": "#/$defs/ReactionActivity"}, "type": "array"}, "read_based_taxonomy_analysis_activity_set": {"description": "This property links a database object to the set of read based analysis activities.", "items": {"$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity"}, "type": "array"}, "read_qc_analysis_activity_set": {"description": "This property links a database object to the set of read QC analysis activities.", "items": {"$ref": "#/$defs/ReadQcAnalysisActivity"}, "type": "array"}, "study_set": {"description": "This property links a database object to the set of studies within it.", "items": {"$ref": "#/$defs/Study"}, "type": "array"}}, "title": "Database", "type": "object"}, "DeposEnvEnum": {"description": "", "enum": ["Continental - Alluvial", "Continental - Aeolian", "Continental - Fluvial", "Continental - Lacustrine", "Transitional - Deltaic", "Transitional - Tidal", "Transitional - Lagoonal", "Transitional - Beach", "Transitional - Lake", "Marine - Shallow", "Marine - Deep", "Marine - Reef", "Other - Evaporite", "Other - Glacial", "Other - Volcanic", "other"], "title": "DeposEnvEnum", "type": "string"}, "DeviceTypeEnum": {"description": "", "enum": ["orbital_shaker", "thermomixer"], "title": "DeviceTypeEnum", "type": "string"}, "DissolvingActivity": {"additionalProperties": false, "description": "", "properties": {"dissolution_aided_by": {"$ref": "#/$defs/LabDevice"}, "dissolution_reagent": {"$ref": "#/$defs/SolventEnum"}, "dissolution_volume": {"$ref": "#/$defs/QuantityValue"}, "dissolved_in": {"$ref": "#/$defs/MaterialContainer"}, "material_input": {"type": "string"}, "material_output": {"type": "string"}}, "title": "DissolvingActivity", "type": "object"}, "DnaContTypeEnum": {"description": "", "enum": ["plate", "tube"], "title": "DnaContTypeEnum", "type": "string"}, "DnaDnaseEnum": {"description": "", "enum": ["no", "yes"], "title": "DnaDnaseEnum", "type": "string"}, "DnaSampleFormatEnum": {"description": "", "enum": ["10 mM Tris-HCl", "DNAStable", "Ethanol", "Low EDTA TE", "MDA reaction buffer", "PBS", "Pellet", "RNAStable", "TE", "Water", "Gentegra-DNA", "Gentegra-RNA"], "title": "DnaSampleFormatEnum", "type": "string"}, "DnaseRnaEnum": {"description": "", "enum": ["no", "yes"], "title": "DnaseRnaEnum", "type": "string"}, "DoorCompTypeEnum": {"description": "", "enum": ["metal covered", "revolving", "sliding", "telescopic"], "title": "DoorCompTypeEnum", "type": "string"}, "DoorCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "DoorCondEnum", "type": "string"}, "DoorDirectEnum": {"description": "", "enum": ["inward", "outward", "sideways"], "title": "DoorDirectEnum", "type": "string"}, "DoorLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "DoorLocEnum", "type": "string"}, "DoorMatEnum": {"description": "", "enum": ["aluminum", "cellular PVC", "engineered plastic", "fiberboard", "fiberglass", "metal", "thermoplastic alloy", "vinyl", "wood", "wood/plastic composite"], "title": "DoorMatEnum", "type": "string"}, "DoorMoveEnum": {"description": "", "enum": ["collapsible", "folding", "revolving", "rolling shutter", "sliding", "swinging"], "title": "DoorMoveEnum", "type": "string"}, "DoorTypeEnum": {"description": "", "enum": ["composite", "metal", "wooden"], "title": "DoorTypeEnum", "type": "string"}, "DoorTypeMetalEnum": {"description": "", "enum": ["collapsible", "corrugated steel", "hollow", "rolling shutters", "steel plate"], "title": "DoorTypeMetalEnum", "type": "string"}, "DoorTypeWoodEnum": {"description": "", "enum": ["bettened and ledged", "battened", "ledged and braced", "ledged and framed", "ledged, braced and frame", "framed and paneled", "glashed or sash", "flush", "louvered", "wire gauged"], "title": "DoorTypeWoodEnum", "type": "string"}, "DrainageClassEnum": {"description": "", "enum": ["very poorly", "poorly", "somewhat poorly", "moderately well", "well", "excessively drained"], "title": "DrainageClassEnum", "type": "string"}, "DrawingsEnum": {"description": "", "enum": ["operation", "as built", "construction", "bid", "design", "building navigation map", "diagram", "sketch"], "title": "DrawingsEnum", "type": "string"}, "EnvironmentalMaterialTerm": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "EnvironmentalMaterialTerm", "type": "object"}, "ExtWallOrientEnum": {"description": "", "enum": ["north", "south", "east", "west", "northeast", "southeast", "southwest", "northwest"], "title": "ExtWallOrientEnum", "type": "string"}, "ExtWindowOrientEnum": {"description": "", "enum": ["north", "south", "east", "west", "northeast", "southeast", "southwest", "northwest"], "title": "ExtWindowOrientEnum", "type": "string"}, "FaoClassEnum": {"description": "", "enum": ["Acrisols", "Andosols", "Arenosols", "Cambisols", "Chernozems", "Ferralsols", "Fluvisols", "Gleysols", "Greyzems", "Gypsisols", "Histosols", "Kastanozems", "Lithosols", "Luvisols", "Nitosols", "Phaeozems", "Planosols", "Podzols", "Podzoluvisols", "Rankers", "Regosols", "Rendzinas", "Solonchaks", "Solonetz", "Vertisols", "Yermosols"], "title": "FaoClassEnum", "type": "string"}, "FieldResearchSite": {"additionalProperties": false, "description": "A site, outside of a laboratory, from which biosamples may be collected.", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "FieldResearchSite", "type": "object"}, "FileTypeEnum": {"description": "", "enum": ["Metagenome Raw Reads", "FT ICR-MS Analysis Results", "GC-MS Metabolomics Results", "Metaproteomics Workflow Statistics", "Protein Report", "Peptide Report", "Unfiltered Metaproteomics Results", "Read Count and RPKM", "QC non-rRNA R2", "QC non-rRNA R1", "Metagenome Bins", "CheckM Statistics", "GOTTCHA2 Krona Plot", "GOTTCHA2 Classification Report", "GOTTCHA2 Report Full", "Kraken2 Krona Plot", "Centrifuge Krona Plot", "Centrifuge output report file", "Kraken2 Classification Report", "Kraken2 Taxonomic Classification", "Centrifuge Classification Report", "Centrifuge Taxonomic Classification", "Structural Annotation GFF", "Functional Annotation GFF", "Annotation Amino Acid FASTA", "Annotation Enzyme Commission", "Annotation KEGG Orthology", "Assembly Coverage BAM", "Assembly AGP", "Assembly Scaffolds", "Assembly Contigs", "Assembly Coverage Stats", "Filtered Sequencing Reads", "QC Statistics", "TIGRFam Annotation GFF", "CRT Annotation GFF", "Genmark Annotation GFF", "Prodigal Annotation GFF", "TRNA Annotation GFF", "Misc Annotation GFF", "RFAM Annotation GFF", "TMRNA Annotation GFF", "KO_EC Annotation GFF", "Product Names", "Gene Phylogeny tsv", "Crisprt Terms", "Clusters of Orthologous Groups (COG) Annotation GFF", "CATH FunFams (Functional Families) Annotation GFF", "SUPERFam Annotation GFF", "SMART Annotation GFF", "Pfam Annotation GFF", "Direct Infusion FT ICR-MS Raw Data"], "title": "FileTypeEnum", "type": "string"}, "FilterTypeEnum": {"description": "", "enum": ["particulate air filter", "chemical air filter", "low-MERV pleated media", "HEPA", "electrostatic", "gas-phase or ultraviolet air treatments"], "title": "FilterTypeEnum", "type": "string"}, "FloorCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "FloorCondEnum", "type": "string"}, "FloorFinishMatEnum": {"description": "", "enum": ["tile", "wood strip or parquet", "carpet", "rug", "laminate wood", "lineoleum", "vinyl composition tile", "sheet vinyl", "stone", "bamboo", "cork", "terrazo", "concrete", "none", "sealed", "clear finish", "paint", "none or unfinished"], "title": "FloorFinishMatEnum", "type": "string"}, "FloorStrucEnum": {"description": "", "enum": ["balcony", "floating floor", "glass floor", "raised floor", "sprung floor", "wood-framed", "concrete"], "title": "FloorStrucEnum", "type": "string"}, "FloorWaterMoldEnum": {"description": "", "enum": ["mold odor", "wet floor", "water stains", "wall discoloration", "floor discoloration", "ceiling discoloration", "peeling paint or wallpaper", "bulging walls", "condensation"], "title": "FloorWaterMoldEnum", "type": "string"}, "FreqCleanEnum": {"description": "", "enum": ["Daily", "Weekly", "Monthly", "Quarterly", "Annually", "other"], "title": "FreqCleanEnum", "type": "string"}, "FunctionalAnnotation": {"additionalProperties": false, "description": "An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods", "properties": {"has_function": {"pattern": "^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$", "type": "string"}, "subject": {"type": "string"}, "was_generated_by": {"description": "provenance for the annotation.", "type": "string"}}, "title": "FunctionalAnnotation", "type": "object"}, "FurnitureEnum": {"description": "", "enum": ["cabinet", "chair", "desks"], "title": "FurnitureEnum", "type": "string"}, "GenderRestroomEnum": {"description": "", "enum": ["all gender", "female", "gender neurtral", "male", "male and female", "unisex"], "title": "GenderRestroomEnum", "type": "string"}, "GeneProduct": {"additionalProperties": false, "description": "A molecule encoded by a gene that has an evolved function", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "GeneProduct", "type": "object"}, "GenomeFeature": {"additionalProperties": false, "description": "A feature localized to an interval along a genome", "title": "GenomeFeature", "type": "object"}, "GeolocationValue": {"additionalProperties": false, "description": "A normalized value for a location on the earth's surface", "properties": {"has_raw_value": {"description": "The raw value for a geolocation should follow {lat} {long}", "type": "string"}, "latitude": {"description": "latitude", "type": "number"}, "longitude": {"description": "longitude", "type": "number"}, "was_generated_by": {"type": "string"}}, "title": "GeolocationValue", "type": "object"}, "GrowthHabitEnum": {"description": "", "enum": ["erect", "semi-erect", "spreading", "prostrate"], "title": "GrowthHabitEnum", "type": "string"}, "HandidnessEnum": {"description": "", "enum": ["ambidexterity", "left handedness", "mixed-handedness", "right handedness"], "title": "HandidnessEnum", "type": "string"}, "HcProducedEnum": {"description": "", "enum": ["Oil", "Gas-Condensate", "Gas", "Bitumen", "Coalbed Methane", "other"], "title": "HcProducedEnum", "type": "string"}, "HcrEnum": {"description": "", "enum": ["Oil Reservoir", "Gas Reservoir", "Oil Sand", "Coalbed", "Shale", "Tight Oil Reservoir", "Tight Gas Reservoir", "other"], "title": "HcrEnum", "type": "string"}, "HcrGeolAgeEnum": {"description": "", "enum": ["Archean", "Cambrian", "Carboniferous", "Cenozoic", "Cretaceous", "Devonian", "Jurassic", "Mesozoic", "Neogene", "Ordovician", "Paleogene", "Paleozoic", "Permian", "Precambrian", "Proterozoic", "Silurian", "Triassic", "other"], "title": "HcrGeolAgeEnum", "type": "string"}, "HeatCoolTypeEnum": {"description": "", "enum": ["radiant system", "heat pump", "forced air system", "steam forced heat", "wood stove"], "title": "HeatCoolTypeEnum", "type": "string"}, "HeatDelivLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "HeatDelivLocEnum", "type": "string"}, "HorizonEnum": {"description": "", "enum": ["O horizon", "A horizon", "E horizon", "B horizon", "C horizon", "R layer", "Permafrost"], "title": "HorizonEnum", "type": "string"}, "HostSexEnum": {"description": "", "enum": ["female", "hermaphrodite", "male", "neuter"], "title": "HostSexEnum", "type": "string"}, "ImageValue": {"additionalProperties": false, "description": "An attribute value representing an image.", "properties": {"description": {"description": "a human-readable description of a thing", "type": "string"}, "display_order": {"description": "When rendering information, this attribute to specify the order in which the information should be rendered.", "type": "string"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "url": {"type": "string"}, "was_generated_by": {"type": "string"}}, "title": "ImageValue", "type": "object"}, "IndoorSpaceEnum": {"description": "", "enum": ["bedroom", "office", "bathroom", "foyer", "kitchen", "locker room", "hallway", "elevator"], "title": "IndoorSpaceEnum", "type": "string"}, "IndoorSurfEnum": {"description": "", "enum": ["cabinet", "ceiling", "counter top", "door", "shelving", "vent cover", "window", "wall"], "title": "IndoorSurfEnum", "type": "string"}, "Instrument": {"additionalProperties": false, "description": "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI].", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Instrument", "type": "object"}, "IntWallCondEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture"], "title": "IntWallCondEnum", "type": "string"}, "IntegerValue": {"additionalProperties": false, "description": "A value that is an integer", "properties": {"has_numeric_value": {"description": "Links a quantity value to a number", "type": "number"}, "has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "IntegerValue", "type": "object"}, "LabDevice": {"additionalProperties": false, "description": "", "properties": {"activity_speed": {"$ref": "#/$defs/QuantityValue"}, "activity_temperature": {"$ref": "#/$defs/QuantityValue"}, "activity_time": {"$ref": "#/$defs/QuantityValue"}, "device_type": {"$ref": "#/$defs/DeviceTypeEnum"}}, "title": "LabDevice", "type": "object"}, "LightTypeEnum": {"description": "", "enum": ["natural light", "electric light", "desk lamp", "flourescent lights", "none"], "title": "LightTypeEnum", "type": "string"}, "LithologyEnum": {"description": "", "enum": ["Basement", "Chalk", "Chert", "Coal", "Conglomerate", "Diatomite", "Dolomite", "Limestone", "Sandstone", "Shale", "Siltstone", "Volcanic", "other"], "title": "LithologyEnum", "type": "string"}, "MagBin": {"additionalProperties": false, "description": "", "properties": {"bin_name": {"type": "string"}, "bin_quality": {"type": "string"}, "completeness": {"type": "number"}, "contamination": {"type": "number"}, "gene_count": {"type": "integer"}, "gtdbtk_class": {"type": "string"}, "gtdbtk_domain": {"type": "string"}, "gtdbtk_family": {"type": "string"}, "gtdbtk_genus": {"type": "string"}, "gtdbtk_order": {"type": "string"}, "gtdbtk_phylum": {"type": "string"}, "gtdbtk_species": {"type": "string"}, "num_16s": {"type": "integer"}, "num_23s": {"type": "integer"}, "num_5s": {"type": "integer"}, "num_t_rna": {"type": "integer"}, "number_of_contig": {"type": "integer"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "title": "MagBin", "type": "object"}, "MagsAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", "properties": {"binned_contig_num": {"type": "integer"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "input_contig_num": {"type": "integer"}, "low_depth_contig_num": {"type": "integer"}, "mags_list": {"items": {"$ref": "#/$defs/MagBin"}, "type": "array"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "too_short_contig_num": {"type": "integer"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "unbinned_contig_num": {"type": "integer"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MagsAnalysisActivity", "type": "object"}, "MaterialContainer": {"additionalProperties": false, "description": "", "properties": {"container_size": {"$ref": "#/$defs/QuantityValue"}, "container_type": {"$ref": "#/$defs/ContainerTypeEnum"}}, "title": "MaterialContainer", "type": "object"}, "MaterialEntity": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "MaterialEntity", "type": "object"}, "MaterialSample": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "MaterialSample", "type": "object"}, "MaterialSamplingActivity": {"additionalProperties": false, "description": "", "properties": {"amount_collected": {"$ref": "#/$defs/QuantityValue"}, "biosample_input": {"type": "string"}, "collected_into": {"$ref": "#/$defs/MaterialContainer"}, "material_output": {"type": "string"}, "sampling_method": {"$ref": "#/$defs/SamplingMethodEnum"}}, "title": "MaterialSamplingActivity", "type": "object"}, "MechStrucEnum": {"description": "", "enum": ["subway", "coach", "carriage", "elevator", "escalator", "boat", "train", "car", "bus"], "title": "MechStrucEnum", "type": "string"}, "MetaboliteQuantification": {"additionalProperties": false, "description": "This is used to link a metabolomics analysis workflow to a specific metabolite", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "MetaboliteQuantification", "type": "object"}, "MetabolomicsAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetabolomicsAnalysisActivity", "type": "object"}, "MetagenomeAnnotationActivity": {"additionalProperties": false, "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "gold_analysis_project_identifiers": {"description": "identifiers for corresponding analysis project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Ga[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetagenomeAnnotationActivity", "type": "object"}, "MetagenomeAssembly": {"additionalProperties": false, "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", "properties": {"asm_score": {"description": "A score for comparing metagenomic assembly quality from same sample.", "type": "number"}, "contig_bp": {"description": "Total size in bp of all contigs.", "type": "number"}, "contigs": {"description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "ctg_l50": {"description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", "type": "number"}, "ctg_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", "type": "number"}, "ctg_logsum": {"description": "Maximum contig length.", "type": "number"}, "ctg_max": {"description": "Maximum contig length.", "type": "number"}, "ctg_n50": {"description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", "type": "number"}, "ctg_n90": {"description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", "type": "number"}, "ctg_powsum": {"description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "gap_pct": {"description": "The gap size percentage of all scaffolds.", "type": "number"}, "gc_avg": {"description": "Average of GC content of all contigs.", "type": "number"}, "gc_std": {"description": "Standard deviation of GC content of all contigs.", "type": "number"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_assembly_identifiers": {"pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "num_aligned_reads": {"description": "The sequence count number of input reads aligned to assembled contigs.", "type": "number"}, "num_input_reads": {"description": "The sequence count number of input reads for assembly.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "scaf_bp": {"description": "Total size in bp of all scaffolds.", "type": "number"}, "scaf_l50": {"description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", "type": "number"}, "scaf_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", "type": "number"}, "scaf_l_gt50k": {"description": "Total size in bp of all scaffolds greater than 50 KB.", "type": "number"}, "scaf_logsum": {"description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "scaf_max": {"description": "Maximum scaffold length.", "type": "number"}, "scaf_n50": {"description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", "type": "number"}, "scaf_n90": {"description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", "type": "number"}, "scaf_n_gt50k": {"description": "Total sequence count of scaffolds greater than 50 KB.", "type": "number"}, "scaf_pct_gt50k": {"description": "Total sequence size percentage of scaffolds greater than 50 KB.", "type": "number"}, "scaf_powsum": {"description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "scaffolds": {"description": "Total sequence count of all scaffolds.", "type": "number"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetagenomeAssembly", "type": "object"}, "MetaproteomicsAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetaproteomicsAnalysisActivity", "type": "object"}, "MetatranscriptomeActivity": {"additionalProperties": false, "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeActivity", "type": "object"}, "MetatranscriptomeAnnotationActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "gold_analysis_project_identifiers": {"description": "identifiers for corresponding analysis project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Ga[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeAnnotationActivity", "type": "object"}, "MetatranscriptomeAssembly": {"additionalProperties": false, "description": "", "properties": {"asm_score": {"description": "A score for comparing metagenomic assembly quality from same sample.", "type": "number"}, "contig_bp": {"description": "Total size in bp of all contigs.", "type": "number"}, "contigs": {"description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "ctg_l50": {"description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", "type": "number"}, "ctg_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", "type": "number"}, "ctg_logsum": {"description": "Maximum contig length.", "type": "number"}, "ctg_max": {"description": "Maximum contig length.", "type": "number"}, "ctg_n50": {"description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", "type": "number"}, "ctg_n90": {"description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", "type": "number"}, "ctg_powsum": {"description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "gap_pct": {"description": "The gap size percentage of all scaffolds.", "type": "number"}, "gc_avg": {"description": "Average of GC content of all contigs.", "type": "number"}, "gc_std": {"description": "Standard deviation of GC content of all contigs.", "type": "number"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_assembly_identifiers": {"pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "num_aligned_reads": {"description": "The sequence count number of input reads aligned to assembled contigs.", "type": "number"}, "num_input_reads": {"description": "The sequence count number of input reads for assembly.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "scaf_bp": {"description": "Total size in bp of all scaffolds.", "type": "number"}, "scaf_l50": {"description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", "type": "number"}, "scaf_l90": {"description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", "type": "number"}, "scaf_l_gt50k": {"description": "Total size in bp of all scaffolds greater than 50 KB.", "type": "number"}, "scaf_logsum": {"description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", "type": "number"}, "scaf_max": {"description": "Maximum scaffold length.", "type": "number"}, "scaf_n50": {"description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", "type": "number"}, "scaf_n90": {"description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", "type": "number"}, "scaf_n_gt50k": {"description": "Total sequence count of scaffolds greater than 50 KB.", "type": "number"}, "scaf_pct_gt50k": {"description": "Total sequence size percentage of scaffolds greater than 50 KB.", "type": "number"}, "scaf_powsum": {"description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", "type": "number"}, "scaffolds": {"description": "Total sequence count of all scaffolds.", "type": "number"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "MetatranscriptomeAssembly", "type": "object"}, "NomAnalysisActivity": {"additionalProperties": false, "description": "", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"description": "The instrument used to collect the data used in the analysis", "type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "NomAnalysisActivity", "type": "object"}, "OccupDocumentEnum": {"description": "", "enum": ["automated count", "estimate", "manual count", "videos"], "title": "OccupDocumentEnum", "type": "string"}, "OmicsProcessing": {"additionalProperties": false, "description": "The methods and processes used to generate omics data from a biosample or organism.", "properties": {"add_date": {"description": "The date on which the information was added to the database.", "type": "string"}, "alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "chimera_check": {"$ref": "#/$defs/TextValue", "description": "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences."}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "gold_sequencing_project_identifiers": {"description": "identifiers for corresponding sequencing project in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Gp[0-9]+$", "type": "array"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "insdc_experiment_identifiers": {"items": {"type": "string"}, "pattern": "^insdc.sra:(E|D|S)RX[0-9]{6,}$", "type": "array"}, "instrument_name": {"description": "The name of the instrument that was used for processing the sample.", "type": "string"}, "mod_date": {"description": "The last date on which the database information was modified.", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "ncbi_project_name": {"type": "string"}, "nucl_acid_amp": {"$ref": "#/$defs/TextValue", "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids"}, "nucl_acid_ext": {"$ref": "#/$defs/TextValue", "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample"}, "omics_type": {"$ref": "#/$defs/ControlledTermValue", "description": "The type of omics data"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "pcr_cond": {"$ref": "#/$defs/TextValue", "description": "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'"}, "pcr_primers": {"$ref": "#/$defs/TextValue", "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters"}, "principal_investigator": {"$ref": "#/$defs/PersonValue", "description": "Principal Investigator who led the study and/or generated the dataset."}, "processing_institution": {"$ref": "#/$defs/ProcessingInstitutionEnum", "description": "The organization that processed the sample."}, "samp_vol_we_dna_ext": {"$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)."}, "seq_meth": {"$ref": "#/$defs/TextValue", "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)."}, "seq_quality_check": {"$ref": "#/$defs/TextValue", "description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA"}, "target_gene": {"$ref": "#/$defs/TextValue", "description": "Targeted gene or locus name for marker gene studies"}, "target_subfragment": {"$ref": "#/$defs/TextValue", "description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}}, "required": ["has_input"], "title": "OmicsProcessing", "type": "object"}, "OntologyClass": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "OntologyClass", "type": "object"}, "OrganismCountEnum": {"description": "", "enum": ["ATP", "MPN", "other"], "title": "OrganismCountEnum", "type": "string"}, "OrthologyGroup": {"additionalProperties": false, "description": "A set of genes or gene products in which all members are orthologous", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "OrthologyGroup", "type": "object"}, "OxyStatSampEnum": {"description": "", "enum": ["aerobic", "anaerobic", "other"], "title": "OxyStatSampEnum", "type": "string"}, "Pathway": {"additionalProperties": false, "description": "A pathway is a sequence of steps/reactions carried out by an organism or community of organisms", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Pathway", "type": "object"}, "PeptideQuantification": {"additionalProperties": false, "description": "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information", "title": "PeptideQuantification", "type": "object"}, "Person": {"additionalProperties": false, "description": "represents a person, such as a researcher", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "Should be an ORCID. Specify in CURIE format. E.g ORCID:0000-1111-...", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Person", "type": "object"}, "PersonValue": {"additionalProperties": false, "description": "An attribute value representing a person", "properties": {"email": {"description": "An email address for an entity such as a person. This should be the primarly email address used.", "type": "string"}, "has_raw_value": {"description": "The full name of the Investigator in format FIRST LAST.", "type": "string"}, "name": {"description": "The full name of the Investigator. It should follow the format FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.", "type": "string"}, "orcid": {"description": "The ORCID of a person.", "type": "string"}, "profile_image_url": {"description": "A url that points to an image of a person.", "type": "string"}, "was_generated_by": {"type": "string"}, "websites": {"description": "A list of websites that are associated with the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "PersonValue", "type": "object"}, "PlannedProcess": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "has_inputs": {"items": {"type": "string"}, "type": "array"}, "has_outputs": {"items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "participating_agent": {"$ref": "#/$defs/Agent"}}, "required": ["id"], "title": "PlannedProcess", "type": "object"}, "PlantGrowthMedEnum": {"description": "", "enum": ["other artificial liquid medium", "other artificial solid medium", "peat moss", "perlite", "pumice", "sand", "soil", "vermiculite", "water"], "title": "PlantGrowthMedEnum", "type": "string"}, "PlantSexEnum": {"description": "", "enum": ["Androdioecious", "Androecious", "Androgynous", "Androgynomonoecious", "Andromonoecious", "Bisexual", "Dichogamous", "Diclinous", "Dioecious", "Gynodioecious", "Gynoecious", "Gynomonoecious", "Hermaphroditic", "Imperfect", "Monoclinous", "Monoecious", "Perfect", "Polygamodioecious", "Polygamomonoecious", "Polygamous", "Protandrous", "Protogynous", "Subandroecious", "Subdioecious", "Subgynoecious", "Synoecious", "Trimonoecious", "Trioecious", "Unisexual"], "title": "PlantSexEnum", "type": "string"}, "ProcessingInstitutionEnum": {"description": "", "enum": ["UCSD", "JGI", "EMSL"], "title": "ProcessingInstitutionEnum", "type": "string"}, "ProfilePositionEnum": {"description": "", "enum": ["summit", "shoulder", "backslope", "footslope", "toeslope"], "title": "ProfilePositionEnum", "type": "string"}, "ProteinQuantification": {"additionalProperties": false, "description": "This is used to link a metaproteomics analysis workflow to a specific protein", "title": "ProteinQuantification", "type": "object"}, "QuadPosEnum": {"description": "", "enum": ["North side", "West side", "South side", "East side"], "title": "QuadPosEnum", "type": "string"}, "QuantityValue": {"additionalProperties": false, "description": "A simple quantity, e.g. 2cm", "properties": {"has_maximum_numeric_value": {"description": "The maximum value part, expressed as number, of the quantity value when the value covers a range.", "type": "number"}, "has_minimum_numeric_value": {"description": "The minimum value part, expressed as number, of the quantity value when the value covers a range.", "type": "number"}, "has_numeric_value": {"description": "The number part of the quantity", "type": "number"}, "has_raw_value": {"description": "Unnormalized atomic string representation, should in syntax {number} {unit}", "type": "string"}, "has_unit": {"description": "The unit of the quantity", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "QuantityValue", "type": "object"}, "Reaction": {"additionalProperties": false, "description": "An individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Reaction", "type": "object"}, "ReactionActivity": {"additionalProperties": false, "description": "", "properties": {"material_input": {"type": "string"}, "material_output": {"type": "string"}, "reaction_aided_by": {"$ref": "#/$defs/LabDevice"}, "reaction_temperature": {"type": "string"}, "reaction_time": {"$ref": "#/$defs/QuantityValue"}}, "title": "ReactionActivity", "type": "object"}, "ReactionParticipant": {"additionalProperties": false, "description": "Instances of this link a reaction to a chemical entity participant", "title": "ReactionParticipant", "type": "object"}, "ReadBasedTaxonomyAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "ReadBasedTaxonomyAnalysisActivity", "type": "object"}, "ReadQcAnalysisActivity": {"additionalProperties": false, "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "input_base_count": {"description": "The nucleotide base count number of input reads for QC analysis.", "type": "number"}, "input_read_count": {"description": "The sequence count number of input reads for QC analysis.", "type": "number"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "output_base_count": {"description": "After QC analysis nucleotide base count number.", "type": "number"}, "output_read_count": {"description": "After QC analysis sequence count number.", "type": "number"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "ReadQcAnalysisActivity", "type": "object"}, "RelSampLocEnum": {"description": "", "enum": ["edge of car", "center of car", "under a seat"], "title": "RelSampLocEnum", "type": "string"}, "RelToOxygenEnum": {"description": "", "enum": ["aerobe", "anaerobe", "facultative", "microaerophilic", "microanaerobe", "obligate aerobe", "obligate anaerobe"], "title": "RelToOxygenEnum", "type": "string"}, "RnaContTypeEnum": {"description": "", "enum": ["plate", "tube"], "title": "RnaContTypeEnum", "type": "string"}, "RnaSampleFormatEnum": {"description": "", "enum": ["10 mM Tris-HCl", "DNAStable", "Ethanol", "Low EDTA TE", "MDA reaction buffer", "PBS", "Pellet", "RNAStable", "TE", "Water", "Gentegra-DNA", "Gentegra-RNA"], "title": "RnaSampleFormatEnum", "type": "string"}, "RoomCondtEnum": {"description": "", "enum": ["new", "visible wear", "needs repair", "damaged", "rupture", "visible signs of mold/mildew"], "title": "RoomCondtEnum", "type": "string"}, "RoomConnectedEnum": {"description": "", "enum": ["attic", "bathroom", "closet", "conference room", "elevator", "examining room", "hallway", "kitchen", "mail room", "office", "stairwell"], "title": "RoomConnectedEnum", "type": "string"}, "RoomLocEnum": {"description": "", "enum": ["corner room", "interior room", "exterior wall"], "title": "RoomLocEnum", "type": "string"}, "RoomSampPosEnum": {"description": "", "enum": ["north corner", "south corner", "west corner", "east corner", "northeast corner", "northwest corner", "southeast corner", "southwest corner", "center"], "title": "RoomSampPosEnum", "type": "string"}, "RoomTypeEnum": {"description": "", "enum": ["attic", "bathroom", "closet", "conference room", "elevator", "examining room", "hallway", "kitchen", "mail room", "private office", "open office", "stairwell", ",restroom", "lobby", "vestibule", "mechanical or electrical room", "data center", "laboratory_wet", "laboratory_dry", "gymnasium", "natatorium", "auditorium", "lockers", "cafe", "warehouse"], "title": "RoomTypeEnum", "type": "string"}, "SampCaptStatusEnum": {"description": "", "enum": ["active surveillance in response to an outbreak", "active surveillance not initiated by an outbreak", "farm sample", "market sample", "other"], "title": "SampCaptStatusEnum", "type": "string"}, "SampCollectPointEnum": {"description": "", "enum": ["well", "test well", "drilling rig", "wellhead", "separator", "storage tank", "other"], "title": "SampCollectPointEnum", "type": "string"}, "SampDisStageEnum": {"description": "", "enum": ["dissemination", "growth and reproduction", "infection", "inoculation", "penetration", "other"], "title": "SampDisStageEnum", "type": "string"}, "SampFloorEnum": {"description": "", "enum": ["1st floor", "2nd floor", "basement", "lobby"], "title": "SampFloorEnum", "type": "string"}, "SampMdEnum": {"description": "", "enum": ["DF", "RT", "KB", "MSL", "other"], "title": "SampMdEnum", "type": "string"}, "SampSubtypeEnum": {"description": "", "enum": ["oil phase", "water phase", "biofilm", "not applicable", "other"], "title": "SampSubtypeEnum", "type": "string"}, "SampWeatherEnum": {"description": "", "enum": ["clear sky", "cloudy", "foggy", "hail", "rain", "snow", "sleet", "sunny", "windy"], "title": "SampWeatherEnum", "type": "string"}, "SampleTypeEnum": {"description": "", "enum": ["soil", "water_extract_soil"], "title": "SampleTypeEnum", "type": "string"}, "SamplingMethodEnum": {"description": "", "enum": ["weighing"], "title": "SamplingMethodEnum", "type": "string"}, "SeasonUseEnum": {"description": "", "enum": ["Spring", "Summer", "Fall", "Winter"], "title": "SeasonUseEnum", "type": "string"}, "SedimentTypeEnum": {"description": "", "enum": ["biogenous", "cosmogenous", "hydrogenous", "lithogenous"], "title": "SedimentTypeEnum", "type": "string"}, "ShadingDeviceCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "ShadingDeviceCondEnum", "type": "string"}, "ShadingDeviceTypeEnum": {"description": "", "enum": ["bahama shutters", "exterior roll blind", "gambrel awning", "hood awning", "porchroller awning", "sarasota shutters", "slatted aluminum", "solid aluminum awning", "sun screen", "tree", "trellis", "venetian awning"], "title": "ShadingDeviceTypeEnum", "type": "string"}, "Site": {"additionalProperties": false, "description": "", "properties": {"alternative_identifiers": {"description": "A list of alternative identifiers for the entity.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "a human-readable description of a thing", "type": "string"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}}, "required": ["id"], "title": "Site", "type": "object"}, "SoilHorizonEnum": {"description": "", "enum": ["O horizon", "A horizon", "E horizon", "B horizon", "C horizon", "R layer", "Permafrost"], "title": "SoilHorizonEnum", "type": "string"}, "SolventEnum": {"description": "", "enum": ["deionized_water", "methanol", "chloroform"], "title": "SolventEnum", "type": "string"}, "SpecificEnum": {"description": "", "enum": ["operation", "as built", "construction", "bid", "design", "photos"], "title": "SpecificEnum", "type": "string"}, "SrDepEnvEnum": {"description": "", "enum": ["Lacustine", "Fluvioldeltaic", "Fluviomarine", "Marine", "other"], "title": "SrDepEnvEnum", "type": "string"}, "SrGeolAgeEnum": {"description": "", "enum": ["Archean", "Cambrian", "Carboniferous", "Cenozoic", "Cretaceous", "Devonian", "Jurassic", "Mesozoic", "Neogene", "Ordovician", "Paleogene", "Paleozoic", "Permian", "Precambrian", "Proterozoic", "Silurian", "Triassic", "other"], "title": "SrGeolAgeEnum", "type": "string"}, "SrKerogTypeEnum": {"description": "", "enum": ["Type I", "Type II", "Type III", "Type IV", "other"], "title": "SrKerogTypeEnum", "type": "string"}, "SrLithologyEnum": {"description": "", "enum": ["Clastic", "Carbonate", "Coal", "Biosilicieous", "other"], "title": "SrLithologyEnum", "type": "string"}, "Study": {"additionalProperties": false, "description": "A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.", "properties": {"abstract": {"description": "The abstract of manuscript/grant associated with the entity; i.e., a summary of the resource.", "type": "string"}, "alternative_descriptions": {"description": "A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.", "items": {"type": "string"}, "type": "array"}, "alternative_identifiers": {"description": "Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC", "items": {"type": "string"}, "type": "array"}, "alternative_names": {"description": "A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.", "items": {"type": "string"}, "type": "array"}, "alternative_titles": {"description": "A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.", "items": {"type": "string"}, "type": "array"}, "description": {"description": "A brief summary that details the study you're submitted to NMDC", "type": "string"}, "doi": {"$ref": "#/$defs/AttributeValue", "description": "The dataset citation for this study"}, "ecosystem": {"description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", "type": "string"}, "ecosystem_category": {"description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", "type": "string"}, "ecosystem_subtype": {"description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", "type": "string"}, "ecosystem_type": {"description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", "type": "string"}, "emsl_proposal_doi": {"description": "The DOI for the EMSL awarded study that relates to the NMDC submitted study", "type": "string"}, "emsl_proposal_identifier": {"description": "The proposal number assigned to the EMSL awarded study that relates to that which is represented in NMDC.", "type": "string"}, "ess_dive_datasets": {"description": "List of ESS-DIVE dataset DOIs", "items": {"type": "string"}, "type": "array"}, "funding_sources": {"items": {"type": "string"}, "type": "array"}, "gold_study_identifiers": {"description": "identifiers for corresponding project(s) in GOLD", "items": {"type": "string"}, "pattern": "^GOLD:Gs[0-9]+$", "type": "array"}, "has_credit_associations": {"description": "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study", "items": {"$ref": "#/$defs/CreditAssociation"}, "type": "array"}, "id": {"description": "An NMDC assigned unique identifier for a sample submitted to NMDC.", "type": "string"}, "mgnify_project_identifiers": {"description": "identifiers for corresponding project in MGnify", "pattern": "^mgnify.proj:[A-Z]+[0-9]+$", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "objective": {"description": "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.", "type": "string"}, "principal_investigator": {"$ref": "#/$defs/PersonValue", "description": "Principal Investigator who led the study and/or generated the dataset."}, "publications": {"description": "A list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.", "items": {"type": "string"}, "type": "array"}, "related_identifiers": {"description": "Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC", "type": "string"}, "relevant_protocols": {"items": {"type": "string"}, "type": "array"}, "specific_ecosystem": {"description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", "type": "string"}, "study_image": {"description": "Links a study to one or more images.", "items": {"$ref": "#/$defs/ImageValue"}, "type": "array"}, "title": {"description": "A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "websites": {"description": "A list of websites that are associated with the entity.", "items": {"type": "string"}, "type": "array"}}, "title": "Study", "type": "object"}, "SubstructureTypeEnum": {"description": "", "enum": ["crawlspace", "slab on grade", "basement"], "title": "SubstructureTypeEnum", "type": "string"}, "SurfAirContEnum": {"description": "", "enum": ["dust", "organic matter", "particulate matter", "volatile organic compounds", "biological contaminants", "radon", "nutrients", "biocides"], "title": "SurfAirContEnum", "type": "string"}, "SurfMaterialEnum": {"description": "", "enum": ["adobe", "carpet", "cinder blocks", "concrete", "hay bales", "glass", "metal", "paint", "plastic", "stainless steel", "stone", "stucco", "tile", "vinyl", "wood"], "title": "SurfMaterialEnum", "type": "string"}, "TextValue": {"additionalProperties": false, "description": "A basic string value", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "language": {"description": "Should use ISO 639-1 code e.g. \"en\", \"fr\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "TextValue", "type": "object"}, "TidalStageEnum": {"description": "", "enum": ["low tide", "ebb tide", "flood tide", "high tide"], "title": "TidalStageEnum", "type": "string"}, "TillageEnum": {"description": "", "enum": ["drill", "cutting disc", "ridge till", "strip tillage", "zonal tillage", "chisel", "tined", "mouldboard", "disc plough"], "title": "TillageEnum", "type": "string"}, "TimestampValue": {"additionalProperties": false, "description": "A value that is a timestamp. The range should be ISO-8601", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "TimestampValue", "type": "object"}, "TrainLineEnum": {"description": "", "enum": ["red", "green", "orange"], "title": "TrainLineEnum", "type": "string"}, "TrainStatLocEnum": {"description": "", "enum": ["south station above ground", "south station underground", "south station amtrak", "forest hills", "riverside"], "title": "TrainStatLocEnum", "type": "string"}, "TrainStopLocEnum": {"description": "", "enum": ["end", "mid", "downtown"], "title": "TrainStopLocEnum", "type": "string"}, "UrlValue": {"additionalProperties": false, "description": "A value that is a string that conforms to URL syntax", "properties": {"has_raw_value": {"description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", "type": "string"}, "was_generated_by": {"type": "string"}}, "title": "UrlValue", "type": "object"}, "VisMediaEnum": {"description": "", "enum": ["photos", "videos", "commonly of the building", "site context (adjacent buildings, vegetation, terrain, streets)", "interiors", "equipment", "3D scans"], "title": "VisMediaEnum", "type": "string"}, "WallConstTypeEnum": {"description": "", "enum": ["frame construction", "joisted masonry", "light noncombustible", "masonry noncombustible", "modified fire resistive", "fire resistive"], "title": "WallConstTypeEnum", "type": "string"}, "WallFinishMatEnum": {"description": "", "enum": ["plaster", "gypsum plaster", "veneer plaster", "gypsum board", "tile", "terrazzo", "stone facing", "acoustical treatment", "wood", "metal", "masonry"], "title": "WallFinishMatEnum", "type": "string"}, "WallLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "WallLocEnum", "type": "string"}, "WallSurfTreatmentEnum": {"description": "", "enum": ["painted", "wall paper", "no treatment", "paneling", "stucco", "fabric"], "title": "WallSurfTreatmentEnum", "type": "string"}, "WallTextureEnum": {"description": "", "enum": ["crows feet", "crows-foot stomp", "double skip", "hawk and trowel", "knockdown", "popcorn", "orange peel", "rosebud stomp", "Santa-Fe texture", "skip trowel", "smooth", "stomp knockdown", "swirl"], "title": "WallTextureEnum", "type": "string"}, "WaterFeatTypeEnum": {"description": "", "enum": ["fountain", "pool", "standing feature", "stream", "waterfall"], "title": "WaterFeatTypeEnum", "type": "string"}, "WeekdayEnum": {"description": "", "enum": ["Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday", "Sunday"], "title": "WeekdayEnum", "type": "string"}, "WindowCondEnum": {"description": "", "enum": ["damaged", "needs repair", "new", "rupture", "visible wear"], "title": "WindowCondEnum", "type": "string"}, "WindowCoverEnum": {"description": "", "enum": ["blinds", "curtains", "none"], "title": "WindowCoverEnum", "type": "string"}, "WindowHorizPosEnum": {"description": "", "enum": ["left", "middle", "right"], "title": "WindowHorizPosEnum", "type": "string"}, "WindowLocEnum": {"description": "", "enum": ["north", "south", "east", "west"], "title": "WindowLocEnum", "type": "string"}, "WindowMatEnum": {"description": "", "enum": ["clad", "fiberglass", "metal", "vinyl", "wood"], "title": "WindowMatEnum", "type": "string"}, "WindowTypeEnum": {"description": "", "enum": ["single-hung sash window", "horizontal sash window", "fixed window"], "title": "WindowTypeEnum", "type": "string"}, "WindowVertPosEnum": {"description": "", "enum": ["bottom", "middle", "top", "low", "high"], "title": "WindowVertPosEnum", "type": "string"}, "WorkflowExecutionActivity": {"additionalProperties": false, "description": "Represents an instance of an execution of a particular workflow", "properties": {"ended_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "execution_resource": {"description": "Example: NERSC-Cori", "type": "string"}, "git_url": {"description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", "type": "string"}, "has_input": {"description": "An input to a process.", "items": {"type": "string"}, "type": "array"}, "has_output": {"description": "An output biosample to a processing step", "items": {"type": "string"}, "type": "array"}, "id": {"description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string"}, "name": {"description": "A human readable label for an entity", "type": "string"}, "part_of": {"description": "Links a resource to another resource that either logically or physically includes it.", "items": {"type": "string"}, "type": "array"}, "started_at_time": {"format": "date-time", "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string"}, "type": {"description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", "type": "string"}, "used": {"type": "string"}, "was_associated_with": {"description": "the agent/entity associated with the generation of the file", "type": "string"}, "was_informed_by": {"type": "string"}}, "required": ["execution_resource", "git_url", "has_input", "has_output", "id", "started_at_time", "ended_at_time", "was_informed_by"], "title": "WorkflowExecutionActivity", "type": "object"}}, "$id": "https://microbiomedata/schema", "$schema": "http://json-schema.org/draft-07/schema#", "additionalProperties": false, "metamodel_version": "1.7.0", "properties": {"activity_set": {"description": "This property links a database object to the set of workflow activities.", "items": {"$ref": "#/$defs/WorkflowExecutionActivity"}, "type": "array"}, "biosample_set": {"description": "This property links a database object to the set of samples within it.", "items": {"$ref": "#/$defs/Biosample"}, "type": "array"}, "collecting_biosamples_from_site_set": {"items": {"$ref": "#/$defs/CollectingBiosamplesFromSite"}, "type": "array"}, "data_object_set": {"description": "This property links a database object to the set of data objects within it.", "items": {"$ref": "#/$defs/DataObject"}, "type": "array"}, "dissolving_activity_set": {"items": {"$ref": "#/$defs/DissolvingActivity"}, "type": "array"}, "field_research_site_set": {"items": {"$ref": "#/$defs/FieldResearchSite"}, "type": "array"}, "functional_annotation_set": {"description": "This property links a database object to the set of all functional annotations", "items": {"$ref": "#/$defs/FunctionalAnnotation"}, "type": "array"}, "genome_feature_set": {"description": "This property links a database object to the set of all features", "items": {"$ref": "#/$defs/GenomeFeature"}, "type": "array"}, "mags_activity_set": {"description": "This property links a database object to the set of MAGs analysis activities.", "items": {"$ref": "#/$defs/MagsAnalysisActivity"}, "type": "array"}, "material_sample_set": {"items": {"$ref": "#/$defs/MaterialSample"}, "type": "array"}, "material_sampling_activity_set": {"items": {"$ref": "#/$defs/MaterialSamplingActivity"}, "type": "array"}, "metabolomics_analysis_activity_set": {"description": "This property links a database object to the set of metabolomics analysis activities.", "items": {"$ref": "#/$defs/MetabolomicsAnalysisActivity"}, "type": "array"}, "metagenome_annotation_activity_set": {"description": "This property links a database object to the set of metagenome annotation activities.", "items": {"$ref": "#/$defs/MetagenomeAnnotationActivity"}, "type": "array"}, "metagenome_assembly_set": {"description": "This property links a database object to the set of metagenome assembly activities.", "items": {"$ref": "#/$defs/MetagenomeAssembly"}, "type": "array"}, "metaproteomics_analysis_activity_set": {"description": "This property links a database object to the set of metaproteomics analysis activities.", "items": {"$ref": "#/$defs/MetaproteomicsAnalysisActivity"}, "type": "array"}, "metatranscriptome_activity_set": {"description": "TODO", "items": {"$ref": "#/$defs/MetatranscriptomeActivity"}, "type": "array"}, "nom_analysis_activity_set": {"description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", "items": {"$ref": "#/$defs/NomAnalysisActivity"}, "type": "array"}, "omics_processing_set": {"description": "This property links a database object to the set of omics processings within it.", "items": {"$ref": "#/$defs/OmicsProcessing"}, "type": "array"}, "reaction_activity_set": {"items": {"$ref": "#/$defs/ReactionActivity"}, "type": "array"}, "read_based_taxonomy_analysis_activity_set": {"description": "This property links a database object to the set of read based analysis activities.", "items": {"$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity"}, "type": "array"}, "read_qc_analysis_activity_set": {"description": "This property links a database object to the set of read QC analysis activities.", "items": {"$ref": "#/$defs/ReadQcAnalysisActivity"}, "type": "array"}, "study_set": {"description": "This property links a database object to the set of studies within it.", "items": {"$ref": "#/$defs/Study"}, "type": "array"}}, "title": "NMDC", "type": "object", "version": "7.0.0"} +{ + "$defs": { + "Activity": { + "additionalProperties": false, + "description": "a provence-generating activity", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):act-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "$ref": "#/$defs/Agent" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "Activity", + "type": "object" + }, + "Agent": { + "additionalProperties": false, + "description": "a provence-generating agent", + "properties": { + "acted_on_behalf_of": { + "$ref": "#/$defs/Agent" + }, + "was_informed_by": { + "type": "string" + } + }, + "title": "Agent", + "type": "object" + }, + "AnalysisTypeEnum": { + "description": "", + "enum": [ + "metabolomics", + "metagenomics", + "metaproteomics", + "metatranscriptomics", + "natural organic matter" + ], + "title": "AnalysisTypeEnum", + "type": "string" + }, + "AnalyticalSample": { + "additionalProperties": false, + "description": "", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):ansm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "AnalyticalSample", + "type": "object" + }, + "ArchStrucEnum": { + "description": "", + "enum": [ + "building", + "shed", + "home" + ], + "title": "ArchStrucEnum", + "type": "string" + }, + "AttributeValue": { + "additionalProperties": false, + "description": "The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value", + "properties": { + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "AttributeValue", + "type": "object" + }, + "BiolStatEnum": { + "description": "", + "enum": [ + "wild", + "natural", + "semi-natural", + "inbred line", + "breeder's line", + "hybrid", + "clonal selection", + "mutant" + ], + "title": "BiolStatEnum", + "type": "string" + }, + "Biosample": { + "additionalProperties": false, + "description": "Biological source material which can be characterized by an experiment.", + "properties": { + "add_date": { + "description": "The date on which the information was added to the database.", + "type": "string" + }, + "agrochem_addition": { + "$ref": "#/$defs/QuantityValue", + "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications" + }, + "air_temp_regm": { + "$ref": "#/$defs/QuantityValue", + "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens" + }, + "al_sat": { + "$ref": "#/$defs/QuantityValue", + "description": "Aluminum saturation (esp. For tropical soils)" + }, + "al_sat_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in determining Al saturation" + }, + "alkalinity": { + "$ref": "#/$defs/QuantityValue", + "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate" + }, + "alkalinity_method": { + "$ref": "#/$defs/TextValue", + "description": "Method used for alkalinity measurement" + }, + "alkyl_diethers": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of alkyl diethers" + }, + "alt": { + "$ref": "#/$defs/QuantityValue", + "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air" + }, + "alternative_identifiers": { + "description": "Unique identifier for a biosample submitted to additional resources. Matches the entity that has been submitted to NMDC", + "items": { + "type": "string" + }, + "type": "array" + }, + "aminopept_act": { + "$ref": "#/$defs/QuantityValue", + "description": "Measurement of aminopeptidase activity" + }, + "ammonium": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of ammonium in the sample" + }, + "ammonium_nitrogen": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of ammonium nitrogen in the sample" + }, + "analysis_type": { + "description": "Select all the data types associated or available for this biosample", + "items": { + "$ref": "#/$defs/AnalysisTypeEnum" + }, + "type": "array" + }, + "annual_precpt": { + "$ref": "#/$defs/QuantityValue", + "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps." + }, + "annual_temp": { + "$ref": "#/$defs/QuantityValue", + "description": "Mean annual temperature" + }, + "bacteria_carb_prod": { + "$ref": "#/$defs/QuantityValue", + "description": "Measurement of bacterial carbon production" + }, + "biosample_categories": { + "items": { + "$ref": "#/$defs/BiosampleCategoryEnum" + }, + "type": "array" + }, + "biotic_regm": { + "$ref": "#/$defs/TextValue", + "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi." + }, + "biotic_relationship": { + "$ref": "#/$defs/TextValue", + "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object" + }, + "bishomohopanol": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of bishomohopanol" + }, + "bromide": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of bromide" + }, + "calcium": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of calcium in the sample" + }, + "carb_nitro_ratio": { + "$ref": "#/$defs/QuantityValue", + "description": "Ratio of amount or concentrations of carbon to nitrogen" + }, + "chem_administration": { + "$ref": "#/$defs/ControlledTermValue", + "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi" + }, + "chloride": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of chloride in the sample" + }, + "chlorophyll": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of chlorophyll" + }, + "climate_environment": { + "$ref": "#/$defs/TextValue", + "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates" + }, + "collected_from": { + "description": "The Site from which a Biosample was collected", + "type": "string" + }, + "collection_date": { + "$ref": "#/$defs/TimestampValue", + "description": "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant" + }, + "collection_date_inc": { + "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "type": "string" + }, + "collection_time": { + "description": "The time of sampling, either as an instance (single point) or interval.", + "type": "string" + }, + "collection_time_inc": { + "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", + "type": "string" + }, + "community": { + "type": "string" + }, + "crop_rotation": { + "$ref": "#/$defs/TextValue", + "description": "Whether or not crop is rotated, and if yes, rotation schedule" + }, + "cur_land_use": { + "$ref": "#/$defs/TextValue", + "description": "Present state of sample site" + }, + "cur_vegetation": { + "$ref": "#/$defs/TextValue", + "description": "Vegetation classification from one or more standard classification systems, or agricultural crop" + }, + "cur_vegetation_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in vegetation classification" + }, + "density": { + "$ref": "#/$defs/QuantityValue", + "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)" + }, + "depth": { + "$ref": "#/$defs/QuantityValue", + "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples." + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "diss_carb_dioxide": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample" + }, + "diss_hydrogen": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of dissolved hydrogen" + }, + "diss_inorg_carb": { + "$ref": "#/$defs/QuantityValue", + "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter" + }, + "diss_inorg_phosp": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of dissolved inorganic phosphorus in the sample" + }, + "diss_org_carb": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid" + }, + "diss_org_nitro": { + "$ref": "#/$defs/QuantityValue", + "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2" + }, + "diss_oxygen": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of dissolved oxygen" + }, + "dna_absorb1": { + "description": "260/280 measurement of DNA sample purity", + "type": "string" + }, + "dna_absorb2": { + "description": "260/230 measurement of DNA sample purity", + "type": "string" + }, + "dna_collect_site": { + "description": "Provide information on the site your DNA sample was collected from", + "type": "string" + }, + "dna_concentration": { + "maximum": 2000, + "minimum": 0, + "type": "string" + }, + "dna_cont_type": { + "$ref": "#/$defs/DnaContTypeEnum", + "description": "Tube or plate (96-well)" + }, + "dna_cont_well": { + "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$", + "type": "string" + }, + "dna_container_id": { + "type": "string" + }, + "dna_dnase": { + "$ref": "#/$defs/DnaDnaseEnum" + }, + "dna_isolate_meth": { + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "type": "string" + }, + "dna_organisms": { + "description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", + "type": "string" + }, + "dna_project_contact": { + "type": "string" + }, + "dna_samp_id": { + "type": "string" + }, + "dna_sample_format": { + "$ref": "#/$defs/DnaSampleFormatEnum", + "description": "Solution in which the DNA sample has been suspended" + }, + "dna_sample_name": { + "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "type": "string" + }, + "dna_seq_project": { + "type": "string" + }, + "dna_seq_project_name": { + "type": "string" + }, + "dna_seq_project_pi": { + "type": "string" + }, + "dna_volume": { + "maximum": 1000, + "minimum": 0, + "type": "string" + }, + "dnase_rna": { + "$ref": "#/$defs/DnaseRnaEnum" + }, + "drainage_class": { + "$ref": "#/$defs/TextValue", + "description": "Drainage classification from a standard system such as the USDA system" + }, + "ecosystem": { + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "type": "string" + }, + "ecosystem_category": { + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "type": "string" + }, + "ecosystem_subtype": { + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "type": "string" + }, + "ecosystem_type": { + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "type": "string" + }, + "elev": { + "$ref": "#/$defs/QuantityValue", + "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit." + }, + "emsl_biosample_identifiers": { + "description": "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.", + "items": { + "type": "string" + }, + "type": "array" + }, + "env_broad_scale": { + "$ref": "#/$defs/ControlledIdentifiedTermValue", + "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS" + }, + "env_local_scale": { + "$ref": "#/$defs/ControlledIdentifiedTermValue", + "description": "Report the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS." + }, + "env_medium": { + "$ref": "#/$defs/ControlledIdentifiedTermValue", + "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top)." + }, + "env_package": { + "$ref": "#/$defs/TextValue", + "description": "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported", + "pattern": "[air|built environment|host\\-associated|human\\-associated|human\\-skin|human\\-oral|human\\-gut|human\\-vaginal|hydrocarbon resources\\-cores|hydrocarbon resources\\-fluids\\/swabs|microbial mat\\/biofilm|misc environment|plant\\-associated|sediment|soil|wastewater\\/sludge|water]" + }, + "experimental_factor": { + "$ref": "#/$defs/ControlledTermValue", + "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI" + }, + "experimental_factor_other": { + "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", + "type": "string" + }, + "extreme_event": { + "description": "Unusual physical events that may have affected microbial populations", + "type": "string" + }, + "fao_class": { + "$ref": "#/$defs/TextValue", + "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups" + }, + "filter_method": { + "description": "Type of filter used or how the sample was filtered", + "type": "string" + }, + "fire": { + "$ref": "#/$defs/TimestampValue", + "description": "Historical and/or physical evidence of fire" + }, + "flooding": { + "$ref": "#/$defs/TimestampValue", + "description": "Historical and/or physical evidence of flooding" + }, + "gaseous_environment": { + "$ref": "#/$defs/QuantityValue", + "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens" + }, + "geo_loc_name": { + "$ref": "#/$defs/TextValue", + "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)" + }, + "glucosidase_act": { + "$ref": "#/$defs/QuantityValue", + "description": "Measurement of glucosidase activity" + }, + "gold_biosample_identifiers": { + "description": "Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample", + "items": { + "type": "string" + }, + "pattern": "^GOLD:Gb[0-9]+$", + "type": "array" + }, + "growth_facil": { + "$ref": "#/$defs/ControlledTermValue", + "description": "Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research" + }, + "habitat": { + "type": "string" + }, + "heavy_metals": { + "$ref": "#/$defs/QuantityValue", + "description": "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field." + }, + "heavy_metals_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in determining heavy metals" + }, + "host_name": { + "type": "string" + }, + "humidity_regm": { + "$ref": "#/$defs/QuantityValue", + "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens" + }, + "id": { + "description": "An NMDC assigned unique identifier for a biosample submitted to NMDC.", + "pattern": "^(nmdc):bsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "igsn_biosample_identifiers": { + "description": "A list of identifiers for the biosample from the IGSN database.", + "items": { + "type": "string" + }, + "type": "array" + }, + "img_identifiers": { + "description": "A list of identifiers that relate the biosample to records in the IMG database.", + "items": { + "type": "string" + }, + "type": "array" + }, + "insdc_biosample_identifiers": { + "description": "identifiers for corresponding sample in INSDC", + "items": { + "type": "string" + }, + "pattern": "^biosample:SAM[NED]([A-Z])?[0-9]+$", + "type": "array" + }, + "isotope_exposure": { + "description": "List isotope exposure or addition applied to your sample.", + "type": "string" + }, + "lat_lon": { + "$ref": "#/$defs/GeolocationValue", + "description": "This is currently a required field but it's not clear if this should be required for human hosts" + }, + "lbc_thirty": { + "$ref": "#/$defs/QuantityValue", + "description": "lime buffer capacity, determined after 30 minute incubation" + }, + "lbceq": { + "$ref": "#/$defs/QuantityValue", + "description": "lime buffer capacity, determined at equilibrium after 5 day incubation" + }, + "light_regm": { + "$ref": "#/$defs/QuantityValue", + "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality." + }, + "link_addit_analys": { + "$ref": "#/$defs/TextValue", + "description": "Link to additional analysis results performed on the sample" + }, + "link_class_info": { + "$ref": "#/$defs/TextValue", + "description": "Link to digitized soil maps or other soil classification information" + }, + "link_climate_info": { + "$ref": "#/$defs/TextValue", + "description": "Link to climate resource" + }, + "local_class": { + "$ref": "#/$defs/TextValue", + "description": "Soil classification based on local soil classification system" + }, + "local_class_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in determining the local soil classification" + }, + "location": { + "type": "string" + }, + "magnesium": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of magnesium in the sample" + }, + "manganese": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of manganese in the sample" + }, + "mean_frict_vel": { + "$ref": "#/$defs/QuantityValue", + "description": "Measurement of mean friction velocity" + }, + "mean_peak_frict_vel": { + "$ref": "#/$defs/QuantityValue", + "description": "Measurement of mean peak friction velocity" + }, + "micro_biomass_c_meth": { + "description": "Reference or method used in determining microbial biomass", + "type": "string" + }, + "micro_biomass_n_meth": { + "description": "Reference or method used in determining microbial biomass nitrogen", + "type": "string" + }, + "microbial_biomass_c": { + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "type": "string" + }, + "microbial_biomass_n": { + "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", + "type": "string" + }, + "misc_param": { + "$ref": "#/$defs/QuantityValue", + "description": "Any other measurement performed or parameter collected, that is not listed here" + }, + "mod_date": { + "description": "The last date on which the database information was modified.", + "type": "string" + }, + "n_alkanes": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of n-alkanes; can include multiple n-alkanes" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "ncbi_taxonomy_name": { + "type": "string" + }, + "nitrate": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of nitrate in the sample" + }, + "nitrate_nitrogen": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of nitrate nitrogen in the sample" + }, + "nitrite": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of nitrite in the sample" + }, + "nitrite_nitrogen": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of nitrite nitrogen in the sample" + }, + "non_microb_biomass": { + "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", + "type": "string" + }, + "non_microb_biomass_method": { + "description": "Reference or method used in determining biomass", + "type": "string" + }, + "org_matter": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of organic matter" + }, + "org_nitro": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of organic nitrogen" + }, + "org_nitro_method": { + "description": "Method used for obtaining organic nitrogen", + "type": "string" + }, + "organism_count": { + "$ref": "#/$defs/QuantityValue", + "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)" + }, + "other_treatment": { + "description": "Other treatments applied to your samples that are not applicable to the provided fields", + "type": "string" + }, + "oxy_stat_samp": { + "$ref": "#/$defs/TextValue", + "description": "Oxygenation status of sample" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "part_org_carb": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of particulate organic carbon" + }, + "perturbation": { + "$ref": "#/$defs/TextValue", + "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types" + }, + "petroleum_hydrocarb": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of petroleum hydrocarbon" + }, + "ph": { + "$ref": "#/$defs/QuantityValue", + "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid" + }, + "ph_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in determining ph" + }, + "phaeopigments": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of phaeopigments; can include multiple phaeopigments" + }, + "phosphate": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of phosphate" + }, + "phosplipid_fatt_acid": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of phospholipid fatty acids; can include multiple values" + }, + "pool_dna_extracts": { + "$ref": "#/$defs/TextValue", + "description": "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given" + }, + "potassium": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of potassium in the sample" + }, + "pressure": { + "$ref": "#/$defs/QuantityValue", + "description": "Pressure to which the sample is subject to, in atmospheres" + }, + "profile_position": { + "$ref": "#/$defs/TextValue", + "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas" + }, + "project_id": { + "description": "Proposal IDs or names associated with dataset", + "type": "string" + }, + "proport_woa_temperature": { + "type": "string" + }, + "proposal_dna": { + "type": "string" + }, + "proposal_rna": { + "type": "string" + }, + "redox_potential": { + "$ref": "#/$defs/QuantityValue", + "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential" + }, + "rel_to_oxygen": { + "$ref": "#/$defs/TextValue", + "description": "Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments" + }, + "replicate_number": { + "description": "If sending biological replicates, indicate the rep number here.", + "type": "string" + }, + "rna_absorb1": { + "description": "260/280 measurement of RNA sample purity", + "type": "string" + }, + "rna_absorb2": { + "description": "260/230 measurement of RNA sample purity", + "type": "string" + }, + "rna_collect_site": { + "description": "Provide information on the site your RNA sample was collected from", + "type": "string" + }, + "rna_concentration": { + "maximum": 1000, + "minimum": 0, + "type": "string" + }, + "rna_cont_type": { + "$ref": "#/$defs/RnaContTypeEnum", + "description": "Tube or plate (96-well)" + }, + "rna_cont_well": { + "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$", + "type": "string" + }, + "rna_container_id": { + "type": "string" + }, + "rna_isolate_meth": { + "description": "Describe the method/protocol/kit used to extract DNA/RNA.", + "type": "string" + }, + "rna_organisms": { + "description": "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.", + "type": "string" + }, + "rna_project_contact": { + "type": "string" + }, + "rna_samp_id": { + "type": "string" + }, + "rna_sample_format": { + "$ref": "#/$defs/RnaSampleFormatEnum", + "description": "Solution in which the RNA sample has been suspended" + }, + "rna_sample_name": { + "description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "maximum": 2000, + "minimum": 0, + "type": "string" + }, + "rna_seq_project": { + "type": "string" + }, + "rna_seq_project_name": { + "type": "string" + }, + "rna_seq_project_pi": { + "type": "string" + }, + "rna_volume": { + "type": "string" + }, + "salinity": { + "$ref": "#/$defs/QuantityValue", + "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater." + }, + "salinity_category": { + "description": "Categorcial description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline", + "type": "string" + }, + "salinity_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in determining salinity" + }, + "samp_collec_method": { + "description": "The method employed for collecting the sample.", + "type": "string" + }, + "samp_mat_process": { + "$ref": "#/$defs/ControlledTermValue", + "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed." + }, + "samp_name": { + "description": "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.", + "type": "string" + }, + "samp_size": { + "$ref": "#/$defs/QuantityValue", + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected." + }, + "samp_store_dur": { + "$ref": "#/$defs/TextValue", + "description": "Duration for which the sample was stored" + }, + "samp_store_loc": { + "$ref": "#/$defs/TextValue", + "description": "Location at which sample was stored, usually name of a specific freezer/room" + }, + "samp_store_temp": { + "$ref": "#/$defs/QuantityValue", + "description": "Temperature at which sample was stored, e.g. -80 degree Celsius" + }, + "samp_vol_we_dna_ext": { + "$ref": "#/$defs/QuantityValue", + "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)." + }, + "sample_collection_site": { + "type": "string" + }, + "sample_link": { + "description": "JsonObj()", + "items": { + "type": "string" + }, + "type": "array" + }, + "sample_shipped": { + "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL", + "type": "string" + }, + "sample_type": { + "$ref": "#/$defs/SampleTypeEnum", + "description": "Type of sample being submitted" + }, + "season_precpt": { + "$ref": "#/$defs/QuantityValue", + "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps." + }, + "season_temp": { + "$ref": "#/$defs/QuantityValue", + "description": "Mean seasonal temperature" + }, + "sieving": { + "$ref": "#/$defs/QuantityValue", + "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved" + }, + "size_frac_low": { + "$ref": "#/$defs/QuantityValue", + "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample" + }, + "size_frac_up": { + "$ref": "#/$defs/QuantityValue", + "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample" + }, + "slope_aspect": { + "$ref": "#/$defs/QuantityValue", + "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration." + }, + "slope_gradient": { + "$ref": "#/$defs/QuantityValue", + "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer" + }, + "sodium": { + "$ref": "#/$defs/QuantityValue", + "description": "Sodium concentration in the sample" + }, + "soil_type": { + "$ref": "#/$defs/TextValue", + "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes." + }, + "soil_type_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in determining soil series name or other lower-level classification" + }, + "soluble_iron_micromol": { + "type": "string" + }, + "source_mat_id": { + "$ref": "#/$defs/TextValue", + "description": "A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2)." + }, + "specific_ecosystem": { + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "type": "string" + }, + "start_date_inc": { + "description": "Date the incubation was started. Only relevant for incubation samples.", + "type": "string" + }, + "start_time_inc": { + "description": "Time the incubation was started. Only relevant for incubation samples.", + "type": "string" + }, + "store_cond": { + "$ref": "#/$defs/TextValue", + "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)." + }, + "subsurface_depth": { + "$ref": "#/$defs/QuantityValue" + }, + "sulfate": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of sulfate in the sample" + }, + "sulfide": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of sulfide in the sample" + }, + "technical_reps": { + "description": "If sending multiple technical replicates of the same sample, indicate how many replicates are being sent", + "type": "string" + }, + "temp": { + "$ref": "#/$defs/QuantityValue", + "description": "Temperature of the sample at the time of sampling." + }, + "tidal_stage": { + "$ref": "#/$defs/TextValue", + "description": "Stage of tide" + }, + "tillage": { + "$ref": "#/$defs/TextValue", + "description": "Note method(s) used for tilling" + }, + "tot_carb": { + "$ref": "#/$defs/QuantityValue", + "description": "Total carbon content" + }, + "tot_depth_water_col": { + "$ref": "#/$defs/QuantityValue", + "description": "Measurement of total depth of water column" + }, + "tot_diss_nitro": { + "$ref": "#/$defs/QuantityValue", + "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen" + }, + "tot_nitro_cont_meth": { + "description": "Reference or method used in determining the total nitrogen", + "type": "string" + }, + "tot_nitro_content": { + "$ref": "#/$defs/QuantityValue", + "description": "Total nitrogen content of the sample" + }, + "tot_org_c_meth": { + "$ref": "#/$defs/TextValue", + "description": "Reference or method used in determining total organic carbon" + }, + "tot_org_carb": { + "$ref": "#/$defs/QuantityValue", + "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content" + }, + "tot_phosp": { + "$ref": "#/$defs/QuantityValue", + "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "water_cont_soil_meth": { + "description": "Reference or method used in determining the water content of soil", + "type": "string" + }, + "water_content": { + "$ref": "#/$defs/QuantityValue", + "description": "Water content measurement" + }, + "watering_regm": { + "$ref": "#/$defs/QuantityValue", + "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens" + }, + "zinc": { + "$ref": "#/$defs/QuantityValue", + "description": "Concentration of zinc in the sample" + } + }, + "required": [ + "part_of", + "id", + "env_broad_scale", + "env_local_scale", + "env_medium" + ], + "title": "Biosample", + "type": "object" + }, + "BiosampleCategoryEnum": { + "description": "Funding-based, sample location-based, or experimental method-based defined categories", + "enum": [ + "LTER", + "SIP", + "SFA", + "FICUS", + "NEON" + ], + "title": "BiosampleCategoryEnum", + "type": "string" + }, + "BiosampleProcessing": { + "additionalProperties": false, + "description": "A process that takes one or more biosamples as inputs and generates one or as outputs. Examples of outputs include samples cultivated from another sample or data objects created by instruments runs.", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):bsmprc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "BiosampleProcessing", + "type": "object" + }, + "BioticRelationshipEnum": { + "description": "", + "enum": [ + "free living", + "parasite", + "commensal", + "symbiont" + ], + "title": "BioticRelationshipEnum", + "type": "string" + }, + "BooleanValue": { + "additionalProperties": false, + "description": "A value that is a boolean", + "properties": { + "has_boolean_value": { + "description": "Links a quantity value to a boolean", + "type": "boolean" + }, + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "BooleanValue", + "type": "object" + }, + "BuildDocsEnum": { + "description": "", + "enum": [ + "building information model", + "commissioning report", + "complaint logs", + "contract administration", + "cost estimate", + "janitorial schedules or logs", + "maintenance plans", + "schedule", + "sections", + "shop drawings", + "submittals", + "ventilation system", + "windows" + ], + "title": "BuildDocsEnum", + "type": "string" + }, + "BuildOccupTypeEnum": { + "description": "", + "enum": [ + "office", + "market", + "restaurant", + "residence", + "school", + "residential", + "commercial", + "low rise", + "high rise", + "wood framed", + "health care", + "airport", + "sports complex" + ], + "title": "BuildOccupTypeEnum", + "type": "string" + }, + "BuildingSettingEnum": { + "description": "", + "enum": [ + "urban", + "suburban", + "exurban", + "rural" + ], + "title": "BuildingSettingEnum", + "type": "string" + }, + "CeilCondEnum": { + "description": "", + "enum": [ + "new", + "visible wear", + "needs repair", + "damaged", + "rupture" + ], + "title": "CeilCondEnum", + "type": "string" + }, + "CeilFinishMatEnum": { + "description": "", + "enum": [ + "drywall", + "mineral fibre", + "tiles", + "PVC", + "plasterboard", + "metal", + "fiberglass", + "stucco", + "mineral wool/calcium silicate", + "wood" + ], + "title": "CeilFinishMatEnum", + "type": "string" + }, + "CeilTextureEnum": { + "description": "", + "enum": [ + "crows feet", + "crows-foot stomp", + "double skip", + "hawk and trowel", + "knockdown", + "popcorn", + "orange peel", + "rosebud stomp", + "Santa-Fe texture", + "skip trowel", + "smooth", + "stomp knockdown", + "swirl" + ], + "title": "CeilTextureEnum", + "type": "string" + }, + "CeilTypeEnum": { + "description": "", + "enum": [ + "cathedral", + "dropped", + "concave", + "barrel-shaped", + "coffered", + "cove", + "stretched" + ], + "title": "CeilTypeEnum", + "type": "string" + }, + "ChemicalEntity": { + "additionalProperties": false, + "description": "An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "ChemicalEntity", + "type": "object" + }, + "CollectingBiosamplesFromSite": { + "additionalProperties": false, + "description": "", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "has_inputs": { + "items": { + "type": "string" + }, + "type": "array" + }, + "has_outputs": { + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):clsite-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "participating_agent": { + "$ref": "#/$defs/Agent" + } + }, + "required": [ + "has_inputs", + "has_outputs", + "id" + ], + "title": "CollectingBiosamplesFromSite", + "type": "object" + }, + "ContainerTypeEnum": { + "description": "", + "enum": [ + "screw_top_conical" + ], + "title": "ContainerTypeEnum", + "type": "string" + }, + "ControlledIdentifiedTermValue": { + "additionalProperties": false, + "description": "A controlled term or class from an ontology, requiring the presence of term with an id", + "properties": { + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "term": { + "$ref": "#/$defs/OntologyClass", + "description": "pointer to an ontology class" + }, + "was_generated_by": { + "type": "string" + } + }, + "required": [ + "term" + ], + "title": "ControlledIdentifiedTermValue", + "type": "object" + }, + "ControlledTermValue": { + "additionalProperties": false, + "description": "A controlled term or class from an ontology", + "properties": { + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "term": { + "$ref": "#/$defs/OntologyClass", + "description": "pointer to an ontology class" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "ControlledTermValue", + "type": "object" + }, + "CreditAssociation": { + "additionalProperties": false, + "description": "This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0", + "properties": { + "applied_role": { + "$ref": "#/$defs/CreditEnum" + }, + "applied_roles": { + "items": { + "$ref": "#/$defs/CreditEnum" + }, + "type": "array" + }, + "applies_to_person": { + "$ref": "#/$defs/PersonValue" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + } + }, + "required": [ + "applies_to_person", + "applied_roles" + ], + "title": "CreditAssociation", + "type": "object" + }, + "CreditEnum": { + "description": "", + "enum": [ + "Conceptualization", + "Data curation", + "Formal Analysis", + "Funding acquisition", + "Investigation", + "Methodology", + "Project administration", + "Resources", + "Software", + "Supervision", + "Validation", + "Visualization", + "Writing original draft", + "Writing review and editing", + "Principal Investigator", + "Submitter" + ], + "title": "CreditEnum", + "type": "string" + }, + "CurLandUseEnum": { + "description": "", + "enum": [ + "cities", + "farmstead", + "industrial areas", + "roads/railroads", + "rock", + "sand", + "gravel", + "mudflats", + "salt flats", + "badlands", + "permanent snow or ice", + "saline seeps", + "mines/quarries", + "oil waste areas", + "small grains", + "row crops", + "vegetable crops", + "horticultural plants (e.g. tulips)", + "marshlands (grass,sedges,rushes)", + "tundra (mosses,lichens)", + "rangeland", + "pastureland (grasslands used for livestock grazing)", + "hayland", + "meadows (grasses,alfalfa,fescue,bromegrass,timothy)", + "shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)", + "successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)", + "shrub crops (blueberries,nursery ornamentals,filberts)", + "vine crops (grapes)", + "conifers (e.g. pine,spruce,fir,cypress)", + "hardwoods (e.g. oak,hickory,elm,aspen)", + "intermixed hardwood and conifers", + "tropical (e.g. mangrove,palms)", + "rainforest (evergreen forest receiving greater than 406 cm annual rainfall)", + "swamp (permanent or semi-permanent water body dominated by woody plants)", + "crop trees (nuts,fruit,christmas trees,nursery trees)" + ], + "title": "CurLandUseEnum", + "type": "string" + }, + "DataObject": { + "additionalProperties": false, + "description": "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "compression_type": { + "description": "If provided, specifies the compression type", + "type": "string" + }, + "data_object_type": { + "$ref": "#/$defs/FileTypeEnum", + "description": "The type of file represented by the data object." + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "file_size_bytes": { + "description": "Size of the file in bytes", + "type": "integer" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):dobj-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "md5_checksum": { + "description": "MD5 checksum of file (pre-compressed)", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "url": { + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "required": [ + "name", + "description" + ], + "title": "DataObject", + "type": "object" + }, + "Database": { + "additionalProperties": false, + "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest", + "properties": { + "activity_set": { + "description": "This property links a database object to the set of workflow activities.", + "items": { + "$ref": "#/$defs/WorkflowExecutionActivity" + }, + "type": "array" + }, + "biosample_set": { + "description": "This property links a database object to the set of samples within it.", + "items": { + "$ref": "#/$defs/Biosample" + }, + "type": "array" + }, + "collecting_biosamples_from_site_set": { + "items": { + "$ref": "#/$defs/CollectingBiosamplesFromSite" + }, + "type": "array" + }, + "data_object_set": { + "description": "This property links a database object to the set of data objects within it.", + "items": { + "$ref": "#/$defs/DataObject" + }, + "type": "array" + }, + "dissolving_activity_set": { + "items": { + "$ref": "#/$defs/DissolvingActivity" + }, + "type": "array" + }, + "field_research_site_set": { + "items": { + "$ref": "#/$defs/FieldResearchSite" + }, + "type": "array" + }, + "functional_annotation_set": { + "description": "This property links a database object to the set of all functional annotations", + "items": { + "$ref": "#/$defs/FunctionalAnnotation" + }, + "type": "array" + }, + "genome_feature_set": { + "description": "This property links a database object to the set of all features", + "items": { + "$ref": "#/$defs/GenomeFeature" + }, + "type": "array" + }, + "mags_activity_set": { + "description": "This property links a database object to the set of MAGs analysis activities.", + "items": { + "$ref": "#/$defs/MagsAnalysisActivity" + }, + "type": "array" + }, + "material_sample_set": { + "items": { + "$ref": "#/$defs/MaterialSample" + }, + "type": "array" + }, + "material_sampling_activity_set": { + "items": { + "$ref": "#/$defs/MaterialSamplingActivity" + }, + "type": "array" + }, + "metabolomics_analysis_activity_set": { + "description": "This property links a database object to the set of metabolomics analysis activities.", + "items": { + "$ref": "#/$defs/MetabolomicsAnalysisActivity" + }, + "type": "array" + }, + "metagenome_annotation_activity_set": { + "description": "This property links a database object to the set of metagenome annotation activities.", + "items": { + "$ref": "#/$defs/MetagenomeAnnotationActivity" + }, + "type": "array" + }, + "metagenome_assembly_set": { + "description": "This property links a database object to the set of metagenome assembly activities.", + "items": { + "$ref": "#/$defs/MetagenomeAssembly" + }, + "type": "array" + }, + "metaproteomics_analysis_activity_set": { + "description": "This property links a database object to the set of metaproteomics analysis activities.", + "items": { + "$ref": "#/$defs/MetaproteomicsAnalysisActivity" + }, + "type": "array" + }, + "metatranscriptome_activity_set": { + "description": "TODO", + "items": { + "$ref": "#/$defs/MetatranscriptomeActivity" + }, + "type": "array" + }, + "nom_analysis_activity_set": { + "description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", + "items": { + "$ref": "#/$defs/NomAnalysisActivity" + }, + "type": "array" + }, + "omics_processing_set": { + "description": "This property links a database object to the set of omics processings within it.", + "items": { + "$ref": "#/$defs/OmicsProcessing" + }, + "type": "array" + }, + "reaction_activity_set": { + "items": { + "$ref": "#/$defs/ReactionActivity" + }, + "type": "array" + }, + "read_based_taxonomy_analysis_activity_set": { + "description": "This property links a database object to the set of read based analysis activities.", + "items": { + "$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity" + }, + "type": "array" + }, + "read_qc_analysis_activity_set": { + "description": "This property links a database object to the set of read QC analysis activities.", + "items": { + "$ref": "#/$defs/ReadQcAnalysisActivity" + }, + "type": "array" + }, + "study_set": { + "description": "This property links a database object to the set of studies within it.", + "items": { + "$ref": "#/$defs/Study" + }, + "type": "array" + } + }, + "title": "Database", + "type": "object" + }, + "DeposEnvEnum": { + "description": "", + "enum": [ + "Continental - Alluvial", + "Continental - Aeolian", + "Continental - Fluvial", + "Continental - Lacustrine", + "Transitional - Deltaic", + "Transitional - Tidal", + "Transitional - Lagoonal", + "Transitional - Beach", + "Transitional - Lake", + "Marine - Shallow", + "Marine - Deep", + "Marine - Reef", + "Other - Evaporite", + "Other - Glacial", + "Other - Volcanic", + "other" + ], + "title": "DeposEnvEnum", + "type": "string" + }, + "DeviceTypeEnum": { + "description": "", + "enum": [ + "orbital_shaker", + "thermomixer" + ], + "title": "DeviceTypeEnum", + "type": "string" + }, + "DissolvingActivity": { + "additionalProperties": false, + "description": "", + "properties": { + "dissolution_aided_by": { + "$ref": "#/$defs/LabDevice" + }, + "dissolution_reagent": { + "$ref": "#/$defs/SolventEnum" + }, + "dissolution_volume": { + "$ref": "#/$defs/QuantityValue" + }, + "dissolved_in": { + "$ref": "#/$defs/MaterialContainer" + }, + "material_input": { + "type": "string" + }, + "material_output": { + "type": "string" + } + }, + "title": "DissolvingActivity", + "type": "object" + }, + "DnaContTypeEnum": { + "description": "", + "enum": [ + "plate", + "tube" + ], + "title": "DnaContTypeEnum", + "type": "string" + }, + "DnaDnaseEnum": { + "description": "", + "enum": [ + "no", + "yes" + ], + "title": "DnaDnaseEnum", + "type": "string" + }, + "DnaSampleFormatEnum": { + "description": "", + "enum": [ + "10 mM Tris-HCl", + "DNAStable", + "Ethanol", + "Low EDTA TE", + "MDA reaction buffer", + "PBS", + "Pellet", + "RNAStable", + "TE", + "Water", + "Gentegra-DNA", + "Gentegra-RNA" + ], + "title": "DnaSampleFormatEnum", + "type": "string" + }, + "DnaseRnaEnum": { + "description": "", + "enum": [ + "no", + "yes" + ], + "title": "DnaseRnaEnum", + "type": "string" + }, + "DoorCompTypeEnum": { + "description": "", + "enum": [ + "metal covered", + "revolving", + "sliding", + "telescopic" + ], + "title": "DoorCompTypeEnum", + "type": "string" + }, + "DoorCondEnum": { + "description": "", + "enum": [ + "damaged", + "needs repair", + "new", + "rupture", + "visible wear" + ], + "title": "DoorCondEnum", + "type": "string" + }, + "DoorDirectEnum": { + "description": "", + "enum": [ + "inward", + "outward", + "sideways" + ], + "title": "DoorDirectEnum", + "type": "string" + }, + "DoorLocEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west" + ], + "title": "DoorLocEnum", + "type": "string" + }, + "DoorMatEnum": { + "description": "", + "enum": [ + "aluminum", + "cellular PVC", + "engineered plastic", + "fiberboard", + "fiberglass", + "metal", + "thermoplastic alloy", + "vinyl", + "wood", + "wood/plastic composite" + ], + "title": "DoorMatEnum", + "type": "string" + }, + "DoorMoveEnum": { + "description": "", + "enum": [ + "collapsible", + "folding", + "revolving", + "rolling shutter", + "sliding", + "swinging" + ], + "title": "DoorMoveEnum", + "type": "string" + }, + "DoorTypeEnum": { + "description": "", + "enum": [ + "composite", + "metal", + "wooden" + ], + "title": "DoorTypeEnum", + "type": "string" + }, + "DoorTypeMetalEnum": { + "description": "", + "enum": [ + "collapsible", + "corrugated steel", + "hollow", + "rolling shutters", + "steel plate" + ], + "title": "DoorTypeMetalEnum", + "type": "string" + }, + "DoorTypeWoodEnum": { + "description": "", + "enum": [ + "bettened and ledged", + "battened", + "ledged and braced", + "ledged and framed", + "ledged, braced and frame", + "framed and paneled", + "glashed or sash", + "flush", + "louvered", + "wire gauged" + ], + "title": "DoorTypeWoodEnum", + "type": "string" + }, + "DrainageClassEnum": { + "description": "", + "enum": [ + "very poorly", + "poorly", + "somewhat poorly", + "moderately well", + "well", + "excessively drained" + ], + "title": "DrainageClassEnum", + "type": "string" + }, + "DrawingsEnum": { + "description": "", + "enum": [ + "operation", + "as built", + "construction", + "bid", + "design", + "building navigation map", + "diagram", + "sketch" + ], + "title": "DrawingsEnum", + "type": "string" + }, + "EnvironmentalMaterialTerm": { + "additionalProperties": false, + "description": "", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "EnvironmentalMaterialTerm", + "type": "object" + }, + "ExtWallOrientEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west", + "northeast", + "southeast", + "southwest", + "northwest" + ], + "title": "ExtWallOrientEnum", + "type": "string" + }, + "ExtWindowOrientEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west", + "northeast", + "southeast", + "southwest", + "northwest" + ], + "title": "ExtWindowOrientEnum", + "type": "string" + }, + "FaoClassEnum": { + "description": "", + "enum": [ + "Acrisols", + "Andosols", + "Arenosols", + "Cambisols", + "Chernozems", + "Ferralsols", + "Fluvisols", + "Gleysols", + "Greyzems", + "Gypsisols", + "Histosols", + "Kastanozems", + "Lithosols", + "Luvisols", + "Nitosols", + "Phaeozems", + "Planosols", + "Podzols", + "Podzoluvisols", + "Rankers", + "Regosols", + "Rendzinas", + "Solonchaks", + "Solonetz", + "Vertisols", + "Yermosols" + ], + "title": "FaoClassEnum", + "type": "string" + }, + "FieldResearchSite": { + "additionalProperties": false, + "description": "A site, outside of a laboratory, from which biosamples may be collected.", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):frsite-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "FieldResearchSite", + "type": "object" + }, + "FileTypeEnum": { + "description": "", + "enum": [ + "Metagenome Raw Reads", + "FT ICR-MS Analysis Results", + "GC-MS Metabolomics Results", + "Metaproteomics Workflow Statistics", + "Protein Report", + "Peptide Report", + "Unfiltered Metaproteomics Results", + "Read Count and RPKM", + "QC non-rRNA R2", + "QC non-rRNA R1", + "Metagenome Bins", + "CheckM Statistics", + "GOTTCHA2 Krona Plot", + "GOTTCHA2 Classification Report", + "GOTTCHA2 Report Full", + "Kraken2 Krona Plot", + "Centrifuge Krona Plot", + "Centrifuge output report file", + "Kraken2 Classification Report", + "Kraken2 Taxonomic Classification", + "Centrifuge Classification Report", + "Centrifuge Taxonomic Classification", + "Structural Annotation GFF", + "Functional Annotation GFF", + "Annotation Amino Acid FASTA", + "Annotation Enzyme Commission", + "Annotation KEGG Orthology", + "Assembly Coverage BAM", + "Assembly AGP", + "Assembly Scaffolds", + "Assembly Contigs", + "Assembly Coverage Stats", + "Filtered Sequencing Reads", + "QC Statistics", + "TIGRFam Annotation GFF", + "CRT Annotation GFF", + "Genmark Annotation GFF", + "Prodigal Annotation GFF", + "TRNA Annotation GFF", + "Misc Annotation GFF", + "RFAM Annotation GFF", + "TMRNA Annotation GFF", + "KO_EC Annotation GFF", + "Product Names", + "Gene Phylogeny tsv", + "Crisprt Terms", + "Clusters of Orthologous Groups (COG) Annotation GFF", + "CATH FunFams (Functional Families) Annotation GFF", + "SUPERFam Annotation GFF", + "SMART Annotation GFF", + "Pfam Annotation GFF", + "Direct Infusion FT ICR-MS Raw Data" + ], + "title": "FileTypeEnum", + "type": "string" + }, + "FilterTypeEnum": { + "description": "", + "enum": [ + "particulate air filter", + "chemical air filter", + "low-MERV pleated media", + "HEPA", + "electrostatic", + "gas-phase or ultraviolet air treatments" + ], + "title": "FilterTypeEnum", + "type": "string" + }, + "FloorCondEnum": { + "description": "", + "enum": [ + "new", + "visible wear", + "needs repair", + "damaged", + "rupture" + ], + "title": "FloorCondEnum", + "type": "string" + }, + "FloorFinishMatEnum": { + "description": "", + "enum": [ + "tile", + "wood strip or parquet", + "carpet", + "rug", + "laminate wood", + "lineoleum", + "vinyl composition tile", + "sheet vinyl", + "stone", + "bamboo", + "cork", + "terrazo", + "concrete", + "none", + "sealed", + "clear finish", + "paint", + "none or unfinished" + ], + "title": "FloorFinishMatEnum", + "type": "string" + }, + "FloorStrucEnum": { + "description": "", + "enum": [ + "balcony", + "floating floor", + "glass floor", + "raised floor", + "sprung floor", + "wood-framed", + "concrete" + ], + "title": "FloorStrucEnum", + "type": "string" + }, + "FloorWaterMoldEnum": { + "description": "", + "enum": [ + "mold odor", + "wet floor", + "water stains", + "wall discoloration", + "floor discoloration", + "ceiling discoloration", + "peeling paint or wallpaper", + "bulging walls", + "condensation" + ], + "title": "FloorWaterMoldEnum", + "type": "string" + }, + "FreqCleanEnum": { + "description": "", + "enum": [ + "Daily", + "Weekly", + "Monthly", + "Quarterly", + "Annually", + "other" + ], + "title": "FreqCleanEnum", + "type": "string" + }, + "FunctionalAnnotation": { + "additionalProperties": false, + "description": "An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods", + "properties": { + "has_function": { + "pattern": "^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$", + "type": "string" + }, + "subject": { + "type": "string" + }, + "was_generated_by": { + "description": "provenance for the annotation.", + "type": "string" + } + }, + "title": "FunctionalAnnotation", + "type": "object" + }, + "FurnitureEnum": { + "description": "", + "enum": [ + "cabinet", + "chair", + "desks" + ], + "title": "FurnitureEnum", + "type": "string" + }, + "GenderRestroomEnum": { + "description": "", + "enum": [ + "all gender", + "female", + "gender neurtral", + "male", + "male and female", + "unisex" + ], + "title": "GenderRestroomEnum", + "type": "string" + }, + "GeneProduct": { + "additionalProperties": false, + "description": "A molecule encoded by a gene that has an evolved function", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "GeneProduct", + "type": "object" + }, + "GenomeFeature": { + "additionalProperties": false, + "description": "A feature localized to an interval along a genome", + "title": "GenomeFeature", + "type": "object" + }, + "GeolocationValue": { + "additionalProperties": false, + "description": "A normalized value for a location on the earth's surface", + "properties": { + "has_raw_value": { + "description": "The raw value for a geolocation should follow {lat} {long}", + "type": "string" + }, + "latitude": { + "description": "latitude", + "type": "number" + }, + "longitude": { + "description": "longitude", + "type": "number" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "GeolocationValue", + "type": "object" + }, + "GrowthHabitEnum": { + "description": "", + "enum": [ + "erect", + "semi-erect", + "spreading", + "prostrate" + ], + "title": "GrowthHabitEnum", + "type": "string" + }, + "HandidnessEnum": { + "description": "", + "enum": [ + "ambidexterity", + "left handedness", + "mixed-handedness", + "right handedness" + ], + "title": "HandidnessEnum", + "type": "string" + }, + "HcProducedEnum": { + "description": "", + "enum": [ + "Oil", + "Gas-Condensate", + "Gas", + "Bitumen", + "Coalbed Methane", + "other" + ], + "title": "HcProducedEnum", + "type": "string" + }, + "HcrEnum": { + "description": "", + "enum": [ + "Oil Reservoir", + "Gas Reservoir", + "Oil Sand", + "Coalbed", + "Shale", + "Tight Oil Reservoir", + "Tight Gas Reservoir", + "other" + ], + "title": "HcrEnum", + "type": "string" + }, + "HcrGeolAgeEnum": { + "description": "", + "enum": [ + "Archean", + "Cambrian", + "Carboniferous", + "Cenozoic", + "Cretaceous", + "Devonian", + "Jurassic", + "Mesozoic", + "Neogene", + "Ordovician", + "Paleogene", + "Paleozoic", + "Permian", + "Precambrian", + "Proterozoic", + "Silurian", + "Triassic", + "other" + ], + "title": "HcrGeolAgeEnum", + "type": "string" + }, + "HeatCoolTypeEnum": { + "description": "", + "enum": [ + "radiant system", + "heat pump", + "forced air system", + "steam forced heat", + "wood stove" + ], + "title": "HeatCoolTypeEnum", + "type": "string" + }, + "HeatDelivLocEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west" + ], + "title": "HeatDelivLocEnum", + "type": "string" + }, + "HorizonEnum": { + "description": "", + "enum": [ + "O horizon", + "A horizon", + "E horizon", + "B horizon", + "C horizon", + "R layer", + "Permafrost" + ], + "title": "HorizonEnum", + "type": "string" + }, + "HostSexEnum": { + "description": "", + "enum": [ + "female", + "hermaphrodite", + "male", + "neuter" + ], + "title": "HostSexEnum", + "type": "string" + }, + "ImageValue": { + "additionalProperties": false, + "description": "An attribute value representing an image.", + "properties": { + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "display_order": { + "description": "When rendering information, this attribute to specify the order in which the information should be rendered.", + "type": "string" + }, + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "url": { + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "ImageValue", + "type": "object" + }, + "IndoorSpaceEnum": { + "description": "", + "enum": [ + "bedroom", + "office", + "bathroom", + "foyer", + "kitchen", + "locker room", + "hallway", + "elevator" + ], + "title": "IndoorSpaceEnum", + "type": "string" + }, + "IndoorSurfEnum": { + "description": "", + "enum": [ + "cabinet", + "ceiling", + "counter top", + "door", + "shelving", + "vent cover", + "window", + "wall" + ], + "title": "IndoorSurfEnum", + "type": "string" + }, + "Instrument": { + "additionalProperties": false, + "description": "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI].", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):inst-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "Instrument", + "type": "object" + }, + "IntWallCondEnum": { + "description": "", + "enum": [ + "new", + "visible wear", + "needs repair", + "damaged", + "rupture" + ], + "title": "IntWallCondEnum", + "type": "string" + }, + "IntegerValue": { + "additionalProperties": false, + "description": "A value that is an integer", + "properties": { + "has_numeric_value": { + "description": "Links a quantity value to a number", + "type": "number" + }, + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "IntegerValue", + "type": "object" + }, + "LabDevice": { + "additionalProperties": false, + "description": "", + "properties": { + "activity_speed": { + "$ref": "#/$defs/QuantityValue" + }, + "activity_temperature": { + "$ref": "#/$defs/QuantityValue" + }, + "activity_time": { + "$ref": "#/$defs/QuantityValue" + }, + "device_type": { + "$ref": "#/$defs/DeviceTypeEnum" + } + }, + "title": "LabDevice", + "type": "object" + }, + "LightTypeEnum": { + "description": "", + "enum": [ + "natural light", + "electric light", + "desk lamp", + "flourescent lights", + "none" + ], + "title": "LightTypeEnum", + "type": "string" + }, + "LithologyEnum": { + "description": "", + "enum": [ + "Basement", + "Chalk", + "Chert", + "Coal", + "Conglomerate", + "Diatomite", + "Dolomite", + "Limestone", + "Sandstone", + "Shale", + "Siltstone", + "Volcanic", + "other" + ], + "title": "LithologyEnum", + "type": "string" + }, + "MagBin": { + "additionalProperties": false, + "description": "", + "properties": { + "bin_name": { + "type": "string" + }, + "bin_quality": { + "type": "string" + }, + "completeness": { + "type": "number" + }, + "contamination": { + "type": "number" + }, + "gene_count": { + "type": "integer" + }, + "gtdbtk_class": { + "type": "string" + }, + "gtdbtk_domain": { + "type": "string" + }, + "gtdbtk_family": { + "type": "string" + }, + "gtdbtk_genus": { + "type": "string" + }, + "gtdbtk_order": { + "type": "string" + }, + "gtdbtk_phylum": { + "type": "string" + }, + "gtdbtk_species": { + "type": "string" + }, + "num_16s": { + "type": "integer" + }, + "num_23s": { + "type": "integer" + }, + "num_5s": { + "type": "integer" + }, + "num_t_rna": { + "type": "integer" + }, + "number_of_contig": { + "type": "integer" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + } + }, + "title": "MagBin", + "type": "object" + }, + "MagsAnalysisActivity": { + "additionalProperties": false, + "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", + "properties": { + "binned_contig_num": { + "type": "integer" + }, + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmag-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "input_contig_num": { + "type": "integer" + }, + "low_depth_contig_num": { + "type": "integer" + }, + "mags_list": { + "items": { + "$ref": "#/$defs/MagBin" + }, + "type": "array" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "too_short_contig_num": { + "type": "integer" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "unbinned_contig_num": { + "type": "integer" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MagsAnalysisActivity", + "type": "object" + }, + "MaterialContainer": { + "additionalProperties": false, + "description": "", + "properties": { + "container_size": { + "$ref": "#/$defs/QuantityValue" + }, + "container_type": { + "$ref": "#/$defs/ContainerTypeEnum" + } + }, + "title": "MaterialContainer", + "type": "object" + }, + "MaterialSample": { + "additionalProperties": false, + "description": "", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):matsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "title": "MaterialSample", + "type": "object" + }, + "MaterialSamplingActivity": { + "additionalProperties": false, + "description": "", + "properties": { + "amount_collected": { + "$ref": "#/$defs/QuantityValue" + }, + "biosample_input": { + "type": "string" + }, + "collected_into": { + "$ref": "#/$defs/MaterialContainer" + }, + "material_output": { + "type": "string" + }, + "sampling_method": { + "$ref": "#/$defs/SamplingMethodEnum" + } + }, + "title": "MaterialSamplingActivity", + "type": "object" + }, + "MechStrucEnum": { + "description": "", + "enum": [ + "subway", + "coach", + "carriage", + "elevator", + "escalator", + "boat", + "train", + "car", + "bus" + ], + "title": "MechStrucEnum", + "type": "string" + }, + "MetaboliteQuantification": { + "additionalProperties": false, + "description": "This is used to link a metabolomics analysis workflow to a specific metabolite", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "title": "MetaboliteQuantification", + "type": "object" + }, + "MetabolomicsAnalysisActivity": { + "additionalProperties": false, + "description": "", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmb-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "description": "The instrument used to collect the data used in the analysis", + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MetabolomicsAnalysisActivity", + "type": "object" + }, + "MetagenomeAnnotationActivity": { + "additionalProperties": false, + "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "gold_analysis_project_identifiers": { + "description": "identifiers for corresponding analysis project in GOLD", + "items": { + "type": "string" + }, + "pattern": "^GOLD:Ga[0-9]+$", + "type": "array" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmgan-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MetagenomeAnnotationActivity", + "type": "object" + }, + "MetagenomeAssembly": { + "additionalProperties": false, + "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", + "properties": { + "asm_score": { + "description": "A score for comparing metagenomic assembly quality from same sample.", + "type": "number" + }, + "contig_bp": { + "description": "Total size in bp of all contigs.", + "type": "number" + }, + "contigs": { + "description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", + "type": "number" + }, + "ctg_l50": { + "description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", + "type": "number" + }, + "ctg_l90": { + "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", + "type": "number" + }, + "ctg_logsum": { + "description": "Maximum contig length.", + "type": "number" + }, + "ctg_max": { + "description": "Maximum contig length.", + "type": "number" + }, + "ctg_n50": { + "description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", + "type": "number" + }, + "ctg_n90": { + "description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", + "type": "number" + }, + "ctg_powsum": { + "description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", + "type": "number" + }, + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "gap_pct": { + "description": "The gap size percentage of all scaffolds.", + "type": "number" + }, + "gc_avg": { + "description": "Average of GC content of all contigs.", + "type": "number" + }, + "gc_std": { + "description": "Standard deviation of GC content of all contigs.", + "type": "number" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmgas-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "insdc_assembly_identifiers": { + "pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "num_aligned_reads": { + "description": "The sequence count number of input reads aligned to assembled contigs.", + "type": "number" + }, + "num_input_reads": { + "description": "The sequence count number of input reads for assembly.", + "type": "number" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "scaf_bp": { + "description": "Total size in bp of all scaffolds.", + "type": "number" + }, + "scaf_l50": { + "description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", + "type": "number" + }, + "scaf_l90": { + "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", + "type": "number" + }, + "scaf_l_gt50k": { + "description": "Total size in bp of all scaffolds greater than 50 KB.", + "type": "number" + }, + "scaf_logsum": { + "description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", + "type": "number" + }, + "scaf_max": { + "description": "Maximum scaffold length.", + "type": "number" + }, + "scaf_n50": { + "description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", + "type": "number" + }, + "scaf_n90": { + "description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", + "type": "number" + }, + "scaf_n_gt50k": { + "description": "Total sequence count of scaffolds greater than 50 KB.", + "type": "number" + }, + "scaf_pct_gt50k": { + "description": "Total sequence size percentage of scaffolds greater than 50 KB.", + "type": "number" + }, + "scaf_powsum": { + "description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", + "type": "number" + }, + "scaffolds": { + "description": "Total sequence count of all scaffolds.", + "type": "number" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MetagenomeAssembly", + "type": "object" + }, + "MetaproteomicsAnalysisActivity": { + "additionalProperties": false, + "description": "", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmp-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "description": "The instrument used to collect the data used in the analysis", + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MetaproteomicsAnalysisActivity", + "type": "object" + }, + "MetatranscriptomeActivity": { + "additionalProperties": false, + "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmt-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MetatranscriptomeActivity", + "type": "object" + }, + "MetatranscriptomeAnnotationActivity": { + "additionalProperties": false, + "description": "", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "gold_analysis_project_identifiers": { + "description": "identifiers for corresponding analysis project in GOLD", + "items": { + "type": "string" + }, + "pattern": "^GOLD:Ga[0-9]+$", + "type": "array" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmtan-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "id", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MetatranscriptomeAnnotationActivity", + "type": "object" + }, + "MetatranscriptomeAssembly": { + "additionalProperties": false, + "description": "", + "properties": { + "asm_score": { + "description": "A score for comparing metagenomic assembly quality from same sample.", + "type": "number" + }, + "contig_bp": { + "description": "Total size in bp of all contigs.", + "type": "number" + }, + "contigs": { + "description": "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase", + "type": "number" + }, + "ctg_l50": { + "description": "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.", + "type": "number" + }, + "ctg_l90": { + "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.", + "type": "number" + }, + "ctg_logsum": { + "description": "Maximum contig length.", + "type": "number" + }, + "ctg_max": { + "description": "Maximum contig length.", + "type": "number" + }, + "ctg_n50": { + "description": "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.", + "type": "number" + }, + "ctg_n90": { + "description": "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.", + "type": "number" + }, + "ctg_powsum": { + "description": "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", + "type": "number" + }, + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "gap_pct": { + "description": "The gap size percentage of all scaffolds.", + "type": "number" + }, + "gc_avg": { + "description": "Average of GC content of all contigs.", + "type": "number" + }, + "gc_std": { + "description": "Standard deviation of GC content of all contigs.", + "type": "number" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfmtas-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "insdc_assembly_identifiers": { + "pattern": "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "num_aligned_reads": { + "description": "The sequence count number of input reads aligned to assembled contigs.", + "type": "number" + }, + "num_input_reads": { + "description": "The sequence count number of input reads for assembly.", + "type": "number" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "scaf_bp": { + "description": "Total size in bp of all scaffolds.", + "type": "number" + }, + "scaf_l50": { + "description": "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.", + "type": "number" + }, + "scaf_l90": { + "description": "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.", + "type": "number" + }, + "scaf_l_gt50k": { + "description": "Total size in bp of all scaffolds greater than 50 KB.", + "type": "number" + }, + "scaf_logsum": { + "description": "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase", + "type": "number" + }, + "scaf_max": { + "description": "Maximum scaffold length.", + "type": "number" + }, + "scaf_n50": { + "description": "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.", + "type": "number" + }, + "scaf_n90": { + "description": "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.", + "type": "number" + }, + "scaf_n_gt50k": { + "description": "Total sequence count of scaffolds greater than 50 KB.", + "type": "number" + }, + "scaf_pct_gt50k": { + "description": "Total sequence size percentage of scaffolds greater than 50 KB.", + "type": "number" + }, + "scaf_powsum": { + "description": "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).", + "type": "number" + }, + "scaffolds": { + "description": "Total sequence count of all scaffolds.", + "type": "number" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "id", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "MetatranscriptomeAssembly", + "type": "object" + }, + "NomAnalysisActivity": { + "additionalProperties": false, + "description": "", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfnom-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "description": "The instrument used to collect the data used in the analysis", + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "NomAnalysisActivity", + "type": "object" + }, + "OccupDocumentEnum": { + "description": "", + "enum": [ + "automated count", + "estimate", + "manual count", + "videos" + ], + "title": "OccupDocumentEnum", + "type": "string" + }, + "OmicsProcessing": { + "additionalProperties": false, + "description": "The methods and processes used to generate omics data from a biosample or organism.", + "properties": { + "add_date": { + "description": "The date on which the information was added to the database.", + "type": "string" + }, + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "chimera_check": { + "$ref": "#/$defs/TextValue", + "description": "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences." + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "gold_sequencing_project_identifiers": { + "description": "identifiers for corresponding sequencing project in GOLD", + "items": { + "type": "string" + }, + "pattern": "^GOLD:Gp[0-9]+$", + "type": "array" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):omprc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "insdc_experiment_identifiers": { + "items": { + "type": "string" + }, + "pattern": "^insdc.sra:(E|D|S)RX[0-9]{6,}$", + "type": "array" + }, + "instrument_name": { + "description": "The name of the instrument that was used for processing the sample.", + "type": "string" + }, + "mod_date": { + "description": "The last date on which the database information was modified.", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "ncbi_project_name": { + "type": "string" + }, + "nucl_acid_amp": { + "$ref": "#/$defs/TextValue", + "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids" + }, + "nucl_acid_ext": { + "$ref": "#/$defs/TextValue", + "description": "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample" + }, + "omics_type": { + "$ref": "#/$defs/ControlledTermValue", + "description": "The type of omics data" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "pcr_cond": { + "$ref": "#/$defs/TextValue", + "description": "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'" + }, + "pcr_primers": { + "$ref": "#/$defs/TextValue", + "description": "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters" + }, + "principal_investigator": { + "$ref": "#/$defs/PersonValue", + "description": "Principal Investigator who led the study and/or generated the dataset." + }, + "processing_institution": { + "$ref": "#/$defs/ProcessingInstitutionEnum", + "description": "The organization that processed the sample." + }, + "samp_vol_we_dna_ext": { + "$ref": "#/$defs/QuantityValue", + "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)." + }, + "seq_meth": { + "$ref": "#/$defs/TextValue", + "description": "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)." + }, + "seq_quality_check": { + "$ref": "#/$defs/TextValue", + "description": "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA" + }, + "target_gene": { + "$ref": "#/$defs/TextValue", + "description": "Targeted gene or locus name for marker gene studies" + }, + "target_subfragment": { + "$ref": "#/$defs/TextValue", + "description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + } + }, + "required": [ + "has_input" + ], + "title": "OmicsProcessing", + "type": "object" + }, + "OntologyClass": { + "additionalProperties": false, + "description": "", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "OntologyClass", + "type": "object" + }, + "OrganismCountEnum": { + "description": "", + "enum": [ + "ATP", + "MPN", + "other" + ], + "title": "OrganismCountEnum", + "type": "string" + }, + "OrthologyGroup": { + "additionalProperties": false, + "description": "A set of genes or gene products in which all members are orthologous", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "OrthologyGroup", + "type": "object" + }, + "OxyStatSampEnum": { + "description": "", + "enum": [ + "aerobic", + "anaerobic", + "other" + ], + "title": "OxyStatSampEnum", + "type": "string" + }, + "Pathway": { + "additionalProperties": false, + "description": "A pathway is a sequence of steps/reactions carried out by an organism or community of organisms", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "Pathway", + "type": "object" + }, + "PeptideQuantification": { + "additionalProperties": false, + "description": "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information", + "title": "PeptideQuantification", + "type": "object" + }, + "Person": { + "additionalProperties": false, + "description": "represents a person, such as a researcher", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "Should be an ORCID. Specify in CURIE format. E.g ORCID:0000-1111-...", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "Person", + "type": "object" + }, + "PersonValue": { + "additionalProperties": false, + "description": "An attribute value representing a person", + "properties": { + "email": { + "description": "An email address for an entity such as a person. This should be the primarly email address used.", + "type": "string" + }, + "has_raw_value": { + "description": "The full name of the Investigator in format FIRST LAST.", + "type": "string" + }, + "name": { + "description": "The full name of the Investigator. It should follow the format FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.", + "type": "string" + }, + "orcid": { + "description": "The ORCID of a person.", + "type": "string" + }, + "profile_image_url": { + "description": "A url that points to an image of a person.", + "type": "string" + }, + "was_generated_by": { + "type": "string" + }, + "websites": { + "description": "A list of websites that are associated with the entity.", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "title": "PersonValue", + "type": "object" + }, + "PlantGrowthMedEnum": { + "description": "", + "enum": [ + "other artificial liquid medium", + "other artificial solid medium", + "peat moss", + "perlite", + "pumice", + "sand", + "soil", + "vermiculite", + "water" + ], + "title": "PlantGrowthMedEnum", + "type": "string" + }, + "PlantSexEnum": { + "description": "", + "enum": [ + "Androdioecious", + "Androecious", + "Androgynous", + "Androgynomonoecious", + "Andromonoecious", + "Bisexual", + "Dichogamous", + "Diclinous", + "Dioecious", + "Gynodioecious", + "Gynoecious", + "Gynomonoecious", + "Hermaphroditic", + "Imperfect", + "Monoclinous", + "Monoecious", + "Perfect", + "Polygamodioecious", + "Polygamomonoecious", + "Polygamous", + "Protandrous", + "Protogynous", + "Subandroecious", + "Subdioecious", + "Subgynoecious", + "Synoecious", + "Trimonoecious", + "Trioecious", + "Unisexual" + ], + "title": "PlantSexEnum", + "type": "string" + }, + "ProcessingInstitutionEnum": { + "description": "", + "enum": [ + "UCSD", + "JGI", + "EMSL" + ], + "title": "ProcessingInstitutionEnum", + "type": "string" + }, + "ProfilePositionEnum": { + "description": "", + "enum": [ + "summit", + "shoulder", + "backslope", + "footslope", + "toeslope" + ], + "title": "ProfilePositionEnum", + "type": "string" + }, + "ProteinQuantification": { + "additionalProperties": false, + "description": "This is used to link a metaproteomics analysis workflow to a specific protein", + "title": "ProteinQuantification", + "type": "object" + }, + "QuadPosEnum": { + "description": "", + "enum": [ + "North side", + "West side", + "South side", + "East side" + ], + "title": "QuadPosEnum", + "type": "string" + }, + "QuantityValue": { + "additionalProperties": false, + "description": "A simple quantity, e.g. 2cm", + "properties": { + "has_maximum_numeric_value": { + "description": "The maximum value part, expressed as number, of the quantity value when the value covers a range.", + "type": "number" + }, + "has_minimum_numeric_value": { + "description": "The minimum value part, expressed as number, of the quantity value when the value covers a range.", + "type": "number" + }, + "has_numeric_value": { + "description": "The number part of the quantity", + "type": "number" + }, + "has_raw_value": { + "description": "Unnormalized atomic string representation, should in syntax {number} {unit}", + "type": "string" + }, + "has_unit": { + "description": "The unit of the quantity", + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "QuantityValue", + "type": "object" + }, + "Reaction": { + "additionalProperties": false, + "description": "An individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters", + "properties": { + "alternative_identifiers": { + "description": "A list of alternative identifiers for the entity.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of a thing", + "type": "string" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "Reaction", + "type": "object" + }, + "ReactionActivity": { + "additionalProperties": false, + "description": "", + "properties": { + "material_input": { + "type": "string" + }, + "material_output": { + "type": "string" + }, + "reaction_aided_by": { + "$ref": "#/$defs/LabDevice" + }, + "reaction_temperature": { + "type": "string" + }, + "reaction_time": { + "$ref": "#/$defs/QuantityValue" + } + }, + "title": "ReactionActivity", + "type": "object" + }, + "ReactionParticipant": { + "additionalProperties": false, + "description": "Instances of this link a reaction to a chemical entity participant", + "title": "ReactionParticipant", + "type": "object" + }, + "ReadBasedTaxonomyAnalysisActivity": { + "additionalProperties": false, + "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfrbt-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "ReadBasedTaxonomyAnalysisActivity", + "type": "object" + }, + "ReadQcAnalysisActivity": { + "additionalProperties": false, + "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wfrqc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "input_base_count": { + "description": "The nucleotide base count number of input reads for QC analysis.", + "type": "number" + }, + "input_read_count": { + "description": "The sequence count number of input reads for QC analysis.", + "type": "number" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "output_base_count": { + "description": "After QC analysis nucleotide base count number.", + "type": "number" + }, + "output_read_count": { + "description": "After QC analysis sequence count number.", + "type": "number" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "ReadQcAnalysisActivity", + "type": "object" + }, + "RelSampLocEnum": { + "description": "", + "enum": [ + "edge of car", + "center of car", + "under a seat" + ], + "title": "RelSampLocEnum", + "type": "string" + }, + "RelToOxygenEnum": { + "description": "", + "enum": [ + "aerobe", + "anaerobe", + "facultative", + "microaerophilic", + "microanaerobe", + "obligate aerobe", + "obligate anaerobe" + ], + "title": "RelToOxygenEnum", + "type": "string" + }, + "RnaContTypeEnum": { + "description": "", + "enum": [ + "plate", + "tube" + ], + "title": "RnaContTypeEnum", + "type": "string" + }, + "RnaSampleFormatEnum": { + "description": "", + "enum": [ + "10 mM Tris-HCl", + "DNAStable", + "Ethanol", + "Low EDTA TE", + "MDA reaction buffer", + "PBS", + "Pellet", + "RNAStable", + "TE", + "Water", + "Gentegra-DNA", + "Gentegra-RNA" + ], + "title": "RnaSampleFormatEnum", + "type": "string" + }, + "RoomCondtEnum": { + "description": "", + "enum": [ + "new", + "visible wear", + "needs repair", + "damaged", + "rupture", + "visible signs of mold/mildew" + ], + "title": "RoomCondtEnum", + "type": "string" + }, + "RoomConnectedEnum": { + "description": "", + "enum": [ + "attic", + "bathroom", + "closet", + "conference room", + "elevator", + "examining room", + "hallway", + "kitchen", + "mail room", + "office", + "stairwell" + ], + "title": "RoomConnectedEnum", + "type": "string" + }, + "RoomLocEnum": { + "description": "", + "enum": [ + "corner room", + "interior room", + "exterior wall" + ], + "title": "RoomLocEnum", + "type": "string" + }, + "RoomSampPosEnum": { + "description": "", + "enum": [ + "north corner", + "south corner", + "west corner", + "east corner", + "northeast corner", + "northwest corner", + "southeast corner", + "southwest corner", + "center" + ], + "title": "RoomSampPosEnum", + "type": "string" + }, + "RoomTypeEnum": { + "description": "", + "enum": [ + "attic", + "bathroom", + "closet", + "conference room", + "elevator", + "examining room", + "hallway", + "kitchen", + "mail room", + "private office", + "open office", + "stairwell", + ",restroom", + "lobby", + "vestibule", + "mechanical or electrical room", + "data center", + "laboratory_wet", + "laboratory_dry", + "gymnasium", + "natatorium", + "auditorium", + "lockers", + "cafe", + "warehouse" + ], + "title": "RoomTypeEnum", + "type": "string" + }, + "SampCaptStatusEnum": { + "description": "", + "enum": [ + "active surveillance in response to an outbreak", + "active surveillance not initiated by an outbreak", + "farm sample", + "market sample", + "other" + ], + "title": "SampCaptStatusEnum", + "type": "string" + }, + "SampCollectPointEnum": { + "description": "", + "enum": [ + "well", + "test well", + "drilling rig", + "wellhead", + "separator", + "storage tank", + "other" + ], + "title": "SampCollectPointEnum", + "type": "string" + }, + "SampDisStageEnum": { + "description": "", + "enum": [ + "dissemination", + "growth and reproduction", + "infection", + "inoculation", + "penetration", + "other" + ], + "title": "SampDisStageEnum", + "type": "string" + }, + "SampFloorEnum": { + "description": "", + "enum": [ + "1st floor", + "2nd floor", + "basement", + "lobby" + ], + "title": "SampFloorEnum", + "type": "string" + }, + "SampMdEnum": { + "description": "", + "enum": [ + "DF", + "RT", + "KB", + "MSL", + "other" + ], + "title": "SampMdEnum", + "type": "string" + }, + "SampSubtypeEnum": { + "description": "", + "enum": [ + "oil phase", + "water phase", + "biofilm", + "not applicable", + "other" + ], + "title": "SampSubtypeEnum", + "type": "string" + }, + "SampWeatherEnum": { + "description": "", + "enum": [ + "clear sky", + "cloudy", + "foggy", + "hail", + "rain", + "snow", + "sleet", + "sunny", + "windy" + ], + "title": "SampWeatherEnum", + "type": "string" + }, + "SampleTypeEnum": { + "description": "", + "enum": [ + "soil", + "water_extract_soil" + ], + "title": "SampleTypeEnum", + "type": "string" + }, + "SamplingMethodEnum": { + "description": "", + "enum": [ + "weighing" + ], + "title": "SamplingMethodEnum", + "type": "string" + }, + "SeasonUseEnum": { + "description": "", + "enum": [ + "Spring", + "Summer", + "Fall", + "Winter" + ], + "title": "SeasonUseEnum", + "type": "string" + }, + "SedimentTypeEnum": { + "description": "", + "enum": [ + "biogenous", + "cosmogenous", + "hydrogenous", + "lithogenous" + ], + "title": "SedimentTypeEnum", + "type": "string" + }, + "ShadingDeviceCondEnum": { + "description": "", + "enum": [ + "damaged", + "needs repair", + "new", + "rupture", + "visible wear" + ], + "title": "ShadingDeviceCondEnum", + "type": "string" + }, + "ShadingDeviceTypeEnum": { + "description": "", + "enum": [ + "bahama shutters", + "exterior roll blind", + "gambrel awning", + "hood awning", + "porchroller awning", + "sarasota shutters", + "slatted aluminum", + "solid aluminum awning", + "sun screen", + "tree", + "trellis", + "venetian awning" + ], + "title": "ShadingDeviceTypeEnum", + "type": "string" + }, + "SoilHorizonEnum": { + "description": "", + "enum": [ + "O horizon", + "A horizon", + "E horizon", + "B horizon", + "C horizon", + "R layer", + "Permafrost" + ], + "title": "SoilHorizonEnum", + "type": "string" + }, + "SolventEnum": { + "description": "", + "enum": [ + "deionized_water", + "methanol", + "chloroform" + ], + "title": "SolventEnum", + "type": "string" + }, + "SpecificEnum": { + "description": "", + "enum": [ + "operation", + "as built", + "construction", + "bid", + "design", + "photos" + ], + "title": "SpecificEnum", + "type": "string" + }, + "SrDepEnvEnum": { + "description": "", + "enum": [ + "Lacustine", + "Fluvioldeltaic", + "Fluviomarine", + "Marine", + "other" + ], + "title": "SrDepEnvEnum", + "type": "string" + }, + "SrGeolAgeEnum": { + "description": "", + "enum": [ + "Archean", + "Cambrian", + "Carboniferous", + "Cenozoic", + "Cretaceous", + "Devonian", + "Jurassic", + "Mesozoic", + "Neogene", + "Ordovician", + "Paleogene", + "Paleozoic", + "Permian", + "Precambrian", + "Proterozoic", + "Silurian", + "Triassic", + "other" + ], + "title": "SrGeolAgeEnum", + "type": "string" + }, + "SrKerogTypeEnum": { + "description": "", + "enum": [ + "Type I", + "Type II", + "Type III", + "Type IV", + "other" + ], + "title": "SrKerogTypeEnum", + "type": "string" + }, + "SrLithologyEnum": { + "description": "", + "enum": [ + "Clastic", + "Carbonate", + "Coal", + "Biosilicieous", + "other" + ], + "title": "SrLithologyEnum", + "type": "string" + }, + "Study": { + "additionalProperties": false, + "description": "A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.", + "properties": { + "abstract": { + "description": "The abstract of manuscript/grant associated with the entity; i.e., a summary of the resource.", + "type": "string" + }, + "alternative_descriptions": { + "description": "A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.", + "items": { + "type": "string" + }, + "type": "array" + }, + "alternative_identifiers": { + "description": "Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC", + "items": { + "type": "string" + }, + "type": "array" + }, + "alternative_names": { + "description": "A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.", + "items": { + "type": "string" + }, + "type": "array" + }, + "alternative_titles": { + "description": "A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "A brief summary that details the study you're submitted to NMDC", + "type": "string" + }, + "doi": { + "$ref": "#/$defs/AttributeValue", + "description": "The dataset citation for this study" + }, + "ecosystem": { + "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", + "type": "string" + }, + "ecosystem_category": { + "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", + "type": "string" + }, + "ecosystem_subtype": { + "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", + "type": "string" + }, + "ecosystem_type": { + "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", + "type": "string" + }, + "emsl_proposal_doi": { + "description": "The DOI for the EMSL awarded study that relates to the NMDC submitted study", + "type": "string" + }, + "emsl_proposal_identifier": { + "description": "The proposal number assigned to the EMSL awarded study that relates to that which is represented in NMDC.", + "type": "string" + }, + "ess_dive_datasets": { + "description": "List of ESS-DIVE dataset DOIs", + "items": { + "type": "string" + }, + "type": "array" + }, + "funding_sources": { + "items": { + "type": "string" + }, + "type": "array" + }, + "gold_study_identifiers": { + "description": "identifiers for corresponding project(s) in GOLD", + "items": { + "type": "string" + }, + "pattern": "^GOLD:Gs[0-9]+$", + "type": "array" + }, + "has_credit_associations": { + "description": "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study", + "items": { + "$ref": "#/$defs/CreditAssociation" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):sty-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "mgnify_project_identifiers": { + "description": "identifiers for corresponding project in MGnify", + "pattern": "^mgnify.proj:[A-Z]+[0-9]+$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "objective": { + "description": "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.", + "type": "string" + }, + "principal_investigator": { + "$ref": "#/$defs/PersonValue", + "description": "Principal Investigator who led the study and/or generated the dataset." + }, + "publications": { + "description": "A list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.", + "items": { + "type": "string" + }, + "type": "array" + }, + "related_identifiers": { + "description": "Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC", + "type": "string" + }, + "relevant_protocols": { + "items": { + "type": "string" + }, + "type": "array" + }, + "specific_ecosystem": { + "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", + "type": "string" + }, + "study_image": { + "description": "Links a study to one or more images.", + "items": { + "$ref": "#/$defs/ImageValue" + }, + "type": "array" + }, + "title": { + "description": "A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "websites": { + "description": "A list of websites that are associated with the entity.", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "title": "Study", + "type": "object" + }, + "SubstructureTypeEnum": { + "description": "", + "enum": [ + "crawlspace", + "slab on grade", + "basement" + ], + "title": "SubstructureTypeEnum", + "type": "string" + }, + "SurfAirContEnum": { + "description": "", + "enum": [ + "dust", + "organic matter", + "particulate matter", + "volatile organic compounds", + "biological contaminants", + "radon", + "nutrients", + "biocides" + ], + "title": "SurfAirContEnum", + "type": "string" + }, + "SurfMaterialEnum": { + "description": "", + "enum": [ + "adobe", + "carpet", + "cinder blocks", + "concrete", + "hay bales", + "glass", + "metal", + "paint", + "plastic", + "stainless steel", + "stone", + "stucco", + "tile", + "vinyl", + "wood" + ], + "title": "SurfMaterialEnum", + "type": "string" + }, + "TextValue": { + "additionalProperties": false, + "description": "A basic string value", + "properties": { + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "language": { + "description": "Should use ISO 639-1 code e.g. \"en\", \"fr\"", + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "TextValue", + "type": "object" + }, + "TidalStageEnum": { + "description": "", + "enum": [ + "low tide", + "ebb tide", + "flood tide", + "high tide" + ], + "title": "TidalStageEnum", + "type": "string" + }, + "TillageEnum": { + "description": "", + "enum": [ + "drill", + "cutting disc", + "ridge till", + "strip tillage", + "zonal tillage", + "chisel", + "tined", + "mouldboard", + "disc plough" + ], + "title": "TillageEnum", + "type": "string" + }, + "TimestampValue": { + "additionalProperties": false, + "description": "A value that is a timestamp. The range should be ISO-8601", + "properties": { + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "TimestampValue", + "type": "object" + }, + "TrainLineEnum": { + "description": "", + "enum": [ + "red", + "green", + "orange" + ], + "title": "TrainLineEnum", + "type": "string" + }, + "TrainStatLocEnum": { + "description": "", + "enum": [ + "south station above ground", + "south station underground", + "south station amtrak", + "forest hills", + "riverside" + ], + "title": "TrainStatLocEnum", + "type": "string" + }, + "TrainStopLocEnum": { + "description": "", + "enum": [ + "end", + "mid", + "downtown" + ], + "title": "TrainStopLocEnum", + "type": "string" + }, + "UrlValue": { + "additionalProperties": false, + "description": "A value that is a string that conforms to URL syntax", + "properties": { + "has_raw_value": { + "description": "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"", + "type": "string" + }, + "was_generated_by": { + "type": "string" + } + }, + "title": "UrlValue", + "type": "object" + }, + "VisMediaEnum": { + "description": "", + "enum": [ + "photos", + "videos", + "commonly of the building", + "site context (adjacent buildings, vegetation, terrain, streets)", + "interiors", + "equipment", + "3D scans" + ], + "title": "VisMediaEnum", + "type": "string" + }, + "WallConstTypeEnum": { + "description": "", + "enum": [ + "frame construction", + "joisted masonry", + "light noncombustible", + "masonry noncombustible", + "modified fire resistive", + "fire resistive" + ], + "title": "WallConstTypeEnum", + "type": "string" + }, + "WallFinishMatEnum": { + "description": "", + "enum": [ + "plaster", + "gypsum plaster", + "veneer plaster", + "gypsum board", + "tile", + "terrazzo", + "stone facing", + "acoustical treatment", + "wood", + "metal", + "masonry" + ], + "title": "WallFinishMatEnum", + "type": "string" + }, + "WallLocEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west" + ], + "title": "WallLocEnum", + "type": "string" + }, + "WallSurfTreatmentEnum": { + "description": "", + "enum": [ + "painted", + "wall paper", + "no treatment", + "paneling", + "stucco", + "fabric" + ], + "title": "WallSurfTreatmentEnum", + "type": "string" + }, + "WallTextureEnum": { + "description": "", + "enum": [ + "crows feet", + "crows-foot stomp", + "double skip", + "hawk and trowel", + "knockdown", + "popcorn", + "orange peel", + "rosebud stomp", + "Santa-Fe texture", + "skip trowel", + "smooth", + "stomp knockdown", + "swirl" + ], + "title": "WallTextureEnum", + "type": "string" + }, + "WaterFeatTypeEnum": { + "description": "", + "enum": [ + "fountain", + "pool", + "standing feature", + "stream", + "waterfall" + ], + "title": "WaterFeatTypeEnum", + "type": "string" + }, + "WeekdayEnum": { + "description": "", + "enum": [ + "Monday", + "Tuesday", + "Wednesday", + "Thursday", + "Friday", + "Saturday", + "Sunday" + ], + "title": "WeekdayEnum", + "type": "string" + }, + "WindowCondEnum": { + "description": "", + "enum": [ + "damaged", + "needs repair", + "new", + "rupture", + "visible wear" + ], + "title": "WindowCondEnum", + "type": "string" + }, + "WindowCoverEnum": { + "description": "", + "enum": [ + "blinds", + "curtains", + "none" + ], + "title": "WindowCoverEnum", + "type": "string" + }, + "WindowHorizPosEnum": { + "description": "", + "enum": [ + "left", + "middle", + "right" + ], + "title": "WindowHorizPosEnum", + "type": "string" + }, + "WindowLocEnum": { + "description": "", + "enum": [ + "north", + "south", + "east", + "west" + ], + "title": "WindowLocEnum", + "type": "string" + }, + "WindowMatEnum": { + "description": "", + "enum": [ + "clad", + "fiberglass", + "metal", + "vinyl", + "wood" + ], + "title": "WindowMatEnum", + "type": "string" + }, + "WindowTypeEnum": { + "description": "", + "enum": [ + "single-hung sash window", + "horizontal sash window", + "fixed window" + ], + "title": "WindowTypeEnum", + "type": "string" + }, + "WindowVertPosEnum": { + "description": "", + "enum": [ + "bottom", + "middle", + "top", + "low", + "high" + ], + "title": "WindowVertPosEnum", + "type": "string" + }, + "WorkflowExecutionActivity": { + "additionalProperties": false, + "description": "Represents an instance of an execution of a particular workflow", + "properties": { + "ended_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "execution_resource": { + "description": "Example: NERSC-Cori", + "type": "string" + }, + "git_url": { + "description": "Example: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1", + "type": "string" + }, + "has_input": { + "description": "An input to a process.", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_output": { + "description": "An output biosample to a processing step", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", + "pattern": "^(nmdc):wf-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$", + "type": "string" + }, + "name": { + "description": "A human readable label for an entity", + "type": "string" + }, + "part_of": { + "description": "Links a resource to another resource that either logically or physically includes it.", + "items": { + "type": "string" + }, + "type": "array" + }, + "started_at_time": { + "format": "date-time", + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "type": "string" + }, + "type": { + "description": "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.", + "type": "string" + }, + "used": { + "type": "string" + }, + "was_associated_with": { + "description": "the agent/entity associated with the generation of the file", + "type": "string" + }, + "was_informed_by": { + "type": "string" + } + }, + "required": [ + "execution_resource", + "git_url", + "has_input", + "has_output", + "started_at_time", + "ended_at_time", + "was_informed_by" + ], + "title": "WorkflowExecutionActivity", + "type": "object" + } + }, + "$id": "https://microbiomedata/schema", + "$schema": "http://json-schema.org/draft-07/schema#", + "additionalProperties": false, + "metamodel_version": "1.7.0", + "properties": { + "activity_set": { + "description": "This property links a database object to the set of workflow activities.", + "items": { + "$ref": "#/$defs/WorkflowExecutionActivity" + }, + "type": "array" + }, + "biosample_set": { + "description": "This property links a database object to the set of samples within it.", + "items": { + "$ref": "#/$defs/Biosample" + }, + "type": "array" + }, + "collecting_biosamples_from_site_set": { + "items": { + "$ref": "#/$defs/CollectingBiosamplesFromSite" + }, + "type": "array" + }, + "data_object_set": { + "description": "This property links a database object to the set of data objects within it.", + "items": { + "$ref": "#/$defs/DataObject" + }, + "type": "array" + }, + "dissolving_activity_set": { + "items": { + "$ref": "#/$defs/DissolvingActivity" + }, + "type": "array" + }, + "field_research_site_set": { + "items": { + "$ref": "#/$defs/FieldResearchSite" + }, + "type": "array" + }, + "functional_annotation_set": { + "description": "This property links a database object to the set of all functional annotations", + "items": { + "$ref": "#/$defs/FunctionalAnnotation" + }, + "type": "array" + }, + "genome_feature_set": { + "description": "This property links a database object to the set of all features", + "items": { + "$ref": "#/$defs/GenomeFeature" + }, + "type": "array" + }, + "mags_activity_set": { + "description": "This property links a database object to the set of MAGs analysis activities.", + "items": { + "$ref": "#/$defs/MagsAnalysisActivity" + }, + "type": "array" + }, + "material_sample_set": { + "items": { + "$ref": "#/$defs/MaterialSample" + }, + "type": "array" + }, + "material_sampling_activity_set": { + "items": { + "$ref": "#/$defs/MaterialSamplingActivity" + }, + "type": "array" + }, + "metabolomics_analysis_activity_set": { + "description": "This property links a database object to the set of metabolomics analysis activities.", + "items": { + "$ref": "#/$defs/MetabolomicsAnalysisActivity" + }, + "type": "array" + }, + "metagenome_annotation_activity_set": { + "description": "This property links a database object to the set of metagenome annotation activities.", + "items": { + "$ref": "#/$defs/MetagenomeAnnotationActivity" + }, + "type": "array" + }, + "metagenome_assembly_set": { + "description": "This property links a database object to the set of metagenome assembly activities.", + "items": { + "$ref": "#/$defs/MetagenomeAssembly" + }, + "type": "array" + }, + "metaproteomics_analysis_activity_set": { + "description": "This property links a database object to the set of metaproteomics analysis activities.", + "items": { + "$ref": "#/$defs/MetaproteomicsAnalysisActivity" + }, + "type": "array" + }, + "metatranscriptome_activity_set": { + "description": "TODO", + "items": { + "$ref": "#/$defs/MetatranscriptomeActivity" + }, + "type": "array" + }, + "nom_analysis_activity_set": { + "description": "This property links a database object to the set of natural organic matter (NOM) analysis activities.", + "items": { + "$ref": "#/$defs/NomAnalysisActivity" + }, + "type": "array" + }, + "omics_processing_set": { + "description": "This property links a database object to the set of omics processings within it.", + "items": { + "$ref": "#/$defs/OmicsProcessing" + }, + "type": "array" + }, + "reaction_activity_set": { + "items": { + "$ref": "#/$defs/ReactionActivity" + }, + "type": "array" + }, + "read_based_taxonomy_analysis_activity_set": { + "description": "This property links a database object to the set of read based analysis activities.", + "items": { + "$ref": "#/$defs/ReadBasedTaxonomyAnalysisActivity" + }, + "type": "array" + }, + "read_qc_analysis_activity_set": { + "description": "This property links a database object to the set of read QC analysis activities.", + "items": { + "$ref": "#/$defs/ReadQcAnalysisActivity" + }, + "type": "array" + }, + "study_set": { + "description": "This property links a database object to the set of studies within it.", + "items": { + "$ref": "#/$defs/Study" + }, + "type": "array" + } + }, + "title": "NMDC", + "type": "object", + "version": "7.0.0" +} diff --git a/nmdc_schema/nmdc.yaml b/nmdc_schema/nmdc.yaml index 78e956aed0..21ed057b1f 100644 --- a/nmdc_schema/nmdc.yaml +++ b/nmdc_schema/nmdc.yaml @@ -7,7 +7,7 @@ notes: - "removed/commented out the comfusing 'identifier' slot" - "removed/commented out all mentions and definitions of depth2 and subsurface_depth2" - "depth2 should now be migrated to the has_maximum_value part of depth" - - "slots requested for Bioscales, but already available for Biosample: tot_phosp, tot_carb, tot_nitro_content, pH" + - "slots requested for Bioscales, but already available for Biosample : tot_phosp, tot_carb, tot_nitro_content, pH" - "informal ## section delimiters should be replaced with subsets ?" - "commented out insdc_biosample_identifiers insdc_secondary_sample_identifiers... need better understanding of id patterns (at least)" - "commented out several MIxS terms assigned to Biosample because the definitions of those terms were commented out in mixs.yaml dues to shared slot uris" @@ -94,16 +94,19 @@ imports: settings: id_nmdc_prefix: "^(nmdc)" - id_typecode: "([a-z]{1,6})" +# id_typecode: "([a-z]{1,6})" id_shoulder: "([0-9][a-z]{0,6}[0-9])" id_blade: "([A-Za-z0-9]{1,})" id_version: "(\\.[A-Za-z0-9]{1,})*" id_locus: "(_[A-Za-z0-9_\\.-]+)?$" # class to typecode associations - id_typecode_biosample: "bsm" - id_typecode_study: "sty" - id_typecode_biosample_processing: "bsmprc" - id_typecode_omics_processing: "omprc" + # id_typecode_biosample: "bsm" + # id_typecode_study: "sty" + # id_typecode_biosample_processing: "bsmprc" + # id_typecode_omics_processing: "omprc" + # id_typecode_dataobject: "dobj" + # id_typecode_activity: "acty" + # id_typecode_named_thing: "nt" subsets: sample subset: @@ -170,6 +173,13 @@ classes: the same plant were obtained at the same site. In this case, the site would correspond to one tree. - "might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833" + slot_usage: + id: + pattern: '^nmdc:frsite' + structured_pattern: + syntax: "{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false CollectingBiosamplesFromSite: is_a: PlannedProcess @@ -187,6 +197,12 @@ classes: has_outputs: range: Biosample required: true + id: + pattern: '^nmdc:clsite' + structured_pattern: + syntax: "{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false DataObject: @@ -194,7 +210,9 @@ classes: in_subset: - data object subset description: 'An object that primarily consists of symbols that represent information. Files, - records, and omics data are examples of data objects. ' + records, and omics data are examples of data objects.' + notes: + - removed previous id_prefixes value of GOLD, since we are now using pattern-based id validation slots: - file_size_bytes - md5_checksum @@ -208,8 +226,14 @@ classes: required: true description: required: true - id_prefixes: - - GOLD + id: + pattern: '^nmdc:dobj' + structured_pattern: + syntax: "{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}" + interpolated: true + partial_match: false + # id_prefixes: + # - GOLD Biosample: is_a: MaterialEntity @@ -224,6 +248,8 @@ classes: Biological source material which can be characterized by an experiment. todos: - could add GOLD and EBI's biosample definitions to the alt_descriptions? + notes: + - removed previous id_prefixes value of GOLD, since we are now using pattern-based id validation alt_descriptions: embl.ena: A sample contains information about the sequenced source material. Samples are associated with checklists, which define the fields used to annotate @@ -491,9 +517,9 @@ classes: id: description: An NMDC assigned unique identifier for a biosample submitted to NMDC. required: true - pattern: '^nmdc:' + pattern: '^nmdc:bsm' structured_pattern: - syntax: "{id_nmdc_prefix}:{id_typecode_biosample}-{id_shoulder}-{id_blade}{id_version}{id_locus}" + syntax: "{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false @@ -533,9 +559,8 @@ classes: tag: expected_value value: date, string range: string - - id_prefixes: - - GOLD + # id_prefixes: + # - GOLD exact_mappings: - OBI:0000747 - NCIT:C43412 @@ -597,11 +622,12 @@ classes: - study_image slot_usage: id: - description: An NMDC assigned unique identifier for a sample submitted to NMDC. + pattern: '^nmdc:sty' structured_pattern: - syntax: "{id_nmdc_prefix}:{id_typecode_study}-{id_shoulder}-{id_blade}{id_version}{id_locus}" + syntax: "{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false + doi: description: >- The dataset citation for this study @@ -676,14 +702,15 @@ classes: - determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor - project_name is redundant with name, so excluding it - id_prefixes: - - GOLD - - insdc.srs - - mgnify + # id_prefixes: + # - GOLD + # - insdc.srs + # - mgnify notes: - "sample GOLD link https://identifiers.org/gold:Gs0110115" - "sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?" - "sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757" + - "GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers, but no longer for the Study.id" BiosampleProcessing: aliases: @@ -696,8 +723,9 @@ classes: - has_input slot_usage: id: + pattern: '^nmdc:bsmprc' structured_pattern: - syntax: "{id_nmdc_prefix}:{id_typecode_biosample_processing}-{id_shoulder}-{id_blade}{id_version}{id_locus}" + syntax: "{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false has_input: @@ -744,10 +772,12 @@ classes: - seq_meth - seq_quality_check - chimera_check + slot_usage: id: + pattern: '^nmdc:omprc' structured_pattern: - syntax: "{id_nmdc_prefix}:{id_typecode_omics_processing}-{id_shoulder}-{id_blade}{id_version}{id_locus}" + syntax: "{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false has_input: diff --git a/nmdc_schema/prov.py b/nmdc_schema/prov.py index 10232a9005..0a3d86016c 100644 --- a/nmdc_schema/prov.py +++ b/nmdc_schema/prov.py @@ -1,5 +1,5 @@ # Auto generated from prov.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:20 +# Generation date: 2023-01-20T13:17:03 # Schema: NMDC-PROV # # id: https://microbiomedata/schema/prov @@ -258,15 +258,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -322,11 +313,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, Agent]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -1234,6 +1220,18 @@ class slots: slots.magBin__gtdbtk_species = Slot(uri=NMDC.gtdbtk_species, name="magBin__gtdbtk_species", curie=NMDC.curie('gtdbtk_species'), model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) + +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1261,6 +1259,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) diff --git a/nmdc_schema/sample_prep.py b/nmdc_schema/sample_prep.py index 88f55268bb..b09c3dfc82 100644 --- a/nmdc_schema/sample_prep.py +++ b/nmdc_schema/sample_prep.py @@ -1,5 +1,5 @@ # Auto generated from sample_prep.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:05 +# Generation date: 2023-01-20T13:16:34 # Schema: sample_prep # # id: https://microbiomedata/schema/sample_prep @@ -71,9 +71,7 @@ BIOLINK = CurieNamespace('biolink', 'https://w3id.org/biolink/vocab/') DCTERMS = CurieNamespace('dcterms', 'http://purl.org/dc/terms/') GTPO = CurieNamespace('gtpo', 'https://unknown.to.linter.org/') -INSDC_SRS = CurieNamespace('insdc_srs', 'https://unknown.to.linter.org/') LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -MGNIFY = CurieNamespace('mgnify', 'https://unknown.to.linter.org/') MIXS = CurieNamespace('mixs', 'https://w3id.org/mixs/') NMDC = CurieNamespace('nmdc', 'https://w3id.org/nmdc/') PROV = CurieNamespace('prov', 'http://www.w3.org/ns/prov#') @@ -1025,15 +1023,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class Biosample(MaterialEntity): """ @@ -2036,11 +2025,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -8327,7 +8311,8 @@ class slots: model_uri=NMDC.dna_cont_type, domain=None, range=Optional[Union[str, "DnaContTypeEnum"]]) slots.dna_cont_well = Slot(uri=NMDC.dna_cont_well, name="dna_cont_well", curie=NMDC.curie('dna_cont_well'), - model_uri=NMDC.dna_cont_well, domain=None, range=Optional[str]) + model_uri=NMDC.dna_cont_well, domain=None, range=Optional[str], + pattern=re.compile(r'^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$')) slots.dna_container_id = Slot(uri=NMDC.dna_container_id, name="dna_container_id", curie=NMDC.curie('dna_container_id'), model_uri=NMDC.dna_container_id, domain=None, range=Optional[str]) @@ -8390,7 +8375,8 @@ class slots: model_uri=NMDC.rna_cont_type, domain=None, range=Optional[Union[str, "RnaContTypeEnum"]]) slots.rna_cont_well = Slot(uri=NMDC.rna_cont_well, name="rna_cont_well", curie=NMDC.curie('rna_cont_well'), - model_uri=NMDC.rna_cont_well, domain=None, range=Optional[str]) + model_uri=NMDC.rna_cont_well, domain=None, range=Optional[str], + pattern=re.compile(r'^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$')) slots.rna_container_id = Slot(uri=NMDC.rna_container_id, name="rna_container_id", curie=NMDC.curie('rna_container_id'), model_uri=NMDC.rna_container_id, domain=None, range=Optional[str]) @@ -8691,6 +8677,10 @@ class slots: slots.DissolvingActivity_material_output = Slot(uri=NMDC.material_output, name="DissolvingActivity_material_output", curie=NMDC.curie('material_output'), model_uri=NMDC.DissolvingActivity_material_output, domain=DissolvingActivity, range=Optional[Union[str, MaterialSampleId]]) +slots.MaterialSample_id = Slot(uri=NMDC.id, name="MaterialSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.MaterialSample_id, domain=MaterialSample, range=Union[str, MaterialSampleId], + pattern=re.compile(r'^nmdc:matsm')) + slots.MaterialSamplingActivity_amount_collected = Slot(uri=NMDC.amount_collected, name="MaterialSamplingActivity_amount_collected", curie=NMDC.curie('amount_collected'), model_uri=NMDC.MaterialSamplingActivity_amount_collected, domain=MaterialSamplingActivity, range=Optional[Union[dict, "QuantityValue"]]) @@ -8724,21 +8714,33 @@ class slots: slots.Database_metatranscriptome_activity_set = Slot(uri=NMDC.metatranscriptome_activity_set, name="Database_metatranscriptome_activity_set", curie=NMDC.curie('metatranscriptome_activity_set'), model_uri=NMDC.Database_metatranscriptome_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]]) +slots.FieldResearchSite_id = Slot(uri=NMDC.id, name="FieldResearchSite_id", curie=NMDC.curie('id'), + model_uri=NMDC.FieldResearchSite_id, domain=FieldResearchSite, range=Union[str, FieldResearchSiteId], + pattern=re.compile(r'^nmdc:frsite')) + slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) slots.CollectingBiosamplesFromSite_has_outputs = Slot(uri=NMDC.has_outputs, name="CollectingBiosamplesFromSite_has_outputs", curie=NMDC.curie('has_outputs'), model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) +slots.CollectingBiosamplesFromSite_id = Slot(uri=NMDC.id, name="CollectingBiosamplesFromSite_id", curie=NMDC.curie('id'), + model_uri=NMDC.CollectingBiosamplesFromSite_id, domain=CollectingBiosamplesFromSite, range=Union[str, CollectingBiosamplesFromSiteId], + pattern=re.compile(r'^nmdc:clsite')) + slots.DataObject_name = Slot(uri=NMDC.name, name="DataObject_name", curie=NMDC.curie('name'), model_uri=NMDC.DataObject_name, domain=DataObject, range=str) slots.DataObject_description = Slot(uri=DCTERMS.description, name="DataObject_description", curie=DCTERMS.curie('description'), model_uri=NMDC.DataObject_description, domain=DataObject, range=str) +slots.DataObject_id = Slot(uri=NMDC.id, name="DataObject_id", curie=NMDC.curie('id'), + model_uri=NMDC.DataObject_id, domain=DataObject, range=Union[str, DataObjectId], + pattern=re.compile(r'^nmdc:dobj')) + slots.Biosample_id = Slot(uri=NMDC.id, name="Biosample_id", curie=NMDC.curie('id'), model_uri=NMDC.Biosample_id, domain=Biosample, range=Union[str, BiosampleId], - pattern=re.compile(r'^nmdc:')) + pattern=re.compile(r'^nmdc:bsm')) slots.Biosample_gold_biosample_identifiers = Slot(uri=NMDC.gold_biosample_identifiers, name="Biosample_gold_biosample_identifiers", curie=NMDC.curie('gold_biosample_identifiers'), model_uri=NMDC.Biosample_gold_biosample_identifiers, domain=Biosample, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]], @@ -8769,7 +8771,8 @@ class slots: model_uri=NMDC.Biosample_extreme_event, domain=Biosample, range=Optional[str]) slots.Study_id = Slot(uri=NMDC.id, name="Study_id", curie=NMDC.curie('id'), - model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId]) + model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId], + pattern=re.compile(r'^nmdc:sty')) slots.Study_doi = Slot(uri=NMDC.doi, name="Study_doi", curie=NMDC.curie('doi'), model_uri=NMDC.Study_doi, domain=Study, range=Optional[Union[dict, "AttributeValue"]]) @@ -8806,17 +8809,27 @@ class slots: model_uri=NMDC.Study_emsl_proposal_doi, domain=Study, range=Optional[str]) slots.BiosampleProcessing_id = Slot(uri=NMDC.id, name="BiosampleProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId]) + model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId], + pattern=re.compile(r'^nmdc:bsmprc')) slots.BiosampleProcessing_has_input = Slot(uri=NMDC.has_input, name="BiosampleProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.BiosampleProcessing_has_input, domain=BiosampleProcessing, range=Optional[Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]]) slots.OmicsProcessing_id = Slot(uri=NMDC.id, name="OmicsProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId]) + model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId], + pattern=re.compile(r'^nmdc:omprc')) slots.OmicsProcessing_has_input = Slot(uri=NMDC.has_input, name="OmicsProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.OmicsProcessing_has_input, domain=OmicsProcessing, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -8844,6 +8857,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -8971,6 +8988,10 @@ class slots: slots.FunctionalAnnotation_was_generated_by = Slot(uri=NMDC.was_generated_by, name="FunctionalAnnotation_was_generated_by", curie=NMDC.curie('was_generated_by'), model_uri=NMDC.FunctionalAnnotation_was_generated_by, domain=FunctionalAnnotation, range=Optional[Union[str, MetagenomeAnnotationActivityId]], mappings = [PROV.wasGeneratedBy]) +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) + slots.WorkflowExecutionActivity_was_associated_with = Slot(uri=NMDC.was_associated_with, name="WorkflowExecutionActivity_was_associated_with", curie=NMDC.curie('was_associated_with'), model_uri=NMDC.WorkflowExecutionActivity_was_associated_with, domain=WorkflowExecutionActivity, range=Optional[Union[str, WorkflowExecutionActivityId]], mappings = [PROV.wasAssociatedWith]) @@ -9000,6 +9021,34 @@ class slots: slots.WorkflowExecutionActivity_type = Slot(uri=NMDC.type, name="WorkflowExecutionActivity_type", curie=NMDC.curie('type'), model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) +slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], + pattern=re.compile(r'^nmdc:wf')) + +slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmgas')) + +slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmtas')) + +slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmgan')) + +slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmtan')) + +slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], + pattern=re.compile(r'^nmdc:wfmt')) + +slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmag')) + slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -9012,6 +9061,14 @@ class slots: slots.ReadQcAnalysisActivity_has_output = Slot(uri=NMDC.has_output, name="ReadQcAnalysisActivity_has_output", curie=NMDC.curie('has_output'), model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) +slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrqc')) + +slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrbt')) + slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9021,14 +9078,26 @@ class slots: slots.MetabolomicsAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="MetabolomicsAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) +slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmb')) + slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.MetaproteomicsAnalysisActivity_has_peptide_quantifications = Slot(uri=NMDC.has_peptide_quantifications, name="MetaproteomicsAnalysisActivity_has_peptide_quantifications", curie=NMDC.curie('has_peptide_quantifications'), model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, PeptideQuantification], List[Union[dict, PeptideQuantification]]]]) +slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmp')) + slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.NomAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="NomAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) + +slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfnom')) diff --git a/nmdc_schema/workflow_execution_activity.py b/nmdc_schema/workflow_execution_activity.py index 0ca0547b61..b0dfd52910 100644 --- a/nmdc_schema/workflow_execution_activity.py +++ b/nmdc_schema/workflow_execution_activity.py @@ -1,5 +1,5 @@ # Auto generated from workflow_execution_activity.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:01 +# Generation date: 2023-01-20T13:17:01 # Schema: NMDC-Workflow-Execution # # id: https://microbiomedata/schema/workflow_execution_activity @@ -1076,15 +1076,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -1140,11 +1131,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, Agent]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -2291,6 +2277,34 @@ class slots: slots.WorkflowExecutionActivity_type = Slot(uri=NMDC.type, name="WorkflowExecutionActivity_type", curie=NMDC.curie('type'), model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) +slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], + pattern=re.compile(r'^nmdc:wf')) + +slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmgas')) + +slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmtas')) + +slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmgan')) + +slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmtan')) + +slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], + pattern=re.compile(r'^nmdc:wfmt')) + +slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmag')) + slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -2303,6 +2317,14 @@ class slots: slots.ReadQcAnalysisActivity_has_output = Slot(uri=NMDC.has_output, name="ReadQcAnalysisActivity_has_output", curie=NMDC.curie('has_output'), model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) +slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrqc')) + +slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrbt')) + slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2312,18 +2334,42 @@ class slots: slots.MetabolomicsAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="MetabolomicsAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) +slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmb')) + slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.MetaproteomicsAnalysisActivity_has_peptide_quantifications = Slot(uri=NMDC.has_peptide_quantifications, name="MetaproteomicsAnalysisActivity_has_peptide_quantifications", curie=NMDC.curie('has_peptide_quantifications'), model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, "PeptideQuantification"], List[Union[dict, "PeptideQuantification"]]]]) +slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmp')) + slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.NomAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="NomAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) +slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfnom')) + +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) + +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -2351,6 +2397,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) diff --git a/python/annotation.py b/python/annotation.py index 0070d5857c..1d35f0330d 100644 --- a/python/annotation.py +++ b/python/annotation.py @@ -1,5 +1,5 @@ # Auto generated from annotation.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:22 +# Generation date: 2023-01-20T13:16:52 # Schema: NMDC-Annotation # # id: https://microbiomedata/schema/annotation @@ -394,15 +394,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -458,11 +449,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -2681,6 +2667,14 @@ class slots: slots.FunctionalAnnotation_was_generated_by = Slot(uri=NMDC.was_generated_by, name="FunctionalAnnotation_was_generated_by", curie=NMDC.curie('was_generated_by'), model_uri=NMDC.FunctionalAnnotation_was_generated_by, domain=FunctionalAnnotation, range=Optional[Union[str, MetagenomeAnnotationActivityId]], mappings = [PROV.wasGeneratedBy]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -2708,6 +2702,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -2765,6 +2763,10 @@ class slots: slots.GeolocationValue_has_raw_value = Slot(uri=NMDC.has_raw_value, name="GeolocationValue_has_raw_value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) + slots.WorkflowExecutionActivity_was_associated_with = Slot(uri=NMDC.was_associated_with, name="WorkflowExecutionActivity_was_associated_with", curie=NMDC.curie('was_associated_with'), model_uri=NMDC.WorkflowExecutionActivity_was_associated_with, domain=WorkflowExecutionActivity, range=Optional[Union[str, WorkflowExecutionActivityId]], mappings = [PROV.wasAssociatedWith]) @@ -2794,6 +2796,34 @@ class slots: slots.WorkflowExecutionActivity_type = Slot(uri=NMDC.type, name="WorkflowExecutionActivity_type", curie=NMDC.curie('type'), model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) +slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], + pattern=re.compile(r'^nmdc:wf')) + +slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmgas')) + +slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmtas')) + +slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmgan')) + +slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmtan')) + +slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], + pattern=re.compile(r'^nmdc:wfmt')) + +slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmag')) + slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -2806,6 +2836,14 @@ class slots: slots.ReadQcAnalysisActivity_has_output = Slot(uri=NMDC.has_output, name="ReadQcAnalysisActivity_has_output", curie=NMDC.curie('has_output'), model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) +slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrqc')) + +slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrbt')) + slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2815,14 +2853,26 @@ class slots: slots.MetabolomicsAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="MetabolomicsAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) +slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmb')) + slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.MetaproteomicsAnalysisActivity_has_peptide_quantifications = Slot(uri=NMDC.has_peptide_quantifications, name="MetaproteomicsAnalysisActivity_has_peptide_quantifications", curie=NMDC.curie('has_peptide_quantifications'), model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, PeptideQuantification], List[Union[dict, PeptideQuantification]]]]) +slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmp')) + slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.NomAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="NomAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) + +slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfnom')) diff --git a/python/basic_slots.py b/python/basic_slots.py index 233a2877f5..3caaf63148 100644 --- a/python/basic_slots.py +++ b/python/basic_slots.py @@ -1,5 +1,5 @@ # Auto generated from basic_slots.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:03 +# Generation date: 2023-01-20T13:16:40 # Schema: NMDC-Basic-Slots # # id: https://microbiomedata/schema/basic_slots @@ -188,15 +188,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -252,11 +243,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -1236,6 +1222,14 @@ class slots: slots.magBin__gtdbtk_species = Slot(uri=NMDC.gtdbtk_species, name="magBin__gtdbtk_species", curie=NMDC.curie('gtdbtk_species'), model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1263,6 +1257,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1319,3 +1317,7 @@ class slots: slots.GeolocationValue_has_raw_value = Slot(uri=NMDC.has_raw_value, name="GeolocationValue_has_raw_value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) + +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) diff --git a/python/bioscales.py b/python/bioscales.py index 0fe7ef5672..c096d0d0dc 100644 --- a/python/bioscales.py +++ b/python/bioscales.py @@ -1,5 +1,5 @@ # Auto generated from bioscales.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:46:59 +# Generation date: 2023-01-20T13:17:05 # Schema: NMDC-Bioscales # # id: https://microbiomedata/schema/bioscales @@ -189,15 +189,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -253,11 +244,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -1258,6 +1244,14 @@ class slots: slots.magBin__gtdbtk_species = Slot(uri=NMDC.gtdbtk_species, name="magBin__gtdbtk_species", curie=NMDC.curie('gtdbtk_species'), model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1285,6 +1279,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1341,3 +1339,7 @@ class slots: slots.GeolocationValue_has_raw_value = Slot(uri=NMDC.has_raw_value, name="GeolocationValue_has_raw_value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) + +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) diff --git a/python/core.py b/python/core.py index 8532137de5..b93015a04e 100644 --- a/python/core.py +++ b/python/core.py @@ -1,5 +1,5 @@ # Auto generated from core.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:24 +# Generation date: 2023-01-20T13:17:14 # Schema: NMDC-Core # # id: https://microbiomedata/schema/core @@ -189,15 +189,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -253,11 +244,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -1237,6 +1223,14 @@ class slots: slots.magBin__gtdbtk_species = Slot(uri=NMDC.gtdbtk_species, name="magBin__gtdbtk_species", curie=NMDC.curie('gtdbtk_species'), model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1264,6 +1258,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1320,3 +1318,7 @@ class slots: slots.GeolocationValue_has_raw_value = Slot(uri=NMDC.has_raw_value, name="GeolocationValue_has_raw_value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) + +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) diff --git a/python/external_identifiers.py b/python/external_identifiers.py index 891ee5f3a9..1215e5e6da 100644 --- a/python/external_identifiers.py +++ b/python/external_identifiers.py @@ -1,5 +1,5 @@ # Auto generated from external_identifiers.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:26 +# Generation date: 2023-01-20T13:16:54 # Schema: external_identifiers # # id: https://microbiomedata/schema/external_identifiers @@ -195,15 +195,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -259,11 +250,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -1321,6 +1307,14 @@ class slots: slots.magBin__gtdbtk_species = Slot(uri=NMDC.gtdbtk_species, name="magBin__gtdbtk_species", curie=NMDC.curie('gtdbtk_species'), model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1348,6 +1342,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1404,3 +1402,7 @@ class slots: slots.GeolocationValue_has_raw_value = Slot(uri=NMDC.has_raw_value, name="GeolocationValue_has_raw_value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) + +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) diff --git a/python/mixs.py b/python/mixs.py index 66a2bd2633..8fcb469f11 100644 --- a/python/mixs.py +++ b/python/mixs.py @@ -1,5 +1,5 @@ # Auto generated from mixs.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:18 +# Generation date: 2023-01-20T13:16:58 # Schema: mixs-schema # # id: https://microbiomedata/schema/mixs @@ -186,15 +186,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -250,11 +241,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -4676,6 +4662,14 @@ class slots: slots.magBin__gtdbtk_species = Slot(uri=NMDC.gtdbtk_species, name="magBin__gtdbtk_species", curie=NMDC.curie('gtdbtk_species'), model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -4703,6 +4697,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -4759,3 +4757,7 @@ class slots: slots.GeolocationValue_has_raw_value = Slot(uri=NMDC.has_raw_value, name="GeolocationValue_has_raw_value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) + +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) diff --git a/python/mixs_legacy.py b/python/mixs_legacy.py deleted file mode 100644 index f9f56e2fa9..0000000000 --- a/python/mixs_legacy.py +++ /dev/null @@ -1,3311 +0,0 @@ -# Auto generated from mixs_legacy.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-05-06T11:21:59 -# Schema: mixs-schema -# -# id: https://microbiomedata/schema/mixs -# description: -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import Boolean, Datetime, Double, Float, Integer, String -from linkml_runtime.utils.metamodelcore import Bool, XSDDateTime - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CAS = CurieNamespace('CAS', 'http://identifiers.org/cas/') -CHEBI = CurieNamespace('CHEBI', 'http://purl.obolibrary.org/obo/CHEBI_') -CHEMBL_COMPOUND = CurieNamespace('CHEMBL_COMPOUND', 'http://identifiers.org/chembl.compound/') -DRUGBANK = CurieNamespace('DRUGBANK', 'http://identifiers.org/drugbank/') -HMDB = CurieNamespace('HMDB', 'http://identifiers.org/hmdb/') -KEGG_COMPOUND = CurieNamespace('KEGG_COMPOUND', 'http://identifiers.org/kegg.compound/') -MESH = CurieNamespace('MESH', 'http://identifiers.org/mesh/') -OBI = CurieNamespace('OBI', 'http://purl.obolibrary.org/obo/OBI_') -PR = CurieNamespace('PR', 'http://purl.obolibrary.org/obo/PR_') -PUBCHEM_COMPOUND = CurieNamespace('PUBCHEM_COMPOUND', 'http://identifiers.org/pubchem.compound/') -UNIPROTKB = CurieNamespace('UniProtKB', 'http://example.org/UNKNOWN/UniProtKB/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -DCTERMS = CurieNamespace('dcterms', 'http://purl.org/dc/terms/') -GTPO = CurieNamespace('gtpo', 'http://example.org/UNKNOWN/gtpo/') -MIXS = CurieNamespace('mixs', 'https://w3id.org/gensc/') -NMDC = CurieNamespace('nmdc', 'https://microbiomedata/meta/') -PROV = CurieNamespace('prov', 'http://www.w3.org/ns/prov#') -QUD = CurieNamespace('qud', 'http://qudt.org/1.1/schema/qudt#') -RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#') -SCHEMA = CurieNamespace('schema', 'http://schema.org/') -SIO = CurieNamespace('sio', 'http://semanticscience.org/resource/SIO_') -SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#') -WGS = CurieNamespace('wgs', 'http://www.w3.org/2003/01/geo/wgs84_pos') -XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#') -DEFAULT_ = CurieNamespace('', 'https://microbiomedata/schema/mixs/') - - -# Types -class Bytes(int): - """ An integer value that corresponds to a size in bytes """ - type_class_uri = XSD.int - type_class_curie = "xsd:int" - type_name = "bytes" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/Bytes") - - -class DecimalDegree(float): - """ A decimal degree expresses latitude or longitude as decimal fractions. """ - type_class_uri = XSD.decimal - type_class_curie = "xsd:decimal" - type_name = "decimal degree" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/DecimalDegree") - - -class LanguageCode(str): - """ A language code conforming to ISO_639-1 """ - type_class_uri = XSD.language - type_class_curie = "xsd:language" - type_name = "language code" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/LanguageCode") - - -class Unit(str): - type_class_uri = XSD.string - type_class_curie = "xsd:string" - type_name = "unit" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/Unit") - - -# Class references -class NamedThingId(extended_str): - pass - - -class OntologyClassId(NamedThingId): - pass - - -class EnvironmentalMaterialTermId(OntologyClassId): - pass - - -class PersonId(NamedThingId): - pass - - -class InstrumentId(NamedThingId): - pass - - -class ChemicalEntityId(OntologyClassId): - pass - - -class GeneProductId(NamedThingId): - pass - - -class ActivityId(extended_str): - pass - - -@dataclass -class NamedThing(YAMLRoot): - """ - a databased entity or concept/class - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.NamedThing - class_class_curie: ClassVar[str] = "nmdc:NamedThing" - class_name: ClassVar[str] = "named thing" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/NamedThing") - - id: Union[str, NamedThingId] = None - name: Optional[str] = None - description: Optional[str] = None - alternative_identifiers: Optional[Union[str, List[str]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedThingId): - self.id = NamedThingId(self.id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.alternative_identifiers, list): - self.alternative_identifiers = [self.alternative_identifiers] if self.alternative_identifiers is not None else [] - self.alternative_identifiers = [v if isinstance(v, str) else str(v) for v in self.alternative_identifiers] - - super().__post_init__(**kwargs) - - -@dataclass -class OntologyClass(NamedThing): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.OntologyClass - class_class_curie: ClassVar[str] = "nmdc:OntologyClass" - class_name: ClassVar[str] = "ontology class" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/OntologyClass") - - id: Union[str, OntologyClassId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OntologyClassId): - self.id = OntologyClassId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class EnvironmentalMaterialTerm(OntologyClass): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.EnvironmentalMaterialTerm - class_class_curie: ClassVar[str] = "nmdc:EnvironmentalMaterialTerm" - class_name: ClassVar[str] = "environmental material term" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/EnvironmentalMaterialTerm") - - id: Union[str, EnvironmentalMaterialTermId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentalMaterialTermId): - self.id = EnvironmentalMaterialTermId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class AttributeValue(YAMLRoot): - """ - The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and - the structured value - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.AttributeValue - class_class_curie: ClassVar[str] = "nmdc:AttributeValue" - class_name: ClassVar[str] = "attribute value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/AttributeValue") - - has_raw_value: Optional[str] = None - was_generated_by: Optional[Union[str, ActivityId]] = None - type: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - if self.was_generated_by is not None and not isinstance(self.was_generated_by, ActivityId): - self.was_generated_by = ActivityId(self.was_generated_by) - - if self.type is not None and not isinstance(self.type, str): - self.type = str(self.type) - - super().__post_init__(**kwargs) - - -@dataclass -class QuantityValue(AttributeValue): - """ - A simple quantity, e.g. 2cm - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.QuantityValue - class_class_curie: ClassVar[str] = "nmdc:QuantityValue" - class_name: ClassVar[str] = "quantity value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/QuantityValue") - - has_unit: Optional[str] = None - has_numeric_value: Optional[float] = None - has_minimum_numeric_value: Optional[float] = None - has_maximum_numeric_value: Optional[float] = None - has_raw_value: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_unit is not None and not isinstance(self.has_unit, str): - self.has_unit = str(self.has_unit) - - if self.has_numeric_value is not None and not isinstance(self.has_numeric_value, float): - self.has_numeric_value = float(self.has_numeric_value) - - if self.has_minimum_numeric_value is not None and not isinstance(self.has_minimum_numeric_value, float): - self.has_minimum_numeric_value = float(self.has_minimum_numeric_value) - - if self.has_maximum_numeric_value is not None and not isinstance(self.has_maximum_numeric_value, float): - self.has_maximum_numeric_value = float(self.has_maximum_numeric_value) - - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - super().__post_init__(**kwargs) - - -@dataclass -class ImageValue(AttributeValue): - """ - An attribute value representing an image. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ImageValue - class_class_curie: ClassVar[str] = "nmdc:ImageValue" - class_name: ClassVar[str] = "image value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ImageValue") - - url: Optional[str] = None - description: Optional[str] = None - display_order: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.url is not None and not isinstance(self.url, str): - self.url = str(self.url) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if self.display_order is not None and not isinstance(self.display_order, str): - self.display_order = str(self.display_order) - - super().__post_init__(**kwargs) - - -@dataclass -class PersonValue(AttributeValue): - """ - An attribute value representing a person - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.PersonValue - class_class_curie: ClassVar[str] = "nmdc:PersonValue" - class_name: ClassVar[str] = "person value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/PersonValue") - - orcid: Optional[str] = None - profile_image_url: Optional[str] = None - email: Optional[str] = None - name: Optional[str] = None - websites: Optional[Union[str, List[str]]] = empty_list() - has_raw_value: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.orcid is not None and not isinstance(self.orcid, str): - self.orcid = str(self.orcid) - - if self.profile_image_url is not None and not isinstance(self.profile_image_url, str): - self.profile_image_url = str(self.profile_image_url) - - if self.email is not None and not isinstance(self.email, str): - self.email = str(self.email) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if not isinstance(self.websites, list): - self.websites = [self.websites] if self.websites is not None else [] - self.websites = [v if isinstance(v, str) else str(v) for v in self.websites] - - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - super().__post_init__(**kwargs) - - -@dataclass -class Person(NamedThing): - """ - represents a person, such as a researcher - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Person - class_class_curie: ClassVar[str] = "nmdc:Person" - class_name: ClassVar[str] = "person" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Person") - - id: Union[str, PersonId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PersonId): - self.id = PersonId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class MAGBin(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.MAGBin - class_class_curie: ClassVar[str] = "nmdc:MAGBin" - class_name: ClassVar[str] = "MAG bin" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/MAGBin") - - type: Optional[str] = None - bin_name: Optional[str] = None - number_of_contig: Optional[int] = None - completeness: Optional[float] = None - contamination: Optional[float] = None - gene_count: Optional[int] = None - bin_quality: Optional[str] = None - num_16s: Optional[int] = None - num_5s: Optional[int] = None - num_23s: Optional[int] = None - num_tRNA: Optional[int] = None - gtdbtk_domain: Optional[str] = None - gtdbtk_phylum: Optional[str] = None - gtdbtk_class: Optional[str] = None - gtdbtk_order: Optional[str] = None - gtdbtk_family: Optional[str] = None - gtdbtk_genus: Optional[str] = None - gtdbtk_species: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.type is not None and not isinstance(self.type, str): - self.type = str(self.type) - - if self.bin_name is not None and not isinstance(self.bin_name, str): - self.bin_name = str(self.bin_name) - - if self.number_of_contig is not None and not isinstance(self.number_of_contig, int): - self.number_of_contig = int(self.number_of_contig) - - if self.completeness is not None and not isinstance(self.completeness, float): - self.completeness = float(self.completeness) - - if self.contamination is not None and not isinstance(self.contamination, float): - self.contamination = float(self.contamination) - - if self.gene_count is not None and not isinstance(self.gene_count, int): - self.gene_count = int(self.gene_count) - - if self.bin_quality is not None and not isinstance(self.bin_quality, str): - self.bin_quality = str(self.bin_quality) - - if self.num_16s is not None and not isinstance(self.num_16s, int): - self.num_16s = int(self.num_16s) - - if self.num_5s is not None and not isinstance(self.num_5s, int): - self.num_5s = int(self.num_5s) - - if self.num_23s is not None and not isinstance(self.num_23s, int): - self.num_23s = int(self.num_23s) - - if self.num_tRNA is not None and not isinstance(self.num_tRNA, int): - self.num_tRNA = int(self.num_tRNA) - - if self.gtdbtk_domain is not None and not isinstance(self.gtdbtk_domain, str): - self.gtdbtk_domain = str(self.gtdbtk_domain) - - if self.gtdbtk_phylum is not None and not isinstance(self.gtdbtk_phylum, str): - self.gtdbtk_phylum = str(self.gtdbtk_phylum) - - if self.gtdbtk_class is not None and not isinstance(self.gtdbtk_class, str): - self.gtdbtk_class = str(self.gtdbtk_class) - - if self.gtdbtk_order is not None and not isinstance(self.gtdbtk_order, str): - self.gtdbtk_order = str(self.gtdbtk_order) - - if self.gtdbtk_family is not None and not isinstance(self.gtdbtk_family, str): - self.gtdbtk_family = str(self.gtdbtk_family) - - if self.gtdbtk_genus is not None and not isinstance(self.gtdbtk_genus, str): - self.gtdbtk_genus = str(self.gtdbtk_genus) - - if self.gtdbtk_species is not None and not isinstance(self.gtdbtk_species, str): - self.gtdbtk_species = str(self.gtdbtk_species) - - super().__post_init__(**kwargs) - - -@dataclass -class Instrument(NamedThing): - """ - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI]. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Instrument - class_class_curie: ClassVar[str] = "nmdc:Instrument" - class_name: ClassVar[str] = "instrument" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Instrument") - - id: Union[str, InstrumentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, InstrumentId): - self.id = InstrumentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class MetaboliteQuantification(YAMLRoot): - """ - This is used to link a metabolomics analysis workflow to a specific metabolite - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.MetaboliteQuantification - class_class_curie: ClassVar[str] = "nmdc:MetaboliteQuantification" - class_name: ClassVar[str] = "metabolite quantification" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/MetaboliteQuantification") - - alternative_identifiers: Optional[Union[str, List[str]]] = empty_list() - metabolite_quantified: Optional[Union[str, ChemicalEntityId]] = None - highest_similarity_score: Optional[float] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.alternative_identifiers, list): - self.alternative_identifiers = [self.alternative_identifiers] if self.alternative_identifiers is not None else [] - self.alternative_identifiers = [v if isinstance(v, str) else str(v) for v in self.alternative_identifiers] - - if self.metabolite_quantified is not None and not isinstance(self.metabolite_quantified, ChemicalEntityId): - self.metabolite_quantified = ChemicalEntityId(self.metabolite_quantified) - - if self.highest_similarity_score is not None and not isinstance(self.highest_similarity_score, float): - self.highest_similarity_score = float(self.highest_similarity_score) - - super().__post_init__(**kwargs) - - -@dataclass -class PeptideQuantification(YAMLRoot): - """ - This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.PeptideQuantification - class_class_curie: ClassVar[str] = "nmdc:PeptideQuantification" - class_name: ClassVar[str] = "peptide quantification" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/PeptideQuantification") - - peptide_sequence: Optional[str] = None - best_protein: Optional[Union[str, GeneProductId]] = None - all_proteins: Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]] = empty_list() - min_q_value: Optional[float] = None - peptide_spectral_count: Optional[int] = None - peptide_sum_masic_abundance: Optional[int] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.peptide_sequence is not None and not isinstance(self.peptide_sequence, str): - self.peptide_sequence = str(self.peptide_sequence) - - if self.best_protein is not None and not isinstance(self.best_protein, GeneProductId): - self.best_protein = GeneProductId(self.best_protein) - - if not isinstance(self.all_proteins, list): - self.all_proteins = [self.all_proteins] if self.all_proteins is not None else [] - self.all_proteins = [v if isinstance(v, GeneProductId) else GeneProductId(v) for v in self.all_proteins] - - if self.min_q_value is not None and not isinstance(self.min_q_value, float): - self.min_q_value = float(self.min_q_value) - - if self.peptide_spectral_count is not None and not isinstance(self.peptide_spectral_count, int): - self.peptide_spectral_count = int(self.peptide_spectral_count) - - if self.peptide_sum_masic_abundance is not None and not isinstance(self.peptide_sum_masic_abundance, int): - self.peptide_sum_masic_abundance = int(self.peptide_sum_masic_abundance) - - super().__post_init__(**kwargs) - - -@dataclass -class ProteinQuantification(YAMLRoot): - """ - This is used to link a metaproteomics analysis workflow to a specific protein - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ProteinQuantification - class_class_curie: ClassVar[str] = "nmdc:ProteinQuantification" - class_name: ClassVar[str] = "protein quantification" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ProteinQuantification") - - best_protein: Optional[Union[str, GeneProductId]] = None - all_proteins: Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]] = empty_list() - peptide_sequence_count: Optional[int] = None - protein_spectral_count: Optional[int] = None - protein_sum_masic_abundance: Optional[int] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.best_protein is not None and not isinstance(self.best_protein, GeneProductId): - self.best_protein = GeneProductId(self.best_protein) - - if not isinstance(self.all_proteins, list): - self.all_proteins = [self.all_proteins] if self.all_proteins is not None else [] - self.all_proteins = [v if isinstance(v, GeneProductId) else GeneProductId(v) for v in self.all_proteins] - - if self.peptide_sequence_count is not None and not isinstance(self.peptide_sequence_count, int): - self.peptide_sequence_count = int(self.peptide_sequence_count) - - if self.protein_spectral_count is not None and not isinstance(self.protein_spectral_count, int): - self.protein_spectral_count = int(self.protein_spectral_count) - - if self.protein_sum_masic_abundance is not None and not isinstance(self.protein_sum_masic_abundance, int): - self.protein_sum_masic_abundance = int(self.protein_sum_masic_abundance) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalEntity(OntologyClass): - """ - An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, - drugs. There may be different terms for distinct acid-base forms, protonation states - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ChemicalEntity - class_class_curie: ClassVar[str] = "nmdc:ChemicalEntity" - class_name: ClassVar[str] = "chemical entity" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ChemicalEntity") - - id: Union[str, ChemicalEntityId] = None - inchi: Optional[str] = None - inchi_key: Optional[str] = None - smiles: Optional[Union[str, List[str]]] = empty_list() - chemical_formula: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalEntityId): - self.id = ChemicalEntityId(self.id) - - if self.inchi is not None and not isinstance(self.inchi, str): - self.inchi = str(self.inchi) - - if self.inchi_key is not None and not isinstance(self.inchi_key, str): - self.inchi_key = str(self.inchi_key) - - if not isinstance(self.smiles, list): - self.smiles = [self.smiles] if self.smiles is not None else [] - self.smiles = [v if isinstance(v, str) else str(v) for v in self.smiles] - - if self.chemical_formula is not None and not isinstance(self.chemical_formula, str): - self.chemical_formula = str(self.chemical_formula) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneProduct(NamedThing): - """ - A molecule encoded by a gene that has an evolved function - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.GeneProduct - class_class_curie: ClassVar[str] = "nmdc:GeneProduct" - class_name: ClassVar[str] = "gene product" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/GeneProduct") - - id: Union[str, GeneProductId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneProductId): - self.id = GeneProductId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class TextValue(AttributeValue): - """ - A basic string value - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.TextValue - class_class_curie: ClassVar[str] = "nmdc:TextValue" - class_name: ClassVar[str] = "text value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/TextValue") - - language: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.language is not None and not isinstance(self.language, str): - self.language = str(self.language) - - super().__post_init__(**kwargs) - - -class UrlValue(AttributeValue): - """ - A value that is a string that conforms to URL syntax - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.UrlValue - class_class_curie: ClassVar[str] = "nmdc:UrlValue" - class_name: ClassVar[str] = "url value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/UrlValue") - - -class TimestampValue(AttributeValue): - """ - A value that is a timestamp. The range should be ISO-8601 - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.TimestampValue - class_class_curie: ClassVar[str] = "nmdc:TimestampValue" - class_name: ClassVar[str] = "timestamp value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/TimestampValue") - - -@dataclass -class IntegerValue(AttributeValue): - """ - A value that is an integer - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.IntegerValue - class_class_curie: ClassVar[str] = "nmdc:IntegerValue" - class_name: ClassVar[str] = "integer value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/IntegerValue") - - has_numeric_value: Optional[float] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_numeric_value is not None and not isinstance(self.has_numeric_value, float): - self.has_numeric_value = float(self.has_numeric_value) - - super().__post_init__(**kwargs) - - -@dataclass -class BooleanValue(AttributeValue): - """ - A value that is a boolean - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.BooleanValue - class_class_curie: ClassVar[str] = "nmdc:BooleanValue" - class_name: ClassVar[str] = "boolean value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/BooleanValue") - - has_boolean_value: Optional[Union[bool, Bool]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_boolean_value is not None and not isinstance(self.has_boolean_value, Bool): - self.has_boolean_value = Bool(self.has_boolean_value) - - super().__post_init__(**kwargs) - - -@dataclass -class ControlledTermValue(AttributeValue): - """ - A controlled term or class from an ontology - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ControlledTermValue - class_class_curie: ClassVar[str] = "nmdc:ControlledTermValue" - class_name: ClassVar[str] = "controlled term value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ControlledTermValue") - - term: Optional[Union[dict, OntologyClass]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.term is not None and not isinstance(self.term, OntologyClass): - self.term = OntologyClass(**as_dict(self.term)) - - super().__post_init__(**kwargs) - - -@dataclass -class GeolocationValue(AttributeValue): - """ - A normalized value for a location on the earth's surface - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.GeolocationValue - class_class_curie: ClassVar[str] = "nmdc:GeolocationValue" - class_name: ClassVar[str] = "geolocation value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/GeolocationValue") - - latitude: Optional[float] = None - longitude: Optional[float] = None - has_raw_value: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.latitude is not None and not isinstance(self.latitude, float): - self.latitude = float(self.latitude) - - if self.longitude is not None and not isinstance(self.longitude, float): - self.longitude = float(self.longitude) - - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - super().__post_init__(**kwargs) - - -@dataclass -class Activity(YAMLRoot): - """ - a provence-generating activity - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Activity - class_class_curie: ClassVar[str] = "nmdc:Activity" - class_name: ClassVar[str] = "activity" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Activity") - - id: Union[str, ActivityId] = None - name: Optional[str] = None - started_at_time: Optional[Union[str, XSDDateTime]] = None - ended_at_time: Optional[Union[str, XSDDateTime]] = None - was_informed_by: Optional[Union[str, ActivityId]] = None - was_associated_with: Optional[Union[dict, "Agent"]] = None - used: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ActivityId): - self.id = ActivityId(self.id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.started_at_time is not None and not isinstance(self.started_at_time, XSDDateTime): - self.started_at_time = XSDDateTime(self.started_at_time) - - if self.ended_at_time is not None and not isinstance(self.ended_at_time, XSDDateTime): - self.ended_at_time = XSDDateTime(self.ended_at_time) - - if self.was_informed_by is not None and not isinstance(self.was_informed_by, ActivityId): - self.was_informed_by = ActivityId(self.was_informed_by) - - if self.was_associated_with is not None and not isinstance(self.was_associated_with, Agent): - self.was_associated_with = Agent(**as_dict(self.was_associated_with)) - - if self.used is not None and not isinstance(self.used, str): - self.used = str(self.used) - - super().__post_init__(**kwargs) - - -@dataclass -class Agent(YAMLRoot): - """ - a provence-generating agent - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Agent - class_class_curie: ClassVar[str] = "nmdc:Agent" - class_name: ClassVar[str] = "agent" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Agent") - - acted_on_behalf_of: Optional[Union[dict, "Agent"]] = None - was_informed_by: Optional[Union[str, ActivityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.acted_on_behalf_of is not None and not isinstance(self.acted_on_behalf_of, Agent): - self.acted_on_behalf_of = Agent(**as_dict(self.acted_on_behalf_of)) - - if self.was_informed_by is not None and not isinstance(self.was_informed_by, ActivityId): - self.was_informed_by = ActivityId(self.was_informed_by) - - super().__post_init__(**kwargs) - - -# Enumerations - - -# Slots -class slots: - pass - -slots.submitted_to_insdc = Slot(uri=DEFAULT_.submitted_to_insdc, name="submitted_to_insdc", curie=DEFAULT_.curie('submitted_to_insdc'), - model_uri=DEFAULT_.submitted_to_insdc, domain=None, range=Optional[Union[dict, BooleanValue]], mappings = [MIXS.submitted_to_insdc], - pattern=re.compile(r'[true|false]')) - -slots.investigation_type = Slot(uri=DEFAULT_.investigation_type, name="investigation_type", curie=DEFAULT_.curie('investigation_type'), - model_uri=DEFAULT_.investigation_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.investigation_type], - pattern=re.compile(r'[eukaryote|bacteria_archaea|plasmid|virus|organelle|metagenome|metatranscriptome|mimarks\-survey|mimarks\-specimen|misag|mimag|miuvig]')) - -slots.project_name = Slot(uri=DEFAULT_.project_name, name="project_name", curie=DEFAULT_.curie('project_name'), - model_uri=DEFAULT_.project_name, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.project_name]) - -slots.experimental_factor = Slot(uri=DEFAULT_.experimental_factor, name="experimental_factor", curie=DEFAULT_.curie('experimental_factor'), - model_uri=DEFAULT_.experimental_factor, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.experimental_factor]) - -slots.lat_lon = Slot(uri=DEFAULT_.lat_lon, name="lat_lon", curie=DEFAULT_.curie('lat_lon'), - model_uri=DEFAULT_.lat_lon, domain=None, range=Optional[Union[dict, GeolocationValue]], mappings = [MIXS.lat_lon], - pattern=re.compile(r'\d+[.\d+] \d+[.\d+]')) - -slots.depth = Slot(uri=DEFAULT_.depth, name="depth", curie=DEFAULT_.curie('depth'), - model_uri=DEFAULT_.depth, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.depth]) - -slots.alt = Slot(uri=DEFAULT_.alt, name="alt", curie=DEFAULT_.curie('alt'), - model_uri=DEFAULT_.alt, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.alt], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.elev = Slot(uri=DEFAULT_.elev, name="elev", curie=DEFAULT_.curie('elev'), - model_uri=DEFAULT_.elev, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.elev], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.geo_loc_name = Slot(uri=DEFAULT_.geo_loc_name, name="geo_loc_name", curie=DEFAULT_.curie('geo_loc_name'), - model_uri=DEFAULT_.geo_loc_name, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.geo_loc_name]) - -slots.collection_date = Slot(uri=DEFAULT_.collection_date, name="collection_date", curie=DEFAULT_.curie('collection_date'), - model_uri=DEFAULT_.collection_date, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.collection_date]) - -slots.env_broad_scale = Slot(uri=DEFAULT_.env_broad_scale, name="env_broad_scale", curie=DEFAULT_.curie('env_broad_scale'), - model_uri=DEFAULT_.env_broad_scale, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.env_broad_scale], - pattern=re.compile(r'.* \S+:\S+')) - -slots.env_local_scale = Slot(uri=DEFAULT_.env_local_scale, name="env_local_scale", curie=DEFAULT_.curie('env_local_scale'), - model_uri=DEFAULT_.env_local_scale, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.env_local_scale], - pattern=re.compile(r'.* \S+:\S+')) - -slots.env_medium = Slot(uri=DEFAULT_.env_medium, name="env_medium", curie=DEFAULT_.curie('env_medium'), - model_uri=DEFAULT_.env_medium, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.env_medium], - pattern=re.compile(r'.* \S+:\S+')) - -slots.env_package = Slot(uri=DEFAULT_.env_package, name="env_package", curie=DEFAULT_.curie('env_package'), - model_uri=DEFAULT_.env_package, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.env_package], - pattern=re.compile(r'[air|built environment|host\-associated|human\-associated|human\-skin|human\-oral|human\-gut|human\-vaginal|hydrocarbon resources\-cores|hydrocarbon resources\-fluids\/swabs|microbial mat\/biofilm|misc environment|plant\-associated|sediment|soil|wastewater\/sludge|water]')) - -slots.subspecf_gen_lin = Slot(uri=DEFAULT_.subspecf_gen_lin, name="subspecf_gen_lin", curie=DEFAULT_.curie('subspecf_gen_lin'), - model_uri=DEFAULT_.subspecf_gen_lin, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.subspecf_gen_lin]) - -slots.ploidy = Slot(uri=DEFAULT_.ploidy, name="ploidy", curie=DEFAULT_.curie('ploidy'), - model_uri=DEFAULT_.ploidy, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.ploidy], - pattern=re.compile(r'.* \S+:\S+')) - -slots.num_replicons = Slot(uri=DEFAULT_.num_replicons, name="num_replicons", curie=DEFAULT_.curie('num_replicons'), - model_uri=DEFAULT_.num_replicons, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.num_replicons]) - -slots.extrachrom_elements = Slot(uri=DEFAULT_.extrachrom_elements, name="extrachrom_elements", curie=DEFAULT_.curie('extrachrom_elements'), - model_uri=DEFAULT_.extrachrom_elements, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.extrachrom_elements]) - -slots.estimated_size = Slot(uri=DEFAULT_.estimated_size, name="estimated_size", curie=DEFAULT_.curie('estimated_size'), - model_uri=DEFAULT_.estimated_size, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.estimated_size]) - -slots.ref_biomaterial = Slot(uri=DEFAULT_.ref_biomaterial, name="ref_biomaterial", curie=DEFAULT_.curie('ref_biomaterial'), - model_uri=DEFAULT_.ref_biomaterial, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ref_biomaterial]) - -slots.source_mat_id = Slot(uri=DEFAULT_.source_mat_id, name="source_mat_id", curie=DEFAULT_.curie('source_mat_id'), - model_uri=DEFAULT_.source_mat_id, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.source_mat_id]) - -slots.pathogenicity = Slot(uri=DEFAULT_.pathogenicity, name="pathogenicity", curie=DEFAULT_.curie('pathogenicity'), - model_uri=DEFAULT_.pathogenicity, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pathogenicity]) - -slots.biotic_relationship = Slot(uri=DEFAULT_.biotic_relationship, name="biotic_relationship", curie=DEFAULT_.curie('biotic_relationship'), - model_uri=DEFAULT_.biotic_relationship, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.biotic_relationship], - pattern=re.compile(r'[free living|parasitism|commensalism|symbiotic|mutualism]')) - -slots.specific_host = Slot(uri=DEFAULT_.specific_host, name="specific_host", curie=DEFAULT_.curie('specific_host'), - model_uri=DEFAULT_.specific_host, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.specific_host]) - -slots.host_spec_range = Slot(uri=DEFAULT_.host_spec_range, name="host_spec_range", curie=DEFAULT_.curie('host_spec_range'), - model_uri=DEFAULT_.host_spec_range, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_spec_range]) - -slots.health_disease_stat = Slot(uri=DEFAULT_.health_disease_stat, name="health_disease_stat", curie=DEFAULT_.curie('health_disease_stat'), - model_uri=DEFAULT_.health_disease_stat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.health_disease_stat], - pattern=re.compile(r'[healthy|diseased|dead|disease\-free|undetermined|recovering|resolving|pre\-existing condition|pathological|life threatening|congenital]')) - -slots.trophic_level = Slot(uri=DEFAULT_.trophic_level, name="trophic_level", curie=DEFAULT_.curie('trophic_level'), - model_uri=DEFAULT_.trophic_level, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.trophic_level], - pattern=re.compile(r'[autotroph|carboxydotroph|chemoautotroph|chemoheterotroph|chemolithoautotroph|chemolithotroph|chemoorganoheterotroph|chemoorganotroph|chemosynthetic|chemotroph|copiotroph|diazotroph|facultative|autotroph|heterotroph|lithoautotroph|lithoheterotroph|lithotroph|methanotroph|methylotroph|mixotroph|obligate|chemoautolithotroph|oligotroph|organoheterotroph|organotroph|photoautotroph|photoheterotroph|photolithoautotroph|photolithotroph|photosynthetic|phototroph]')) - -slots.propagation = Slot(uri=DEFAULT_.propagation, name="propagation", curie=DEFAULT_.curie('propagation'), - model_uri=DEFAULT_.propagation, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.propagation]) - -slots.encoded_traits = Slot(uri=DEFAULT_.encoded_traits, name="encoded_traits", curie=DEFAULT_.curie('encoded_traits'), - model_uri=DEFAULT_.encoded_traits, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.encoded_traits]) - -slots.rel_to_oxygen = Slot(uri=DEFAULT_.rel_to_oxygen, name="rel_to_oxygen", curie=DEFAULT_.curie('rel_to_oxygen'), - model_uri=DEFAULT_.rel_to_oxygen, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.rel_to_oxygen], - pattern=re.compile(r'[aerobe|anaerobe|facultative|microaerophilic|microanaerobe|obligate aerobe|obligate anaerobe]')) - -slots.isol_growth_condt = Slot(uri=DEFAULT_.isol_growth_condt, name="isol_growth_condt", curie=DEFAULT_.curie('isol_growth_condt'), - model_uri=DEFAULT_.isol_growth_condt, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.isol_growth_condt]) - -slots.samp_collect_device = Slot(uri=DEFAULT_.samp_collect_device, name="samp_collect_device", curie=DEFAULT_.curie('samp_collect_device'), - model_uri=DEFAULT_.samp_collect_device, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_collect_device]) - -slots.samp_mat_process = Slot(uri=DEFAULT_.samp_mat_process, name="samp_mat_process", curie=DEFAULT_.curie('samp_mat_process'), - model_uri=DEFAULT_.samp_mat_process, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.samp_mat_process]) - -slots.size_frac = Slot(uri=DEFAULT_.size_frac, name="size_frac", curie=DEFAULT_.curie('size_frac'), - model_uri=DEFAULT_.size_frac, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.size_frac], - pattern=re.compile(r'\d+[.\d+]\-\d+[.\d+] \S+')) - -slots.samp_size = Slot(uri=DEFAULT_.samp_size, name="samp_size", curie=DEFAULT_.curie('samp_size'), - model_uri=DEFAULT_.samp_size, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_size], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.source_uvig = Slot(uri=DEFAULT_.source_uvig, name="source_uvig", curie=DEFAULT_.curie('source_uvig'), - model_uri=DEFAULT_.source_uvig, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.source_uvig], - pattern=re.compile(r'[metagenome (not viral targeted)|viral fraction metagenome (virome)|sequence\-targeted metagenome|metatranscriptome (not viral targeted)|viral fraction RNA metagenome (RNA virome)|sequence\-targeted RNA metagenome|microbial single amplified genome (SAG)|viral single amplified genome (vSAG)|isolate microbial genome|other]')) - -slots.virus_enrich_appr = Slot(uri=DEFAULT_.virus_enrich_appr, name="virus_enrich_appr", curie=DEFAULT_.curie('virus_enrich_appr'), - model_uri=DEFAULT_.virus_enrich_appr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.virus_enrich_appr], - pattern=re.compile(r'[filtration|ultrafiltration|centrifugation|ultracentrifugation|PEG Precipitation|FeCl Precipitation|CsCl density gradient|DNAse|RNAse|targeted sequence capture|other|none]')) - -slots.nucl_acid_ext = Slot(uri=DEFAULT_.nucl_acid_ext, name="nucl_acid_ext", curie=DEFAULT_.curie('nucl_acid_ext'), - model_uri=DEFAULT_.nucl_acid_ext, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.nucl_acid_ext]) - -slots.nucl_acid_amp = Slot(uri=DEFAULT_.nucl_acid_amp, name="nucl_acid_amp", curie=DEFAULT_.curie('nucl_acid_amp'), - model_uri=DEFAULT_.nucl_acid_amp, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.nucl_acid_amp]) - -slots.lib_size = Slot(uri=DEFAULT_.lib_size, name="lib_size", curie=DEFAULT_.curie('lib_size'), - model_uri=DEFAULT_.lib_size, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.lib_size]) - -slots.lib_reads_seqd = Slot(uri=DEFAULT_.lib_reads_seqd, name="lib_reads_seqd", curie=DEFAULT_.curie('lib_reads_seqd'), - model_uri=DEFAULT_.lib_reads_seqd, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.lib_reads_seqd]) - -slots.lib_layout = Slot(uri=DEFAULT_.lib_layout, name="lib_layout", curie=DEFAULT_.curie('lib_layout'), - model_uri=DEFAULT_.lib_layout, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.lib_layout], - pattern=re.compile(r'[paired|single|vector|other]')) - -slots.lib_vector = Slot(uri=DEFAULT_.lib_vector, name="lib_vector", curie=DEFAULT_.curie('lib_vector'), - model_uri=DEFAULT_.lib_vector, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.lib_vector]) - -slots.lib_screen = Slot(uri=DEFAULT_.lib_screen, name="lib_screen", curie=DEFAULT_.curie('lib_screen'), - model_uri=DEFAULT_.lib_screen, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.lib_screen]) - -slots.target_gene = Slot(uri=DEFAULT_.target_gene, name="target_gene", curie=DEFAULT_.curie('target_gene'), - model_uri=DEFAULT_.target_gene, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.target_gene]) - -slots.target_subfragment = Slot(uri=DEFAULT_.target_subfragment, name="target_subfragment", curie=DEFAULT_.curie('target_subfragment'), - model_uri=DEFAULT_.target_subfragment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.target_subfragment]) - -slots.pcr_primers = Slot(uri=DEFAULT_.pcr_primers, name="pcr_primers", curie=DEFAULT_.curie('pcr_primers'), - model_uri=DEFAULT_.pcr_primers, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pcr_primers]) - -slots.mid = Slot(uri=DEFAULT_.mid, name="mid", curie=DEFAULT_.curie('mid'), - model_uri=DEFAULT_.mid, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.mid]) - -slots.adapters = Slot(uri=DEFAULT_.adapters, name="adapters", curie=DEFAULT_.curie('adapters'), - model_uri=DEFAULT_.adapters, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.adapters]) - -slots.pcr_cond = Slot(uri=DEFAULT_.pcr_cond, name="pcr_cond", curie=DEFAULT_.curie('pcr_cond'), - model_uri=DEFAULT_.pcr_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pcr_cond], - pattern=re.compile(r'initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles')) - -slots.seq_meth = Slot(uri=DEFAULT_.seq_meth, name="seq_meth", curie=DEFAULT_.curie('seq_meth'), - model_uri=DEFAULT_.seq_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.seq_meth], - pattern=re.compile(r'[MinION|GridION|PromethION|454 GS|454 GS 20|454 GS FLX|454 GS FLX+|454 GS FLX Titanium|454 GS Junior|Illumina Genome Analyzer|Illumina Genome Analyzer II|Illumina Genome Analyzer IIx|Illumina HiSeq 4000|Illumina HiSeq 3000|Illumina HiSeq 2500|Illumina HiSeq 2000|Illumina HiSeq 1500|Illumina HiSeq 1000|Illumina HiScanSQ|Illumina MiSeq|Illumina HiSeq X Five|Illumina HiSeq X Ten|Illumina NextSeq 500|Illumina NextSeq 550|AB SOLiD System|AB SOLiD System 2.0|AB SOLiD System 3.0|AB SOLiD 3 Plus System|AB SOLiD 4 System|AB SOLiD 4hq System|AB SOLiD PI System|AB 5500 Genetic Analyzer|AB 5500xl Genetic Analyzer|AB 5500xl\-W Genetic Analysis System|Ion Torrent PGM|Ion Torrent Proton|Ion Torrent S5|Ion Torrent S5 XL|PacBio RS|PacBio RS II|Sequel|AB 3730xL Genetic Analyzer|AB 3730 Genetic Analyzer|AB 3500xL Genetic Analyzer|AB 3500 Genetic Analyzer|AB 3130xL Genetic Analyzer|AB 3130 Genetic Analyzer|AB 310 Genetic Analyzer|BGISEQ\-500]')) - -slots.seq_quality_check = Slot(uri=DEFAULT_.seq_quality_check, name="seq_quality_check", curie=DEFAULT_.curie('seq_quality_check'), - model_uri=DEFAULT_.seq_quality_check, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.seq_quality_check], - pattern=re.compile(r'[none|manually edited]')) - -slots.chimera_check = Slot(uri=DEFAULT_.chimera_check, name="chimera_check", curie=DEFAULT_.curie('chimera_check'), - model_uri=DEFAULT_.chimera_check, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.chimera_check]) - -slots.tax_ident = Slot(uri=DEFAULT_.tax_ident, name="tax_ident", curie=DEFAULT_.curie('tax_ident'), - model_uri=DEFAULT_.tax_ident, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tax_ident], - pattern=re.compile(r'[16S rRNA gene|multi\-marker approach|other]')) - -slots.assembly_qual = Slot(uri=DEFAULT_.assembly_qual, name="assembly_qual", curie=DEFAULT_.curie('assembly_qual'), - model_uri=DEFAULT_.assembly_qual, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.assembly_qual], - pattern=re.compile(r'[Finished genome|High\-quality draft genome|Medium\-quality draft genome|Low\-quality draft genome|Genome fragment(s)]')) - -slots.assembly_name = Slot(uri=DEFAULT_.assembly_name, name="assembly_name", curie=DEFAULT_.curie('assembly_name'), - model_uri=DEFAULT_.assembly_name, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.assembly_name]) - -slots.assembly_software = Slot(uri=DEFAULT_.assembly_software, name="assembly_software", curie=DEFAULT_.curie('assembly_software'), - model_uri=DEFAULT_.assembly_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.assembly_software]) - -slots.annot = Slot(uri=DEFAULT_.annot, name="annot", curie=DEFAULT_.curie('annot'), - model_uri=DEFAULT_.annot, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.annot]) - -slots.number_contig = Slot(uri=DEFAULT_.number_contig, name="number_contig", curie=DEFAULT_.curie('number_contig'), - model_uri=DEFAULT_.number_contig, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.number_contig]) - -slots.feat_pred = Slot(uri=DEFAULT_.feat_pred, name="feat_pred", curie=DEFAULT_.curie('feat_pred'), - model_uri=DEFAULT_.feat_pred, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.feat_pred]) - -slots.ref_db = Slot(uri=DEFAULT_.ref_db, name="ref_db", curie=DEFAULT_.curie('ref_db'), - model_uri=DEFAULT_.ref_db, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ref_db]) - -slots.sim_search_meth = Slot(uri=DEFAULT_.sim_search_meth, name="sim_search_meth", curie=DEFAULT_.curie('sim_search_meth'), - model_uri=DEFAULT_.sim_search_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sim_search_meth]) - -slots.tax_class = Slot(uri=DEFAULT_.tax_class, name="tax_class", curie=DEFAULT_.curie('tax_class'), - model_uri=DEFAULT_.tax_class, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tax_class]) - -slots._16s_recover = Slot(uri=DEFAULT_._16s_recover, name="_16s_recover", curie=DEFAULT_.curie('_16s_recover'), - model_uri=DEFAULT_._16s_recover, domain=None, range=Optional[Union[dict, BooleanValue]], mappings = [MIXS._16s_recover], - pattern=re.compile(r'[true|false]')) - -slots._16s_recover_software = Slot(uri=DEFAULT_._16s_recover_software, name="_16s_recover_software", curie=DEFAULT_.curie('_16s_recover_software'), - model_uri=DEFAULT_._16s_recover_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS._16s_recover_software]) - -slots.trnas = Slot(uri=DEFAULT_.trnas, name="trnas", curie=DEFAULT_.curie('trnas'), - model_uri=DEFAULT_.trnas, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.trnas]) - -slots.trna_ext_software = Slot(uri=DEFAULT_.trna_ext_software, name="trna_ext_software", curie=DEFAULT_.curie('trna_ext_software'), - model_uri=DEFAULT_.trna_ext_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.trna_ext_software]) - -slots.compl_score = Slot(uri=DEFAULT_.compl_score, name="compl_score", curie=DEFAULT_.curie('compl_score'), - model_uri=DEFAULT_.compl_score, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.compl_score]) - -slots.compl_software = Slot(uri=DEFAULT_.compl_software, name="compl_software", curie=DEFAULT_.curie('compl_software'), - model_uri=DEFAULT_.compl_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.compl_software]) - -slots.compl_appr = Slot(uri=DEFAULT_.compl_appr, name="compl_appr", curie=DEFAULT_.curie('compl_appr'), - model_uri=DEFAULT_.compl_appr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.compl_appr], - pattern=re.compile(r'[marker gene|reference based|other]')) - -slots.contam_score = Slot(uri=DEFAULT_.contam_score, name="contam_score", curie=DEFAULT_.curie('contam_score'), - model_uri=DEFAULT_.contam_score, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.contam_score], - pattern=re.compile(r'\d+[.\d+] percentage')) - -slots.contam_screen_input = Slot(uri=DEFAULT_.contam_screen_input, name="contam_screen_input", curie=DEFAULT_.curie('contam_screen_input'), - model_uri=DEFAULT_.contam_screen_input, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.contam_screen_input], - pattern=re.compile(r'[reads| contigs]')) - -slots.contam_screen_param = Slot(uri=DEFAULT_.contam_screen_param, name="contam_screen_param", curie=DEFAULT_.curie('contam_screen_param'), - model_uri=DEFAULT_.contam_screen_param, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.contam_screen_param]) - -slots.decontam_software = Slot(uri=DEFAULT_.decontam_software, name="decontam_software", curie=DEFAULT_.curie('decontam_software'), - model_uri=DEFAULT_.decontam_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.decontam_software], - pattern=re.compile(r'[checkm\/refinem|anvi\'o|prodege|bbtools:decontaminate.sh|acdc|combination]')) - -slots.sort_tech = Slot(uri=DEFAULT_.sort_tech, name="sort_tech", curie=DEFAULT_.curie('sort_tech'), - model_uri=DEFAULT_.sort_tech, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sort_tech], - pattern=re.compile(r'[flow cytometric cell sorting|microfluidics|lazer\-tweezing|optical manipulation|micromanipulation|other]')) - -slots.single_cell_lysis_appr = Slot(uri=DEFAULT_.single_cell_lysis_appr, name="single_cell_lysis_appr", curie=DEFAULT_.curie('single_cell_lysis_appr'), - model_uri=DEFAULT_.single_cell_lysis_appr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.single_cell_lysis_appr], - pattern=re.compile(r'[chemical|enzymatic|physical|combination]')) - -slots.single_cell_lysis_prot = Slot(uri=DEFAULT_.single_cell_lysis_prot, name="single_cell_lysis_prot", curie=DEFAULT_.curie('single_cell_lysis_prot'), - model_uri=DEFAULT_.single_cell_lysis_prot, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.single_cell_lysis_prot]) - -slots.wga_amp_appr = Slot(uri=DEFAULT_.wga_amp_appr, name="wga_amp_appr", curie=DEFAULT_.curie('wga_amp_appr'), - model_uri=DEFAULT_.wga_amp_appr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wga_amp_appr], - pattern=re.compile(r'[pcr based|mda based]')) - -slots.wga_amp_kit = Slot(uri=DEFAULT_.wga_amp_kit, name="wga_amp_kit", curie=DEFAULT_.curie('wga_amp_kit'), - model_uri=DEFAULT_.wga_amp_kit, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wga_amp_kit]) - -slots.bin_param = Slot(uri=DEFAULT_.bin_param, name="bin_param", curie=DEFAULT_.curie('bin_param'), - model_uri=DEFAULT_.bin_param, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.bin_param], - pattern=re.compile(r'[homology search|kmer|coverage|codon usage|combination]')) - -slots.bin_software = Slot(uri=DEFAULT_.bin_software, name="bin_software", curie=DEFAULT_.curie('bin_software'), - model_uri=DEFAULT_.bin_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.bin_software], - pattern=re.compile(r'[metabat|maxbin|concoct|groupm|esom|metawatt|combination|other]')) - -slots.reassembly_bin = Slot(uri=DEFAULT_.reassembly_bin, name="reassembly_bin", curie=DEFAULT_.curie('reassembly_bin'), - model_uri=DEFAULT_.reassembly_bin, domain=None, range=Optional[Union[dict, BooleanValue]], mappings = [MIXS.reassembly_bin], - pattern=re.compile(r'[true|false]')) - -slots.mag_cov_software = Slot(uri=DEFAULT_.mag_cov_software, name="mag_cov_software", curie=DEFAULT_.curie('mag_cov_software'), - model_uri=DEFAULT_.mag_cov_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.mag_cov_software], - pattern=re.compile(r'[bwa|bbmap|bowtie|other]')) - -slots.vir_ident_software = Slot(uri=DEFAULT_.vir_ident_software, name="vir_ident_software", curie=DEFAULT_.curie('vir_ident_software'), - model_uri=DEFAULT_.vir_ident_software, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.vir_ident_software]) - -slots.pred_genome_type = Slot(uri=DEFAULT_.pred_genome_type, name="pred_genome_type", curie=DEFAULT_.curie('pred_genome_type'), - model_uri=DEFAULT_.pred_genome_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pred_genome_type], - pattern=re.compile(r'[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (\-)|mixed|uncharacterized]')) - -slots.pred_genome_struc = Slot(uri=DEFAULT_.pred_genome_struc, name="pred_genome_struc", curie=DEFAULT_.curie('pred_genome_struc'), - model_uri=DEFAULT_.pred_genome_struc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pred_genome_struc], - pattern=re.compile(r'[segmented|non\-segmented|undetermined]')) - -slots.detec_type = Slot(uri=DEFAULT_.detec_type, name="detec_type", curie=DEFAULT_.curie('detec_type'), - model_uri=DEFAULT_.detec_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.detec_type], - pattern=re.compile(r'[independent sequence (UViG)|provirus (UpViG)]')) - -slots.votu_class_appr = Slot(uri=DEFAULT_.votu_class_appr, name="votu_class_appr", curie=DEFAULT_.curie('votu_class_appr'), - model_uri=DEFAULT_.votu_class_appr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.votu_class_appr]) - -slots.votu_seq_comp_appr = Slot(uri=DEFAULT_.votu_seq_comp_appr, name="votu_seq_comp_appr", curie=DEFAULT_.curie('votu_seq_comp_appr'), - model_uri=DEFAULT_.votu_seq_comp_appr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.votu_seq_comp_appr]) - -slots.votu_db = Slot(uri=DEFAULT_.votu_db, name="votu_db", curie=DEFAULT_.curie('votu_db'), - model_uri=DEFAULT_.votu_db, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.votu_db]) - -slots.host_pred_appr = Slot(uri=DEFAULT_.host_pred_appr, name="host_pred_appr", curie=DEFAULT_.curie('host_pred_appr'), - model_uri=DEFAULT_.host_pred_appr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_pred_appr], - pattern=re.compile(r'[provirus|host sequence similarity|CRISPR spacer match|kmer similarity|co\-occurrence|combination|other]')) - -slots.host_pred_est_acc = Slot(uri=DEFAULT_.host_pred_est_acc, name="host_pred_est_acc", curie=DEFAULT_.curie('host_pred_est_acc'), - model_uri=DEFAULT_.host_pred_est_acc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_pred_est_acc]) - -slots.mixs_url = Slot(uri=DEFAULT_.mixs_url, name="mixs_url", curie=DEFAULT_.curie('mixs_url'), - model_uri=DEFAULT_.mixs_url, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.mixs_url]) - -slots.sop = Slot(uri=DEFAULT_.sop, name="sop", curie=DEFAULT_.curie('sop'), - model_uri=DEFAULT_.sop, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sop]) - -slots.barometric_press = Slot(uri=DEFAULT_.barometric_press, name="barometric_press", curie=DEFAULT_.curie('barometric_press'), - model_uri=DEFAULT_.barometric_press, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.barometric_press], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.carb_dioxide = Slot(uri=DEFAULT_.carb_dioxide, name="carb_dioxide", curie=DEFAULT_.curie('carb_dioxide'), - model_uri=DEFAULT_.carb_dioxide, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.carb_dioxide], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.carb_monoxide = Slot(uri=DEFAULT_.carb_monoxide, name="carb_monoxide", curie=DEFAULT_.curie('carb_monoxide'), - model_uri=DEFAULT_.carb_monoxide, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.carb_monoxide], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.chem_administration = Slot(uri=DEFAULT_.chem_administration, name="chem_administration", curie=DEFAULT_.curie('chem_administration'), - model_uri=DEFAULT_.chem_administration, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.chem_administration]) - -slots.humidity = Slot(uri=DEFAULT_.humidity, name="humidity", curie=DEFAULT_.curie('humidity'), - model_uri=DEFAULT_.humidity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.humidity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.methane = Slot(uri=DEFAULT_.methane, name="methane", curie=DEFAULT_.curie('methane'), - model_uri=DEFAULT_.methane, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.methane], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.misc_param = Slot(uri=DEFAULT_.misc_param, name="misc_param", curie=DEFAULT_.curie('misc_param'), - model_uri=DEFAULT_.misc_param, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.misc_param]) - -slots.organism_count = Slot(uri=DEFAULT_.organism_count, name="organism_count", curie=DEFAULT_.curie('organism_count'), - model_uri=DEFAULT_.organism_count, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.organism_count]) - -slots.oxygen = Slot(uri=DEFAULT_.oxygen, name="oxygen", curie=DEFAULT_.curie('oxygen'), - model_uri=DEFAULT_.oxygen, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.oxygen], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.oxy_stat_samp = Slot(uri=DEFAULT_.oxy_stat_samp, name="oxy_stat_samp", curie=DEFAULT_.curie('oxy_stat_samp'), - model_uri=DEFAULT_.oxy_stat_samp, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.oxy_stat_samp], - pattern=re.compile(r'[aerobic|anaerobic|other]')) - -slots.perturbation = Slot(uri=DEFAULT_.perturbation, name="perturbation", curie=DEFAULT_.curie('perturbation'), - model_uri=DEFAULT_.perturbation, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.perturbation]) - -slots.pollutants = Slot(uri=DEFAULT_.pollutants, name="pollutants", curie=DEFAULT_.curie('pollutants'), - model_uri=DEFAULT_.pollutants, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.pollutants]) - -slots.resp_part_matter = Slot(uri=DEFAULT_.resp_part_matter, name="resp_part_matter", curie=DEFAULT_.curie('resp_part_matter'), - model_uri=DEFAULT_.resp_part_matter, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.resp_part_matter]) - -slots.samp_salinity = Slot(uri=DEFAULT_.samp_salinity, name="samp_salinity", curie=DEFAULT_.curie('samp_salinity'), - model_uri=DEFAULT_.samp_salinity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_salinity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.samp_store_dur = Slot(uri=DEFAULT_.samp_store_dur, name="samp_store_dur", curie=DEFAULT_.curie('samp_store_dur'), - model_uri=DEFAULT_.samp_store_dur, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_store_dur]) - -slots.samp_store_loc = Slot(uri=DEFAULT_.samp_store_loc, name="samp_store_loc", curie=DEFAULT_.curie('samp_store_loc'), - model_uri=DEFAULT_.samp_store_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_store_loc]) - -slots.samp_store_temp = Slot(uri=DEFAULT_.samp_store_temp, name="samp_store_temp", curie=DEFAULT_.curie('samp_store_temp'), - model_uri=DEFAULT_.samp_store_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_store_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.samp_vol_we_dna_ext = Slot(uri=DEFAULT_.samp_vol_we_dna_ext, name="samp_vol_we_dna_ext", curie=DEFAULT_.curie('samp_vol_we_dna_ext'), - model_uri=DEFAULT_.samp_vol_we_dna_ext, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_vol_we_dna_ext], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.solar_irradiance = Slot(uri=DEFAULT_.solar_irradiance, name="solar_irradiance", curie=DEFAULT_.curie('solar_irradiance'), - model_uri=DEFAULT_.solar_irradiance, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.solar_irradiance], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.temp = Slot(uri=DEFAULT_.temp, name="temp", curie=DEFAULT_.curie('temp'), - model_uri=DEFAULT_.temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.ventilation_rate = Slot(uri=DEFAULT_.ventilation_rate, name="ventilation_rate", curie=DEFAULT_.curie('ventilation_rate'), - model_uri=DEFAULT_.ventilation_rate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.ventilation_rate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.ventilation_type = Slot(uri=DEFAULT_.ventilation_type, name="ventilation_type", curie=DEFAULT_.curie('ventilation_type'), - model_uri=DEFAULT_.ventilation_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ventilation_type]) - -slots.volatile_org_comp = Slot(uri=DEFAULT_.volatile_org_comp, name="volatile_org_comp", curie=DEFAULT_.curie('volatile_org_comp'), - model_uri=DEFAULT_.volatile_org_comp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.volatile_org_comp]) - -slots.wind_direction = Slot(uri=DEFAULT_.wind_direction, name="wind_direction", curie=DEFAULT_.curie('wind_direction'), - model_uri=DEFAULT_.wind_direction, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wind_direction]) - -slots.wind_speed = Slot(uri=DEFAULT_.wind_speed, name="wind_speed", curie=DEFAULT_.curie('wind_speed'), - model_uri=DEFAULT_.wind_speed, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.wind_speed], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.surf_material = Slot(uri=DEFAULT_.surf_material, name="surf_material", curie=DEFAULT_.curie('surf_material'), - model_uri=DEFAULT_.surf_material, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.surf_material], - pattern=re.compile(r'[concrete|wood|stone|tile|plastic|glass|vinyl|metal|carpet|stainless steel|paint|cinder blocks|hay bales|stucco|adobe]')) - -slots.surf_air_cont = Slot(uri=DEFAULT_.surf_air_cont, name="surf_air_cont", curie=DEFAULT_.curie('surf_air_cont'), - model_uri=DEFAULT_.surf_air_cont, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.surf_air_cont], - pattern=re.compile(r'[dust|organic matter|particulate matter|volatile organic compounds|biological contaminants|radon|nutrients|biocides]')) - -slots.rel_air_humidity = Slot(uri=DEFAULT_.rel_air_humidity, name="rel_air_humidity", curie=DEFAULT_.curie('rel_air_humidity'), - model_uri=DEFAULT_.rel_air_humidity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.rel_air_humidity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.abs_air_humidity = Slot(uri=DEFAULT_.abs_air_humidity, name="abs_air_humidity", curie=DEFAULT_.curie('abs_air_humidity'), - model_uri=DEFAULT_.abs_air_humidity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.abs_air_humidity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.surf_humidity = Slot(uri=DEFAULT_.surf_humidity, name="surf_humidity", curie=DEFAULT_.curie('surf_humidity'), - model_uri=DEFAULT_.surf_humidity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.surf_humidity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.air_temp = Slot(uri=DEFAULT_.air_temp, name="air_temp", curie=DEFAULT_.curie('air_temp'), - model_uri=DEFAULT_.air_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.air_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.surf_temp = Slot(uri=DEFAULT_.surf_temp, name="surf_temp", curie=DEFAULT_.curie('surf_temp'), - model_uri=DEFAULT_.surf_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.surf_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.surf_moisture_ph = Slot(uri=DEFAULT_.surf_moisture_ph, name="surf_moisture_ph", curie=DEFAULT_.curie('surf_moisture_ph'), - model_uri=DEFAULT_.surf_moisture_ph, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.surf_moisture_ph], - pattern=re.compile(r'\d+[.\d+]')) - -slots.build_occup_type = Slot(uri=DEFAULT_.build_occup_type, name="build_occup_type", curie=DEFAULT_.curie('build_occup_type'), - model_uri=DEFAULT_.build_occup_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.build_occup_type], - pattern=re.compile(r'[office|market|restaurant|residence|school|residential|commercial|low rise|high rise|wood framed|office|health care|school|airport|sports complex]')) - -slots.surf_moisture = Slot(uri=DEFAULT_.surf_moisture, name="surf_moisture", curie=DEFAULT_.curie('surf_moisture'), - model_uri=DEFAULT_.surf_moisture, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.surf_moisture], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.dew_point = Slot(uri=DEFAULT_.dew_point, name="dew_point", curie=DEFAULT_.curie('dew_point'), - model_uri=DEFAULT_.dew_point, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.dew_point], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.indoor_space = Slot(uri=DEFAULT_.indoor_space, name="indoor_space", curie=DEFAULT_.curie('indoor_space'), - model_uri=DEFAULT_.indoor_space, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.indoor_space], - pattern=re.compile(r'[bedroom|office|bathroom|foyer|kitchen|locker room|hallway|elevator]')) - -slots.indoor_surf = Slot(uri=DEFAULT_.indoor_surf, name="indoor_surf", curie=DEFAULT_.curie('indoor_surf'), - model_uri=DEFAULT_.indoor_surf, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.indoor_surf], - pattern=re.compile(r'[counter top|window|wall|cabinet|ceiling|door|shelving|vent cover]')) - -slots.filter_type = Slot(uri=DEFAULT_.filter_type, name="filter_type", curie=DEFAULT_.curie('filter_type'), - model_uri=DEFAULT_.filter_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.filter_type], - pattern=re.compile(r'[particulate air filter|chemical air filter|low\-MERV pleated media|HEPA|electrostatic|gas\-phase or ultraviolet air treatments]')) - -slots.heat_cool_type = Slot(uri=DEFAULT_.heat_cool_type, name="heat_cool_type", curie=DEFAULT_.curie('heat_cool_type'), - model_uri=DEFAULT_.heat_cool_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.heat_cool_type], - pattern=re.compile(r'[radiant system|heat pump|forced air system|steam forced heat|wood stove]')) - -slots.substructure_type = Slot(uri=DEFAULT_.substructure_type, name="substructure_type", curie=DEFAULT_.curie('substructure_type'), - model_uri=DEFAULT_.substructure_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.substructure_type], - pattern=re.compile(r'[crawlspace|slab on grade|basement]')) - -slots.building_setting = Slot(uri=DEFAULT_.building_setting, name="building_setting", curie=DEFAULT_.curie('building_setting'), - model_uri=DEFAULT_.building_setting, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.building_setting], - pattern=re.compile(r'[urban|suburban|exurban|rural]')) - -slots.light_type = Slot(uri=DEFAULT_.light_type, name="light_type", curie=DEFAULT_.curie('light_type'), - model_uri=DEFAULT_.light_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.light_type], - pattern=re.compile(r'[natural light|electric light|desk lamp|flourescent lights|natural light|none]')) - -slots.samp_sort_meth = Slot(uri=DEFAULT_.samp_sort_meth, name="samp_sort_meth", curie=DEFAULT_.curie('samp_sort_meth'), - model_uri=DEFAULT_.samp_sort_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_sort_meth]) - -slots.space_typ_state = Slot(uri=DEFAULT_.space_typ_state, name="space_typ_state", curie=DEFAULT_.curie('space_typ_state'), - model_uri=DEFAULT_.space_typ_state, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.space_typ_state], - pattern=re.compile(r'[typically occupied|typically unoccupied]')) - -slots.typ_occup_density = Slot(uri=DEFAULT_.typ_occup_density, name="typ_occup_density", curie=DEFAULT_.curie('typ_occup_density'), - model_uri=DEFAULT_.typ_occup_density, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.typ_occup_density], - pattern=re.compile(r'\d+[.\d+]')) - -slots.occup_samp = Slot(uri=DEFAULT_.occup_samp, name="occup_samp", curie=DEFAULT_.curie('occup_samp'), - model_uri=DEFAULT_.occup_samp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.occup_samp]) - -slots.occup_density_samp = Slot(uri=DEFAULT_.occup_density_samp, name="occup_density_samp", curie=DEFAULT_.curie('occup_density_samp'), - model_uri=DEFAULT_.occup_density_samp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.occup_density_samp], - pattern=re.compile(r'\d+[.\d+]')) - -slots.address = Slot(uri=DEFAULT_.address, name="address", curie=DEFAULT_.curie('address'), - model_uri=DEFAULT_.address, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.address]) - -slots.adj_room = Slot(uri=DEFAULT_.adj_room, name="adj_room", curie=DEFAULT_.curie('adj_room'), - model_uri=DEFAULT_.adj_room, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.adj_room]) - -slots.aero_struc = Slot(uri=DEFAULT_.aero_struc, name="aero_struc", curie=DEFAULT_.curie('aero_struc'), - model_uri=DEFAULT_.aero_struc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.aero_struc], - pattern=re.compile(r'[plane|glider]')) - -slots.amount_light = Slot(uri=DEFAULT_.amount_light, name="amount_light", curie=DEFAULT_.curie('amount_light'), - model_uri=DEFAULT_.amount_light, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.amount_light], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.arch_struc = Slot(uri=DEFAULT_.arch_struc, name="arch_struc", curie=DEFAULT_.curie('arch_struc'), - model_uri=DEFAULT_.arch_struc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.arch_struc], - pattern=re.compile(r'[building|shed|home]')) - -slots.avg_occup = Slot(uri=DEFAULT_.avg_occup, name="avg_occup", curie=DEFAULT_.curie('avg_occup'), - model_uri=DEFAULT_.avg_occup, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.avg_occup], - pattern=re.compile(r'\d+[.\d+]')) - -slots.avg_dew_point = Slot(uri=DEFAULT_.avg_dew_point, name="avg_dew_point", curie=DEFAULT_.curie('avg_dew_point'), - model_uri=DEFAULT_.avg_dew_point, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.avg_dew_point], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.avg_temp = Slot(uri=DEFAULT_.avg_temp, name="avg_temp", curie=DEFAULT_.curie('avg_temp'), - model_uri=DEFAULT_.avg_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.avg_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.bathroom_count = Slot(uri=DEFAULT_.bathroom_count, name="bathroom_count", curie=DEFAULT_.curie('bathroom_count'), - model_uri=DEFAULT_.bathroom_count, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.bathroom_count]) - -slots.bedroom_count = Slot(uri=DEFAULT_.bedroom_count, name="bedroom_count", curie=DEFAULT_.curie('bedroom_count'), - model_uri=DEFAULT_.bedroom_count, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.bedroom_count]) - -slots.built_struc_age = Slot(uri=DEFAULT_.built_struc_age, name="built_struc_age", curie=DEFAULT_.curie('built_struc_age'), - model_uri=DEFAULT_.built_struc_age, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.built_struc_age], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.built_struc_set = Slot(uri=DEFAULT_.built_struc_set, name="built_struc_set", curie=DEFAULT_.curie('built_struc_set'), - model_uri=DEFAULT_.built_struc_set, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.built_struc_set], - pattern=re.compile(r'[urban|rural]')) - -slots.built_struc_type = Slot(uri=DEFAULT_.built_struc_type, name="built_struc_type", curie=DEFAULT_.curie('built_struc_type'), - model_uri=DEFAULT_.built_struc_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.built_struc_type]) - -slots.ceil_area = Slot(uri=DEFAULT_.ceil_area, name="ceil_area", curie=DEFAULT_.curie('ceil_area'), - model_uri=DEFAULT_.ceil_area, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.ceil_area], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.ceil_cond = Slot(uri=DEFAULT_.ceil_cond, name="ceil_cond", curie=DEFAULT_.curie('ceil_cond'), - model_uri=DEFAULT_.ceil_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ceil_cond], - pattern=re.compile(r'[new|visible wear|needs repair|damaged|rupture]')) - -slots.ceil_finish_mat = Slot(uri=DEFAULT_.ceil_finish_mat, name="ceil_finish_mat", curie=DEFAULT_.curie('ceil_finish_mat'), - model_uri=DEFAULT_.ceil_finish_mat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ceil_finish_mat], - pattern=re.compile(r'[drywall|mineral fibre|tiles|PVC|plasterboard|metal|fiberglass|stucco|mineral wool\/calcium silicate|wood]')) - -slots.ceil_water_mold = Slot(uri=DEFAULT_.ceil_water_mold, name="ceil_water_mold", curie=DEFAULT_.curie('ceil_water_mold'), - model_uri=DEFAULT_.ceil_water_mold, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ceil_water_mold], - pattern=re.compile(r'[presence of mold visible|no presence of mold visible]')) - -slots.ceil_struc = Slot(uri=DEFAULT_.ceil_struc, name="ceil_struc", curie=DEFAULT_.curie('ceil_struc'), - model_uri=DEFAULT_.ceil_struc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ceil_struc], - pattern=re.compile(r'[wood frame|concrete]')) - -slots.ceil_texture = Slot(uri=DEFAULT_.ceil_texture, name="ceil_texture", curie=DEFAULT_.curie('ceil_texture'), - model_uri=DEFAULT_.ceil_texture, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ceil_texture], - pattern=re.compile(r'[crows feet|crows\-foot stomp|double skip|hawk and trowel|knockdown|popcorn|orange peel|rosebud stomp|Santa\-Fe texture|skip trowel|smooth|stomp knockdown|swirl]')) - -slots.ceil_thermal_mass = Slot(uri=DEFAULT_.ceil_thermal_mass, name="ceil_thermal_mass", curie=DEFAULT_.curie('ceil_thermal_mass'), - model_uri=DEFAULT_.ceil_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.ceil_thermal_mass], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.ceil_type = Slot(uri=DEFAULT_.ceil_type, name="ceil_type", curie=DEFAULT_.curie('ceil_type'), - model_uri=DEFAULT_.ceil_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ceil_type], - pattern=re.compile(r'[cathedral|dropped|concave|barrel\-shaped|coffered|cove|stretched]')) - -slots.cool_syst_id = Slot(uri=DEFAULT_.cool_syst_id, name="cool_syst_id", curie=DEFAULT_.curie('cool_syst_id'), - model_uri=DEFAULT_.cool_syst_id, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.cool_syst_id]) - -slots.date_last_rain = Slot(uri=DEFAULT_.date_last_rain, name="date_last_rain", curie=DEFAULT_.curie('date_last_rain'), - model_uri=DEFAULT_.date_last_rain, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.date_last_rain]) - -slots.build_docs = Slot(uri=DEFAULT_.build_docs, name="build_docs", curie=DEFAULT_.curie('build_docs'), - model_uri=DEFAULT_.build_docs, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.build_docs], - pattern=re.compile(r'[building information model|commissioning report|complaint logs|contract administration|cost estimate|janitorial schedules or logs|maintenance plans|schedule|sections|shop drawings|submittals|ventilation system|windows] ')) - -slots.door_size = Slot(uri=DEFAULT_.door_size, name="door_size", curie=DEFAULT_.curie('door_size'), - model_uri=DEFAULT_.door_size, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.door_size], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.door_cond = Slot(uri=DEFAULT_.door_cond, name="door_cond", curie=DEFAULT_.curie('door_cond'), - model_uri=DEFAULT_.door_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_cond], - pattern=re.compile(r'[damaged|needs repair|new|rupture|visible wear]')) - -slots.door_direct = Slot(uri=DEFAULT_.door_direct, name="door_direct", curie=DEFAULT_.curie('door_direct'), - model_uri=DEFAULT_.door_direct, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_direct], - pattern=re.compile(r'[inward|outward|sideways]')) - -slots.door_loc = Slot(uri=DEFAULT_.door_loc, name="door_loc", curie=DEFAULT_.curie('door_loc'), - model_uri=DEFAULT_.door_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_loc], - pattern=re.compile(r'[north|south|east|west]')) - -slots.door_mat = Slot(uri=DEFAULT_.door_mat, name="door_mat", curie=DEFAULT_.curie('door_mat'), - model_uri=DEFAULT_.door_mat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_mat], - pattern=re.compile(r'[aluminum|cellular PVC|engineered plastic|fiberboard|fiberglass|metal|thermoplastic alloy|vinyl|wood|wood\/plastic composite]')) - -slots.door_move = Slot(uri=DEFAULT_.door_move, name="door_move", curie=DEFAULT_.curie('door_move'), - model_uri=DEFAULT_.door_move, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_move], - pattern=re.compile(r'[collapsible|folding|revolving|rolling shutter|sliding|swinging] ')) - -slots.door_water_mold = Slot(uri=DEFAULT_.door_water_mold, name="door_water_mold", curie=DEFAULT_.curie('door_water_mold'), - model_uri=DEFAULT_.door_water_mold, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_water_mold], - pattern=re.compile(r'[presence of mold visible|no presence of mold visible]')) - -slots.door_type = Slot(uri=DEFAULT_.door_type, name="door_type", curie=DEFAULT_.curie('door_type'), - model_uri=DEFAULT_.door_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_type], - pattern=re.compile(r'[composite|metal|wooden]')) - -slots.door_comp_type = Slot(uri=DEFAULT_.door_comp_type, name="door_comp_type", curie=DEFAULT_.curie('door_comp_type'), - model_uri=DEFAULT_.door_comp_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_comp_type], - pattern=re.compile(r'[metal covered|revolving|sliding|telescopic]')) - -slots.door_type_metal = Slot(uri=DEFAULT_.door_type_metal, name="door_type_metal", curie=DEFAULT_.curie('door_type_metal'), - model_uri=DEFAULT_.door_type_metal, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_type_metal], - pattern=re.compile(r'[collapsible|corrugated steel|hollow|rolling shutters|steel plate]')) - -slots.door_type_wood = Slot(uri=DEFAULT_.door_type_wood, name="door_type_wood", curie=DEFAULT_.curie('door_type_wood'), - model_uri=DEFAULT_.door_type_wood, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.door_type_wood], - pattern=re.compile(r'[bettened and ledged|battened|ledged and braced|battened|ledged and framed|battened|ledged, braced and frame|framed and paneled|glashed or sash|flush|louvered|wire gauged]')) - -slots.drawings = Slot(uri=DEFAULT_.drawings, name="drawings", curie=DEFAULT_.curie('drawings'), - model_uri=DEFAULT_.drawings, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.drawings], - pattern=re.compile(r'[operation|as built|construction|bid|design|building navigation map|diagram|sketch]')) - -slots.elevator = Slot(uri=DEFAULT_.elevator, name="elevator", curie=DEFAULT_.curie('elevator'), - model_uri=DEFAULT_.elevator, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.elevator]) - -slots.escalator = Slot(uri=DEFAULT_.escalator, name="escalator", curie=DEFAULT_.curie('escalator'), - model_uri=DEFAULT_.escalator, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.escalator]) - -slots.exp_duct = Slot(uri=DEFAULT_.exp_duct, name="exp_duct", curie=DEFAULT_.curie('exp_duct'), - model_uri=DEFAULT_.exp_duct, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.exp_duct], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.exp_pipe = Slot(uri=DEFAULT_.exp_pipe, name="exp_pipe", curie=DEFAULT_.curie('exp_pipe'), - model_uri=DEFAULT_.exp_pipe, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.exp_pipe]) - -slots.ext_door = Slot(uri=DEFAULT_.ext_door, name="ext_door", curie=DEFAULT_.curie('ext_door'), - model_uri=DEFAULT_.ext_door, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ext_door]) - -slots.fireplace_type = Slot(uri=DEFAULT_.fireplace_type, name="fireplace_type", curie=DEFAULT_.curie('fireplace_type'), - model_uri=DEFAULT_.fireplace_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.fireplace_type], - pattern=re.compile(r'[gas burning|wood burning]')) - -slots.floor_age = Slot(uri=DEFAULT_.floor_age, name="floor_age", curie=DEFAULT_.curie('floor_age'), - model_uri=DEFAULT_.floor_age, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.floor_age], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.floor_area = Slot(uri=DEFAULT_.floor_area, name="floor_area", curie=DEFAULT_.curie('floor_area'), - model_uri=DEFAULT_.floor_area, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.floor_area], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.floor_cond = Slot(uri=DEFAULT_.floor_cond, name="floor_cond", curie=DEFAULT_.curie('floor_cond'), - model_uri=DEFAULT_.floor_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.floor_cond], - pattern=re.compile(r'[new|visible wear|needs repair|damaged|rupture]')) - -slots.floor_count = Slot(uri=DEFAULT_.floor_count, name="floor_count", curie=DEFAULT_.curie('floor_count'), - model_uri=DEFAULT_.floor_count, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.floor_count]) - -slots.floor_finish_mat = Slot(uri=DEFAULT_.floor_finish_mat, name="floor_finish_mat", curie=DEFAULT_.curie('floor_finish_mat'), - model_uri=DEFAULT_.floor_finish_mat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.floor_finish_mat], - pattern=re.compile(r'[tile|wood strip or parquet|carpet|rug|laminate wood|lineoleum|vinyl composition tile|sheet vinyl|stone|bamboo|cork|terrazo|concrete|none;specify unfinished|sealed|clear finish|paint]')) - -slots.floor_water_mold = Slot(uri=DEFAULT_.floor_water_mold, name="floor_water_mold", curie=DEFAULT_.curie('floor_water_mold'), - model_uri=DEFAULT_.floor_water_mold, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.floor_water_mold], - pattern=re.compile(r'[mold odor|wet floor|water stains|wall discoloration|floor discoloration|ceiling discoloration|peeling paint or wallpaper|bulging walls|condensation]')) - -slots.floor_struc = Slot(uri=DEFAULT_.floor_struc, name="floor_struc", curie=DEFAULT_.curie('floor_struc'), - model_uri=DEFAULT_.floor_struc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.floor_struc], - pattern=re.compile(r'[balcony|floating floor|glass floor|raised floor|sprung floor|wood\-framed|concrete]')) - -slots.floor_thermal_mass = Slot(uri=DEFAULT_.floor_thermal_mass, name="floor_thermal_mass", curie=DEFAULT_.curie('floor_thermal_mass'), - model_uri=DEFAULT_.floor_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.floor_thermal_mass], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.freq_clean = Slot(uri=DEFAULT_.freq_clean, name="freq_clean", curie=DEFAULT_.curie('freq_clean'), - model_uri=DEFAULT_.freq_clean, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.freq_clean]) - -slots.freq_cook = Slot(uri=DEFAULT_.freq_cook, name="freq_cook", curie=DEFAULT_.curie('freq_cook'), - model_uri=DEFAULT_.freq_cook, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.freq_cook]) - -slots.furniture = Slot(uri=DEFAULT_.furniture, name="furniture", curie=DEFAULT_.curie('furniture'), - model_uri=DEFAULT_.furniture, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.furniture], - pattern=re.compile(r'[cabinet|chair|desks]')) - -slots.gender_restroom = Slot(uri=DEFAULT_.gender_restroom, name="gender_restroom", curie=DEFAULT_.curie('gender_restroom'), - model_uri=DEFAULT_.gender_restroom, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.gender_restroom], - pattern=re.compile(r'[male|female]')) - -slots.hall_count = Slot(uri=DEFAULT_.hall_count, name="hall_count", curie=DEFAULT_.curie('hall_count'), - model_uri=DEFAULT_.hall_count, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.hall_count]) - -slots.handidness = Slot(uri=DEFAULT_.handidness, name="handidness", curie=DEFAULT_.curie('handidness'), - model_uri=DEFAULT_.handidness, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.handidness], - pattern=re.compile(r'[ambidexterity|left handedness|mixed\-handedness|right handedness]')) - -slots.heat_deliv_loc = Slot(uri=DEFAULT_.heat_deliv_loc, name="heat_deliv_loc", curie=DEFAULT_.curie('heat_deliv_loc'), - model_uri=DEFAULT_.heat_deliv_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.heat_deliv_loc], - pattern=re.compile(r'[north|south|east|west]')) - -slots.heat_system_deliv_meth = Slot(uri=DEFAULT_.heat_system_deliv_meth, name="heat_system_deliv_meth", curie=DEFAULT_.curie('heat_system_deliv_meth'), - model_uri=DEFAULT_.heat_system_deliv_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.heat_system_deliv_meth], - pattern=re.compile(r'[conductive|radiant]')) - -slots.heat_system_id = Slot(uri=DEFAULT_.heat_system_id, name="heat_system_id", curie=DEFAULT_.curie('heat_system_id'), - model_uri=DEFAULT_.heat_system_id, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.heat_system_id]) - -slots.height_carper_fiber = Slot(uri=DEFAULT_.height_carper_fiber, name="height_carper_fiber", curie=DEFAULT_.curie('height_carper_fiber'), - model_uri=DEFAULT_.height_carper_fiber, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.height_carper_fiber], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.inside_lux = Slot(uri=DEFAULT_.inside_lux, name="inside_lux", curie=DEFAULT_.curie('inside_lux'), - model_uri=DEFAULT_.inside_lux, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.inside_lux], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.int_wall_cond = Slot(uri=DEFAULT_.int_wall_cond, name="int_wall_cond", curie=DEFAULT_.curie('int_wall_cond'), - model_uri=DEFAULT_.int_wall_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.int_wall_cond], - pattern=re.compile(r'[new|visible wear|needs repair|damaged|rupture]')) - -slots.last_clean = Slot(uri=DEFAULT_.last_clean, name="last_clean", curie=DEFAULT_.curie('last_clean'), - model_uri=DEFAULT_.last_clean, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.last_clean]) - -slots.max_occup = Slot(uri=DEFAULT_.max_occup, name="max_occup", curie=DEFAULT_.curie('max_occup'), - model_uri=DEFAULT_.max_occup, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.max_occup]) - -slots.mech_struc = Slot(uri=DEFAULT_.mech_struc, name="mech_struc", curie=DEFAULT_.curie('mech_struc'), - model_uri=DEFAULT_.mech_struc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.mech_struc], - pattern=re.compile(r'[subway|coach|carriage|elevator|escalator|boat|train|car|bus]')) - -slots.number_plants = Slot(uri=DEFAULT_.number_plants, name="number_plants", curie=DEFAULT_.curie('number_plants'), - model_uri=DEFAULT_.number_plants, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.number_plants]) - -slots.number_pets = Slot(uri=DEFAULT_.number_pets, name="number_pets", curie=DEFAULT_.curie('number_pets'), - model_uri=DEFAULT_.number_pets, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.number_pets]) - -slots.number_resident = Slot(uri=DEFAULT_.number_resident, name="number_resident", curie=DEFAULT_.curie('number_resident'), - model_uri=DEFAULT_.number_resident, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.number_resident]) - -slots.occup_document = Slot(uri=DEFAULT_.occup_document, name="occup_document", curie=DEFAULT_.curie('occup_document'), - model_uri=DEFAULT_.occup_document, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.occup_document], - pattern=re.compile(r'[automated count|estimate|manual count|videos]')) - -slots.ext_wall_orient = Slot(uri=DEFAULT_.ext_wall_orient, name="ext_wall_orient", curie=DEFAULT_.curie('ext_wall_orient'), - model_uri=DEFAULT_.ext_wall_orient, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ext_wall_orient], - pattern=re.compile(r'[north|south|east|west|northeast|southeast|southwest|northwest]')) - -slots.ext_window_orient = Slot(uri=DEFAULT_.ext_window_orient, name="ext_window_orient", curie=DEFAULT_.curie('ext_window_orient'), - model_uri=DEFAULT_.ext_window_orient, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ext_window_orient], - pattern=re.compile(r'[north|south|east|west|northeast|southeast|southwest|northwest]')) - -slots.rel_humidity_out = Slot(uri=DEFAULT_.rel_humidity_out, name="rel_humidity_out", curie=DEFAULT_.curie('rel_humidity_out'), - model_uri=DEFAULT_.rel_humidity_out, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.rel_humidity_out], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.pres_animal = Slot(uri=DEFAULT_.pres_animal, name="pres_animal", curie=DEFAULT_.curie('pres_animal'), - model_uri=DEFAULT_.pres_animal, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pres_animal]) - -slots.quad_pos = Slot(uri=DEFAULT_.quad_pos, name="quad_pos", curie=DEFAULT_.curie('quad_pos'), - model_uri=DEFAULT_.quad_pos, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.quad_pos], - pattern=re.compile(r'[North side|West side|South side|East side]')) - -slots.rel_samp_loc = Slot(uri=DEFAULT_.rel_samp_loc, name="rel_samp_loc", curie=DEFAULT_.curie('rel_samp_loc'), - model_uri=DEFAULT_.rel_samp_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.rel_samp_loc], - pattern=re.compile(r'[edge of car|center of car|under a seat]')) - -slots.room_air_exch_rate = Slot(uri=DEFAULT_.room_air_exch_rate, name="room_air_exch_rate", curie=DEFAULT_.curie('room_air_exch_rate'), - model_uri=DEFAULT_.room_air_exch_rate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.room_air_exch_rate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.room_architec_element = Slot(uri=DEFAULT_.room_architec_element, name="room_architec_element", curie=DEFAULT_.curie('room_architec_element'), - model_uri=DEFAULT_.room_architec_element, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_architec_element]) - -slots.room_condt = Slot(uri=DEFAULT_.room_condt, name="room_condt", curie=DEFAULT_.curie('room_condt'), - model_uri=DEFAULT_.room_condt, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_condt], - pattern=re.compile(r'[new|visible wear|needs repair|damaged|rupture|visible signs of mold\/mildew]')) - -slots.room_count = Slot(uri=DEFAULT_.room_count, name="room_count", curie=DEFAULT_.curie('room_count'), - model_uri=DEFAULT_.room_count, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_count]) - -slots.room_dim = Slot(uri=DEFAULT_.room_dim, name="room_dim", curie=DEFAULT_.curie('room_dim'), - model_uri=DEFAULT_.room_dim, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.room_dim]) - -slots.room_door_dist = Slot(uri=DEFAULT_.room_door_dist, name="room_door_dist", curie=DEFAULT_.curie('room_door_dist'), - model_uri=DEFAULT_.room_door_dist, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.room_door_dist]) - -slots.room_loc = Slot(uri=DEFAULT_.room_loc, name="room_loc", curie=DEFAULT_.curie('room_loc'), - model_uri=DEFAULT_.room_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_loc], - pattern=re.compile(r'[corner room|interior room|exterior wall]')) - -slots.room_moist_damage_hist = Slot(uri=DEFAULT_.room_moist_damage_hist, name="room_moist_damage_hist", curie=DEFAULT_.curie('room_moist_damage_hist'), - model_uri=DEFAULT_.room_moist_damage_hist, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_moist_damage_hist]) - -slots.room_net_area = Slot(uri=DEFAULT_.room_net_area, name="room_net_area", curie=DEFAULT_.curie('room_net_area'), - model_uri=DEFAULT_.room_net_area, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.room_net_area]) - -slots.room_occup = Slot(uri=DEFAULT_.room_occup, name="room_occup", curie=DEFAULT_.curie('room_occup'), - model_uri=DEFAULT_.room_occup, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.room_occup]) - -slots.room_samp_pos = Slot(uri=DEFAULT_.room_samp_pos, name="room_samp_pos", curie=DEFAULT_.curie('room_samp_pos'), - model_uri=DEFAULT_.room_samp_pos, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_samp_pos], - pattern=re.compile(r'[north corner|south corner|west corner|east corner|northeast corner|northwest corner|southeast corner|southwest corner|center]')) - -slots.room_type = Slot(uri=DEFAULT_.room_type, name="room_type", curie=DEFAULT_.curie('room_type'), - model_uri=DEFAULT_.room_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_type], - pattern=re.compile(r'[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail room|private office|open office|stairwell|,restroom|lobby|vestibule|mechanical or electrical room|data center|laboratory_wet|laboratory_dry|gymnasium|natatorium|auditorium|lockers|cafe|warehouse]')) - -slots.room_vol = Slot(uri=DEFAULT_.room_vol, name="room_vol", curie=DEFAULT_.curie('room_vol'), - model_uri=DEFAULT_.room_vol, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.room_vol]) - -slots.room_window_count = Slot(uri=DEFAULT_.room_window_count, name="room_window_count", curie=DEFAULT_.curie('room_window_count'), - model_uri=DEFAULT_.room_window_count, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_window_count]) - -slots.room_connected = Slot(uri=DEFAULT_.room_connected, name="room_connected", curie=DEFAULT_.curie('room_connected'), - model_uri=DEFAULT_.room_connected, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_connected], - pattern=re.compile(r'[attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|mail room|office|stairwell]')) - -slots.room_hallway = Slot(uri=DEFAULT_.room_hallway, name="room_hallway", curie=DEFAULT_.curie('room_hallway'), - model_uri=DEFAULT_.room_hallway, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_hallway]) - -slots.room_door_share = Slot(uri=DEFAULT_.room_door_share, name="room_door_share", curie=DEFAULT_.curie('room_door_share'), - model_uri=DEFAULT_.room_door_share, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_door_share]) - -slots.room_wall_share = Slot(uri=DEFAULT_.room_wall_share, name="room_wall_share", curie=DEFAULT_.curie('room_wall_share'), - model_uri=DEFAULT_.room_wall_share, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.room_wall_share]) - -slots.samp_weather = Slot(uri=DEFAULT_.samp_weather, name="samp_weather", curie=DEFAULT_.curie('samp_weather'), - model_uri=DEFAULT_.samp_weather, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_weather], - pattern=re.compile(r'[clear sky|cloudy|foggy|hail|rain|snow|sleet|sunny|windy]')) - -slots.samp_floor = Slot(uri=DEFAULT_.samp_floor, name="samp_floor", curie=DEFAULT_.curie('samp_floor'), - model_uri=DEFAULT_.samp_floor, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_floor]) - -slots.samp_room_id = Slot(uri=DEFAULT_.samp_room_id, name="samp_room_id", curie=DEFAULT_.curie('samp_room_id'), - model_uri=DEFAULT_.samp_room_id, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_room_id]) - -slots.samp_time_out = Slot(uri=DEFAULT_.samp_time_out, name="samp_time_out", curie=DEFAULT_.curie('samp_time_out'), - model_uri=DEFAULT_.samp_time_out, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_time_out], - pattern=re.compile(r'\d+[.\d+]')) - -slots.season = Slot(uri=DEFAULT_.season, name="season", curie=DEFAULT_.curie('season'), - model_uri=DEFAULT_.season, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.season], - pattern=re.compile(r'[Spring|Summer|Fall|Winter]')) - -slots.season_use = Slot(uri=DEFAULT_.season_use, name="season_use", curie=DEFAULT_.curie('season_use'), - model_uri=DEFAULT_.season_use, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.season_use], - pattern=re.compile(r'[Spring|Summer|Fall|Winter]')) - -slots.shading_device_cond = Slot(uri=DEFAULT_.shading_device_cond, name="shading_device_cond", curie=DEFAULT_.curie('shading_device_cond'), - model_uri=DEFAULT_.shading_device_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.shading_device_cond], - pattern=re.compile(r'[damaged|needs repair|new|rupture|visible wear]')) - -slots.shading_device_loc = Slot(uri=DEFAULT_.shading_device_loc, name="shading_device_loc", curie=DEFAULT_.curie('shading_device_loc'), - model_uri=DEFAULT_.shading_device_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.shading_device_loc], - pattern=re.compile(r'[exterior|interior]')) - -slots.shading_device_mat = Slot(uri=DEFAULT_.shading_device_mat, name="shading_device_mat", curie=DEFAULT_.curie('shading_device_mat'), - model_uri=DEFAULT_.shading_device_mat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.shading_device_mat]) - -slots.shading_device_water_mold = Slot(uri=DEFAULT_.shading_device_water_mold, name="shading_device_water_mold", curie=DEFAULT_.curie('shading_device_water_mold'), - model_uri=DEFAULT_.shading_device_water_mold, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.shading_device_water_mold], - pattern=re.compile(r'[presence of mold visible|no presence of mold visible]')) - -slots.shading_device_type = Slot(uri=DEFAULT_.shading_device_type, name="shading_device_type", curie=DEFAULT_.curie('shading_device_type'), - model_uri=DEFAULT_.shading_device_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.shading_device_type], - pattern=re.compile(r'[bahama shutters|exterior roll blind|gambrel awning|hood awning|porchroller awning|sarasota shutters|slatted aluminum|solid aluminum awning|sun screen|tree|trellis|venetian awning]')) - -slots.specific_humidity = Slot(uri=DEFAULT_.specific_humidity, name="specific_humidity", curie=DEFAULT_.curie('specific_humidity'), - model_uri=DEFAULT_.specific_humidity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.specific_humidity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.specific = Slot(uri=DEFAULT_.specific, name="specific", curie=DEFAULT_.curie('specific'), - model_uri=DEFAULT_.specific, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.specific], - pattern=re.compile(r'[operation|as built|construction|bid|design|photos]')) - -slots.temp_out = Slot(uri=DEFAULT_.temp_out, name="temp_out", curie=DEFAULT_.curie('temp_out'), - model_uri=DEFAULT_.temp_out, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.temp_out], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.train_line = Slot(uri=DEFAULT_.train_line, name="train_line", curie=DEFAULT_.curie('train_line'), - model_uri=DEFAULT_.train_line, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.train_line], - pattern=re.compile(r'[red|green|orange]')) - -slots.train_stat_loc = Slot(uri=DEFAULT_.train_stat_loc, name="train_stat_loc", curie=DEFAULT_.curie('train_stat_loc'), - model_uri=DEFAULT_.train_stat_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.train_stat_loc], - pattern=re.compile(r'[south station above ground|south station underground|south station amtrak|forest hills|riverside]')) - -slots.train_stop_loc = Slot(uri=DEFAULT_.train_stop_loc, name="train_stop_loc", curie=DEFAULT_.curie('train_stop_loc'), - model_uri=DEFAULT_.train_stop_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.train_stop_loc], - pattern=re.compile(r'[end|mid|downtown]')) - -slots.vis_media = Slot(uri=DEFAULT_.vis_media, name="vis_media", curie=DEFAULT_.curie('vis_media'), - model_uri=DEFAULT_.vis_media, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.vis_media], - pattern=re.compile(r'[photos|videos|commonly of the building|site context (adjacent buildings, vegetation, terrain, streets)|interiors|equipment|3D scans]')) - -slots.wall_area = Slot(uri=DEFAULT_.wall_area, name="wall_area", curie=DEFAULT_.curie('wall_area'), - model_uri=DEFAULT_.wall_area, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.wall_area], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.wall_const_type = Slot(uri=DEFAULT_.wall_const_type, name="wall_const_type", curie=DEFAULT_.curie('wall_const_type'), - model_uri=DEFAULT_.wall_const_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wall_const_type], - pattern=re.compile(r'[frame construction|joisted masonry|light noncombustible|masonry noncombustible|modified fire resistive|fire resistive]')) - -slots.wall_finish_mat = Slot(uri=DEFAULT_.wall_finish_mat, name="wall_finish_mat", curie=DEFAULT_.curie('wall_finish_mat'), - model_uri=DEFAULT_.wall_finish_mat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wall_finish_mat], - pattern=re.compile(r'[plaster|gypsum plaster|veneer plaster|gypsum board|tile|terrazzo|stone facing|acoustical treatment|wood|metal|masonry]')) - -slots.wall_height = Slot(uri=DEFAULT_.wall_height, name="wall_height", curie=DEFAULT_.curie('wall_height'), - model_uri=DEFAULT_.wall_height, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.wall_height], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.wall_loc = Slot(uri=DEFAULT_.wall_loc, name="wall_loc", curie=DEFAULT_.curie('wall_loc'), - model_uri=DEFAULT_.wall_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wall_loc], - pattern=re.compile(r'[north|south|east|west]')) - -slots.wall_water_mold = Slot(uri=DEFAULT_.wall_water_mold, name="wall_water_mold", curie=DEFAULT_.curie('wall_water_mold'), - model_uri=DEFAULT_.wall_water_mold, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wall_water_mold], - pattern=re.compile(r'[presence of mold visible|no presence of mold visible]')) - -slots.wall_surf_treatment = Slot(uri=DEFAULT_.wall_surf_treatment, name="wall_surf_treatment", curie=DEFAULT_.curie('wall_surf_treatment'), - model_uri=DEFAULT_.wall_surf_treatment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wall_surf_treatment], - pattern=re.compile(r'[painted|wall paper|no treatment|paneling|stucco|fabric]')) - -slots.wall_texture = Slot(uri=DEFAULT_.wall_texture, name="wall_texture", curie=DEFAULT_.curie('wall_texture'), - model_uri=DEFAULT_.wall_texture, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wall_texture], - pattern=re.compile(r'[crows feet|crows\-foot stomp|double skip|hawk and trowel|knockdown|popcorn|orange peel|rosebud stomp|Santa\-Fe texture|skip trowel|smooth|stomp knockdown|swirl]')) - -slots.wall_thermal_mass = Slot(uri=DEFAULT_.wall_thermal_mass, name="wall_thermal_mass", curie=DEFAULT_.curie('wall_thermal_mass'), - model_uri=DEFAULT_.wall_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.wall_thermal_mass], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.water_feat_size = Slot(uri=DEFAULT_.water_feat_size, name="water_feat_size", curie=DEFAULT_.curie('water_feat_size'), - model_uri=DEFAULT_.water_feat_size, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.water_feat_size], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.water_feat_type = Slot(uri=DEFAULT_.water_feat_type, name="water_feat_type", curie=DEFAULT_.curie('water_feat_type'), - model_uri=DEFAULT_.water_feat_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.water_feat_type], - pattern=re.compile(r'[fountain|pool|standing feature|stream|waterfall]')) - -slots.weekday = Slot(uri=DEFAULT_.weekday, name="weekday", curie=DEFAULT_.curie('weekday'), - model_uri=DEFAULT_.weekday, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.weekday], - pattern=re.compile(r'[Monday|Tuesday|Wednesday|Thursday|Friday|Saturday|Sunday]')) - -slots.window_size = Slot(uri=DEFAULT_.window_size, name="window_size", curie=DEFAULT_.curie('window_size'), - model_uri=DEFAULT_.window_size, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.window_size], - pattern=re.compile(r'\d+[.\d+] \S+ x \d+[.\d+] \S+')) - -slots.window_cond = Slot(uri=DEFAULT_.window_cond, name="window_cond", curie=DEFAULT_.curie('window_cond'), - model_uri=DEFAULT_.window_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_cond], - pattern=re.compile(r'[damaged|needs repair|new|rupture|visible wear]')) - -slots.window_cover = Slot(uri=DEFAULT_.window_cover, name="window_cover", curie=DEFAULT_.curie('window_cover'), - model_uri=DEFAULT_.window_cover, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_cover], - pattern=re.compile(r'[blinds|curtains|none]')) - -slots.window_horiz_pos = Slot(uri=DEFAULT_.window_horiz_pos, name="window_horiz_pos", curie=DEFAULT_.curie('window_horiz_pos'), - model_uri=DEFAULT_.window_horiz_pos, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_horiz_pos], - pattern=re.compile(r'[left|middle|right]')) - -slots.window_loc = Slot(uri=DEFAULT_.window_loc, name="window_loc", curie=DEFAULT_.curie('window_loc'), - model_uri=DEFAULT_.window_loc, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_loc], - pattern=re.compile(r'[north|south|east|west]')) - -slots.window_mat = Slot(uri=DEFAULT_.window_mat, name="window_mat", curie=DEFAULT_.curie('window_mat'), - model_uri=DEFAULT_.window_mat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_mat], - pattern=re.compile(r'[clad|fiberglass|metal|vinyl|wood]')) - -slots.window_open_freq = Slot(uri=DEFAULT_.window_open_freq, name="window_open_freq", curie=DEFAULT_.curie('window_open_freq'), - model_uri=DEFAULT_.window_open_freq, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_open_freq]) - -slots.window_water_mold = Slot(uri=DEFAULT_.window_water_mold, name="window_water_mold", curie=DEFAULT_.curie('window_water_mold'), - model_uri=DEFAULT_.window_water_mold, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_water_mold], - pattern=re.compile(r'[presence of mold visible|no presence of mold visible]')) - -slots.window_status = Slot(uri=DEFAULT_.window_status, name="window_status", curie=DEFAULT_.curie('window_status'), - model_uri=DEFAULT_.window_status, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_status], - pattern=re.compile(r'[closed|open]')) - -slots.window_type = Slot(uri=DEFAULT_.window_type, name="window_type", curie=DEFAULT_.curie('window_type'), - model_uri=DEFAULT_.window_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_type], - pattern=re.compile(r'[single\-hung sash window|horizontal sash window|fixed window] ')) - -slots.window_vert_pos = Slot(uri=DEFAULT_.window_vert_pos, name="window_vert_pos", curie=DEFAULT_.curie('window_vert_pos'), - model_uri=DEFAULT_.window_vert_pos, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.window_vert_pos], - pattern=re.compile(r'[bottom|middle|top|low|middle|high]')) - -slots.ances_data = Slot(uri=DEFAULT_.ances_data, name="ances_data", curie=DEFAULT_.curie('ances_data'), - model_uri=DEFAULT_.ances_data, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ances_data]) - -slots.biol_stat = Slot(uri=DEFAULT_.biol_stat, name="biol_stat", curie=DEFAULT_.curie('biol_stat'), - model_uri=DEFAULT_.biol_stat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.biol_stat], - pattern=re.compile(r'[wild|natural|semi\-natural|inbred line|breeder\'s line|hybrid|clonal selection|mutant]')) - -slots.genetic_mod = Slot(uri=DEFAULT_.genetic_mod, name="genetic_mod", curie=DEFAULT_.curie('genetic_mod'), - model_uri=DEFAULT_.genetic_mod, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.genetic_mod]) - -slots.host_common_name = Slot(uri=DEFAULT_.host_common_name, name="host_common_name", curie=DEFAULT_.curie('host_common_name'), - model_uri=DEFAULT_.host_common_name, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_common_name]) - -slots.samp_capt_status = Slot(uri=DEFAULT_.samp_capt_status, name="samp_capt_status", curie=DEFAULT_.curie('samp_capt_status'), - model_uri=DEFAULT_.samp_capt_status, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_capt_status], - pattern=re.compile(r'[active surveillance in response to an outbreak|active surveillance not initiated by an outbreak|farm sample|market sample|other]')) - -slots.samp_dis_stage = Slot(uri=DEFAULT_.samp_dis_stage, name="samp_dis_stage", curie=DEFAULT_.curie('samp_dis_stage'), - model_uri=DEFAULT_.samp_dis_stage, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_dis_stage]) - -slots.host_taxid = Slot(uri=DEFAULT_.host_taxid, name="host_taxid", curie=DEFAULT_.curie('host_taxid'), - model_uri=DEFAULT_.host_taxid, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_taxid]) - -slots.host_subject_id = Slot(uri=DEFAULT_.host_subject_id, name="host_subject_id", curie=DEFAULT_.curie('host_subject_id'), - model_uri=DEFAULT_.host_subject_id, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_subject_id]) - -slots.host_age = Slot(uri=DEFAULT_.host_age, name="host_age", curie=DEFAULT_.curie('host_age'), - model_uri=DEFAULT_.host_age, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_age], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_life_stage = Slot(uri=DEFAULT_.host_life_stage, name="host_life_stage", curie=DEFAULT_.curie('host_life_stage'), - model_uri=DEFAULT_.host_life_stage, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_life_stage]) - -slots.host_sex = Slot(uri=DEFAULT_.host_sex, name="host_sex", curie=DEFAULT_.curie('host_sex'), - model_uri=DEFAULT_.host_sex, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_sex], - pattern=re.compile(r'[male|female|neuter|hermaphrodite|not determined]')) - -slots.host_disease_stat = Slot(uri=DEFAULT_.host_disease_stat, name="host_disease_stat", curie=DEFAULT_.curie('host_disease_stat'), - model_uri=DEFAULT_.host_disease_stat, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.host_disease_stat]) - -slots.host_body_habitat = Slot(uri=DEFAULT_.host_body_habitat, name="host_body_habitat", curie=DEFAULT_.curie('host_body_habitat'), - model_uri=DEFAULT_.host_body_habitat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_body_habitat]) - -slots.host_body_site = Slot(uri=DEFAULT_.host_body_site, name="host_body_site", curie=DEFAULT_.curie('host_body_site'), - model_uri=DEFAULT_.host_body_site, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.host_body_site], - pattern=re.compile(r'.* \S+:\S+')) - -slots.host_body_product = Slot(uri=DEFAULT_.host_body_product, name="host_body_product", curie=DEFAULT_.curie('host_body_product'), - model_uri=DEFAULT_.host_body_product, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.host_body_product], - pattern=re.compile(r'.* \S+:\S+')) - -slots.host_tot_mass = Slot(uri=DEFAULT_.host_tot_mass, name="host_tot_mass", curie=DEFAULT_.curie('host_tot_mass'), - model_uri=DEFAULT_.host_tot_mass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_tot_mass], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_height = Slot(uri=DEFAULT_.host_height, name="host_height", curie=DEFAULT_.curie('host_height'), - model_uri=DEFAULT_.host_height, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_height], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_length = Slot(uri=DEFAULT_.host_length, name="host_length", curie=DEFAULT_.curie('host_length'), - model_uri=DEFAULT_.host_length, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_length], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_diet = Slot(uri=DEFAULT_.host_diet, name="host_diet", curie=DEFAULT_.curie('host_diet'), - model_uri=DEFAULT_.host_diet, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_diet]) - -slots.host_last_meal = Slot(uri=DEFAULT_.host_last_meal, name="host_last_meal", curie=DEFAULT_.curie('host_last_meal'), - model_uri=DEFAULT_.host_last_meal, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_last_meal]) - -slots.host_growth_cond = Slot(uri=DEFAULT_.host_growth_cond, name="host_growth_cond", curie=DEFAULT_.curie('host_growth_cond'), - model_uri=DEFAULT_.host_growth_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_growth_cond]) - -slots.host_substrate = Slot(uri=DEFAULT_.host_substrate, name="host_substrate", curie=DEFAULT_.curie('host_substrate'), - model_uri=DEFAULT_.host_substrate, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_substrate]) - -slots.host_family_relationship = Slot(uri=DEFAULT_.host_family_relationship, name="host_family_relationship", curie=DEFAULT_.curie('host_family_relationship'), - model_uri=DEFAULT_.host_family_relationship, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_family_relationship]) - -slots.host_infra_specific_name = Slot(uri=DEFAULT_.host_infra_specific_name, name="host_infra_specific_name", curie=DEFAULT_.curie('host_infra_specific_name'), - model_uri=DEFAULT_.host_infra_specific_name, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_infra_specific_name]) - -slots.host_infra_specific_rank = Slot(uri=DEFAULT_.host_infra_specific_rank, name="host_infra_specific_rank", curie=DEFAULT_.curie('host_infra_specific_rank'), - model_uri=DEFAULT_.host_infra_specific_rank, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_infra_specific_rank]) - -slots.host_genotype = Slot(uri=DEFAULT_.host_genotype, name="host_genotype", curie=DEFAULT_.curie('host_genotype'), - model_uri=DEFAULT_.host_genotype, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_genotype]) - -slots.host_phenotype = Slot(uri=DEFAULT_.host_phenotype, name="host_phenotype", curie=DEFAULT_.curie('host_phenotype'), - model_uri=DEFAULT_.host_phenotype, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.host_phenotype], - pattern=re.compile(r'.* \S+:\S+')) - -slots.host_body_temp = Slot(uri=DEFAULT_.host_body_temp, name="host_body_temp", curie=DEFAULT_.curie('host_body_temp'), - model_uri=DEFAULT_.host_body_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_body_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_dry_mass = Slot(uri=DEFAULT_.host_dry_mass, name="host_dry_mass", curie=DEFAULT_.curie('host_dry_mass'), - model_uri=DEFAULT_.host_dry_mass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_dry_mass], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_blood_press_diast = Slot(uri=DEFAULT_.host_blood_press_diast, name="host_blood_press_diast", curie=DEFAULT_.curie('host_blood_press_diast'), - model_uri=DEFAULT_.host_blood_press_diast, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_blood_press_diast], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_blood_press_syst = Slot(uri=DEFAULT_.host_blood_press_syst, name="host_blood_press_syst", curie=DEFAULT_.curie('host_blood_press_syst'), - model_uri=DEFAULT_.host_blood_press_syst, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_blood_press_syst], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.host_color = Slot(uri=DEFAULT_.host_color, name="host_color", curie=DEFAULT_.curie('host_color'), - model_uri=DEFAULT_.host_color, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_color]) - -slots.host_shape = Slot(uri=DEFAULT_.host_shape, name="host_shape", curie=DEFAULT_.curie('host_shape'), - model_uri=DEFAULT_.host_shape, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_shape]) - -slots.gravidity = Slot(uri=DEFAULT_.gravidity, name="gravidity", curie=DEFAULT_.curie('gravidity'), - model_uri=DEFAULT_.gravidity, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.gravidity]) - -slots.ihmc_medication_code = Slot(uri=DEFAULT_.ihmc_medication_code, name="ihmc_medication_code", curie=DEFAULT_.curie('ihmc_medication_code'), - model_uri=DEFAULT_.ihmc_medication_code, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ihmc_medication_code]) - -slots.smoker = Slot(uri=DEFAULT_.smoker, name="smoker", curie=DEFAULT_.curie('smoker'), - model_uri=DEFAULT_.smoker, domain=None, range=Optional[Union[dict, BooleanValue]], mappings = [MIXS.smoker], - pattern=re.compile(r'[true|false]')) - -slots.host_hiv_stat = Slot(uri=DEFAULT_.host_hiv_stat, name="host_hiv_stat", curie=DEFAULT_.curie('host_hiv_stat'), - model_uri=DEFAULT_.host_hiv_stat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_hiv_stat], - pattern=re.compile(r'[true|false];[true|false]')) - -slots.drug_usage = Slot(uri=DEFAULT_.drug_usage, name="drug_usage", curie=DEFAULT_.curie('drug_usage'), - model_uri=DEFAULT_.drug_usage, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.drug_usage]) - -slots.host_body_mass_index = Slot(uri=DEFAULT_.host_body_mass_index, name="host_body_mass_index", curie=DEFAULT_.curie('host_body_mass_index'), - model_uri=DEFAULT_.host_body_mass_index, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_body_mass_index], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diet_last_six_month = Slot(uri=DEFAULT_.diet_last_six_month, name="diet_last_six_month", curie=DEFAULT_.curie('diet_last_six_month'), - model_uri=DEFAULT_.diet_last_six_month, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.diet_last_six_month]) - -slots.weight_loss_3_month = Slot(uri=DEFAULT_.weight_loss_3_month, name="weight_loss_3_month", curie=DEFAULT_.curie('weight_loss_3_month'), - model_uri=DEFAULT_.weight_loss_3_month, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.weight_loss_3_month], - pattern=re.compile(r'[true|false];\d+[.\d+] \S+')) - -slots.ihmc_ethnicity = Slot(uri=DEFAULT_.ihmc_ethnicity, name="ihmc_ethnicity", curie=DEFAULT_.curie('ihmc_ethnicity'), - model_uri=DEFAULT_.ihmc_ethnicity, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ihmc_ethnicity]) - -slots.host_occupation = Slot(uri=DEFAULT_.host_occupation, name="host_occupation", curie=DEFAULT_.curie('host_occupation'), - model_uri=DEFAULT_.host_occupation, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.host_occupation]) - -slots.pet_farm_animal = Slot(uri=DEFAULT_.pet_farm_animal, name="pet_farm_animal", curie=DEFAULT_.curie('pet_farm_animal'), - model_uri=DEFAULT_.pet_farm_animal, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pet_farm_animal]) - -slots.travel_out_six_month = Slot(uri=DEFAULT_.travel_out_six_month, name="travel_out_six_month", curie=DEFAULT_.curie('travel_out_six_month'), - model_uri=DEFAULT_.travel_out_six_month, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.travel_out_six_month]) - -slots.twin_sibling = Slot(uri=DEFAULT_.twin_sibling, name="twin_sibling", curie=DEFAULT_.curie('twin_sibling'), - model_uri=DEFAULT_.twin_sibling, domain=None, range=Optional[Union[dict, BooleanValue]], mappings = [MIXS.twin_sibling], - pattern=re.compile(r'[true|false]')) - -slots.medic_hist_perform = Slot(uri=DEFAULT_.medic_hist_perform, name="medic_hist_perform", curie=DEFAULT_.curie('medic_hist_perform'), - model_uri=DEFAULT_.medic_hist_perform, domain=None, range=Optional[Union[dict, BooleanValue]], mappings = [MIXS.medic_hist_perform], - pattern=re.compile(r'[true|false]')) - -slots.study_complt_stat = Slot(uri=DEFAULT_.study_complt_stat, name="study_complt_stat", curie=DEFAULT_.curie('study_complt_stat'), - model_uri=DEFAULT_.study_complt_stat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.study_complt_stat], - pattern=re.compile(r'[true|false];[adverse event|non\-compliance|lost to follow up|other\-specify]')) - -slots.pulmonary_disord = Slot(uri=DEFAULT_.pulmonary_disord, name="pulmonary_disord", curie=DEFAULT_.curie('pulmonary_disord'), - model_uri=DEFAULT_.pulmonary_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pulmonary_disord]) - -slots.nose_throat_disord = Slot(uri=DEFAULT_.nose_throat_disord, name="nose_throat_disord", curie=DEFAULT_.curie('nose_throat_disord'), - model_uri=DEFAULT_.nose_throat_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.nose_throat_disord]) - -slots.blood_blood_disord = Slot(uri=DEFAULT_.blood_blood_disord, name="blood_blood_disord", curie=DEFAULT_.curie('blood_blood_disord'), - model_uri=DEFAULT_.blood_blood_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.blood_blood_disord]) - -slots.host_pulse = Slot(uri=DEFAULT_.host_pulse, name="host_pulse", curie=DEFAULT_.curie('host_pulse'), - model_uri=DEFAULT_.host_pulse, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_pulse], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.gestation_state = Slot(uri=DEFAULT_.gestation_state, name="gestation_state", curie=DEFAULT_.curie('gestation_state'), - model_uri=DEFAULT_.gestation_state, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.gestation_state]) - -slots.maternal_health_stat = Slot(uri=DEFAULT_.maternal_health_stat, name="maternal_health_stat", curie=DEFAULT_.curie('maternal_health_stat'), - model_uri=DEFAULT_.maternal_health_stat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.maternal_health_stat]) - -slots.foetal_health_stat = Slot(uri=DEFAULT_.foetal_health_stat, name="foetal_health_stat", curie=DEFAULT_.curie('foetal_health_stat'), - model_uri=DEFAULT_.foetal_health_stat, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.foetal_health_stat]) - -slots.amniotic_fluid_color = Slot(uri=DEFAULT_.amniotic_fluid_color, name="amniotic_fluid_color", curie=DEFAULT_.curie('amniotic_fluid_color'), - model_uri=DEFAULT_.amniotic_fluid_color, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.amniotic_fluid_color]) - -slots.kidney_disord = Slot(uri=DEFAULT_.kidney_disord, name="kidney_disord", curie=DEFAULT_.curie('kidney_disord'), - model_uri=DEFAULT_.kidney_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.kidney_disord]) - -slots.urogenit_tract_disor = Slot(uri=DEFAULT_.urogenit_tract_disor, name="urogenit_tract_disor", curie=DEFAULT_.curie('urogenit_tract_disor'), - model_uri=DEFAULT_.urogenit_tract_disor, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.urogenit_tract_disor]) - -slots.urine_collect_meth = Slot(uri=DEFAULT_.urine_collect_meth, name="urine_collect_meth", curie=DEFAULT_.curie('urine_collect_meth'), - model_uri=DEFAULT_.urine_collect_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.urine_collect_meth], - pattern=re.compile(r'[clean catch|catheter]')) - -slots.gastrointest_disord = Slot(uri=DEFAULT_.gastrointest_disord, name="gastrointest_disord", curie=DEFAULT_.curie('gastrointest_disord'), - model_uri=DEFAULT_.gastrointest_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.gastrointest_disord]) - -slots.liver_disord = Slot(uri=DEFAULT_.liver_disord, name="liver_disord", curie=DEFAULT_.curie('liver_disord'), - model_uri=DEFAULT_.liver_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.liver_disord]) - -slots.special_diet = Slot(uri=DEFAULT_.special_diet, name="special_diet", curie=DEFAULT_.curie('special_diet'), - model_uri=DEFAULT_.special_diet, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.special_diet], - pattern=re.compile(r'[low carb|reduced calorie|vegetarian|other(to be specified)]')) - -slots.nose_mouth_teeth_throat_disord = Slot(uri=DEFAULT_.nose_mouth_teeth_throat_disord, name="nose_mouth_teeth_throat_disord", curie=DEFAULT_.curie('nose_mouth_teeth_throat_disord'), - model_uri=DEFAULT_.nose_mouth_teeth_throat_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.nose_mouth_teeth_throat_disord]) - -slots.time_last_toothbrush = Slot(uri=DEFAULT_.time_last_toothbrush, name="time_last_toothbrush", curie=DEFAULT_.curie('time_last_toothbrush'), - model_uri=DEFAULT_.time_last_toothbrush, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.time_last_toothbrush]) - -slots.dermatology_disord = Slot(uri=DEFAULT_.dermatology_disord, name="dermatology_disord", curie=DEFAULT_.curie('dermatology_disord'), - model_uri=DEFAULT_.dermatology_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.dermatology_disord]) - -slots.time_since_last_wash = Slot(uri=DEFAULT_.time_since_last_wash, name="time_since_last_wash", curie=DEFAULT_.curie('time_since_last_wash'), - model_uri=DEFAULT_.time_since_last_wash, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.time_since_last_wash]) - -slots.dominant_hand = Slot(uri=DEFAULT_.dominant_hand, name="dominant_hand", curie=DEFAULT_.curie('dominant_hand'), - model_uri=DEFAULT_.dominant_hand, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.dominant_hand], - pattern=re.compile(r'[left|right|ambidextrous]')) - -slots.menarche = Slot(uri=DEFAULT_.menarche, name="menarche", curie=DEFAULT_.curie('menarche'), - model_uri=DEFAULT_.menarche, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.menarche]) - -slots.sexual_act = Slot(uri=DEFAULT_.sexual_act, name="sexual_act", curie=DEFAULT_.curie('sexual_act'), - model_uri=DEFAULT_.sexual_act, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sexual_act]) - -slots.pregnancy = Slot(uri=DEFAULT_.pregnancy, name="pregnancy", curie=DEFAULT_.curie('pregnancy'), - model_uri=DEFAULT_.pregnancy, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.pregnancy]) - -slots.douche = Slot(uri=DEFAULT_.douche, name="douche", curie=DEFAULT_.curie('douche'), - model_uri=DEFAULT_.douche, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.douche]) - -slots.birth_control = Slot(uri=DEFAULT_.birth_control, name="birth_control", curie=DEFAULT_.curie('birth_control'), - model_uri=DEFAULT_.birth_control, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.birth_control]) - -slots.menopause = Slot(uri=DEFAULT_.menopause, name="menopause", curie=DEFAULT_.curie('menopause'), - model_uri=DEFAULT_.menopause, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.menopause]) - -slots.hrt = Slot(uri=DEFAULT_.hrt, name="hrt", curie=DEFAULT_.curie('hrt'), - model_uri=DEFAULT_.hrt, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.hrt]) - -slots.hysterectomy = Slot(uri=DEFAULT_.hysterectomy, name="hysterectomy", curie=DEFAULT_.curie('hysterectomy'), - model_uri=DEFAULT_.hysterectomy, domain=None, range=Optional[Union[dict, BooleanValue]], mappings = [MIXS.hysterectomy], - pattern=re.compile(r'[true|false]')) - -slots.gynecologic_disord = Slot(uri=DEFAULT_.gynecologic_disord, name="gynecologic_disord", curie=DEFAULT_.curie('gynecologic_disord'), - model_uri=DEFAULT_.gynecologic_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.gynecologic_disord]) - -slots.urogenit_disord = Slot(uri=DEFAULT_.urogenit_disord, name="urogenit_disord", curie=DEFAULT_.curie('urogenit_disord'), - model_uri=DEFAULT_.urogenit_disord, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.urogenit_disord]) - -slots.hcr = Slot(uri=DEFAULT_.hcr, name="hcr", curie=DEFAULT_.curie('hcr'), - model_uri=DEFAULT_.hcr, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.hcr], - pattern=re.compile(r'[Oil Reservoir|Gas Reservoir|Oil Sand|Coalbed|Shale|Tight Oil Reservoir|Tight Gas Reservoir|other]')) - -slots.hc_produced = Slot(uri=DEFAULT_.hc_produced, name="hc_produced", curie=DEFAULT_.curie('hc_produced'), - model_uri=DEFAULT_.hc_produced, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.hc_produced], - pattern=re.compile(r'[Oil|Gas\-Condensate|Gas|Bitumen|Coalbed Methane|other]')) - -slots.basin = Slot(uri=DEFAULT_.basin, name="basin", curie=DEFAULT_.curie('basin'), - model_uri=DEFAULT_.basin, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.basin]) - -slots.field = Slot(uri=DEFAULT_.field, name="field", curie=DEFAULT_.curie('field'), - model_uri=DEFAULT_.field, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.field]) - -slots.reservoir = Slot(uri=DEFAULT_.reservoir, name="reservoir", curie=DEFAULT_.curie('reservoir'), - model_uri=DEFAULT_.reservoir, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.reservoir]) - -slots.hcr_temp = Slot(uri=DEFAULT_.hcr_temp, name="hcr_temp", curie=DEFAULT_.curie('hcr_temp'), - model_uri=DEFAULT_.hcr_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.hcr_temp], - pattern=re.compile(r'\d+[.\d+] \- \d+[.\d+] \S+')) - -slots.tvdss_of_hcr_temp = Slot(uri=DEFAULT_.tvdss_of_hcr_temp, name="tvdss_of_hcr_temp", curie=DEFAULT_.curie('tvdss_of_hcr_temp'), - model_uri=DEFAULT_.tvdss_of_hcr_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tvdss_of_hcr_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.hcr_pressure = Slot(uri=DEFAULT_.hcr_pressure, name="hcr_pressure", curie=DEFAULT_.curie('hcr_pressure'), - model_uri=DEFAULT_.hcr_pressure, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.hcr_pressure], - pattern=re.compile(r'\d+[.\d+] \- \d+[.\d+] \S+')) - -slots.tvdss_of_hcr_pressure = Slot(uri=DEFAULT_.tvdss_of_hcr_pressure, name="tvdss_of_hcr_pressure", curie=DEFAULT_.curie('tvdss_of_hcr_pressure'), - model_uri=DEFAULT_.tvdss_of_hcr_pressure, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tvdss_of_hcr_pressure], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.permeability = Slot(uri=DEFAULT_.permeability, name="permeability", curie=DEFAULT_.curie('permeability'), - model_uri=DEFAULT_.permeability, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.permeability]) - -slots.porosity = Slot(uri=DEFAULT_.porosity, name="porosity", curie=DEFAULT_.curie('porosity'), - model_uri=DEFAULT_.porosity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.porosity], - pattern=re.compile(r'\d+[.\d+] \- \d+[.\d+] \S+')) - -slots.lithology = Slot(uri=DEFAULT_.lithology, name="lithology", curie=DEFAULT_.curie('lithology'), - model_uri=DEFAULT_.lithology, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.lithology], - pattern=re.compile(r'[Basement|Chalk|Chert|Coal|Conglomerate|Diatomite|Dolomite|Limestone|Sandstone|Shale|Siltstone|Volcanic|other]')) - -slots.depos_env = Slot(uri=DEFAULT_.depos_env, name="depos_env", curie=DEFAULT_.curie('depos_env'), - model_uri=DEFAULT_.depos_env, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.depos_env], - pattern=re.compile(r'[Continental \- Alluvial|Continental \- Aeolian|Continental \- Fluvial|Continental \- Lacustrine|Transitional \- Deltaic|Transitional \- Tidal|Transitional \- Lagoonal|Transitional \- Beach|Transitional \- Lake|Marine \- Shallow|Marine \- Deep|Marine \- Reef|Other \- Evaporite|Other \- Glacial|Other \- Volcanic|other]')) - -slots.hcr_geol_age = Slot(uri=DEFAULT_.hcr_geol_age, name="hcr_geol_age", curie=DEFAULT_.curie('hcr_geol_age'), - model_uri=DEFAULT_.hcr_geol_age, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.hcr_geol_age], - pattern=re.compile(r'[Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other]')) - -slots.owc_tvdss = Slot(uri=DEFAULT_.owc_tvdss, name="owc_tvdss", curie=DEFAULT_.curie('owc_tvdss'), - model_uri=DEFAULT_.owc_tvdss, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.owc_tvdss], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.hcr_fw_salinity = Slot(uri=DEFAULT_.hcr_fw_salinity, name="hcr_fw_salinity", curie=DEFAULT_.curie('hcr_fw_salinity'), - model_uri=DEFAULT_.hcr_fw_salinity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.hcr_fw_salinity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.sulfate_fw = Slot(uri=DEFAULT_.sulfate_fw, name="sulfate_fw", curie=DEFAULT_.curie('sulfate_fw'), - model_uri=DEFAULT_.sulfate_fw, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.sulfate_fw], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.vfa_fw = Slot(uri=DEFAULT_.vfa_fw, name="vfa_fw", curie=DEFAULT_.curie('vfa_fw'), - model_uri=DEFAULT_.vfa_fw, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.vfa_fw], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.sr_kerog_type = Slot(uri=DEFAULT_.sr_kerog_type, name="sr_kerog_type", curie=DEFAULT_.curie('sr_kerog_type'), - model_uri=DEFAULT_.sr_kerog_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sr_kerog_type], - pattern=re.compile(r'[Type I|Type II|Type III|Type IV|other]')) - -slots.sr_lithology = Slot(uri=DEFAULT_.sr_lithology, name="sr_lithology", curie=DEFAULT_.curie('sr_lithology'), - model_uri=DEFAULT_.sr_lithology, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sr_lithology], - pattern=re.compile(r'[Clastic|Carbonate|Coal|Biosilicieous|other]')) - -slots.sr_dep_env = Slot(uri=DEFAULT_.sr_dep_env, name="sr_dep_env", curie=DEFAULT_.curie('sr_dep_env'), - model_uri=DEFAULT_.sr_dep_env, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sr_dep_env], - pattern=re.compile(r'[Lacustine|Fluvioldeltaic|Fluviomarine|Marine|other]')) - -slots.sr_geol_age = Slot(uri=DEFAULT_.sr_geol_age, name="sr_geol_age", curie=DEFAULT_.curie('sr_geol_age'), - model_uri=DEFAULT_.sr_geol_age, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sr_geol_age], - pattern=re.compile(r'[Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other]')) - -slots.samp_well_name = Slot(uri=DEFAULT_.samp_well_name, name="samp_well_name", curie=DEFAULT_.curie('samp_well_name'), - model_uri=DEFAULT_.samp_well_name, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_well_name]) - -slots.win = Slot(uri=DEFAULT_.win, name="win", curie=DEFAULT_.curie('win'), - model_uri=DEFAULT_.win, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.win]) - -slots.samp_type = Slot(uri=DEFAULT_.samp_type, name="samp_type", curie=DEFAULT_.curie('samp_type'), - model_uri=DEFAULT_.samp_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_type], - pattern=re.compile(r'[core|rock trimmings|drill cuttings|piping section|coupon|pigging debris|solid deposit|produced fluid|produced water|injected water|water from treatment plant|fresh water|sea water|drilling fluid|procedural blank|positive control|negative control|other]')) - -slots.samp_subtype = Slot(uri=DEFAULT_.samp_subtype, name="samp_subtype", curie=DEFAULT_.curie('samp_subtype'), - model_uri=DEFAULT_.samp_subtype, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_subtype], - pattern=re.compile(r'[oil phase|water phase|biofilm|not applicable|other]')) - -slots.pressure = Slot(uri=DEFAULT_.pressure, name="pressure", curie=DEFAULT_.curie('pressure'), - model_uri=DEFAULT_.pressure, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.pressure], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.samp_tvdss = Slot(uri=DEFAULT_.samp_tvdss, name="samp_tvdss", curie=DEFAULT_.curie('samp_tvdss'), - model_uri=DEFAULT_.samp_tvdss, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_tvdss], - pattern=re.compile(r'\d+[.\d+]\-\d+[.\d+] \S+')) - -slots.samp_md = Slot(uri=DEFAULT_.samp_md, name="samp_md", curie=DEFAULT_.curie('samp_md'), - model_uri=DEFAULT_.samp_md, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_md], - pattern=re.compile(r'\d+[.\d+] \S+;[GL|DF|RT|KB|MSL|other]')) - -slots.samp_transport_cond = Slot(uri=DEFAULT_.samp_transport_cond, name="samp_transport_cond", curie=DEFAULT_.curie('samp_transport_cond'), - model_uri=DEFAULT_.samp_transport_cond, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_transport_cond], - pattern=re.compile(r'\d+[.\d+] \S+;\d+[.\d+] \S+')) - -slots.organism_count_qpcr_info = Slot(uri=DEFAULT_.organism_count_qpcr_info, name="organism_count_qpcr_info", curie=DEFAULT_.curie('organism_count_qpcr_info'), - model_uri=DEFAULT_.organism_count_qpcr_info, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.organism_count_qpcr_info]) - -slots.ph = Slot(uri=DEFAULT_.ph, name="ph", curie=DEFAULT_.curie('ph'), - model_uri=DEFAULT_.ph, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.ph], - pattern=re.compile(r'\d+[.\d+]')) - -slots.alkalinity = Slot(uri=DEFAULT_.alkalinity, name="alkalinity", curie=DEFAULT_.curie('alkalinity'), - model_uri=DEFAULT_.alkalinity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.alkalinity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.alkalinity_method = Slot(uri=DEFAULT_.alkalinity_method, name="alkalinity_method", curie=DEFAULT_.curie('alkalinity_method'), - model_uri=DEFAULT_.alkalinity_method, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.alkalinity_method]) - -slots.sulfate = Slot(uri=DEFAULT_.sulfate, name="sulfate", curie=DEFAULT_.curie('sulfate'), - model_uri=DEFAULT_.sulfate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.sulfate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.sulfide = Slot(uri=DEFAULT_.sulfide, name="sulfide", curie=DEFAULT_.curie('sulfide'), - model_uri=DEFAULT_.sulfide, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.sulfide], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_sulfur = Slot(uri=DEFAULT_.tot_sulfur, name="tot_sulfur", curie=DEFAULT_.curie('tot_sulfur'), - model_uri=DEFAULT_.tot_sulfur, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_sulfur], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.nitrate = Slot(uri=DEFAULT_.nitrate, name="nitrate", curie=DEFAULT_.curie('nitrate'), - model_uri=DEFAULT_.nitrate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.nitrate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.nitrite = Slot(uri=DEFAULT_.nitrite, name="nitrite", curie=DEFAULT_.curie('nitrite'), - model_uri=DEFAULT_.nitrite, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.nitrite], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.ammonium = Slot(uri=DEFAULT_.ammonium, name="ammonium", curie=DEFAULT_.curie('ammonium'), - model_uri=DEFAULT_.ammonium, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.ammonium], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_nitro = Slot(uri=DEFAULT_.tot_nitro, name="tot_nitro", curie=DEFAULT_.curie('tot_nitro'), - model_uri=DEFAULT_.tot_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_iron = Slot(uri=DEFAULT_.diss_iron, name="diss_iron", curie=DEFAULT_.curie('diss_iron'), - model_uri=DEFAULT_.diss_iron, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_iron], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.sodium = Slot(uri=DEFAULT_.sodium, name="sodium", curie=DEFAULT_.curie('sodium'), - model_uri=DEFAULT_.sodium, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.sodium], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.chloride = Slot(uri=DEFAULT_.chloride, name="chloride", curie=DEFAULT_.curie('chloride'), - model_uri=DEFAULT_.chloride, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.chloride], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.potassium = Slot(uri=DEFAULT_.potassium, name="potassium", curie=DEFAULT_.curie('potassium'), - model_uri=DEFAULT_.potassium, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.potassium], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.magnesium = Slot(uri=DEFAULT_.magnesium, name="magnesium", curie=DEFAULT_.curie('magnesium'), - model_uri=DEFAULT_.magnesium, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.magnesium], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.calcium = Slot(uri=DEFAULT_.calcium, name="calcium", curie=DEFAULT_.curie('calcium'), - model_uri=DEFAULT_.calcium, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.calcium], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_iron = Slot(uri=DEFAULT_.tot_iron, name="tot_iron", curie=DEFAULT_.curie('tot_iron'), - model_uri=DEFAULT_.tot_iron, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_iron], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_org_carb = Slot(uri=DEFAULT_.diss_org_carb, name="diss_org_carb", curie=DEFAULT_.curie('diss_org_carb'), - model_uri=DEFAULT_.diss_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_org_carb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_inorg_carb = Slot(uri=DEFAULT_.diss_inorg_carb, name="diss_inorg_carb", curie=DEFAULT_.curie('diss_inorg_carb'), - model_uri=DEFAULT_.diss_inorg_carb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_inorg_carb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_inorg_phosp = Slot(uri=DEFAULT_.diss_inorg_phosp, name="diss_inorg_phosp", curie=DEFAULT_.curie('diss_inorg_phosp'), - model_uri=DEFAULT_.diss_inorg_phosp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_inorg_phosp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_phosp = Slot(uri=DEFAULT_.tot_phosp, name="tot_phosp", curie=DEFAULT_.curie('tot_phosp'), - model_uri=DEFAULT_.tot_phosp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_phosp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.suspend_solids = Slot(uri=DEFAULT_.suspend_solids, name="suspend_solids", curie=DEFAULT_.curie('suspend_solids'), - model_uri=DEFAULT_.suspend_solids, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.suspend_solids]) - -slots.density = Slot(uri=DEFAULT_.density, name="density", curie=DEFAULT_.curie('density'), - model_uri=DEFAULT_.density, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.density], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_carb_dioxide = Slot(uri=DEFAULT_.diss_carb_dioxide, name="diss_carb_dioxide", curie=DEFAULT_.curie('diss_carb_dioxide'), - model_uri=DEFAULT_.diss_carb_dioxide, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_carb_dioxide], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_oxygen_fluid = Slot(uri=DEFAULT_.diss_oxygen_fluid, name="diss_oxygen_fluid", curie=DEFAULT_.curie('diss_oxygen_fluid'), - model_uri=DEFAULT_.diss_oxygen_fluid, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_oxygen_fluid], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.vfa = Slot(uri=DEFAULT_.vfa, name="vfa", curie=DEFAULT_.curie('vfa'), - model_uri=DEFAULT_.vfa, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.vfa], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.benzene = Slot(uri=DEFAULT_.benzene, name="benzene", curie=DEFAULT_.curie('benzene'), - model_uri=DEFAULT_.benzene, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.benzene], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.toluene = Slot(uri=DEFAULT_.toluene, name="toluene", curie=DEFAULT_.curie('toluene'), - model_uri=DEFAULT_.toluene, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.toluene], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.ethylbenzene = Slot(uri=DEFAULT_.ethylbenzene, name="ethylbenzene", curie=DEFAULT_.curie('ethylbenzene'), - model_uri=DEFAULT_.ethylbenzene, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.ethylbenzene], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.xylene = Slot(uri=DEFAULT_.xylene, name="xylene", curie=DEFAULT_.curie('xylene'), - model_uri=DEFAULT_.xylene, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.xylene], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.api = Slot(uri=DEFAULT_.api, name="api", curie=DEFAULT_.curie('api'), - model_uri=DEFAULT_.api, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.api], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tan = Slot(uri=DEFAULT_.tan, name="tan", curie=DEFAULT_.curie('tan'), - model_uri=DEFAULT_.tan, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tan], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.viscosity = Slot(uri=DEFAULT_.viscosity, name="viscosity", curie=DEFAULT_.curie('viscosity'), - model_uri=DEFAULT_.viscosity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.viscosity], - pattern=re.compile(r'\d+[.\d+] \S+;\d+[.\d+] \S+')) - -slots.pour_point = Slot(uri=DEFAULT_.pour_point, name="pour_point", curie=DEFAULT_.curie('pour_point'), - model_uri=DEFAULT_.pour_point, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.pour_point], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.saturates_pc = Slot(uri=DEFAULT_.saturates_pc, name="saturates_pc", curie=DEFAULT_.curie('saturates_pc'), - model_uri=DEFAULT_.saturates_pc, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.saturates_pc]) - -slots.aromatics_pc = Slot(uri=DEFAULT_.aromatics_pc, name="aromatics_pc", curie=DEFAULT_.curie('aromatics_pc'), - model_uri=DEFAULT_.aromatics_pc, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.aromatics_pc]) - -slots.resins_pc = Slot(uri=DEFAULT_.resins_pc, name="resins_pc", curie=DEFAULT_.curie('resins_pc'), - model_uri=DEFAULT_.resins_pc, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.resins_pc]) - -slots.asphaltenes_pc = Slot(uri=DEFAULT_.asphaltenes_pc, name="asphaltenes_pc", curie=DEFAULT_.curie('asphaltenes_pc'), - model_uri=DEFAULT_.asphaltenes_pc, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.asphaltenes_pc]) - -slots.additional_info = Slot(uri=DEFAULT_.additional_info, name="additional_info", curie=DEFAULT_.curie('additional_info'), - model_uri=DEFAULT_.additional_info, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.additional_info]) - -slots.prod_start_date = Slot(uri=DEFAULT_.prod_start_date, name="prod_start_date", curie=DEFAULT_.curie('prod_start_date'), - model_uri=DEFAULT_.prod_start_date, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.prod_start_date]) - -slots.prod_rate = Slot(uri=DEFAULT_.prod_rate, name="prod_rate", curie=DEFAULT_.curie('prod_rate'), - model_uri=DEFAULT_.prod_rate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.prod_rate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.water_production_rate = Slot(uri=DEFAULT_.water_production_rate, name="water_production_rate", curie=DEFAULT_.curie('water_production_rate'), - model_uri=DEFAULT_.water_production_rate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.water_production_rate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.water_cut = Slot(uri=DEFAULT_.water_cut, name="water_cut", curie=DEFAULT_.curie('water_cut'), - model_uri=DEFAULT_.water_cut, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.water_cut], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.iwf = Slot(uri=DEFAULT_.iwf, name="iwf", curie=DEFAULT_.curie('iwf'), - model_uri=DEFAULT_.iwf, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.iwf], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.add_recov_method = Slot(uri=DEFAULT_.add_recov_method, name="add_recov_method", curie=DEFAULT_.curie('add_recov_method'), - model_uri=DEFAULT_.add_recov_method, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.add_recov_method]) - -slots.iw_bt_date_well = Slot(uri=DEFAULT_.iw_bt_date_well, name="iw_bt_date_well", curie=DEFAULT_.curie('iw_bt_date_well'), - model_uri=DEFAULT_.iw_bt_date_well, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.iw_bt_date_well]) - -slots.biocide = Slot(uri=DEFAULT_.biocide, name="biocide", curie=DEFAULT_.curie('biocide'), - model_uri=DEFAULT_.biocide, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.biocide]) - -slots.biocide_admin_method = Slot(uri=DEFAULT_.biocide_admin_method, name="biocide_admin_method", curie=DEFAULT_.curie('biocide_admin_method'), - model_uri=DEFAULT_.biocide_admin_method, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.biocide_admin_method]) - -slots.chem_treatment = Slot(uri=DEFAULT_.chem_treatment, name="chem_treatment", curie=DEFAULT_.curie('chem_treatment'), - model_uri=DEFAULT_.chem_treatment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.chem_treatment]) - -slots.chem_treatment_method = Slot(uri=DEFAULT_.chem_treatment_method, name="chem_treatment_method", curie=DEFAULT_.curie('chem_treatment_method'), - model_uri=DEFAULT_.chem_treatment_method, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.chem_treatment_method]) - -slots.samp_loc_corr_rate = Slot(uri=DEFAULT_.samp_loc_corr_rate, name="samp_loc_corr_rate", curie=DEFAULT_.curie('samp_loc_corr_rate'), - model_uri=DEFAULT_.samp_loc_corr_rate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_loc_corr_rate], - pattern=re.compile(r'\d+[.\d+] \- \d+[.\d+] \S+')) - -slots.samp_collection_point = Slot(uri=DEFAULT_.samp_collection_point, name="samp_collection_point", curie=DEFAULT_.curie('samp_collection_point'), - model_uri=DEFAULT_.samp_collection_point, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.samp_collection_point], - pattern=re.compile(r'[well|test well|drilling rig|wellhead|separator|storage tank|other]')) - -slots.samp_preserv = Slot(uri=DEFAULT_.samp_preserv, name="samp_preserv", curie=DEFAULT_.curie('samp_preserv'), - model_uri=DEFAULT_.samp_preserv, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.samp_preserv]) - -slots.alkyl_diethers = Slot(uri=DEFAULT_.alkyl_diethers, name="alkyl_diethers", curie=DEFAULT_.curie('alkyl_diethers'), - model_uri=DEFAULT_.alkyl_diethers, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.alkyl_diethers], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.aminopept_act = Slot(uri=DEFAULT_.aminopept_act, name="aminopept_act", curie=DEFAULT_.curie('aminopept_act'), - model_uri=DEFAULT_.aminopept_act, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.aminopept_act], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.bacteria_carb_prod = Slot(uri=DEFAULT_.bacteria_carb_prod, name="bacteria_carb_prod", curie=DEFAULT_.curie('bacteria_carb_prod'), - model_uri=DEFAULT_.bacteria_carb_prod, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.bacteria_carb_prod], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.biomass = Slot(uri=DEFAULT_.biomass, name="biomass", curie=DEFAULT_.curie('biomass'), - model_uri=DEFAULT_.biomass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.biomass]) - -slots.bishomohopanol = Slot(uri=DEFAULT_.bishomohopanol, name="bishomohopanol", curie=DEFAULT_.curie('bishomohopanol'), - model_uri=DEFAULT_.bishomohopanol, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.bishomohopanol], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.bromide = Slot(uri=DEFAULT_.bromide, name="bromide", curie=DEFAULT_.curie('bromide'), - model_uri=DEFAULT_.bromide, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.bromide], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.carb_nitro_ratio = Slot(uri=DEFAULT_.carb_nitro_ratio, name="carb_nitro_ratio", curie=DEFAULT_.curie('carb_nitro_ratio'), - model_uri=DEFAULT_.carb_nitro_ratio, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.carb_nitro_ratio], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.chlorophyll = Slot(uri=DEFAULT_.chlorophyll, name="chlorophyll", curie=DEFAULT_.curie('chlorophyll'), - model_uri=DEFAULT_.chlorophyll, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.chlorophyll], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diether_lipids = Slot(uri=DEFAULT_.diether_lipids, name="diether_lipids", curie=DEFAULT_.curie('diether_lipids'), - model_uri=DEFAULT_.diether_lipids, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diether_lipids]) - -slots.diss_hydrogen = Slot(uri=DEFAULT_.diss_hydrogen, name="diss_hydrogen", curie=DEFAULT_.curie('diss_hydrogen'), - model_uri=DEFAULT_.diss_hydrogen, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_hydrogen], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_org_nitro = Slot(uri=DEFAULT_.diss_org_nitro, name="diss_org_nitro", curie=DEFAULT_.curie('diss_org_nitro'), - model_uri=DEFAULT_.diss_org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_org_nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_oxygen = Slot(uri=DEFAULT_.diss_oxygen, name="diss_oxygen", curie=DEFAULT_.curie('diss_oxygen'), - model_uri=DEFAULT_.diss_oxygen, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_oxygen], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.glucosidase_act = Slot(uri=DEFAULT_.glucosidase_act, name="glucosidase_act", curie=DEFAULT_.curie('glucosidase_act'), - model_uri=DEFAULT_.glucosidase_act, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.glucosidase_act], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.mean_frict_vel = Slot(uri=DEFAULT_.mean_frict_vel, name="mean_frict_vel", curie=DEFAULT_.curie('mean_frict_vel'), - model_uri=DEFAULT_.mean_frict_vel, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.mean_frict_vel], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.mean_peak_frict_vel = Slot(uri=DEFAULT_.mean_peak_frict_vel, name="mean_peak_frict_vel", curie=DEFAULT_.curie('mean_peak_frict_vel'), - model_uri=DEFAULT_.mean_peak_frict_vel, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.mean_peak_frict_vel], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.n_alkanes = Slot(uri=DEFAULT_.n_alkanes, name="n_alkanes", curie=DEFAULT_.curie('n_alkanes'), - model_uri=DEFAULT_.n_alkanes, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.n_alkanes]) - -slots.nitro = Slot(uri=DEFAULT_.nitro, name="nitro", curie=DEFAULT_.curie('nitro'), - model_uri=DEFAULT_.nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.org_carb = Slot(uri=DEFAULT_.org_carb, name="org_carb", curie=DEFAULT_.curie('org_carb'), - model_uri=DEFAULT_.org_carb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.org_carb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.org_matter = Slot(uri=DEFAULT_.org_matter, name="org_matter", curie=DEFAULT_.curie('org_matter'), - model_uri=DEFAULT_.org_matter, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.org_matter], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.org_nitro = Slot(uri=DEFAULT_.org_nitro, name="org_nitro", curie=DEFAULT_.curie('org_nitro'), - model_uri=DEFAULT_.org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.org_nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.part_org_carb = Slot(uri=DEFAULT_.part_org_carb, name="part_org_carb", curie=DEFAULT_.curie('part_org_carb'), - model_uri=DEFAULT_.part_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.part_org_carb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.petroleum_hydrocarb = Slot(uri=DEFAULT_.petroleum_hydrocarb, name="petroleum_hydrocarb", curie=DEFAULT_.curie('petroleum_hydrocarb'), - model_uri=DEFAULT_.petroleum_hydrocarb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.petroleum_hydrocarb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.phaeopigments = Slot(uri=DEFAULT_.phaeopigments, name="phaeopigments", curie=DEFAULT_.curie('phaeopigments'), - model_uri=DEFAULT_.phaeopigments, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.phaeopigments]) - -slots.phosphate = Slot(uri=DEFAULT_.phosphate, name="phosphate", curie=DEFAULT_.curie('phosphate'), - model_uri=DEFAULT_.phosphate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.phosphate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.phosplipid_fatt_acid = Slot(uri=DEFAULT_.phosplipid_fatt_acid, name="phosplipid_fatt_acid", curie=DEFAULT_.curie('phosplipid_fatt_acid'), - model_uri=DEFAULT_.phosplipid_fatt_acid, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.phosplipid_fatt_acid]) - -slots.redox_potential = Slot(uri=DEFAULT_.redox_potential, name="redox_potential", curie=DEFAULT_.curie('redox_potential'), - model_uri=DEFAULT_.redox_potential, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.redox_potential], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.salinity = Slot(uri=DEFAULT_.salinity, name="salinity", curie=DEFAULT_.curie('salinity'), - model_uri=DEFAULT_.salinity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.salinity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.silicate = Slot(uri=DEFAULT_.silicate, name="silicate", curie=DEFAULT_.curie('silicate'), - model_uri=DEFAULT_.silicate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.silicate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_carb = Slot(uri=DEFAULT_.tot_carb, name="tot_carb", curie=DEFAULT_.curie('tot_carb'), - model_uri=DEFAULT_.tot_carb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_carb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_nitro_content = Slot(uri=DEFAULT_.tot_nitro_content, name="tot_nitro_content", curie=DEFAULT_.curie('tot_nitro_content'), - model_uri=DEFAULT_.tot_nitro_content, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_nitro_content], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_org_carb = Slot(uri=DEFAULT_.tot_org_carb, name="tot_org_carb", curie=DEFAULT_.curie('tot_org_carb'), - model_uri=DEFAULT_.tot_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_org_carb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.turbidity = Slot(uri=DEFAULT_.turbidity, name="turbidity", curie=DEFAULT_.curie('turbidity'), - model_uri=DEFAULT_.turbidity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.turbidity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.water_content = Slot(uri=DEFAULT_.water_content, name="water_content", curie=DEFAULT_.curie('water_content'), - model_uri=DEFAULT_.water_content, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.water_content], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.water_current = Slot(uri=DEFAULT_.water_current, name="water_current", curie=DEFAULT_.curie('water_current'), - model_uri=DEFAULT_.water_current, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.water_current], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.air_temp_regm = Slot(uri=DEFAULT_.air_temp_regm, name="air_temp_regm", curie=DEFAULT_.curie('air_temp_regm'), - model_uri=DEFAULT_.air_temp_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.air_temp_regm]) - -slots.antibiotic_regm = Slot(uri=DEFAULT_.antibiotic_regm, name="antibiotic_regm", curie=DEFAULT_.curie('antibiotic_regm'), - model_uri=DEFAULT_.antibiotic_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.antibiotic_regm]) - -slots.biotic_regm = Slot(uri=DEFAULT_.biotic_regm, name="biotic_regm", curie=DEFAULT_.curie('biotic_regm'), - model_uri=DEFAULT_.biotic_regm, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.biotic_regm]) - -slots.chem_mutagen = Slot(uri=DEFAULT_.chem_mutagen, name="chem_mutagen", curie=DEFAULT_.curie('chem_mutagen'), - model_uri=DEFAULT_.chem_mutagen, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.chem_mutagen]) - -slots.climate_environment = Slot(uri=DEFAULT_.climate_environment, name="climate_environment", curie=DEFAULT_.curie('climate_environment'), - model_uri=DEFAULT_.climate_environment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.climate_environment]) - -slots.cult_root_med = Slot(uri=DEFAULT_.cult_root_med, name="cult_root_med", curie=DEFAULT_.curie('cult_root_med'), - model_uri=DEFAULT_.cult_root_med, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.cult_root_med]) - -slots.fertilizer_regm = Slot(uri=DEFAULT_.fertilizer_regm, name="fertilizer_regm", curie=DEFAULT_.curie('fertilizer_regm'), - model_uri=DEFAULT_.fertilizer_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.fertilizer_regm]) - -slots.fungicide_regm = Slot(uri=DEFAULT_.fungicide_regm, name="fungicide_regm", curie=DEFAULT_.curie('fungicide_regm'), - model_uri=DEFAULT_.fungicide_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.fungicide_regm]) - -slots.gaseous_environment = Slot(uri=DEFAULT_.gaseous_environment, name="gaseous_environment", curie=DEFAULT_.curie('gaseous_environment'), - model_uri=DEFAULT_.gaseous_environment, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.gaseous_environment]) - -slots.gravity = Slot(uri=DEFAULT_.gravity, name="gravity", curie=DEFAULT_.curie('gravity'), - model_uri=DEFAULT_.gravity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.gravity]) - -slots.growth_facil = Slot(uri=DEFAULT_.growth_facil, name="growth_facil", curie=DEFAULT_.curie('growth_facil'), - model_uri=DEFAULT_.growth_facil, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.growth_facil]) - -slots.growth_habit = Slot(uri=DEFAULT_.growth_habit, name="growth_habit", curie=DEFAULT_.curie('growth_habit'), - model_uri=DEFAULT_.growth_habit, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.growth_habit], - pattern=re.compile(r'[erect|semi\-erect|spreading|prostrate] ')) - -slots.growth_hormone_regm = Slot(uri=DEFAULT_.growth_hormone_regm, name="growth_hormone_regm", curie=DEFAULT_.curie('growth_hormone_regm'), - model_uri=DEFAULT_.growth_hormone_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.growth_hormone_regm]) - -slots.herbicide_regm = Slot(uri=DEFAULT_.herbicide_regm, name="herbicide_regm", curie=DEFAULT_.curie('herbicide_regm'), - model_uri=DEFAULT_.herbicide_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.herbicide_regm]) - -slots.host_wet_mass = Slot(uri=DEFAULT_.host_wet_mass, name="host_wet_mass", curie=DEFAULT_.curie('host_wet_mass'), - model_uri=DEFAULT_.host_wet_mass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.host_wet_mass], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.humidity_regm = Slot(uri=DEFAULT_.humidity_regm, name="humidity_regm", curie=DEFAULT_.curie('humidity_regm'), - model_uri=DEFAULT_.humidity_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.humidity_regm]) - -slots.light_regm = Slot(uri=DEFAULT_.light_regm, name="light_regm", curie=DEFAULT_.curie('light_regm'), - model_uri=DEFAULT_.light_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.light_regm]) - -slots.mechanical_damage = Slot(uri=DEFAULT_.mechanical_damage, name="mechanical_damage", curie=DEFAULT_.curie('mechanical_damage'), - model_uri=DEFAULT_.mechanical_damage, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.mechanical_damage]) - -slots.mineral_nutr_regm = Slot(uri=DEFAULT_.mineral_nutr_regm, name="mineral_nutr_regm", curie=DEFAULT_.curie('mineral_nutr_regm'), - model_uri=DEFAULT_.mineral_nutr_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.mineral_nutr_regm]) - -slots.non_mineral_nutr_regm = Slot(uri=DEFAULT_.non_mineral_nutr_regm, name="non_mineral_nutr_regm", curie=DEFAULT_.curie('non_mineral_nutr_regm'), - model_uri=DEFAULT_.non_mineral_nutr_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.non_mineral_nutr_regm]) - -slots.ph_regm = Slot(uri=DEFAULT_.ph_regm, name="ph_regm", curie=DEFAULT_.curie('ph_regm'), - model_uri=DEFAULT_.ph_regm, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ph_regm]) - -slots.pesticide_regm = Slot(uri=DEFAULT_.pesticide_regm, name="pesticide_regm", curie=DEFAULT_.curie('pesticide_regm'), - model_uri=DEFAULT_.pesticide_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.pesticide_regm]) - -slots.plant_growth_med = Slot(uri=DEFAULT_.plant_growth_med, name="plant_growth_med", curie=DEFAULT_.curie('plant_growth_med'), - model_uri=DEFAULT_.plant_growth_med, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.plant_growth_med], - pattern=re.compile(r'.* \S+:\S+')) - -slots.plant_product = Slot(uri=DEFAULT_.plant_product, name="plant_product", curie=DEFAULT_.curie('plant_product'), - model_uri=DEFAULT_.plant_product, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.plant_product]) - -slots.plant_sex = Slot(uri=DEFAULT_.plant_sex, name="plant_sex", curie=DEFAULT_.curie('plant_sex'), - model_uri=DEFAULT_.plant_sex, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.plant_sex], - pattern=re.compile(r'[Androdioecious|Androecious|Androgynous|Androgynomonoecious|Andromonoecious|Bisexual|Dichogamous|Diclinous|Dioecious|Gynodioecious|Gynoecious|Gynomonoecious|Hermaphroditic|Imperfect|Monoclinous|Monoecious|Perfect|Polygamodioecious|Polygamomonoecious|Polygamous|Protandrous|Protogynous|Subandroecious|Subdioecious|Subgynoecious|Synoecious|Trimonoecious|Trioecious|Unisexual]')) - -slots.plant_struc = Slot(uri=DEFAULT_.plant_struc, name="plant_struc", curie=DEFAULT_.curie('plant_struc'), - model_uri=DEFAULT_.plant_struc, domain=None, range=Optional[Union[dict, ControlledTermValue]], mappings = [MIXS.plant_struc], - pattern=re.compile(r'.* \S+:\S+')) - -slots.radiation_regm = Slot(uri=DEFAULT_.radiation_regm, name="radiation_regm", curie=DEFAULT_.curie('radiation_regm'), - model_uri=DEFAULT_.radiation_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.radiation_regm]) - -slots.rainfall_regm = Slot(uri=DEFAULT_.rainfall_regm, name="rainfall_regm", curie=DEFAULT_.curie('rainfall_regm'), - model_uri=DEFAULT_.rainfall_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.rainfall_regm]) - -slots.root_cond = Slot(uri=DEFAULT_.root_cond, name="root_cond", curie=DEFAULT_.curie('root_cond'), - model_uri=DEFAULT_.root_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.root_cond]) - -slots.root_med_carbon = Slot(uri=DEFAULT_.root_med_carbon, name="root_med_carbon", curie=DEFAULT_.curie('root_med_carbon'), - model_uri=DEFAULT_.root_med_carbon, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.root_med_carbon]) - -slots.root_med_macronutr = Slot(uri=DEFAULT_.root_med_macronutr, name="root_med_macronutr", curie=DEFAULT_.curie('root_med_macronutr'), - model_uri=DEFAULT_.root_med_macronutr, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.root_med_macronutr]) - -slots.root_med_micronutr = Slot(uri=DEFAULT_.root_med_micronutr, name="root_med_micronutr", curie=DEFAULT_.curie('root_med_micronutr'), - model_uri=DEFAULT_.root_med_micronutr, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.root_med_micronutr]) - -slots.root_med_suppl = Slot(uri=DEFAULT_.root_med_suppl, name="root_med_suppl", curie=DEFAULT_.curie('root_med_suppl'), - model_uri=DEFAULT_.root_med_suppl, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.root_med_suppl]) - -slots.root_med_ph = Slot(uri=DEFAULT_.root_med_ph, name="root_med_ph", curie=DEFAULT_.curie('root_med_ph'), - model_uri=DEFAULT_.root_med_ph, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.root_med_ph], - pattern=re.compile(r'\d+[.\d+]')) - -slots.root_med_regl = Slot(uri=DEFAULT_.root_med_regl, name="root_med_regl", curie=DEFAULT_.curie('root_med_regl'), - model_uri=DEFAULT_.root_med_regl, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.root_med_regl]) - -slots.root_med_solid = Slot(uri=DEFAULT_.root_med_solid, name="root_med_solid", curie=DEFAULT_.curie('root_med_solid'), - model_uri=DEFAULT_.root_med_solid, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.root_med_solid]) - -slots.salt_regm = Slot(uri=DEFAULT_.salt_regm, name="salt_regm", curie=DEFAULT_.curie('salt_regm'), - model_uri=DEFAULT_.salt_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.salt_regm]) - -slots.season_environment = Slot(uri=DEFAULT_.season_environment, name="season_environment", curie=DEFAULT_.curie('season_environment'), - model_uri=DEFAULT_.season_environment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.season_environment]) - -slots.standing_water_regm = Slot(uri=DEFAULT_.standing_water_regm, name="standing_water_regm", curie=DEFAULT_.curie('standing_water_regm'), - model_uri=DEFAULT_.standing_water_regm, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.standing_water_regm]) - -slots.tiss_cult_growth_med = Slot(uri=DEFAULT_.tiss_cult_growth_med, name="tiss_cult_growth_med", curie=DEFAULT_.curie('tiss_cult_growth_med'), - model_uri=DEFAULT_.tiss_cult_growth_med, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tiss_cult_growth_med]) - -slots.water_temp_regm = Slot(uri=DEFAULT_.water_temp_regm, name="water_temp_regm", curie=DEFAULT_.curie('water_temp_regm'), - model_uri=DEFAULT_.water_temp_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.water_temp_regm]) - -slots.watering_regm = Slot(uri=DEFAULT_.watering_regm, name="watering_regm", curie=DEFAULT_.curie('watering_regm'), - model_uri=DEFAULT_.watering_regm, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.watering_regm]) - -slots.particle_class = Slot(uri=DEFAULT_.particle_class, name="particle_class", curie=DEFAULT_.curie('particle_class'), - model_uri=DEFAULT_.particle_class, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.particle_class]) - -slots.sediment_type = Slot(uri=DEFAULT_.sediment_type, name="sediment_type", curie=DEFAULT_.curie('sediment_type'), - model_uri=DEFAULT_.sediment_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sediment_type], - pattern=re.compile(r'[biogenous|cosmogenous|hydrogenous|lithogenous]')) - -slots.tidal_stage = Slot(uri=DEFAULT_.tidal_stage, name="tidal_stage", curie=DEFAULT_.curie('tidal_stage'), - model_uri=DEFAULT_.tidal_stage, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tidal_stage], - pattern=re.compile(r'[low tide|ebb tide|flood tide|high tide]')) - -slots.tot_depth_water_col = Slot(uri=DEFAULT_.tot_depth_water_col, name="tot_depth_water_col", curie=DEFAULT_.curie('tot_depth_water_col'), - model_uri=DEFAULT_.tot_depth_water_col, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_depth_water_col], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.cur_land_use = Slot(uri=DEFAULT_.cur_land_use, name="cur_land_use", curie=DEFAULT_.curie('cur_land_use'), - model_uri=DEFAULT_.cur_land_use, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.cur_land_use], - pattern=re.compile(r'[cities|farmstead|industrial areas|roads\/railroads|rock|sand|gravel|mudflats|salt flats|badlands|permanent snow or ice|saline seeps|mines\/quarries|oil waste areas|small grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands (grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands used for livestock grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub land (e.g. mesquite,sage\-brush,creosote bush,shrub oak,eucalyptus)|successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub crops (blueberries,nursery ornamentals,filberts)|vine crops (grapes)|conifers (e.g. pine,spruce,fir,cypress)|hardwoods (e.g. oak,hickory,elm,aspen)|intermixed hardwood and conifers|tropical (e.g. mangrove,palms)|rainforest (evergreen forest receiving >406 cm annual rainfall)|swamp (permanent or semi\-permanent water body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery trees)]')) - -slots.cur_vegetation = Slot(uri=DEFAULT_.cur_vegetation, name="cur_vegetation", curie=DEFAULT_.curie('cur_vegetation'), - model_uri=DEFAULT_.cur_vegetation, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.cur_vegetation]) - -slots.cur_vegetation_meth = Slot(uri=DEFAULT_.cur_vegetation_meth, name="cur_vegetation_meth", curie=DEFAULT_.curie('cur_vegetation_meth'), - model_uri=DEFAULT_.cur_vegetation_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.cur_vegetation_meth]) - -slots.previous_land_use = Slot(uri=DEFAULT_.previous_land_use, name="previous_land_use", curie=DEFAULT_.curie('previous_land_use'), - model_uri=DEFAULT_.previous_land_use, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.previous_land_use]) - -slots.previous_land_use_meth = Slot(uri=DEFAULT_.previous_land_use_meth, name="previous_land_use_meth", curie=DEFAULT_.curie('previous_land_use_meth'), - model_uri=DEFAULT_.previous_land_use_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.previous_land_use_meth]) - -slots.crop_rotation = Slot(uri=DEFAULT_.crop_rotation, name="crop_rotation", curie=DEFAULT_.curie('crop_rotation'), - model_uri=DEFAULT_.crop_rotation, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.crop_rotation]) - -slots.agrochem_addition = Slot(uri=DEFAULT_.agrochem_addition, name="agrochem_addition", curie=DEFAULT_.curie('agrochem_addition'), - model_uri=DEFAULT_.agrochem_addition, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.agrochem_addition]) - -slots.tillage = Slot(uri=DEFAULT_.tillage, name="tillage", curie=DEFAULT_.curie('tillage'), - model_uri=DEFAULT_.tillage, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tillage], - pattern=re.compile(r'[drill|cutting disc|ridge till|strip tillage|zonal tillage|chisel|tined|mouldboard|disc plough]')) - -slots.fire = Slot(uri=DEFAULT_.fire, name="fire", curie=DEFAULT_.curie('fire'), - model_uri=DEFAULT_.fire, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.fire]) - -slots.flooding = Slot(uri=DEFAULT_.flooding, name="flooding", curie=DEFAULT_.curie('flooding'), - model_uri=DEFAULT_.flooding, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.flooding]) - -slots.extreme_event = Slot(uri=DEFAULT_.extreme_event, name="extreme_event", curie=DEFAULT_.curie('extreme_event'), - model_uri=DEFAULT_.extreme_event, domain=None, range=Optional[Union[dict, TimestampValue]], mappings = [MIXS.extreme_event]) - -slots.horizon = Slot(uri=DEFAULT_.horizon, name="horizon", curie=DEFAULT_.curie('horizon'), - model_uri=DEFAULT_.horizon, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.horizon], - pattern=re.compile(r'[O horizon|A horizon|E horizon|B horizon|C horizon|R layer|Permafrost]')) - -slots.horizon_meth = Slot(uri=DEFAULT_.horizon_meth, name="horizon_meth", curie=DEFAULT_.curie('horizon_meth'), - model_uri=DEFAULT_.horizon_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.horizon_meth]) - -slots.sieving = Slot(uri=DEFAULT_.sieving, name="sieving", curie=DEFAULT_.curie('sieving'), - model_uri=DEFAULT_.sieving, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.sieving]) - -slots.water_content_soil_meth = Slot(uri=DEFAULT_.water_content_soil_meth, name="water_content_soil_meth", curie=DEFAULT_.curie('water_content_soil_meth'), - model_uri=DEFAULT_.water_content_soil_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.water_content_soil_meth]) - -slots.pool_dna_extracts = Slot(uri=DEFAULT_.pool_dna_extracts, name="pool_dna_extracts", curie=DEFAULT_.curie('pool_dna_extracts'), - model_uri=DEFAULT_.pool_dna_extracts, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pool_dna_extracts]) - -slots.store_cond = Slot(uri=DEFAULT_.store_cond, name="store_cond", curie=DEFAULT_.curie('store_cond'), - model_uri=DEFAULT_.store_cond, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.store_cond]) - -slots.link_climate_info = Slot(uri=DEFAULT_.link_climate_info, name="link_climate_info", curie=DEFAULT_.curie('link_climate_info'), - model_uri=DEFAULT_.link_climate_info, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.link_climate_info]) - -slots.annual_temp = Slot(uri=DEFAULT_.annual_temp, name="annual_temp", curie=DEFAULT_.curie('annual_temp'), - model_uri=DEFAULT_.annual_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.annual_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.season_temp = Slot(uri=DEFAULT_.season_temp, name="season_temp", curie=DEFAULT_.curie('season_temp'), - model_uri=DEFAULT_.season_temp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.season_temp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.annual_precpt = Slot(uri=DEFAULT_.annual_precpt, name="annual_precpt", curie=DEFAULT_.curie('annual_precpt'), - model_uri=DEFAULT_.annual_precpt, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.annual_precpt], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.season_precpt = Slot(uri=DEFAULT_.season_precpt, name="season_precpt", curie=DEFAULT_.curie('season_precpt'), - model_uri=DEFAULT_.season_precpt, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.season_precpt], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.link_class_info = Slot(uri=DEFAULT_.link_class_info, name="link_class_info", curie=DEFAULT_.curie('link_class_info'), - model_uri=DEFAULT_.link_class_info, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.link_class_info]) - -slots.fao_class = Slot(uri=DEFAULT_.fao_class, name="fao_class", curie=DEFAULT_.curie('fao_class'), - model_uri=DEFAULT_.fao_class, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.fao_class], - pattern=re.compile(r'[Acrisols|Andosols|Arenosols|Cambisols|Chernozems|Ferralsols|Fluvisols|Gleysols|Greyzems|Gypsisols|Histosols|Kastanozems|Lithosols|Luvisols|Nitosols|Phaeozems|Planosols|Podzols|Podzoluvisols|Rankers|Regosols|Rendzinas|Solonchaks|Solonetz|Vertisols|Yermosols]')) - -slots.local_class = Slot(uri=DEFAULT_.local_class, name="local_class", curie=DEFAULT_.curie('local_class'), - model_uri=DEFAULT_.local_class, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.local_class]) - -slots.local_class_meth = Slot(uri=DEFAULT_.local_class_meth, name="local_class_meth", curie=DEFAULT_.curie('local_class_meth'), - model_uri=DEFAULT_.local_class_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.local_class_meth]) - -slots.soil_type = Slot(uri=DEFAULT_.soil_type, name="soil_type", curie=DEFAULT_.curie('soil_type'), - model_uri=DEFAULT_.soil_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.soil_type]) - -slots.soil_type_meth = Slot(uri=DEFAULT_.soil_type_meth, name="soil_type_meth", curie=DEFAULT_.curie('soil_type_meth'), - model_uri=DEFAULT_.soil_type_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.soil_type_meth]) - -slots.slope_gradient = Slot(uri=DEFAULT_.slope_gradient, name="slope_gradient", curie=DEFAULT_.curie('slope_gradient'), - model_uri=DEFAULT_.slope_gradient, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.slope_gradient], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.slope_aspect = Slot(uri=DEFAULT_.slope_aspect, name="slope_aspect", curie=DEFAULT_.curie('slope_aspect'), - model_uri=DEFAULT_.slope_aspect, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.slope_aspect], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.profile_position = Slot(uri=DEFAULT_.profile_position, name="profile_position", curie=DEFAULT_.curie('profile_position'), - model_uri=DEFAULT_.profile_position, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.profile_position], - pattern=re.compile(r'[summit|shoulder|backslope|footslope|toeslope]')) - -slots.drainage_class = Slot(uri=DEFAULT_.drainage_class, name="drainage_class", curie=DEFAULT_.curie('drainage_class'), - model_uri=DEFAULT_.drainage_class, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.drainage_class], - pattern=re.compile(r'[very poorly|poorly|somewhat poorly|moderately well|well|excessively drained]')) - -slots.texture = Slot(uri=DEFAULT_.texture, name="texture", curie=DEFAULT_.curie('texture'), - model_uri=DEFAULT_.texture, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.texture], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.texture_meth = Slot(uri=DEFAULT_.texture_meth, name="texture_meth", curie=DEFAULT_.curie('texture_meth'), - model_uri=DEFAULT_.texture_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.texture_meth]) - -slots.ph_meth = Slot(uri=DEFAULT_.ph_meth, name="ph_meth", curie=DEFAULT_.curie('ph_meth'), - model_uri=DEFAULT_.ph_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.ph_meth]) - -slots.tot_org_c_meth = Slot(uri=DEFAULT_.tot_org_c_meth, name="tot_org_c_meth", curie=DEFAULT_.curie('tot_org_c_meth'), - model_uri=DEFAULT_.tot_org_c_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tot_org_c_meth]) - -slots.tot_nitro_content_meth = Slot(uri=DEFAULT_.tot_nitro_content_meth, name="tot_nitro_content_meth", curie=DEFAULT_.curie('tot_nitro_content_meth'), - model_uri=DEFAULT_.tot_nitro_content_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tot_nitro_content_meth]) - -slots.microbial_biomass = Slot(uri=DEFAULT_.microbial_biomass, name="microbial_biomass", curie=DEFAULT_.curie('microbial_biomass'), - model_uri=DEFAULT_.microbial_biomass, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.microbial_biomass], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.microbial_biomass_meth = Slot(uri=DEFAULT_.microbial_biomass_meth, name="microbial_biomass_meth", curie=DEFAULT_.curie('microbial_biomass_meth'), - model_uri=DEFAULT_.microbial_biomass_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.microbial_biomass_meth]) - -slots.link_addit_analys = Slot(uri=DEFAULT_.link_addit_analys, name="link_addit_analys", curie=DEFAULT_.curie('link_addit_analys'), - model_uri=DEFAULT_.link_addit_analys, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.link_addit_analys]) - -slots.extreme_salinity = Slot(uri=DEFAULT_.extreme_salinity, name="extreme_salinity", curie=DEFAULT_.curie('extreme_salinity'), - model_uri=DEFAULT_.extreme_salinity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.extreme_salinity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.salinity_meth = Slot(uri=DEFAULT_.salinity_meth, name="salinity_meth", curie=DEFAULT_.curie('salinity_meth'), - model_uri=DEFAULT_.salinity_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.salinity_meth]) - -slots.heavy_metals = Slot(uri=DEFAULT_.heavy_metals, name="heavy_metals", curie=DEFAULT_.curie('heavy_metals'), - model_uri=DEFAULT_.heavy_metals, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.heavy_metals]) - -slots.heavy_metals_meth = Slot(uri=DEFAULT_.heavy_metals_meth, name="heavy_metals_meth", curie=DEFAULT_.curie('heavy_metals_meth'), - model_uri=DEFAULT_.heavy_metals_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.heavy_metals_meth]) - -slots.al_sat = Slot(uri=DEFAULT_.al_sat, name="al_sat", curie=DEFAULT_.curie('al_sat'), - model_uri=DEFAULT_.al_sat, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.al_sat], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.al_sat_meth = Slot(uri=DEFAULT_.al_sat_meth, name="al_sat_meth", curie=DEFAULT_.curie('al_sat_meth'), - model_uri=DEFAULT_.al_sat_meth, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.al_sat_meth]) - -slots.biochem_oxygen_dem = Slot(uri=DEFAULT_.biochem_oxygen_dem, name="biochem_oxygen_dem", curie=DEFAULT_.curie('biochem_oxygen_dem'), - model_uri=DEFAULT_.biochem_oxygen_dem, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.biochem_oxygen_dem], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.chem_oxygen_dem = Slot(uri=DEFAULT_.chem_oxygen_dem, name="chem_oxygen_dem", curie=DEFAULT_.curie('chem_oxygen_dem'), - model_uri=DEFAULT_.chem_oxygen_dem, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.chem_oxygen_dem], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.efficiency_percent = Slot(uri=DEFAULT_.efficiency_percent, name="efficiency_percent", curie=DEFAULT_.curie('efficiency_percent'), - model_uri=DEFAULT_.efficiency_percent, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.efficiency_percent], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.emulsions = Slot(uri=DEFAULT_.emulsions, name="emulsions", curie=DEFAULT_.curie('emulsions'), - model_uri=DEFAULT_.emulsions, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.emulsions]) - -slots.gaseous_substances = Slot(uri=DEFAULT_.gaseous_substances, name="gaseous_substances", curie=DEFAULT_.curie('gaseous_substances'), - model_uri=DEFAULT_.gaseous_substances, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.gaseous_substances]) - -slots.indust_eff_percent = Slot(uri=DEFAULT_.indust_eff_percent, name="indust_eff_percent", curie=DEFAULT_.curie('indust_eff_percent'), - model_uri=DEFAULT_.indust_eff_percent, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.indust_eff_percent], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.inorg_particles = Slot(uri=DEFAULT_.inorg_particles, name="inorg_particles", curie=DEFAULT_.curie('inorg_particles'), - model_uri=DEFAULT_.inorg_particles, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.inorg_particles]) - -slots.org_particles = Slot(uri=DEFAULT_.org_particles, name="org_particles", curie=DEFAULT_.curie('org_particles'), - model_uri=DEFAULT_.org_particles, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.org_particles]) - -slots.pre_treatment = Slot(uri=DEFAULT_.pre_treatment, name="pre_treatment", curie=DEFAULT_.curie('pre_treatment'), - model_uri=DEFAULT_.pre_treatment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.pre_treatment]) - -slots.primary_treatment = Slot(uri=DEFAULT_.primary_treatment, name="primary_treatment", curie=DEFAULT_.curie('primary_treatment'), - model_uri=DEFAULT_.primary_treatment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.primary_treatment]) - -slots.reactor_type = Slot(uri=DEFAULT_.reactor_type, name="reactor_type", curie=DEFAULT_.curie('reactor_type'), - model_uri=DEFAULT_.reactor_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.reactor_type]) - -slots.secondary_treatment = Slot(uri=DEFAULT_.secondary_treatment, name="secondary_treatment", curie=DEFAULT_.curie('secondary_treatment'), - model_uri=DEFAULT_.secondary_treatment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.secondary_treatment]) - -slots.sewage_type = Slot(uri=DEFAULT_.sewage_type, name="sewage_type", curie=DEFAULT_.curie('sewage_type'), - model_uri=DEFAULT_.sewage_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.sewage_type]) - -slots.sludge_retent_time = Slot(uri=DEFAULT_.sludge_retent_time, name="sludge_retent_time", curie=DEFAULT_.curie('sludge_retent_time'), - model_uri=DEFAULT_.sludge_retent_time, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.sludge_retent_time], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.soluble_inorg_mat = Slot(uri=DEFAULT_.soluble_inorg_mat, name="soluble_inorg_mat", curie=DEFAULT_.curie('soluble_inorg_mat'), - model_uri=DEFAULT_.soluble_inorg_mat, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.soluble_inorg_mat]) - -slots.soluble_org_mat = Slot(uri=DEFAULT_.soluble_org_mat, name="soluble_org_mat", curie=DEFAULT_.curie('soluble_org_mat'), - model_uri=DEFAULT_.soluble_org_mat, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.soluble_org_mat]) - -slots.tertiary_treatment = Slot(uri=DEFAULT_.tertiary_treatment, name="tertiary_treatment", curie=DEFAULT_.curie('tertiary_treatment'), - model_uri=DEFAULT_.tertiary_treatment, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.tertiary_treatment]) - -slots.tot_phosphate = Slot(uri=DEFAULT_.tot_phosphate, name="tot_phosphate", curie=DEFAULT_.curie('tot_phosphate'), - model_uri=DEFAULT_.tot_phosphate, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_phosphate], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.wastewater_type = Slot(uri=DEFAULT_.wastewater_type, name="wastewater_type", curie=DEFAULT_.curie('wastewater_type'), - model_uri=DEFAULT_.wastewater_type, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.wastewater_type]) - -slots.atmospheric_data = Slot(uri=DEFAULT_.atmospheric_data, name="atmospheric_data", curie=DEFAULT_.curie('atmospheric_data'), - model_uri=DEFAULT_.atmospheric_data, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.atmospheric_data]) - -slots.bac_prod = Slot(uri=DEFAULT_.bac_prod, name="bac_prod", curie=DEFAULT_.curie('bac_prod'), - model_uri=DEFAULT_.bac_prod, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.bac_prod], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.bac_resp = Slot(uri=DEFAULT_.bac_resp, name="bac_resp", curie=DEFAULT_.curie('bac_resp'), - model_uri=DEFAULT_.bac_resp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.bac_resp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.conduc = Slot(uri=DEFAULT_.conduc, name="conduc", curie=DEFAULT_.curie('conduc'), - model_uri=DEFAULT_.conduc, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.conduc], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.diss_inorg_nitro = Slot(uri=DEFAULT_.diss_inorg_nitro, name="diss_inorg_nitro", curie=DEFAULT_.curie('diss_inorg_nitro'), - model_uri=DEFAULT_.diss_inorg_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.diss_inorg_nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.down_par = Slot(uri=DEFAULT_.down_par, name="down_par", curie=DEFAULT_.curie('down_par'), - model_uri=DEFAULT_.down_par, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.down_par], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.fluor = Slot(uri=DEFAULT_.fluor, name="fluor", curie=DEFAULT_.curie('fluor'), - model_uri=DEFAULT_.fluor, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.fluor], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.light_intensity = Slot(uri=DEFAULT_.light_intensity, name="light_intensity", curie=DEFAULT_.curie('light_intensity'), - model_uri=DEFAULT_.light_intensity, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.light_intensity], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.part_org_nitro = Slot(uri=DEFAULT_.part_org_nitro, name="part_org_nitro", curie=DEFAULT_.curie('part_org_nitro'), - model_uri=DEFAULT_.part_org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.part_org_nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.photon_flux = Slot(uri=DEFAULT_.photon_flux, name="photon_flux", curie=DEFAULT_.curie('photon_flux'), - model_uri=DEFAULT_.photon_flux, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.photon_flux], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.primary_prod = Slot(uri=DEFAULT_.primary_prod, name="primary_prod", curie=DEFAULT_.curie('primary_prod'), - model_uri=DEFAULT_.primary_prod, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.primary_prod], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.size_frac_low = Slot(uri=DEFAULT_.size_frac_low, name="size_frac_low", curie=DEFAULT_.curie('size_frac_low'), - model_uri=DEFAULT_.size_frac_low, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.size_frac_low], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.size_frac_up = Slot(uri=DEFAULT_.size_frac_up, name="size_frac_up", curie=DEFAULT_.curie('size_frac_up'), - model_uri=DEFAULT_.size_frac_up, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.size_frac_up], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.soluble_react_phosp = Slot(uri=DEFAULT_.soluble_react_phosp, name="soluble_react_phosp", curie=DEFAULT_.curie('soluble_react_phosp'), - model_uri=DEFAULT_.soluble_react_phosp, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.soluble_react_phosp], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.suspend_part_matter = Slot(uri=DEFAULT_.suspend_part_matter, name="suspend_part_matter", curie=DEFAULT_.curie('suspend_part_matter'), - model_uri=DEFAULT_.suspend_part_matter, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.suspend_part_matter], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_diss_nitro = Slot(uri=DEFAULT_.tot_diss_nitro, name="tot_diss_nitro", curie=DEFAULT_.curie('tot_diss_nitro'), - model_uri=DEFAULT_.tot_diss_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_diss_nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_inorg_nitro = Slot(uri=DEFAULT_.tot_inorg_nitro, name="tot_inorg_nitro", curie=DEFAULT_.curie('tot_inorg_nitro'), - model_uri=DEFAULT_.tot_inorg_nitro, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_inorg_nitro], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.tot_part_carb = Slot(uri=DEFAULT_.tot_part_carb, name="tot_part_carb", curie=DEFAULT_.curie('tot_part_carb'), - model_uri=DEFAULT_.tot_part_carb, domain=None, range=Optional[Union[dict, QuantityValue]], mappings = [MIXS.tot_part_carb], - pattern=re.compile(r'\d+[.\d+] \S+')) - -slots.language = Slot(uri=NMDC.language, name="language", curie=NMDC.curie('language'), - model_uri=DEFAULT_.language, domain=None, range=Optional[str]) - -slots.attribute = Slot(uri=NMDC.attribute, name="attribute", curie=NMDC.curie('attribute'), - model_uri=DEFAULT_.attribute, domain=None, range=Optional[str]) - -slots.has_raw_value = Slot(uri=NMDC.has_raw_value, name="has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.has_raw_value, domain=AttributeValue, range=Optional[str]) - -slots.has_unit = Slot(uri=NMDC.has_unit, name="has unit", curie=NMDC.curie('has_unit'), - model_uri=DEFAULT_.has_unit, domain=None, range=Optional[str], mappings = [QUD.unit, SCHEMA.unitCode]) - -slots.has_numeric_value = Slot(uri=NMDC.has_numeric_value, name="has numeric value", curie=NMDC.curie('has_numeric_value'), - model_uri=DEFAULT_.has_numeric_value, domain=None, range=Optional[float], mappings = [QUD.quantityValue, SCHEMA.value]) - -slots.has_minimum_numeric_value = Slot(uri=NMDC.has_minimum_numeric_value, name="has minimum numeric value", curie=NMDC.curie('has_minimum_numeric_value'), - model_uri=DEFAULT_.has_minimum_numeric_value, domain=None, range=Optional[float]) - -slots.has_maximum_numeric_value = Slot(uri=NMDC.has_maximum_numeric_value, name="has maximum numeric value", curie=NMDC.curie('has_maximum_numeric_value'), - model_uri=DEFAULT_.has_maximum_numeric_value, domain=None, range=Optional[float]) - -slots.has_boolean_value = Slot(uri=NMDC.has_boolean_value, name="has boolean value", curie=NMDC.curie('has_boolean_value'), - model_uri=DEFAULT_.has_boolean_value, domain=None, range=Optional[Union[bool, Bool]]) - -slots.latitude = Slot(uri=WGS.lat, name="latitude", curie=WGS.curie('lat'), - model_uri=DEFAULT_.latitude, domain=GeolocationValue, range=Optional[float], mappings = [SCHEMA.latitude]) - -slots.longitude = Slot(uri=WGS.long, name="longitude", curie=WGS.curie('long'), - model_uri=DEFAULT_.longitude, domain=GeolocationValue, range=Optional[float], mappings = [SCHEMA.longitude]) - -slots.term = Slot(uri=RDF.type, name="term", curie=RDF.curie('type'), - model_uri=DEFAULT_.term, domain=ControlledTermValue, range=Optional[Union[dict, OntologyClass]]) - -slots.orcid = Slot(uri=NMDC.orcid, name="orcid", curie=NMDC.curie('orcid'), - model_uri=DEFAULT_.orcid, domain=PersonValue, range=Optional[str]) - -slots.email = Slot(uri=SCHEMA.email, name="email", curie=SCHEMA.curie('email'), - model_uri=DEFAULT_.email, domain=None, range=Optional[str]) - -slots.alternate_emails = Slot(uri=NMDC.alternate_emails, name="alternate emails", curie=NMDC.curie('alternate_emails'), - model_uri=DEFAULT_.alternate_emails, domain=None, range=Optional[str]) - -slots.profile_image_url = Slot(uri=NMDC.profile_image_url, name="profile image url", curie=NMDC.curie('profile_image_url'), - model_uri=DEFAULT_.profile_image_url, domain=PersonValue, range=Optional[str]) - -slots.has_input = Slot(uri=NMDC.has_input, name="has input", curie=NMDC.curie('has_input'), - model_uri=DEFAULT_.has_input, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) - -slots.has_output = Slot(uri=NMDC.has_output, name="has output", curie=NMDC.curie('has_output'), - model_uri=DEFAULT_.has_output, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) - -slots.part_of = Slot(uri=DCTERMS.isPartOf, name="part of", curie=DCTERMS.curie('isPartOf'), - model_uri=DEFAULT_.part_of, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) - -slots.execution_resource = Slot(uri=NMDC.execution_resource, name="execution resource", curie=NMDC.curie('execution_resource'), - model_uri=DEFAULT_.execution_resource, domain=None, range=Optional[str]) - -slots.url = Slot(uri=NMDC.url, name="url", curie=NMDC.curie('url'), - model_uri=DEFAULT_.url, domain=None, range=Optional[str]) - -slots.display_order = Slot(uri=NMDC.display_order, name="display order", curie=NMDC.curie('display_order'), - model_uri=DEFAULT_.display_order, domain=None, range=Optional[str]) - -slots.git_url = Slot(uri=NMDC.git_url, name="git url", curie=NMDC.curie('git_url'), - model_uri=DEFAULT_.git_url, domain=None, range=Optional[str]) - -slots.file_size_bytes = Slot(uri=NMDC.file_size_bytes, name="file size bytes", curie=NMDC.curie('file_size_bytes'), - model_uri=DEFAULT_.file_size_bytes, domain=None, range=Optional[int]) - -slots.md5_checksum = Slot(uri=NMDC.md5_checksum, name="md5 checksum", curie=NMDC.curie('md5_checksum'), - model_uri=DEFAULT_.md5_checksum, domain=None, range=Optional[str]) - -slots.abstract = Slot(uri=NMDC.abstract, name="abstract", curie=NMDC.curie('abstract'), - model_uri=DEFAULT_.abstract, domain=None, range=Optional[str]) - -slots.keywords = Slot(uri=NMDC.keywords, name="keywords", curie=NMDC.curie('keywords'), - model_uri=DEFAULT_.keywords, domain=None, range=Optional[Union[str, List[str]]], mappings = [DCTERMS.subject]) - -slots.objective = Slot(uri=NMDC.objective, name="objective", curie=NMDC.curie('objective'), - model_uri=DEFAULT_.objective, domain=None, range=Optional[str], mappings = [SIO["000337"]]) - -slots.websites = Slot(uri=NMDC.websites, name="websites", curie=NMDC.curie('websites'), - model_uri=DEFAULT_.websites, domain=None, range=Optional[Union[str, List[str]]]) - -slots.publications = Slot(uri=NMDC.publications, name="publications", curie=NMDC.curie('publications'), - model_uri=DEFAULT_.publications, domain=None, range=Optional[Union[str, List[str]]]) - -slots.id = Slot(uri=NMDC.id, name="id", curie=NMDC.curie('id'), - model_uri=DEFAULT_.id, domain=None, range=URIRef) - -slots.name = Slot(uri=NMDC.name, name="name", curie=NMDC.curie('name'), - model_uri=DEFAULT_.name, domain=None, range=Optional[str]) - -slots.description = Slot(uri=DCTERMS.description, name="description", curie=DCTERMS.curie('description'), - model_uri=DEFAULT_.description, domain=None, range=Optional[str]) - -slots.type = Slot(uri=NMDC.type, name="type", curie=NMDC.curie('type'), - model_uri=DEFAULT_.type, domain=None, range=Optional[str]) - -slots.title = Slot(uri=NMDC.title, name="title", curie=NMDC.curie('title'), - model_uri=DEFAULT_.title, domain=None, range=Optional[str]) - -slots.alternative_titles = Slot(uri=NMDC.alternative_titles, name="alternative titles", curie=NMDC.curie('alternative_titles'), - model_uri=DEFAULT_.alternative_titles, domain=None, range=Optional[Union[str, List[str]]]) - -slots.alternative_names = Slot(uri=NMDC.alternative_names, name="alternative names", curie=NMDC.curie('alternative_names'), - model_uri=DEFAULT_.alternative_names, domain=None, range=Optional[Union[str, List[str]]]) - -slots.alternative_descriptions = Slot(uri=NMDC.alternative_descriptions, name="alternative descriptions", curie=NMDC.curie('alternative_descriptions'), - model_uri=DEFAULT_.alternative_descriptions, domain=None, range=Optional[Union[str, List[str]]]) - -slots.alternative_identifiers = Slot(uri=NMDC.alternative_identifiers, name="alternative identifiers", curie=NMDC.curie('alternative_identifiers'), - model_uri=DEFAULT_.alternative_identifiers, domain=None, range=Optional[Union[str, List[str]]]) - -slots.started_at_time = Slot(uri=NMDC.started_at_time, name="started at time", curie=NMDC.curie('started_at_time'), - model_uri=DEFAULT_.started_at_time, domain=None, range=Optional[Union[str, XSDDateTime]], mappings = [PROV.startedAtTime], - pattern=re.compile(r'^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$')) - -slots.ended_at_time = Slot(uri=NMDC.ended_at_time, name="ended at time", curie=NMDC.curie('ended_at_time'), - model_uri=DEFAULT_.ended_at_time, domain=None, range=Optional[Union[str, XSDDateTime]], mappings = [PROV.endedAtTime], - pattern=re.compile(r'^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$')) - -slots.was_informed_by = Slot(uri=NMDC.was_informed_by, name="was informed by", curie=NMDC.curie('was_informed_by'), - model_uri=DEFAULT_.was_informed_by, domain=None, range=Optional[Union[str, ActivityId]], mappings = [PROV.wasInformedBy]) - -slots.was_associated_with = Slot(uri=NMDC.was_associated_with, name="was associated with", curie=NMDC.curie('was_associated_with'), - model_uri=DEFAULT_.was_associated_with, domain=None, range=Optional[Union[dict, Agent]], mappings = [PROV.wasAssociatedWith]) - -slots.acted_on_behalf_of = Slot(uri=NMDC.acted_on_behalf_of, name="acted on behalf of", curie=NMDC.curie('acted_on_behalf_of'), - model_uri=DEFAULT_.acted_on_behalf_of, domain=None, range=Optional[Union[dict, Agent]], mappings = [PROV.actedOnBehalfOf]) - -slots.was_generated_by = Slot(uri=NMDC.was_generated_by, name="was generated by", curie=NMDC.curie('was_generated_by'), - model_uri=DEFAULT_.was_generated_by, domain=None, range=Optional[Union[str, ActivityId]], mappings = [PROV.wasGeneratedBy]) - -slots.used = Slot(uri=NMDC.used, name="used", curie=NMDC.curie('used'), - model_uri=DEFAULT_.used, domain=Activity, range=Optional[str], mappings = [PROV.used]) - -slots.mAGBin__bin_name = Slot(uri=DEFAULT_.bin_name, name="mAGBin__bin_name", curie=DEFAULT_.curie('bin_name'), - model_uri=DEFAULT_.mAGBin__bin_name, domain=None, range=Optional[str]) - -slots.mAGBin__number_of_contig = Slot(uri=DEFAULT_.number_of_contig, name="mAGBin__number_of_contig", curie=DEFAULT_.curie('number_of_contig'), - model_uri=DEFAULT_.mAGBin__number_of_contig, domain=None, range=Optional[int]) - -slots.mAGBin__completeness = Slot(uri=DEFAULT_.completeness, name="mAGBin__completeness", curie=DEFAULT_.curie('completeness'), - model_uri=DEFAULT_.mAGBin__completeness, domain=None, range=Optional[float]) - -slots.mAGBin__contamination = Slot(uri=DEFAULT_.contamination, name="mAGBin__contamination", curie=DEFAULT_.curie('contamination'), - model_uri=DEFAULT_.mAGBin__contamination, domain=None, range=Optional[float]) - -slots.mAGBin__gene_count = Slot(uri=DEFAULT_.gene_count, name="mAGBin__gene_count", curie=DEFAULT_.curie('gene_count'), - model_uri=DEFAULT_.mAGBin__gene_count, domain=None, range=Optional[int]) - -slots.mAGBin__bin_quality = Slot(uri=DEFAULT_.bin_quality, name="mAGBin__bin_quality", curie=DEFAULT_.curie('bin_quality'), - model_uri=DEFAULT_.mAGBin__bin_quality, domain=None, range=Optional[str]) - -slots.mAGBin__num_16s = Slot(uri=DEFAULT_.num_16s, name="mAGBin__num_16s", curie=DEFAULT_.curie('num_16s'), - model_uri=DEFAULT_.mAGBin__num_16s, domain=None, range=Optional[int]) - -slots.mAGBin__num_5s = Slot(uri=DEFAULT_.num_5s, name="mAGBin__num_5s", curie=DEFAULT_.curie('num_5s'), - model_uri=DEFAULT_.mAGBin__num_5s, domain=None, range=Optional[int]) - -slots.mAGBin__num_23s = Slot(uri=DEFAULT_.num_23s, name="mAGBin__num_23s", curie=DEFAULT_.curie('num_23s'), - model_uri=DEFAULT_.mAGBin__num_23s, domain=None, range=Optional[int]) - -slots.mAGBin__num_tRNA = Slot(uri=DEFAULT_.num_tRNA, name="mAGBin__num_tRNA", curie=DEFAULT_.curie('num_tRNA'), - model_uri=DEFAULT_.mAGBin__num_tRNA, domain=None, range=Optional[int]) - -slots.mAGBin__gtdbtk_domain = Slot(uri=DEFAULT_.gtdbtk_domain, name="mAGBin__gtdbtk_domain", curie=DEFAULT_.curie('gtdbtk_domain'), - model_uri=DEFAULT_.mAGBin__gtdbtk_domain, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_phylum = Slot(uri=DEFAULT_.gtdbtk_phylum, name="mAGBin__gtdbtk_phylum", curie=DEFAULT_.curie('gtdbtk_phylum'), - model_uri=DEFAULT_.mAGBin__gtdbtk_phylum, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_class = Slot(uri=DEFAULT_.gtdbtk_class, name="mAGBin__gtdbtk_class", curie=DEFAULT_.curie('gtdbtk_class'), - model_uri=DEFAULT_.mAGBin__gtdbtk_class, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_order = Slot(uri=DEFAULT_.gtdbtk_order, name="mAGBin__gtdbtk_order", curie=DEFAULT_.curie('gtdbtk_order'), - model_uri=DEFAULT_.mAGBin__gtdbtk_order, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_family = Slot(uri=DEFAULT_.gtdbtk_family, name="mAGBin__gtdbtk_family", curie=DEFAULT_.curie('gtdbtk_family'), - model_uri=DEFAULT_.mAGBin__gtdbtk_family, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_genus = Slot(uri=DEFAULT_.gtdbtk_genus, name="mAGBin__gtdbtk_genus", curie=DEFAULT_.curie('gtdbtk_genus'), - model_uri=DEFAULT_.mAGBin__gtdbtk_genus, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_species = Slot(uri=DEFAULT_.gtdbtk_species, name="mAGBin__gtdbtk_species", curie=DEFAULT_.curie('gtdbtk_species'), - model_uri=DEFAULT_.mAGBin__gtdbtk_species, domain=None, range=Optional[str]) - -slots.metabolite_quantified = Slot(uri=DEFAULT_.metabolite_quantified, name="metabolite quantified", curie=DEFAULT_.curie('metabolite_quantified'), - model_uri=DEFAULT_.metabolite_quantified, domain=None, range=Optional[Union[str, ChemicalEntityId]]) - -slots.highest_similarity_score = Slot(uri=DEFAULT_.highest_similarity_score, name="highest similarity score", curie=DEFAULT_.curie('highest_similarity_score'), - model_uri=DEFAULT_.highest_similarity_score, domain=None, range=Optional[float]) - -slots.peptide_sequence = Slot(uri=DEFAULT_.peptide_sequence, name="peptide sequence", curie=DEFAULT_.curie('peptide_sequence'), - model_uri=DEFAULT_.peptide_sequence, domain=None, range=Optional[str]) - -slots.best_protein = Slot(uri=DEFAULT_.best_protein, name="best protein", curie=DEFAULT_.curie('best_protein'), - model_uri=DEFAULT_.best_protein, domain=None, range=Optional[Union[str, GeneProductId]]) - -slots.all_proteins = Slot(uri=DEFAULT_.all_proteins, name="all proteins", curie=DEFAULT_.curie('all_proteins'), - model_uri=DEFAULT_.all_proteins, domain=None, range=Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]]) - -slots.min_q_value = Slot(uri=DEFAULT_.min_q_value, name="min_q_value", curie=DEFAULT_.curie('min_q_value'), - model_uri=DEFAULT_.min_q_value, domain=None, range=Optional[float]) - -slots.peptide_spectral_count = Slot(uri=DEFAULT_.peptide_spectral_count, name="peptide_spectral_count", curie=DEFAULT_.curie('peptide_spectral_count'), - model_uri=DEFAULT_.peptide_spectral_count, domain=None, range=Optional[int]) - -slots.peptide_sum_masic_abundance = Slot(uri=DEFAULT_.peptide_sum_masic_abundance, name="peptide_sum_masic_abundance", curie=DEFAULT_.curie('peptide_sum_masic_abundance'), - model_uri=DEFAULT_.peptide_sum_masic_abundance, domain=None, range=Optional[int]) - -slots.peptide_sequence_count = Slot(uri=DEFAULT_.peptide_sequence_count, name="peptide_sequence_count", curie=DEFAULT_.curie('peptide_sequence_count'), - model_uri=DEFAULT_.peptide_sequence_count, domain=None, range=Optional[int]) - -slots.protein_spectral_count = Slot(uri=DEFAULT_.protein_spectral_count, name="protein_spectral_count", curie=DEFAULT_.curie('protein_spectral_count'), - model_uri=DEFAULT_.protein_spectral_count, domain=None, range=Optional[int]) - -slots.protein_sum_masic_abundance = Slot(uri=DEFAULT_.protein_sum_masic_abundance, name="protein_sum_masic_abundance", curie=DEFAULT_.curie('protein_sum_masic_abundance'), - model_uri=DEFAULT_.protein_sum_masic_abundance, domain=None, range=Optional[int]) - -slots.inchi = Slot(uri=DEFAULT_.inchi, name="inchi", curie=DEFAULT_.curie('inchi'), - model_uri=DEFAULT_.inchi, domain=None, range=Optional[str]) - -slots.inchi_key = Slot(uri=DEFAULT_.inchi_key, name="inchi key", curie=DEFAULT_.curie('inchi_key'), - model_uri=DEFAULT_.inchi_key, domain=None, range=Optional[str]) - -slots.smiles = Slot(uri=DEFAULT_.smiles, name="smiles", curie=DEFAULT_.curie('smiles'), - model_uri=DEFAULT_.smiles, domain=None, range=Optional[Union[str, List[str]]]) - -slots.chemical_formula = Slot(uri=DEFAULT_.chemical_formula, name="chemical formula", curie=DEFAULT_.curie('chemical_formula'), - model_uri=DEFAULT_.chemical_formula, domain=None, range=Optional[str]) - -slots.attribute_value_type = Slot(uri=NMDC.type, name="attribute value_type", curie=NMDC.curie('type'), - model_uri=DEFAULT_.attribute_value_type, domain=AttributeValue, range=Optional[str]) - -slots.quantity_value_has_raw_value = Slot(uri=NMDC.has_raw_value, name="quantity value_has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.quantity_value_has_raw_value, domain=QuantityValue, range=Optional[str]) - -slots.quantity_value_has_unit = Slot(uri=NMDC.has_unit, name="quantity value_has unit", curie=NMDC.curie('has_unit'), - model_uri=DEFAULT_.quantity_value_has_unit, domain=QuantityValue, range=Optional[str], mappings = [QUD.unit, SCHEMA.unitCode]) - -slots.quantity_value_has_numeric_value = Slot(uri=NMDC.has_numeric_value, name="quantity value_has numeric value", curie=NMDC.curie('has_numeric_value'), - model_uri=DEFAULT_.quantity_value_has_numeric_value, domain=QuantityValue, range=Optional[float], mappings = [QUD.quantityValue, SCHEMA.value]) - -slots.person_value_orcid = Slot(uri=NMDC.orcid, name="person value_orcid", curie=NMDC.curie('orcid'), - model_uri=DEFAULT_.person_value_orcid, domain=PersonValue, range=Optional[str]) - -slots.person_value_email = Slot(uri=SCHEMA.email, name="person value_email", curie=SCHEMA.curie('email'), - model_uri=DEFAULT_.person_value_email, domain=PersonValue, range=Optional[str]) - -slots.person_value_has_raw_value = Slot(uri=NMDC.has_raw_value, name="person value_has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.person_value_has_raw_value, domain=PersonValue, range=Optional[str]) - -slots.person_value_name = Slot(uri=NMDC.name, name="person value_name", curie=NMDC.curie('name'), - model_uri=DEFAULT_.person_value_name, domain=PersonValue, range=Optional[str]) - -slots.person_id = Slot(uri=NMDC.id, name="person_id", curie=NMDC.curie('id'), - model_uri=DEFAULT_.person_id, domain=Person, range=Union[str, PersonId]) - -slots.metabolite_quantification_metabolite_quantified = Slot(uri=DEFAULT_.metabolite_quantified, name="metabolite quantification_metabolite quantified", curie=DEFAULT_.curie('metabolite_quantified'), - model_uri=DEFAULT_.metabolite_quantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) - -slots.metabolite_quantification_highest_similarity_score = Slot(uri=DEFAULT_.highest_similarity_score, name="metabolite quantification_highest similarity score", curie=DEFAULT_.curie('highest_similarity_score'), - model_uri=DEFAULT_.metabolite_quantification_highest_similarity_score, domain=MetaboliteQuantification, range=Optional[float]) - -slots.peptide_quantification_peptide_sequence = Slot(uri=DEFAULT_.peptide_sequence, name="peptide quantification_peptide sequence", curie=DEFAULT_.curie('peptide_sequence'), - model_uri=DEFAULT_.peptide_quantification_peptide_sequence, domain=PeptideQuantification, range=Optional[str]) - -slots.peptide_quantification_best_protein = Slot(uri=DEFAULT_.best_protein, name="peptide quantification_best protein", curie=DEFAULT_.curie('best_protein'), - model_uri=DEFAULT_.peptide_quantification_best_protein, domain=PeptideQuantification, range=Optional[Union[str, GeneProductId]]) - -slots.peptide_quantification_all_proteins = Slot(uri=DEFAULT_.all_proteins, name="peptide quantification_all proteins", curie=DEFAULT_.curie('all_proteins'), - model_uri=DEFAULT_.peptide_quantification_all_proteins, domain=PeptideQuantification, range=Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]]) - -slots.peptide_quantification_min_q_value = Slot(uri=DEFAULT_.min_q_value, name="peptide quantification_min_q_value", curie=DEFAULT_.curie('min_q_value'), - model_uri=DEFAULT_.peptide_quantification_min_q_value, domain=PeptideQuantification, range=Optional[float]) - -slots.peptide_quantification_peptide_spectral_count = Slot(uri=DEFAULT_.peptide_spectral_count, name="peptide quantification_peptide_spectral_count", curie=DEFAULT_.curie('peptide_spectral_count'), - model_uri=DEFAULT_.peptide_quantification_peptide_spectral_count, domain=PeptideQuantification, range=Optional[int]) - -slots.peptide_quantification_peptide_sum_masic_abundance = Slot(uri=DEFAULT_.peptide_sum_masic_abundance, name="peptide quantification_peptide_sum_masic_abundance", curie=DEFAULT_.curie('peptide_sum_masic_abundance'), - model_uri=DEFAULT_.peptide_quantification_peptide_sum_masic_abundance, domain=PeptideQuantification, range=Optional[int]) - -slots.protein_quantification_best_protein = Slot(uri=DEFAULT_.best_protein, name="protein quantification_best protein", curie=DEFAULT_.curie('best_protein'), - model_uri=DEFAULT_.protein_quantification_best_protein, domain=ProteinQuantification, range=Optional[Union[str, GeneProductId]]) - -slots.protein_quantification_all_proteins = Slot(uri=DEFAULT_.all_proteins, name="protein quantification_all proteins", curie=DEFAULT_.curie('all_proteins'), - model_uri=DEFAULT_.protein_quantification_all_proteins, domain=ProteinQuantification, range=Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]]) - -slots.protein_quantification_peptide_sequence_count = Slot(uri=DEFAULT_.peptide_sequence_count, name="protein quantification_peptide_sequence_count", curie=DEFAULT_.curie('peptide_sequence_count'), - model_uri=DEFAULT_.protein_quantification_peptide_sequence_count, domain=ProteinQuantification, range=Optional[int]) - -slots.protein_quantification_protein_spectral_count = Slot(uri=DEFAULT_.protein_spectral_count, name="protein quantification_protein_spectral_count", curie=DEFAULT_.curie('protein_spectral_count'), - model_uri=DEFAULT_.protein_quantification_protein_spectral_count, domain=ProteinQuantification, range=Optional[int]) - -slots.protein_quantification_protein_sum_masic_abundance = Slot(uri=DEFAULT_.protein_sum_masic_abundance, name="protein quantification_protein_sum_masic_abundance", curie=DEFAULT_.curie('protein_sum_masic_abundance'), - model_uri=DEFAULT_.protein_quantification_protein_sum_masic_abundance, domain=ProteinQuantification, range=Optional[int]) - -slots.chemical_entity_inchi = Slot(uri=DEFAULT_.inchi, name="chemical entity_inchi", curie=DEFAULT_.curie('inchi'), - model_uri=DEFAULT_.chemical_entity_inchi, domain=ChemicalEntity, range=Optional[str]) - -slots.chemical_entity_inchi_key = Slot(uri=DEFAULT_.inchi_key, name="chemical entity_inchi key", curie=DEFAULT_.curie('inchi_key'), - model_uri=DEFAULT_.chemical_entity_inchi_key, domain=ChemicalEntity, range=Optional[str]) - -slots.chemical_entity_smiles = Slot(uri=DEFAULT_.smiles, name="chemical entity_smiles", curie=DEFAULT_.curie('smiles'), - model_uri=DEFAULT_.chemical_entity_smiles, domain=ChemicalEntity, range=Optional[Union[str, List[str]]]) - -slots.chemical_entity_chemical_formula = Slot(uri=DEFAULT_.chemical_formula, name="chemical entity_chemical formula", curie=DEFAULT_.curie('chemical_formula'), - model_uri=DEFAULT_.chemical_entity_chemical_formula, domain=ChemicalEntity, range=Optional[str]) - -slots.geolocation_value_has_raw_value = Slot(uri=NMDC.has_raw_value, name="geolocation value_has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.geolocation_value_has_raw_value, domain=GeolocationValue, range=Optional[str]) diff --git a/python/mixs_new.py b/python/mixs_new.py deleted file mode 100644 index f0376ed9db..0000000000 --- a/python/mixs_new.py +++ /dev/null @@ -1,4656 +0,0 @@ -# Auto generated from mixs_new.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-05-06T11:21:42 -# Schema: mixs-schema -# -# id: https://microbiomedata/schema/mixs -# description: -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import Boolean, Datetime, Double, Float, Integer, String -from linkml_runtime.utils.metamodelcore import Bool, XSDDateTime - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CAS = CurieNamespace('CAS', 'http://identifiers.org/cas/') -CHEBI = CurieNamespace('CHEBI', 'http://purl.obolibrary.org/obo/CHEBI_') -CHEMBL_COMPOUND = CurieNamespace('CHEMBL_COMPOUND', 'http://identifiers.org/chembl.compound/') -DRUGBANK = CurieNamespace('DRUGBANK', 'http://identifiers.org/drugbank/') -HMDB = CurieNamespace('HMDB', 'http://identifiers.org/hmdb/') -KEGG_COMPOUND = CurieNamespace('KEGG_COMPOUND', 'http://identifiers.org/kegg.compound/') -MESH = CurieNamespace('MESH', 'http://identifiers.org/mesh/') -MIXS = CurieNamespace('MIXS', 'https://w3id.org/gensc/') -OBI = CurieNamespace('OBI', 'http://purl.obolibrary.org/obo/OBI_') -PR = CurieNamespace('PR', 'http://purl.obolibrary.org/obo/PR_') -PUBCHEM_COMPOUND = CurieNamespace('PUBCHEM_COMPOUND', 'http://identifiers.org/pubchem.compound/') -UNIPROTKB = CurieNamespace('UniProtKB', 'http://example.org/UNKNOWN/UniProtKB/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -DCTERMS = CurieNamespace('dcterms', 'http://purl.org/dc/terms/') -GTPO = CurieNamespace('gtpo', 'http://example.org/UNKNOWN/gtpo/') -MIXS = CurieNamespace('mixs', 'https://w3id.org/gensc/') -NMDC = CurieNamespace('nmdc', 'https://microbiomedata/meta/') -PROV = CurieNamespace('prov', 'http://www.w3.org/ns/prov#') -QUD = CurieNamespace('qud', 'http://qudt.org/1.1/schema/qudt#') -RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#') -SCHEMA = CurieNamespace('schema', 'http://schema.org/') -SIO = CurieNamespace('sio', 'http://semanticscience.org/resource/SIO_') -SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#') -WGS = CurieNamespace('wgs', 'http://www.w3.org/2003/01/geo/wgs84_pos') -XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#') -DEFAULT_ = CurieNamespace('', 'https://microbiomedata/schema/mixs/') - - -# Types -class Bytes(int): - """ An integer value that corresponds to a size in bytes """ - type_class_uri = XSD.int - type_class_curie = "xsd:int" - type_name = "bytes" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/Bytes") - - -class DecimalDegree(float): - """ A decimal degree expresses latitude or longitude as decimal fractions. """ - type_class_uri = XSD.decimal - type_class_curie = "xsd:decimal" - type_name = "decimal degree" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/DecimalDegree") - - -class LanguageCode(str): - """ A language code conforming to ISO_639-1 """ - type_class_uri = XSD.language - type_class_curie = "xsd:language" - type_name = "language code" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/LanguageCode") - - -class Unit(str): - type_class_uri = XSD.string - type_class_curie = "xsd:string" - type_name = "unit" - type_model_uri = URIRef("https://microbiomedata/schema/mixs/Unit") - - -# Class references -class NamedThingId(extended_str): - pass - - -class OntologyClassId(NamedThingId): - pass - - -class EnvironmentalMaterialTermId(OntologyClassId): - pass - - -class PersonId(NamedThingId): - pass - - -class InstrumentId(NamedThingId): - pass - - -class ChemicalEntityId(OntologyClassId): - pass - - -class GeneProductId(NamedThingId): - pass - - -class ActivityId(extended_str): - pass - - -@dataclass -class NamedThing(YAMLRoot): - """ - a databased entity or concept/class - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.NamedThing - class_class_curie: ClassVar[str] = "nmdc:NamedThing" - class_name: ClassVar[str] = "named thing" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/NamedThing") - - id: Union[str, NamedThingId] = None - name: Optional[str] = None - description: Optional[str] = None - alternative_identifiers: Optional[Union[str, List[str]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedThingId): - self.id = NamedThingId(self.id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.alternative_identifiers, list): - self.alternative_identifiers = [self.alternative_identifiers] if self.alternative_identifiers is not None else [] - self.alternative_identifiers = [v if isinstance(v, str) else str(v) for v in self.alternative_identifiers] - - super().__post_init__(**kwargs) - - -@dataclass -class OntologyClass(NamedThing): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.OntologyClass - class_class_curie: ClassVar[str] = "nmdc:OntologyClass" - class_name: ClassVar[str] = "ontology class" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/OntologyClass") - - id: Union[str, OntologyClassId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OntologyClassId): - self.id = OntologyClassId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class EnvironmentalMaterialTerm(OntologyClass): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.EnvironmentalMaterialTerm - class_class_curie: ClassVar[str] = "nmdc:EnvironmentalMaterialTerm" - class_name: ClassVar[str] = "environmental material term" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/EnvironmentalMaterialTerm") - - id: Union[str, EnvironmentalMaterialTermId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentalMaterialTermId): - self.id = EnvironmentalMaterialTermId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class AttributeValue(YAMLRoot): - """ - The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and - the structured value - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.AttributeValue - class_class_curie: ClassVar[str] = "nmdc:AttributeValue" - class_name: ClassVar[str] = "attribute value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/AttributeValue") - - has_raw_value: Optional[str] = None - was_generated_by: Optional[Union[str, ActivityId]] = None - type: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - if self.was_generated_by is not None and not isinstance(self.was_generated_by, ActivityId): - self.was_generated_by = ActivityId(self.was_generated_by) - - if self.type is not None and not isinstance(self.type, str): - self.type = str(self.type) - - super().__post_init__(**kwargs) - - -@dataclass -class QuantityValue(AttributeValue): - """ - A simple quantity, e.g. 2cm - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.QuantityValue - class_class_curie: ClassVar[str] = "nmdc:QuantityValue" - class_name: ClassVar[str] = "quantity value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/QuantityValue") - - has_unit: Optional[str] = None - has_numeric_value: Optional[float] = None - has_minimum_numeric_value: Optional[float] = None - has_maximum_numeric_value: Optional[float] = None - has_raw_value: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_unit is not None and not isinstance(self.has_unit, str): - self.has_unit = str(self.has_unit) - - if self.has_numeric_value is not None and not isinstance(self.has_numeric_value, float): - self.has_numeric_value = float(self.has_numeric_value) - - if self.has_minimum_numeric_value is not None and not isinstance(self.has_minimum_numeric_value, float): - self.has_minimum_numeric_value = float(self.has_minimum_numeric_value) - - if self.has_maximum_numeric_value is not None and not isinstance(self.has_maximum_numeric_value, float): - self.has_maximum_numeric_value = float(self.has_maximum_numeric_value) - - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - super().__post_init__(**kwargs) - - -@dataclass -class ImageValue(AttributeValue): - """ - An attribute value representing an image. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ImageValue - class_class_curie: ClassVar[str] = "nmdc:ImageValue" - class_name: ClassVar[str] = "image value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ImageValue") - - url: Optional[str] = None - description: Optional[str] = None - display_order: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.url is not None and not isinstance(self.url, str): - self.url = str(self.url) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if self.display_order is not None and not isinstance(self.display_order, str): - self.display_order = str(self.display_order) - - super().__post_init__(**kwargs) - - -@dataclass -class PersonValue(AttributeValue): - """ - An attribute value representing a person - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.PersonValue - class_class_curie: ClassVar[str] = "nmdc:PersonValue" - class_name: ClassVar[str] = "person value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/PersonValue") - - orcid: Optional[str] = None - profile_image_url: Optional[str] = None - email: Optional[str] = None - name: Optional[str] = None - websites: Optional[Union[str, List[str]]] = empty_list() - has_raw_value: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.orcid is not None and not isinstance(self.orcid, str): - self.orcid = str(self.orcid) - - if self.profile_image_url is not None and not isinstance(self.profile_image_url, str): - self.profile_image_url = str(self.profile_image_url) - - if self.email is not None and not isinstance(self.email, str): - self.email = str(self.email) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if not isinstance(self.websites, list): - self.websites = [self.websites] if self.websites is not None else [] - self.websites = [v if isinstance(v, str) else str(v) for v in self.websites] - - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - super().__post_init__(**kwargs) - - -@dataclass -class Person(NamedThing): - """ - represents a person, such as a researcher - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Person - class_class_curie: ClassVar[str] = "nmdc:Person" - class_name: ClassVar[str] = "person" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Person") - - id: Union[str, PersonId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PersonId): - self.id = PersonId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class MAGBin(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.MAGBin - class_class_curie: ClassVar[str] = "nmdc:MAGBin" - class_name: ClassVar[str] = "MAG bin" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/MAGBin") - - type: Optional[str] = None - bin_name: Optional[str] = None - number_of_contig: Optional[int] = None - completeness: Optional[float] = None - contamination: Optional[float] = None - gene_count: Optional[int] = None - bin_quality: Optional[str] = None - num_16s: Optional[int] = None - num_5s: Optional[int] = None - num_23s: Optional[int] = None - num_tRNA: Optional[int] = None - gtdbtk_domain: Optional[str] = None - gtdbtk_phylum: Optional[str] = None - gtdbtk_class: Optional[str] = None - gtdbtk_order: Optional[str] = None - gtdbtk_family: Optional[str] = None - gtdbtk_genus: Optional[str] = None - gtdbtk_species: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.type is not None and not isinstance(self.type, str): - self.type = str(self.type) - - if self.bin_name is not None and not isinstance(self.bin_name, str): - self.bin_name = str(self.bin_name) - - if self.number_of_contig is not None and not isinstance(self.number_of_contig, int): - self.number_of_contig = int(self.number_of_contig) - - if self.completeness is not None and not isinstance(self.completeness, float): - self.completeness = float(self.completeness) - - if self.contamination is not None and not isinstance(self.contamination, float): - self.contamination = float(self.contamination) - - if self.gene_count is not None and not isinstance(self.gene_count, int): - self.gene_count = int(self.gene_count) - - if self.bin_quality is not None and not isinstance(self.bin_quality, str): - self.bin_quality = str(self.bin_quality) - - if self.num_16s is not None and not isinstance(self.num_16s, int): - self.num_16s = int(self.num_16s) - - if self.num_5s is not None and not isinstance(self.num_5s, int): - self.num_5s = int(self.num_5s) - - if self.num_23s is not None and not isinstance(self.num_23s, int): - self.num_23s = int(self.num_23s) - - if self.num_tRNA is not None and not isinstance(self.num_tRNA, int): - self.num_tRNA = int(self.num_tRNA) - - if self.gtdbtk_domain is not None and not isinstance(self.gtdbtk_domain, str): - self.gtdbtk_domain = str(self.gtdbtk_domain) - - if self.gtdbtk_phylum is not None and not isinstance(self.gtdbtk_phylum, str): - self.gtdbtk_phylum = str(self.gtdbtk_phylum) - - if self.gtdbtk_class is not None and not isinstance(self.gtdbtk_class, str): - self.gtdbtk_class = str(self.gtdbtk_class) - - if self.gtdbtk_order is not None and not isinstance(self.gtdbtk_order, str): - self.gtdbtk_order = str(self.gtdbtk_order) - - if self.gtdbtk_family is not None and not isinstance(self.gtdbtk_family, str): - self.gtdbtk_family = str(self.gtdbtk_family) - - if self.gtdbtk_genus is not None and not isinstance(self.gtdbtk_genus, str): - self.gtdbtk_genus = str(self.gtdbtk_genus) - - if self.gtdbtk_species is not None and not isinstance(self.gtdbtk_species, str): - self.gtdbtk_species = str(self.gtdbtk_species) - - super().__post_init__(**kwargs) - - -@dataclass -class Instrument(NamedThing): - """ - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI]. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Instrument - class_class_curie: ClassVar[str] = "nmdc:Instrument" - class_name: ClassVar[str] = "instrument" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Instrument") - - id: Union[str, InstrumentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, InstrumentId): - self.id = InstrumentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class MetaboliteQuantification(YAMLRoot): - """ - This is used to link a metabolomics analysis workflow to a specific metabolite - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.MetaboliteQuantification - class_class_curie: ClassVar[str] = "nmdc:MetaboliteQuantification" - class_name: ClassVar[str] = "metabolite quantification" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/MetaboliteQuantification") - - alternative_identifiers: Optional[Union[str, List[str]]] = empty_list() - metabolite_quantified: Optional[Union[str, ChemicalEntityId]] = None - highest_similarity_score: Optional[float] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.alternative_identifiers, list): - self.alternative_identifiers = [self.alternative_identifiers] if self.alternative_identifiers is not None else [] - self.alternative_identifiers = [v if isinstance(v, str) else str(v) for v in self.alternative_identifiers] - - if self.metabolite_quantified is not None and not isinstance(self.metabolite_quantified, ChemicalEntityId): - self.metabolite_quantified = ChemicalEntityId(self.metabolite_quantified) - - if self.highest_similarity_score is not None and not isinstance(self.highest_similarity_score, float): - self.highest_similarity_score = float(self.highest_similarity_score) - - super().__post_init__(**kwargs) - - -@dataclass -class PeptideQuantification(YAMLRoot): - """ - This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.PeptideQuantification - class_class_curie: ClassVar[str] = "nmdc:PeptideQuantification" - class_name: ClassVar[str] = "peptide quantification" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/PeptideQuantification") - - peptide_sequence: Optional[str] = None - best_protein: Optional[Union[str, GeneProductId]] = None - all_proteins: Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]] = empty_list() - min_q_value: Optional[float] = None - peptide_spectral_count: Optional[int] = None - peptide_sum_masic_abundance: Optional[int] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.peptide_sequence is not None and not isinstance(self.peptide_sequence, str): - self.peptide_sequence = str(self.peptide_sequence) - - if self.best_protein is not None and not isinstance(self.best_protein, GeneProductId): - self.best_protein = GeneProductId(self.best_protein) - - if not isinstance(self.all_proteins, list): - self.all_proteins = [self.all_proteins] if self.all_proteins is not None else [] - self.all_proteins = [v if isinstance(v, GeneProductId) else GeneProductId(v) for v in self.all_proteins] - - if self.min_q_value is not None and not isinstance(self.min_q_value, float): - self.min_q_value = float(self.min_q_value) - - if self.peptide_spectral_count is not None and not isinstance(self.peptide_spectral_count, int): - self.peptide_spectral_count = int(self.peptide_spectral_count) - - if self.peptide_sum_masic_abundance is not None and not isinstance(self.peptide_sum_masic_abundance, int): - self.peptide_sum_masic_abundance = int(self.peptide_sum_masic_abundance) - - super().__post_init__(**kwargs) - - -@dataclass -class ProteinQuantification(YAMLRoot): - """ - This is used to link a metaproteomics analysis workflow to a specific protein - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ProteinQuantification - class_class_curie: ClassVar[str] = "nmdc:ProteinQuantification" - class_name: ClassVar[str] = "protein quantification" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ProteinQuantification") - - best_protein: Optional[Union[str, GeneProductId]] = None - all_proteins: Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]] = empty_list() - peptide_sequence_count: Optional[int] = None - protein_spectral_count: Optional[int] = None - protein_sum_masic_abundance: Optional[int] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.best_protein is not None and not isinstance(self.best_protein, GeneProductId): - self.best_protein = GeneProductId(self.best_protein) - - if not isinstance(self.all_proteins, list): - self.all_proteins = [self.all_proteins] if self.all_proteins is not None else [] - self.all_proteins = [v if isinstance(v, GeneProductId) else GeneProductId(v) for v in self.all_proteins] - - if self.peptide_sequence_count is not None and not isinstance(self.peptide_sequence_count, int): - self.peptide_sequence_count = int(self.peptide_sequence_count) - - if self.protein_spectral_count is not None and not isinstance(self.protein_spectral_count, int): - self.protein_spectral_count = int(self.protein_spectral_count) - - if self.protein_sum_masic_abundance is not None and not isinstance(self.protein_sum_masic_abundance, int): - self.protein_sum_masic_abundance = int(self.protein_sum_masic_abundance) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalEntity(OntologyClass): - """ - An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, - drugs. There may be different terms for distinct acid-base forms, protonation states - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ChemicalEntity - class_class_curie: ClassVar[str] = "nmdc:ChemicalEntity" - class_name: ClassVar[str] = "chemical entity" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ChemicalEntity") - - id: Union[str, ChemicalEntityId] = None - inchi: Optional[str] = None - inchi_key: Optional[str] = None - smiles: Optional[Union[str, List[str]]] = empty_list() - chemical_formula: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalEntityId): - self.id = ChemicalEntityId(self.id) - - if self.inchi is not None and not isinstance(self.inchi, str): - self.inchi = str(self.inchi) - - if self.inchi_key is not None and not isinstance(self.inchi_key, str): - self.inchi_key = str(self.inchi_key) - - if not isinstance(self.smiles, list): - self.smiles = [self.smiles] if self.smiles is not None else [] - self.smiles = [v if isinstance(v, str) else str(v) for v in self.smiles] - - if self.chemical_formula is not None and not isinstance(self.chemical_formula, str): - self.chemical_formula = str(self.chemical_formula) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneProduct(NamedThing): - """ - A molecule encoded by a gene that has an evolved function - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.GeneProduct - class_class_curie: ClassVar[str] = "nmdc:GeneProduct" - class_name: ClassVar[str] = "gene product" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/GeneProduct") - - id: Union[str, GeneProductId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneProductId): - self.id = GeneProductId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class TextValue(AttributeValue): - """ - A basic string value - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.TextValue - class_class_curie: ClassVar[str] = "nmdc:TextValue" - class_name: ClassVar[str] = "text value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/TextValue") - - language: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.language is not None and not isinstance(self.language, str): - self.language = str(self.language) - - super().__post_init__(**kwargs) - - -class UrlValue(AttributeValue): - """ - A value that is a string that conforms to URL syntax - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.UrlValue - class_class_curie: ClassVar[str] = "nmdc:UrlValue" - class_name: ClassVar[str] = "url value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/UrlValue") - - -class TimestampValue(AttributeValue): - """ - A value that is a timestamp. The range should be ISO-8601 - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.TimestampValue - class_class_curie: ClassVar[str] = "nmdc:TimestampValue" - class_name: ClassVar[str] = "timestamp value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/TimestampValue") - - -@dataclass -class IntegerValue(AttributeValue): - """ - A value that is an integer - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.IntegerValue - class_class_curie: ClassVar[str] = "nmdc:IntegerValue" - class_name: ClassVar[str] = "integer value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/IntegerValue") - - has_numeric_value: Optional[float] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_numeric_value is not None and not isinstance(self.has_numeric_value, float): - self.has_numeric_value = float(self.has_numeric_value) - - super().__post_init__(**kwargs) - - -@dataclass -class BooleanValue(AttributeValue): - """ - A value that is a boolean - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.BooleanValue - class_class_curie: ClassVar[str] = "nmdc:BooleanValue" - class_name: ClassVar[str] = "boolean value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/BooleanValue") - - has_boolean_value: Optional[Union[bool, Bool]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.has_boolean_value is not None and not isinstance(self.has_boolean_value, Bool): - self.has_boolean_value = Bool(self.has_boolean_value) - - super().__post_init__(**kwargs) - - -@dataclass -class ControlledTermValue(AttributeValue): - """ - A controlled term or class from an ontology - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.ControlledTermValue - class_class_curie: ClassVar[str] = "nmdc:ControlledTermValue" - class_name: ClassVar[str] = "controlled term value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/ControlledTermValue") - - term: Optional[Union[dict, OntologyClass]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.term is not None and not isinstance(self.term, OntologyClass): - self.term = OntologyClass(**as_dict(self.term)) - - super().__post_init__(**kwargs) - - -@dataclass -class GeolocationValue(AttributeValue): - """ - A normalized value for a location on the earth's surface - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.GeolocationValue - class_class_curie: ClassVar[str] = "nmdc:GeolocationValue" - class_name: ClassVar[str] = "geolocation value" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/GeolocationValue") - - latitude: Optional[float] = None - longitude: Optional[float] = None - has_raw_value: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.latitude is not None and not isinstance(self.latitude, float): - self.latitude = float(self.latitude) - - if self.longitude is not None and not isinstance(self.longitude, float): - self.longitude = float(self.longitude) - - if self.has_raw_value is not None and not isinstance(self.has_raw_value, str): - self.has_raw_value = str(self.has_raw_value) - - super().__post_init__(**kwargs) - - -@dataclass -class Activity(YAMLRoot): - """ - a provence-generating activity - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Activity - class_class_curie: ClassVar[str] = "nmdc:Activity" - class_name: ClassVar[str] = "activity" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Activity") - - id: Union[str, ActivityId] = None - name: Optional[str] = None - started_at_time: Optional[Union[str, XSDDateTime]] = None - ended_at_time: Optional[Union[str, XSDDateTime]] = None - was_informed_by: Optional[Union[str, ActivityId]] = None - was_associated_with: Optional[Union[dict, "Agent"]] = None - used: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ActivityId): - self.id = ActivityId(self.id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.started_at_time is not None and not isinstance(self.started_at_time, XSDDateTime): - self.started_at_time = XSDDateTime(self.started_at_time) - - if self.ended_at_time is not None and not isinstance(self.ended_at_time, XSDDateTime): - self.ended_at_time = XSDDateTime(self.ended_at_time) - - if self.was_informed_by is not None and not isinstance(self.was_informed_by, ActivityId): - self.was_informed_by = ActivityId(self.was_informed_by) - - if self.was_associated_with is not None and not isinstance(self.was_associated_with, Agent): - self.was_associated_with = Agent(**as_dict(self.was_associated_with)) - - if self.used is not None and not isinstance(self.used, str): - self.used = str(self.used) - - super().__post_init__(**kwargs) - - -@dataclass -class Agent(YAMLRoot): - """ - a provence-generating agent - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC.Agent - class_class_curie: ClassVar[str] = "nmdc:Agent" - class_name: ClassVar[str] = "agent" - class_model_uri: ClassVar[URIRef] = URIRef("https://microbiomedata/schema/mixs/Agent") - - acted_on_behalf_of: Optional[Union[dict, "Agent"]] = None - was_informed_by: Optional[Union[str, ActivityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.acted_on_behalf_of is not None and not isinstance(self.acted_on_behalf_of, Agent): - self.acted_on_behalf_of = Agent(**as_dict(self.acted_on_behalf_of)) - - if self.was_informed_by is not None and not isinstance(self.was_informed_by, ActivityId): - self.was_informed_by = ActivityId(self.was_informed_by) - - super().__post_init__(**kwargs) - - -# Enumerations -class ArchStrucEnum(EnumDefinitionImpl): - - building = PermissibleValue(text="building") - shed = PermissibleValue(text="shed") - home = PermissibleValue(text="home") - - _defn = EnumDefinition( - name="ArchStrucEnum", - ) - -class BiolStatEnum(EnumDefinitionImpl): - - wild = PermissibleValue(text="wild") - natural = PermissibleValue(text="natural") - hybrid = PermissibleValue(text="hybrid") - mutant = PermissibleValue(text="mutant") - - _defn = EnumDefinition( - name="BiolStatEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "semi-natural", - PermissibleValue(text="semi-natural") ) - setattr(cls, "inbred line", - PermissibleValue(text="inbred line") ) - setattr(cls, "breeder's line", - PermissibleValue(text="breeder's line") ) - setattr(cls, "clonal selection", - PermissibleValue(text="clonal selection") ) - -class BioticRelationshipEnum(EnumDefinitionImpl): - - parasite = PermissibleValue(text="parasite") - commensal = PermissibleValue(text="commensal") - symbiont = PermissibleValue(text="symbiont") - - _defn = EnumDefinition( - name="BioticRelationshipEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "free living", - PermissibleValue(text="free living") ) - -class BuildDocsEnum(EnumDefinitionImpl): - - schedule = PermissibleValue(text="schedule") - sections = PermissibleValue(text="sections") - submittals = PermissibleValue(text="submittals") - windows = PermissibleValue(text="windows") - - _defn = EnumDefinition( - name="BuildDocsEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "building information model", - PermissibleValue(text="building information model") ) - setattr(cls, "commissioning report", - PermissibleValue(text="commissioning report") ) - setattr(cls, "complaint logs", - PermissibleValue(text="complaint logs") ) - setattr(cls, "contract administration", - PermissibleValue(text="contract administration") ) - setattr(cls, "cost estimate", - PermissibleValue(text="cost estimate") ) - setattr(cls, "janitorial schedules or logs", - PermissibleValue(text="janitorial schedules or logs") ) - setattr(cls, "maintenance plans", - PermissibleValue(text="maintenance plans") ) - setattr(cls, "shop drawings", - PermissibleValue(text="shop drawings") ) - setattr(cls, "ventilation system", - PermissibleValue(text="ventilation system") ) - -class BuildOccupTypeEnum(EnumDefinitionImpl): - - office = PermissibleValue(text="office") - market = PermissibleValue(text="market") - restaurant = PermissibleValue(text="restaurant") - residence = PermissibleValue(text="residence") - school = PermissibleValue(text="school") - residential = PermissibleValue(text="residential") - commercial = PermissibleValue(text="commercial") - airport = PermissibleValue(text="airport") - - _defn = EnumDefinition( - name="BuildOccupTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "low rise", - PermissibleValue(text="low rise") ) - setattr(cls, "high rise", - PermissibleValue(text="high rise") ) - setattr(cls, "wood framed", - PermissibleValue(text="wood framed") ) - setattr(cls, "health care", - PermissibleValue(text="health care") ) - setattr(cls, "sports complex", - PermissibleValue(text="sports complex") ) - -class BuildingSettingEnum(EnumDefinitionImpl): - - urban = PermissibleValue(text="urban") - suburban = PermissibleValue(text="suburban") - exurban = PermissibleValue(text="exurban") - rural = PermissibleValue(text="rural") - - _defn = EnumDefinition( - name="BuildingSettingEnum", - ) - -class CeilCondEnum(EnumDefinitionImpl): - - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="CeilCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear") ) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair") ) - -class CeilFinishMatEnum(EnumDefinitionImpl): - - drywall = PermissibleValue(text="drywall") - tiles = PermissibleValue(text="tiles") - PVC = PermissibleValue(text="PVC") - plasterboard = PermissibleValue(text="plasterboard") - metal = PermissibleValue(text="metal") - fiberglass = PermissibleValue(text="fiberglass") - stucco = PermissibleValue(text="stucco") - wood = PermissibleValue(text="wood") - - _defn = EnumDefinition( - name="CeilFinishMatEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "mineral fibre", - PermissibleValue(text="mineral fibre") ) - setattr(cls, "mineral wool/calcium silicate", - PermissibleValue(text="mineral wool/calcium silicate") ) - -class CeilTextureEnum(EnumDefinitionImpl): - - knockdown = PermissibleValue(text="knockdown") - popcorn = PermissibleValue(text="popcorn") - smooth = PermissibleValue(text="smooth") - swirl = PermissibleValue(text="swirl") - - _defn = EnumDefinition( - name="CeilTextureEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "crows feet", - PermissibleValue(text="crows feet") ) - setattr(cls, "crows-foot stomp", - PermissibleValue(text="crows-foot stomp") ) - setattr(cls, "double skip", - PermissibleValue(text="double skip") ) - setattr(cls, "hawk and trowel", - PermissibleValue(text="hawk and trowel") ) - setattr(cls, "orange peel", - PermissibleValue(text="orange peel") ) - setattr(cls, "rosebud stomp", - PermissibleValue(text="rosebud stomp") ) - setattr(cls, "Santa-Fe texture", - PermissibleValue(text="Santa-Fe texture") ) - setattr(cls, "skip trowel", - PermissibleValue(text="skip trowel") ) - setattr(cls, "stomp knockdown", - PermissibleValue(text="stomp knockdown") ) - -class CeilTypeEnum(EnumDefinitionImpl): - - cathedral = PermissibleValue(text="cathedral") - dropped = PermissibleValue(text="dropped") - concave = PermissibleValue(text="concave") - coffered = PermissibleValue(text="coffered") - cove = PermissibleValue(text="cove") - stretched = PermissibleValue(text="stretched") - - _defn = EnumDefinition( - name="CeilTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "barrel-shaped", - PermissibleValue(text="barrel-shaped") ) - -class CurLandUseEnum(EnumDefinitionImpl): - - cities = PermissibleValue(text="cities") - farmstead = PermissibleValue(text="farmstead") - rock = PermissibleValue(text="rock") - sand = PermissibleValue(text="sand") - gravel = PermissibleValue(text="gravel") - mudflats = PermissibleValue(text="mudflats") - badlands = PermissibleValue(text="badlands") - rangeland = PermissibleValue(text="rangeland") - hayland = PermissibleValue(text="hayland") - - _defn = EnumDefinition( - name="CurLandUseEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "industrial areas", - PermissibleValue(text="industrial areas") ) - setattr(cls, "roads/railroads", - PermissibleValue(text="roads/railroads") ) - setattr(cls, "salt flats", - PermissibleValue(text="salt flats") ) - setattr(cls, "permanent snow or ice", - PermissibleValue(text="permanent snow or ice") ) - setattr(cls, "saline seeps", - PermissibleValue(text="saline seeps") ) - setattr(cls, "mines/quarries", - PermissibleValue(text="mines/quarries") ) - setattr(cls, "oil waste areas", - PermissibleValue(text="oil waste areas") ) - setattr(cls, "small grains", - PermissibleValue(text="small grains") ) - setattr(cls, "row crops", - PermissibleValue(text="row crops") ) - setattr(cls, "vegetable crops", - PermissibleValue(text="vegetable crops") ) - setattr(cls, "horticultural plants (e.g. tulips)", - PermissibleValue(text="horticultural plants (e.g. tulips)") ) - setattr(cls, "marshlands (grass,sedges,rushes)", - PermissibleValue(text="marshlands (grass,sedges,rushes)") ) - setattr(cls, "tundra (mosses,lichens)", - PermissibleValue(text="tundra (mosses,lichens)") ) - setattr(cls, "pastureland (grasslands used for livestock grazing)", - PermissibleValue(text="pastureland (grasslands used for livestock grazing)") ) - setattr(cls, "meadows (grasses,alfalfa,fescue,bromegrass,timothy)", - PermissibleValue(text="meadows (grasses,alfalfa,fescue,bromegrass,timothy)") ) - setattr(cls, "shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)", - PermissibleValue(text="shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)") ) - setattr(cls, "successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)", - PermissibleValue(text="successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)") ) - setattr(cls, "shrub crops (blueberries,nursery ornamentals,filberts)", - PermissibleValue(text="shrub crops (blueberries,nursery ornamentals,filberts)") ) - setattr(cls, "vine crops (grapes)", - PermissibleValue(text="vine crops (grapes)") ) - setattr(cls, "conifers (e.g. pine,spruce,fir,cypress)", - PermissibleValue(text="conifers (e.g. pine,spruce,fir,cypress)") ) - setattr(cls, "hardwoods (e.g. oak,hickory,elm,aspen)", - PermissibleValue(text="hardwoods (e.g. oak,hickory,elm,aspen)") ) - setattr(cls, "intermixed hardwood and conifers", - PermissibleValue(text="intermixed hardwood and conifers") ) - setattr(cls, "tropical (e.g. mangrove,palms)", - PermissibleValue(text="tropical (e.g. mangrove,palms)") ) - setattr(cls, "rainforest (evergreen forest receiving greater than 406 cm annual rainfall)", - PermissibleValue(text="rainforest (evergreen forest receiving greater than 406 cm annual rainfall)") ) - setattr(cls, "swamp (permanent or semi-permanent water body dominated by woody plants)", - PermissibleValue(text="swamp (permanent or semi-permanent water body dominated by woody plants)") ) - setattr(cls, "crop trees (nuts,fruit,christmas trees,nursery trees)", - PermissibleValue(text="crop trees (nuts,fruit,christmas trees,nursery trees)") ) - -class DeposEnvEnum(EnumDefinitionImpl): - - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="DeposEnvEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "Continental - Alluvial", - PermissibleValue(text="Continental - Alluvial") ) - setattr(cls, "Continental - Aeolian", - PermissibleValue(text="Continental - Aeolian") ) - setattr(cls, "Continental - Fluvial", - PermissibleValue(text="Continental - Fluvial") ) - setattr(cls, "Continental - Lacustrine", - PermissibleValue(text="Continental - Lacustrine") ) - setattr(cls, "Transitional - Deltaic", - PermissibleValue(text="Transitional - Deltaic") ) - setattr(cls, "Transitional - Tidal", - PermissibleValue(text="Transitional - Tidal") ) - setattr(cls, "Transitional - Lagoonal", - PermissibleValue(text="Transitional - Lagoonal") ) - setattr(cls, "Transitional - Beach", - PermissibleValue(text="Transitional - Beach") ) - setattr(cls, "Transitional - Lake", - PermissibleValue(text="Transitional - Lake") ) - setattr(cls, "Marine - Shallow", - PermissibleValue(text="Marine - Shallow") ) - setattr(cls, "Marine - Deep", - PermissibleValue(text="Marine - Deep") ) - setattr(cls, "Marine - Reef", - PermissibleValue(text="Marine - Reef") ) - setattr(cls, "Other - Evaporite", - PermissibleValue(text="Other - Evaporite") ) - setattr(cls, "Other - Glacial", - PermissibleValue(text="Other - Glacial") ) - setattr(cls, "Other - Volcanic", - PermissibleValue(text="Other - Volcanic") ) - -class DoorCompTypeEnum(EnumDefinitionImpl): - - revolving = PermissibleValue(text="revolving") - sliding = PermissibleValue(text="sliding") - telescopic = PermissibleValue(text="telescopic") - - _defn = EnumDefinition( - name="DoorCompTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "metal covered", - PermissibleValue(text="metal covered") ) - -class DoorCondEnum(EnumDefinitionImpl): - - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="DoorCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair") ) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear") ) - -class DoorDirectEnum(EnumDefinitionImpl): - - inward = PermissibleValue(text="inward") - outward = PermissibleValue(text="outward") - sideways = PermissibleValue(text="sideways") - - _defn = EnumDefinition( - name="DoorDirectEnum", - ) - -class DoorLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="DoorLocEnum", - ) - -class DoorMatEnum(EnumDefinitionImpl): - - aluminum = PermissibleValue(text="aluminum") - fiberboard = PermissibleValue(text="fiberboard") - fiberglass = PermissibleValue(text="fiberglass") - metal = PermissibleValue(text="metal") - vinyl = PermissibleValue(text="vinyl") - wood = PermissibleValue(text="wood") - - _defn = EnumDefinition( - name="DoorMatEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "cellular PVC", - PermissibleValue(text="cellular PVC") ) - setattr(cls, "engineered plastic", - PermissibleValue(text="engineered plastic") ) - setattr(cls, "thermoplastic alloy", - PermissibleValue(text="thermoplastic alloy") ) - setattr(cls, "wood/plastic composite", - PermissibleValue(text="wood/plastic composite") ) - -class DoorMoveEnum(EnumDefinitionImpl): - - collapsible = PermissibleValue(text="collapsible") - folding = PermissibleValue(text="folding") - revolving = PermissibleValue(text="revolving") - sliding = PermissibleValue(text="sliding") - swinging = PermissibleValue(text="swinging") - - _defn = EnumDefinition( - name="DoorMoveEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "rolling shutter", - PermissibleValue(text="rolling shutter") ) - -class DoorTypeEnum(EnumDefinitionImpl): - - composite = PermissibleValue(text="composite") - metal = PermissibleValue(text="metal") - wooden = PermissibleValue(text="wooden") - - _defn = EnumDefinition( - name="DoorTypeEnum", - ) - -class DoorTypeMetalEnum(EnumDefinitionImpl): - - collapsible = PermissibleValue(text="collapsible") - hollow = PermissibleValue(text="hollow") - - _defn = EnumDefinition( - name="DoorTypeMetalEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "corrugated steel", - PermissibleValue(text="corrugated steel") ) - setattr(cls, "rolling shutters", - PermissibleValue(text="rolling shutters") ) - setattr(cls, "steel plate", - PermissibleValue(text="steel plate") ) - -class DoorTypeWoodEnum(EnumDefinitionImpl): - - battened = PermissibleValue(text="battened") - flush = PermissibleValue(text="flush") - louvered = PermissibleValue(text="louvered") - - _defn = EnumDefinition( - name="DoorTypeWoodEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "bettened and ledged", - PermissibleValue(text="bettened and ledged") ) - setattr(cls, "ledged and braced", - PermissibleValue(text="ledged and braced") ) - setattr(cls, "ledged and framed", - PermissibleValue(text="ledged and framed") ) - setattr(cls, "ledged, braced and frame", - PermissibleValue(text="ledged, braced and frame") ) - setattr(cls, "framed and paneled", - PermissibleValue(text="framed and paneled") ) - setattr(cls, "glashed or sash", - PermissibleValue(text="glashed or sash") ) - setattr(cls, "wire gauged", - PermissibleValue(text="wire gauged") ) - -class DrainageClassEnum(EnumDefinitionImpl): - - poorly = PermissibleValue(text="poorly") - well = PermissibleValue(text="well") - - _defn = EnumDefinition( - name="DrainageClassEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "very poorly", - PermissibleValue(text="very poorly") ) - setattr(cls, "somewhat poorly", - PermissibleValue(text="somewhat poorly") ) - setattr(cls, "moderately well", - PermissibleValue(text="moderately well") ) - setattr(cls, "excessively drained", - PermissibleValue(text="excessively drained") ) - -class DrawingsEnum(EnumDefinitionImpl): - - operation = PermissibleValue(text="operation") - construction = PermissibleValue(text="construction") - bid = PermissibleValue(text="bid") - design = PermissibleValue(text="design") - diagram = PermissibleValue(text="diagram") - sketch = PermissibleValue(text="sketch") - - _defn = EnumDefinition( - name="DrawingsEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "as built", - PermissibleValue(text="as built") ) - setattr(cls, "building navigation map", - PermissibleValue(text="building navigation map") ) - -class ExtWallOrientEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - northeast = PermissibleValue(text="northeast") - southeast = PermissibleValue(text="southeast") - southwest = PermissibleValue(text="southwest") - northwest = PermissibleValue(text="northwest") - - _defn = EnumDefinition( - name="ExtWallOrientEnum", - ) - -class ExtWindowOrientEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - northeast = PermissibleValue(text="northeast") - southeast = PermissibleValue(text="southeast") - southwest = PermissibleValue(text="southwest") - northwest = PermissibleValue(text="northwest") - - _defn = EnumDefinition( - name="ExtWindowOrientEnum", - ) - -class FaoClassEnum(EnumDefinitionImpl): - - Acrisols = PermissibleValue(text="Acrisols") - Andosols = PermissibleValue(text="Andosols") - Arenosols = PermissibleValue(text="Arenosols") - Cambisols = PermissibleValue(text="Cambisols") - Chernozems = PermissibleValue(text="Chernozems") - Ferralsols = PermissibleValue(text="Ferralsols") - Fluvisols = PermissibleValue(text="Fluvisols") - Gleysols = PermissibleValue(text="Gleysols") - Greyzems = PermissibleValue(text="Greyzems") - Gypsisols = PermissibleValue(text="Gypsisols") - Histosols = PermissibleValue(text="Histosols") - Kastanozems = PermissibleValue(text="Kastanozems") - Lithosols = PermissibleValue(text="Lithosols") - Luvisols = PermissibleValue(text="Luvisols") - Nitosols = PermissibleValue(text="Nitosols") - Phaeozems = PermissibleValue(text="Phaeozems") - Planosols = PermissibleValue(text="Planosols") - Podzols = PermissibleValue(text="Podzols") - Podzoluvisols = PermissibleValue(text="Podzoluvisols") - Rankers = PermissibleValue(text="Rankers") - Regosols = PermissibleValue(text="Regosols") - Rendzinas = PermissibleValue(text="Rendzinas") - Solonchaks = PermissibleValue(text="Solonchaks") - Solonetz = PermissibleValue(text="Solonetz") - Vertisols = PermissibleValue(text="Vertisols") - Yermosols = PermissibleValue(text="Yermosols") - - _defn = EnumDefinition( - name="FaoClassEnum", - ) - -class FilterTypeEnum(EnumDefinitionImpl): - - HEPA = PermissibleValue(text="HEPA") - electrostatic = PermissibleValue(text="electrostatic") - - _defn = EnumDefinition( - name="FilterTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "particulate air filter", - PermissibleValue(text="particulate air filter") ) - setattr(cls, "chemical air filter", - PermissibleValue(text="chemical air filter") ) - setattr(cls, "low-MERV pleated media", - PermissibleValue(text="low-MERV pleated media") ) - setattr(cls, "gas-phase or ultraviolet air treatments", - PermissibleValue(text="gas-phase or ultraviolet air treatments") ) - -class FloorCondEnum(EnumDefinitionImpl): - - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="FloorCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear") ) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair") ) - -class FloorFinishMatEnum(EnumDefinitionImpl): - - tile = PermissibleValue(text="tile") - carpet = PermissibleValue(text="carpet") - rug = PermissibleValue(text="rug") - lineoleum = PermissibleValue(text="lineoleum") - stone = PermissibleValue(text="stone") - bamboo = PermissibleValue(text="bamboo") - cork = PermissibleValue(text="cork") - terrazo = PermissibleValue(text="terrazo") - concrete = PermissibleValue(text="concrete") - none = PermissibleValue(text="none") - sealed = PermissibleValue(text="sealed") - paint = PermissibleValue(text="paint") - - _defn = EnumDefinition( - name="FloorFinishMatEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "wood strip or parquet", - PermissibleValue(text="wood strip or parquet") ) - setattr(cls, "laminate wood", - PermissibleValue(text="laminate wood") ) - setattr(cls, "vinyl composition tile", - PermissibleValue(text="vinyl composition tile") ) - setattr(cls, "sheet vinyl", - PermissibleValue(text="sheet vinyl") ) - setattr(cls, "clear finish", - PermissibleValue(text="clear finish") ) - setattr(cls, "none or unfinished", - PermissibleValue(text="none or unfinished") ) - -class FloorStrucEnum(EnumDefinitionImpl): - - balcony = PermissibleValue(text="balcony") - concrete = PermissibleValue(text="concrete") - - _defn = EnumDefinition( - name="FloorStrucEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "floating floor", - PermissibleValue(text="floating floor") ) - setattr(cls, "glass floor", - PermissibleValue(text="glass floor") ) - setattr(cls, "raised floor", - PermissibleValue(text="raised floor") ) - setattr(cls, "sprung floor", - PermissibleValue(text="sprung floor") ) - setattr(cls, "wood-framed", - PermissibleValue(text="wood-framed") ) - -class FloorWaterMoldEnum(EnumDefinitionImpl): - - condensation = PermissibleValue(text="condensation") - - _defn = EnumDefinition( - name="FloorWaterMoldEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "mold odor", - PermissibleValue(text="mold odor") ) - setattr(cls, "wet floor", - PermissibleValue(text="wet floor") ) - setattr(cls, "water stains", - PermissibleValue(text="water stains") ) - setattr(cls, "wall discoloration", - PermissibleValue(text="wall discoloration") ) - setattr(cls, "floor discoloration", - PermissibleValue(text="floor discoloration") ) - setattr(cls, "ceiling discoloration", - PermissibleValue(text="ceiling discoloration") ) - setattr(cls, "peeling paint or wallpaper", - PermissibleValue(text="peeling paint or wallpaper") ) - setattr(cls, "bulging walls", - PermissibleValue(text="bulging walls") ) - -class FreqCleanEnum(EnumDefinitionImpl): - - Daily = PermissibleValue(text="Daily") - Weekly = PermissibleValue(text="Weekly") - Monthly = PermissibleValue(text="Monthly") - Quarterly = PermissibleValue(text="Quarterly") - Annually = PermissibleValue(text="Annually") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="FreqCleanEnum", - ) - -class FurnitureEnum(EnumDefinitionImpl): - - cabinet = PermissibleValue(text="cabinet") - chair = PermissibleValue(text="chair") - desks = PermissibleValue(text="desks") - - _defn = EnumDefinition( - name="FurnitureEnum", - ) - -class GenderRestroomEnum(EnumDefinitionImpl): - - female = PermissibleValue(text="female") - male = PermissibleValue(text="male") - unisex = PermissibleValue(text="unisex") - - _defn = EnumDefinition( - name="GenderRestroomEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "all gender", - PermissibleValue(text="all gender") ) - setattr(cls, "gender neurtral", - PermissibleValue(text="gender neurtral") ) - setattr(cls, "male and female", - PermissibleValue(text="male and female") ) - -class GrowthHabitEnum(EnumDefinitionImpl): - - erect = PermissibleValue(text="erect") - spreading = PermissibleValue(text="spreading") - prostrate = PermissibleValue(text="prostrate") - - _defn = EnumDefinition( - name="GrowthHabitEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "semi-erect", - PermissibleValue(text="semi-erect") ) - -class HandidnessEnum(EnumDefinitionImpl): - - ambidexterity = PermissibleValue(text="ambidexterity") - - _defn = EnumDefinition( - name="HandidnessEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "left handedness", - PermissibleValue(text="left handedness") ) - setattr(cls, "mixed-handedness", - PermissibleValue(text="mixed-handedness") ) - setattr(cls, "right handedness", - PermissibleValue(text="right handedness") ) - -class HcProducedEnum(EnumDefinitionImpl): - - Oil = PermissibleValue(text="Oil") - Gas = PermissibleValue(text="Gas") - Bitumen = PermissibleValue(text="Bitumen") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="HcProducedEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "Gas-Condensate", - PermissibleValue(text="Gas-Condensate") ) - setattr(cls, "Coalbed Methane", - PermissibleValue(text="Coalbed Methane") ) - -class HcrEnum(EnumDefinitionImpl): - - Coalbed = PermissibleValue(text="Coalbed") - Shale = PermissibleValue(text="Shale") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="HcrEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "Oil Reservoir", - PermissibleValue(text="Oil Reservoir") ) - setattr(cls, "Gas Reservoir", - PermissibleValue(text="Gas Reservoir") ) - setattr(cls, "Oil Sand", - PermissibleValue(text="Oil Sand") ) - setattr(cls, "Tight Oil Reservoir", - PermissibleValue(text="Tight Oil Reservoir") ) - setattr(cls, "Tight Gas Reservoir", - PermissibleValue(text="Tight Gas Reservoir") ) - -class HcrGeolAgeEnum(EnumDefinitionImpl): - - Archean = PermissibleValue(text="Archean") - Cambrian = PermissibleValue(text="Cambrian") - Carboniferous = PermissibleValue(text="Carboniferous") - Cenozoic = PermissibleValue(text="Cenozoic") - Cretaceous = PermissibleValue(text="Cretaceous") - Devonian = PermissibleValue(text="Devonian") - Jurassic = PermissibleValue(text="Jurassic") - Mesozoic = PermissibleValue(text="Mesozoic") - Neogene = PermissibleValue(text="Neogene") - Ordovician = PermissibleValue(text="Ordovician") - Paleogene = PermissibleValue(text="Paleogene") - Paleozoic = PermissibleValue(text="Paleozoic") - Permian = PermissibleValue(text="Permian") - Precambrian = PermissibleValue(text="Precambrian") - Proterozoic = PermissibleValue(text="Proterozoic") - Silurian = PermissibleValue(text="Silurian") - Triassic = PermissibleValue(text="Triassic") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="HcrGeolAgeEnum", - ) - -class HeatCoolTypeEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="HeatCoolTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "radiant system", - PermissibleValue(text="radiant system") ) - setattr(cls, "heat pump", - PermissibleValue(text="heat pump") ) - setattr(cls, "forced air system", - PermissibleValue(text="forced air system") ) - setattr(cls, "steam forced heat", - PermissibleValue(text="steam forced heat") ) - setattr(cls, "wood stove", - PermissibleValue(text="wood stove") ) - -class HeatDelivLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="HeatDelivLocEnum", - ) - -class HorizonEnum(EnumDefinitionImpl): - - Permafrost = PermissibleValue(text="Permafrost") - - _defn = EnumDefinition( - name="HorizonEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "O horizon", - PermissibleValue(text="O horizon") ) - setattr(cls, "A horizon", - PermissibleValue(text="A horizon") ) - setattr(cls, "E horizon", - PermissibleValue(text="E horizon") ) - setattr(cls, "B horizon", - PermissibleValue(text="B horizon") ) - setattr(cls, "C horizon", - PermissibleValue(text="C horizon") ) - setattr(cls, "R layer", - PermissibleValue(text="R layer") ) - -class HostSexEnum(EnumDefinitionImpl): - - female = PermissibleValue(text="female") - hermaphrodite = PermissibleValue(text="hermaphrodite") - male = PermissibleValue(text="male") - neuter = PermissibleValue(text="neuter") - - _defn = EnumDefinition( - name="HostSexEnum", - ) - -class IndoorSpaceEnum(EnumDefinitionImpl): - - bedroom = PermissibleValue(text="bedroom") - office = PermissibleValue(text="office") - bathroom = PermissibleValue(text="bathroom") - foyer = PermissibleValue(text="foyer") - kitchen = PermissibleValue(text="kitchen") - hallway = PermissibleValue(text="hallway") - elevator = PermissibleValue(text="elevator") - - _defn = EnumDefinition( - name="IndoorSpaceEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "locker room", - PermissibleValue(text="locker room") ) - -class IndoorSurfEnum(EnumDefinitionImpl): - - cabinet = PermissibleValue(text="cabinet") - ceiling = PermissibleValue(text="ceiling") - door = PermissibleValue(text="door") - shelving = PermissibleValue(text="shelving") - window = PermissibleValue(text="window") - wall = PermissibleValue(text="wall") - - _defn = EnumDefinition( - name="IndoorSurfEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "counter top", - PermissibleValue(text="counter top") ) - setattr(cls, "vent cover", - PermissibleValue(text="vent cover") ) - -class IntWallCondEnum(EnumDefinitionImpl): - - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="IntWallCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear") ) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair") ) - -class LightTypeEnum(EnumDefinitionImpl): - - none = PermissibleValue(text="none") - - _defn = EnumDefinition( - name="LightTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "natural light", - PermissibleValue(text="natural light") ) - setattr(cls, "electric light", - PermissibleValue(text="electric light") ) - setattr(cls, "desk lamp", - PermissibleValue(text="desk lamp") ) - setattr(cls, "flourescent lights", - PermissibleValue(text="flourescent lights") ) - -class LithologyEnum(EnumDefinitionImpl): - - Basement = PermissibleValue(text="Basement") - Chalk = PermissibleValue(text="Chalk") - Chert = PermissibleValue(text="Chert") - Coal = PermissibleValue(text="Coal") - Conglomerate = PermissibleValue(text="Conglomerate") - Diatomite = PermissibleValue(text="Diatomite") - Dolomite = PermissibleValue(text="Dolomite") - Limestone = PermissibleValue(text="Limestone") - Sandstone = PermissibleValue(text="Sandstone") - Shale = PermissibleValue(text="Shale") - Siltstone = PermissibleValue(text="Siltstone") - Volcanic = PermissibleValue(text="Volcanic") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="LithologyEnum", - ) - -class MechStrucEnum(EnumDefinitionImpl): - - subway = PermissibleValue(text="subway") - coach = PermissibleValue(text="coach") - carriage = PermissibleValue(text="carriage") - elevator = PermissibleValue(text="elevator") - escalator = PermissibleValue(text="escalator") - boat = PermissibleValue(text="boat") - train = PermissibleValue(text="train") - car = PermissibleValue(text="car") - bus = PermissibleValue(text="bus") - - _defn = EnumDefinition( - name="MechStrucEnum", - ) - -class OccupDocumentEnum(EnumDefinitionImpl): - - estimate = PermissibleValue(text="estimate") - videos = PermissibleValue(text="videos") - - _defn = EnumDefinition( - name="OccupDocumentEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "automated count", - PermissibleValue(text="automated count") ) - setattr(cls, "manual count", - PermissibleValue(text="manual count") ) - -class OrganismCountEnum(EnumDefinitionImpl): - - ATP = PermissibleValue(text="ATP") - MPN = PermissibleValue(text="MPN") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="OrganismCountEnum", - ) - -class OxyStatSampEnum(EnumDefinitionImpl): - - aerobic = PermissibleValue(text="aerobic") - anaerobic = PermissibleValue(text="anaerobic") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="OxyStatSampEnum", - ) - -class PlantGrowthMedEnum(EnumDefinitionImpl): - - perlite = PermissibleValue(text="perlite") - pumice = PermissibleValue(text="pumice") - sand = PermissibleValue(text="sand") - soil = PermissibleValue(text="soil") - vermiculite = PermissibleValue(text="vermiculite") - water = PermissibleValue(text="water") - - _defn = EnumDefinition( - name="PlantGrowthMedEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "other artificial liquid medium", - PermissibleValue(text="other artificial liquid medium") ) - setattr(cls, "other artificial solid medium", - PermissibleValue(text="other artificial solid medium") ) - setattr(cls, "peat moss", - PermissibleValue(text="peat moss") ) - -class PlantSexEnum(EnumDefinitionImpl): - - Androdioecious = PermissibleValue(text="Androdioecious") - Androecious = PermissibleValue(text="Androecious") - Androgynous = PermissibleValue(text="Androgynous") - Androgynomonoecious = PermissibleValue(text="Androgynomonoecious") - Andromonoecious = PermissibleValue(text="Andromonoecious") - Bisexual = PermissibleValue(text="Bisexual") - Dichogamous = PermissibleValue(text="Dichogamous") - Diclinous = PermissibleValue(text="Diclinous") - Dioecious = PermissibleValue(text="Dioecious") - Gynodioecious = PermissibleValue(text="Gynodioecious") - Gynoecious = PermissibleValue(text="Gynoecious") - Gynomonoecious = PermissibleValue(text="Gynomonoecious") - Hermaphroditic = PermissibleValue(text="Hermaphroditic") - Imperfect = PermissibleValue(text="Imperfect") - Monoclinous = PermissibleValue(text="Monoclinous") - Monoecious = PermissibleValue(text="Monoecious") - Perfect = PermissibleValue(text="Perfect") - Polygamodioecious = PermissibleValue(text="Polygamodioecious") - Polygamomonoecious = PermissibleValue(text="Polygamomonoecious") - Polygamous = PermissibleValue(text="Polygamous") - Protandrous = PermissibleValue(text="Protandrous") - Protogynous = PermissibleValue(text="Protogynous") - Subandroecious = PermissibleValue(text="Subandroecious") - Subdioecious = PermissibleValue(text="Subdioecious") - Subgynoecious = PermissibleValue(text="Subgynoecious") - Synoecious = PermissibleValue(text="Synoecious") - Trimonoecious = PermissibleValue(text="Trimonoecious") - Trioecious = PermissibleValue(text="Trioecious") - Unisexual = PermissibleValue(text="Unisexual") - - _defn = EnumDefinition( - name="PlantSexEnum", - ) - -class ProfilePositionEnum(EnumDefinitionImpl): - - summit = PermissibleValue(text="summit") - shoulder = PermissibleValue(text="shoulder") - backslope = PermissibleValue(text="backslope") - footslope = PermissibleValue(text="footslope") - toeslope = PermissibleValue(text="toeslope") - - _defn = EnumDefinition( - name="ProfilePositionEnum", - ) - -class QuadPosEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="QuadPosEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "North side", - PermissibleValue(text="North side") ) - setattr(cls, "West side", - PermissibleValue(text="West side") ) - setattr(cls, "South side", - PermissibleValue(text="South side") ) - setattr(cls, "East side", - PermissibleValue(text="East side") ) - -class RelSampLocEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="RelSampLocEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "edge of car", - PermissibleValue(text="edge of car") ) - setattr(cls, "center of car", - PermissibleValue(text="center of car") ) - setattr(cls, "under a seat", - PermissibleValue(text="under a seat") ) - -class RelToOxygenEnum(EnumDefinitionImpl): - - aerobe = PermissibleValue(text="aerobe") - anaerobe = PermissibleValue(text="anaerobe") - facultative = PermissibleValue(text="facultative") - microaerophilic = PermissibleValue(text="microaerophilic") - microanaerobe = PermissibleValue(text="microanaerobe") - - _defn = EnumDefinition( - name="RelToOxygenEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "obligate aerobe", - PermissibleValue(text="obligate aerobe") ) - setattr(cls, "obligate anaerobe", - PermissibleValue(text="obligate anaerobe") ) - -class RoomCondtEnum(EnumDefinitionImpl): - - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="RoomCondtEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear") ) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair") ) - setattr(cls, "visible signs of mold/mildew", - PermissibleValue(text="visible signs of mold/mildew") ) - -class RoomConnectedEnum(EnumDefinitionImpl): - - attic = PermissibleValue(text="attic") - bathroom = PermissibleValue(text="bathroom") - closet = PermissibleValue(text="closet") - elevator = PermissibleValue(text="elevator") - hallway = PermissibleValue(text="hallway") - kitchen = PermissibleValue(text="kitchen") - office = PermissibleValue(text="office") - stairwell = PermissibleValue(text="stairwell") - - _defn = EnumDefinition( - name="RoomConnectedEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "conference room", - PermissibleValue(text="conference room") ) - setattr(cls, "examining room", - PermissibleValue(text="examining room") ) - setattr(cls, "mail room", - PermissibleValue(text="mail room") ) - -class RoomLocEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="RoomLocEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "corner room", - PermissibleValue(text="corner room") ) - setattr(cls, "interior room", - PermissibleValue(text="interior room") ) - setattr(cls, "exterior wall", - PermissibleValue(text="exterior wall") ) - -class RoomSampPosEnum(EnumDefinitionImpl): - - center = PermissibleValue(text="center") - - _defn = EnumDefinition( - name="RoomSampPosEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "north corner", - PermissibleValue(text="north corner") ) - setattr(cls, "south corner", - PermissibleValue(text="south corner") ) - setattr(cls, "west corner", - PermissibleValue(text="west corner") ) - setattr(cls, "east corner", - PermissibleValue(text="east corner") ) - setattr(cls, "northeast corner", - PermissibleValue(text="northeast corner") ) - setattr(cls, "northwest corner", - PermissibleValue(text="northwest corner") ) - setattr(cls, "southeast corner", - PermissibleValue(text="southeast corner") ) - setattr(cls, "southwest corner", - PermissibleValue(text="southwest corner") ) - -class RoomTypeEnum(EnumDefinitionImpl): - - attic = PermissibleValue(text="attic") - bathroom = PermissibleValue(text="bathroom") - closet = PermissibleValue(text="closet") - elevator = PermissibleValue(text="elevator") - hallway = PermissibleValue(text="hallway") - kitchen = PermissibleValue(text="kitchen") - stairwell = PermissibleValue(text="stairwell") - lobby = PermissibleValue(text="lobby") - vestibule = PermissibleValue(text="vestibule") - laboratory_wet = PermissibleValue(text="laboratory_wet") - laboratory_dry = PermissibleValue(text="laboratory_dry") - gymnasium = PermissibleValue(text="gymnasium") - natatorium = PermissibleValue(text="natatorium") - auditorium = PermissibleValue(text="auditorium") - lockers = PermissibleValue(text="lockers") - cafe = PermissibleValue(text="cafe") - warehouse = PermissibleValue(text="warehouse") - - _defn = EnumDefinition( - name="RoomTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "conference room", - PermissibleValue(text="conference room") ) - setattr(cls, "examining room", - PermissibleValue(text="examining room") ) - setattr(cls, "mail room", - PermissibleValue(text="mail room") ) - setattr(cls, "private office", - PermissibleValue(text="private office") ) - setattr(cls, "open office", - PermissibleValue(text="open office") ) - setattr(cls, ",restroom", - PermissibleValue(text=",restroom") ) - setattr(cls, "mechanical or electrical room", - PermissibleValue(text="mechanical or electrical room") ) - setattr(cls, "data center", - PermissibleValue(text="data center") ) - -class SampCaptStatusEnum(EnumDefinitionImpl): - - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SampCaptStatusEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "active surveillance in response to an outbreak", - PermissibleValue(text="active surveillance in response to an outbreak") ) - setattr(cls, "active surveillance not initiated by an outbreak", - PermissibleValue(text="active surveillance not initiated by an outbreak") ) - setattr(cls, "farm sample", - PermissibleValue(text="farm sample") ) - setattr(cls, "market sample", - PermissibleValue(text="market sample") ) - -class SampCollectPointEnum(EnumDefinitionImpl): - - well = PermissibleValue(text="well") - wellhead = PermissibleValue(text="wellhead") - separator = PermissibleValue(text="separator") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SampCollectPointEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "test well", - PermissibleValue(text="test well") ) - setattr(cls, "drilling rig", - PermissibleValue(text="drilling rig") ) - setattr(cls, "storage tank", - PermissibleValue(text="storage tank") ) - -class SampDisStageEnum(EnumDefinitionImpl): - - dissemination = PermissibleValue(text="dissemination") - infection = PermissibleValue(text="infection") - inoculation = PermissibleValue(text="inoculation") - penetration = PermissibleValue(text="penetration") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SampDisStageEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "growth and reproduction", - PermissibleValue(text="growth and reproduction") ) - -class SampFloorEnum(EnumDefinitionImpl): - - basement = PermissibleValue(text="basement") - lobby = PermissibleValue(text="lobby") - - _defn = EnumDefinition( - name="SampFloorEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "1st floor", - PermissibleValue(text="1st floor") ) - setattr(cls, "2nd floor", - PermissibleValue(text="2nd floor") ) - -class SampMdEnum(EnumDefinitionImpl): - - DF = PermissibleValue(text="DF") - RT = PermissibleValue(text="RT") - KB = PermissibleValue(text="KB") - MSL = PermissibleValue(text="MSL") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SampMdEnum", - ) - -class SampSubtypeEnum(EnumDefinitionImpl): - - biofilm = PermissibleValue(text="biofilm") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SampSubtypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "oil phase", - PermissibleValue(text="oil phase") ) - setattr(cls, "water phase", - PermissibleValue(text="water phase") ) - setattr(cls, "not applicable", - PermissibleValue(text="not applicable") ) - -class SampWeatherEnum(EnumDefinitionImpl): - - cloudy = PermissibleValue(text="cloudy") - foggy = PermissibleValue(text="foggy") - hail = PermissibleValue(text="hail") - rain = PermissibleValue(text="rain") - snow = PermissibleValue(text="snow") - sleet = PermissibleValue(text="sleet") - sunny = PermissibleValue(text="sunny") - windy = PermissibleValue(text="windy") - - _defn = EnumDefinition( - name="SampWeatherEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "clear sky", - PermissibleValue(text="clear sky") ) - -class SeasonUseEnum(EnumDefinitionImpl): - - Spring = PermissibleValue(text="Spring") - Summer = PermissibleValue(text="Summer") - Fall = PermissibleValue(text="Fall") - Winter = PermissibleValue(text="Winter") - - _defn = EnumDefinition( - name="SeasonUseEnum", - ) - -class SedimentTypeEnum(EnumDefinitionImpl): - - biogenous = PermissibleValue(text="biogenous") - cosmogenous = PermissibleValue(text="cosmogenous") - hydrogenous = PermissibleValue(text="hydrogenous") - lithogenous = PermissibleValue(text="lithogenous") - - _defn = EnumDefinition( - name="SedimentTypeEnum", - ) - -class ShadingDeviceCondEnum(EnumDefinitionImpl): - - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="ShadingDeviceCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair") ) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear") ) - -class ShadingDeviceTypeEnum(EnumDefinitionImpl): - - tree = PermissibleValue(text="tree") - trellis = PermissibleValue(text="trellis") - - _defn = EnumDefinition( - name="ShadingDeviceTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "bahama shutters", - PermissibleValue(text="bahama shutters") ) - setattr(cls, "exterior roll blind", - PermissibleValue(text="exterior roll blind") ) - setattr(cls, "gambrel awning", - PermissibleValue(text="gambrel awning") ) - setattr(cls, "hood awning", - PermissibleValue(text="hood awning") ) - setattr(cls, "porchroller awning", - PermissibleValue(text="porchroller awning") ) - setattr(cls, "sarasota shutters", - PermissibleValue(text="sarasota shutters") ) - setattr(cls, "slatted aluminum", - PermissibleValue(text="slatted aluminum") ) - setattr(cls, "solid aluminum awning", - PermissibleValue(text="solid aluminum awning") ) - setattr(cls, "sun screen", - PermissibleValue(text="sun screen") ) - setattr(cls, "venetian awning", - PermissibleValue(text="venetian awning") ) - -class SoilHorizonEnum(EnumDefinitionImpl): - - Permafrost = PermissibleValue(text="Permafrost") - - _defn = EnumDefinition( - name="SoilHorizonEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "O horizon", - PermissibleValue(text="O horizon") ) - setattr(cls, "A horizon", - PermissibleValue(text="A horizon") ) - setattr(cls, "E horizon", - PermissibleValue(text="E horizon") ) - setattr(cls, "B horizon", - PermissibleValue(text="B horizon") ) - setattr(cls, "C horizon", - PermissibleValue(text="C horizon") ) - setattr(cls, "R layer", - PermissibleValue(text="R layer") ) - -class SpecificEnum(EnumDefinitionImpl): - - operation = PermissibleValue(text="operation") - construction = PermissibleValue(text="construction") - bid = PermissibleValue(text="bid") - design = PermissibleValue(text="design") - photos = PermissibleValue(text="photos") - - _defn = EnumDefinition( - name="SpecificEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "as built", - PermissibleValue(text="as built") ) - -class SrDepEnvEnum(EnumDefinitionImpl): - - Lacustine = PermissibleValue(text="Lacustine") - Fluvioldeltaic = PermissibleValue(text="Fluvioldeltaic") - Fluviomarine = PermissibleValue(text="Fluviomarine") - Marine = PermissibleValue(text="Marine") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SrDepEnvEnum", - ) - -class SrGeolAgeEnum(EnumDefinitionImpl): - - Archean = PermissibleValue(text="Archean") - Cambrian = PermissibleValue(text="Cambrian") - Carboniferous = PermissibleValue(text="Carboniferous") - Cenozoic = PermissibleValue(text="Cenozoic") - Cretaceous = PermissibleValue(text="Cretaceous") - Devonian = PermissibleValue(text="Devonian") - Jurassic = PermissibleValue(text="Jurassic") - Mesozoic = PermissibleValue(text="Mesozoic") - Neogene = PermissibleValue(text="Neogene") - Ordovician = PermissibleValue(text="Ordovician") - Paleogene = PermissibleValue(text="Paleogene") - Paleozoic = PermissibleValue(text="Paleozoic") - Permian = PermissibleValue(text="Permian") - Precambrian = PermissibleValue(text="Precambrian") - Proterozoic = PermissibleValue(text="Proterozoic") - Silurian = PermissibleValue(text="Silurian") - Triassic = PermissibleValue(text="Triassic") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SrGeolAgeEnum", - ) - -class SrKerogTypeEnum(EnumDefinitionImpl): - - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SrKerogTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "Type I", - PermissibleValue(text="Type I") ) - setattr(cls, "Type II", - PermissibleValue(text="Type II") ) - setattr(cls, "Type III", - PermissibleValue(text="Type III") ) - setattr(cls, "Type IV", - PermissibleValue(text="Type IV") ) - -class SrLithologyEnum(EnumDefinitionImpl): - - Clastic = PermissibleValue(text="Clastic") - Carbonate = PermissibleValue(text="Carbonate") - Coal = PermissibleValue(text="Coal") - Biosilicieous = PermissibleValue(text="Biosilicieous") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SrLithologyEnum", - ) - -class SubstructureTypeEnum(EnumDefinitionImpl): - - crawlspace = PermissibleValue(text="crawlspace") - basement = PermissibleValue(text="basement") - - _defn = EnumDefinition( - name="SubstructureTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "slab on grade", - PermissibleValue(text="slab on grade") ) - -class SurfAirContEnum(EnumDefinitionImpl): - - dust = PermissibleValue(text="dust") - radon = PermissibleValue(text="radon") - nutrients = PermissibleValue(text="nutrients") - biocides = PermissibleValue(text="biocides") - - _defn = EnumDefinition( - name="SurfAirContEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "organic matter", - PermissibleValue(text="organic matter") ) - setattr(cls, "particulate matter", - PermissibleValue(text="particulate matter") ) - setattr(cls, "volatile organic compounds", - PermissibleValue(text="volatile organic compounds") ) - setattr(cls, "biological contaminants", - PermissibleValue(text="biological contaminants") ) - -class SurfMaterialEnum(EnumDefinitionImpl): - - adobe = PermissibleValue(text="adobe") - carpet = PermissibleValue(text="carpet") - concrete = PermissibleValue(text="concrete") - glass = PermissibleValue(text="glass") - metal = PermissibleValue(text="metal") - paint = PermissibleValue(text="paint") - plastic = PermissibleValue(text="plastic") - stone = PermissibleValue(text="stone") - stucco = PermissibleValue(text="stucco") - tile = PermissibleValue(text="tile") - vinyl = PermissibleValue(text="vinyl") - wood = PermissibleValue(text="wood") - - _defn = EnumDefinition( - name="SurfMaterialEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "cinder blocks", - PermissibleValue(text="cinder blocks") ) - setattr(cls, "hay bales", - PermissibleValue(text="hay bales") ) - setattr(cls, "stainless steel", - PermissibleValue(text="stainless steel") ) - -class TidalStageEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="TidalStageEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "low tide", - PermissibleValue(text="low tide") ) - setattr(cls, "ebb tide", - PermissibleValue(text="ebb tide") ) - setattr(cls, "flood tide", - PermissibleValue(text="flood tide") ) - setattr(cls, "high tide", - PermissibleValue(text="high tide") ) - -class TillageEnum(EnumDefinitionImpl): - - drill = PermissibleValue(text="drill") - chisel = PermissibleValue(text="chisel") - tined = PermissibleValue(text="tined") - mouldboard = PermissibleValue(text="mouldboard") - - _defn = EnumDefinition( - name="TillageEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "cutting disc", - PermissibleValue(text="cutting disc") ) - setattr(cls, "ridge till", - PermissibleValue(text="ridge till") ) - setattr(cls, "strip tillage", - PermissibleValue(text="strip tillage") ) - setattr(cls, "zonal tillage", - PermissibleValue(text="zonal tillage") ) - setattr(cls, "disc plough", - PermissibleValue(text="disc plough") ) - -class TrainLineEnum(EnumDefinitionImpl): - - red = PermissibleValue(text="red") - green = PermissibleValue(text="green") - orange = PermissibleValue(text="orange") - - _defn = EnumDefinition( - name="TrainLineEnum", - ) - -class TrainStatLocEnum(EnumDefinitionImpl): - - riverside = PermissibleValue(text="riverside") - - _defn = EnumDefinition( - name="TrainStatLocEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "south station above ground", - PermissibleValue(text="south station above ground") ) - setattr(cls, "south station underground", - PermissibleValue(text="south station underground") ) - setattr(cls, "south station amtrak", - PermissibleValue(text="south station amtrak") ) - setattr(cls, "forest hills", - PermissibleValue(text="forest hills") ) - -class TrainStopLocEnum(EnumDefinitionImpl): - - end = PermissibleValue(text="end") - mid = PermissibleValue(text="mid") - downtown = PermissibleValue(text="downtown") - - _defn = EnumDefinition( - name="TrainStopLocEnum", - ) - -class VisMediaEnum(EnumDefinitionImpl): - - photos = PermissibleValue(text="photos") - videos = PermissibleValue(text="videos") - interiors = PermissibleValue(text="interiors") - equipment = PermissibleValue(text="equipment") - - _defn = EnumDefinition( - name="VisMediaEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "commonly of the building", - PermissibleValue(text="commonly of the building") ) - setattr(cls, "site context (adjacent buildings, vegetation, terrain, streets)", - PermissibleValue(text="site context (adjacent buildings, vegetation, terrain, streets)") ) - setattr(cls, "3D scans", - PermissibleValue(text="3D scans") ) - -class WallConstTypeEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="WallConstTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "frame construction", - PermissibleValue(text="frame construction") ) - setattr(cls, "joisted masonry", - PermissibleValue(text="joisted masonry") ) - setattr(cls, "light noncombustible", - PermissibleValue(text="light noncombustible") ) - setattr(cls, "masonry noncombustible", - PermissibleValue(text="masonry noncombustible") ) - setattr(cls, "modified fire resistive", - PermissibleValue(text="modified fire resistive") ) - setattr(cls, "fire resistive", - PermissibleValue(text="fire resistive") ) - -class WallFinishMatEnum(EnumDefinitionImpl): - - plaster = PermissibleValue(text="plaster") - tile = PermissibleValue(text="tile") - terrazzo = PermissibleValue(text="terrazzo") - wood = PermissibleValue(text="wood") - metal = PermissibleValue(text="metal") - masonry = PermissibleValue(text="masonry") - - _defn = EnumDefinition( - name="WallFinishMatEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "gypsum plaster", - PermissibleValue(text="gypsum plaster") ) - setattr(cls, "veneer plaster", - PermissibleValue(text="veneer plaster") ) - setattr(cls, "gypsum board", - PermissibleValue(text="gypsum board") ) - setattr(cls, "stone facing", - PermissibleValue(text="stone facing") ) - setattr(cls, "acoustical treatment", - PermissibleValue(text="acoustical treatment") ) - -class WallLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="WallLocEnum", - ) - -class WallSurfTreatmentEnum(EnumDefinitionImpl): - - painted = PermissibleValue(text="painted") - paneling = PermissibleValue(text="paneling") - stucco = PermissibleValue(text="stucco") - fabric = PermissibleValue(text="fabric") - - _defn = EnumDefinition( - name="WallSurfTreatmentEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "wall paper", - PermissibleValue(text="wall paper") ) - setattr(cls, "no treatment", - PermissibleValue(text="no treatment") ) - -class WallTextureEnum(EnumDefinitionImpl): - - knockdown = PermissibleValue(text="knockdown") - popcorn = PermissibleValue(text="popcorn") - smooth = PermissibleValue(text="smooth") - swirl = PermissibleValue(text="swirl") - - _defn = EnumDefinition( - name="WallTextureEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "crows feet", - PermissibleValue(text="crows feet") ) - setattr(cls, "crows-foot stomp", - PermissibleValue(text="crows-foot stomp") ) - setattr(cls, "", - PermissibleValue(text="") ) - setattr(cls, "double skip", - PermissibleValue(text="double skip") ) - setattr(cls, "hawk and trowel", - PermissibleValue(text="hawk and trowel") ) - setattr(cls, "orange peel", - PermissibleValue(text="orange peel") ) - setattr(cls, "rosebud stomp", - PermissibleValue(text="rosebud stomp") ) - setattr(cls, "Santa-Fe texture", - PermissibleValue(text="Santa-Fe texture") ) - setattr(cls, "skip trowel", - PermissibleValue(text="skip trowel") ) - setattr(cls, "stomp knockdown", - PermissibleValue(text="stomp knockdown") ) - -class WaterFeatTypeEnum(EnumDefinitionImpl): - - fountain = PermissibleValue(text="fountain") - pool = PermissibleValue(text="pool") - stream = PermissibleValue(text="stream") - waterfall = PermissibleValue(text="waterfall") - - _defn = EnumDefinition( - name="WaterFeatTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "standing feature", - PermissibleValue(text="standing feature") ) - -class WeekdayEnum(EnumDefinitionImpl): - - Monday = PermissibleValue(text="Monday") - Tuesday = PermissibleValue(text="Tuesday") - Wednesday = PermissibleValue(text="Wednesday") - Thursday = PermissibleValue(text="Thursday") - Friday = PermissibleValue(text="Friday") - Saturday = PermissibleValue(text="Saturday") - Sunday = PermissibleValue(text="Sunday") - - _defn = EnumDefinition( - name="WeekdayEnum", - ) - -class WindowCondEnum(EnumDefinitionImpl): - - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="WindowCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair") ) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear") ) - -class WindowCoverEnum(EnumDefinitionImpl): - - blinds = PermissibleValue(text="blinds") - curtains = PermissibleValue(text="curtains") - none = PermissibleValue(text="none") - - _defn = EnumDefinition( - name="WindowCoverEnum", - ) - -class WindowHorizPosEnum(EnumDefinitionImpl): - - left = PermissibleValue(text="left") - middle = PermissibleValue(text="middle") - right = PermissibleValue(text="right") - - _defn = EnumDefinition( - name="WindowHorizPosEnum", - ) - -class WindowLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="WindowLocEnum", - ) - -class WindowMatEnum(EnumDefinitionImpl): - - clad = PermissibleValue(text="clad") - fiberglass = PermissibleValue(text="fiberglass") - metal = PermissibleValue(text="metal") - vinyl = PermissibleValue(text="vinyl") - wood = PermissibleValue(text="wood") - - _defn = EnumDefinition( - name="WindowMatEnum", - ) - -class WindowTypeEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="WindowTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "single-hung sash window", - PermissibleValue(text="single-hung sash window") ) - setattr(cls, "horizontal sash window", - PermissibleValue(text="horizontal sash window") ) - setattr(cls, "fixed window", - PermissibleValue(text="fixed window") ) - -class WindowVertPosEnum(EnumDefinitionImpl): - - bottom = PermissibleValue(text="bottom") - middle = PermissibleValue(text="middle") - top = PermissibleValue(text="top") - low = PermissibleValue(text="low") - high = PermissibleValue(text="high") - - _defn = EnumDefinition( - name="WindowVertPosEnum", - ) - -# Slots -class slots: - pass - -slots.abs_air_humidity = Slot(uri=MIXS['0000122'], name="abs_air_humidity", curie=MIXS.curie('0000122'), - model_uri=DEFAULT_.abs_air_humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.core_field = Slot(uri=DEFAULT_.core_field, name="core field", curie=DEFAULT_.curie('core_field'), - model_uri=DEFAULT_.core_field, domain=None, range=Optional[str]) - -slots.add_recov_method = Slot(uri=MIXS['0001009'], name="add_recov_method", curie=MIXS.curie('0001009'), - model_uri=DEFAULT_.add_recov_method, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.additional_info = Slot(uri=MIXS['0000300'], name="additional_info", curie=MIXS.curie('0000300'), - model_uri=DEFAULT_.additional_info, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.address = Slot(uri=MIXS['0000218'], name="address", curie=MIXS.curie('0000218'), - model_uri=DEFAULT_.address, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.adj_room = Slot(uri=MIXS['0000219'], name="adj_room", curie=MIXS.curie('0000219'), - model_uri=DEFAULT_.adj_room, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.aero_struc = Slot(uri=MIXS['0000773'], name="aero_struc", curie=MIXS.curie('0000773'), - model_uri=DEFAULT_.aero_struc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.agrochem_addition = Slot(uri=MIXS['0000639'], name="agrochem_addition", curie=MIXS.curie('0000639'), - model_uri=DEFAULT_.agrochem_addition, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.air_temp = Slot(uri=MIXS['0000124'], name="air_temp", curie=MIXS.curie('0000124'), - model_uri=DEFAULT_.air_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.air_temp_regm = Slot(uri=MIXS['0000551'], name="air_temp_regm", curie=MIXS.curie('0000551'), - model_uri=DEFAULT_.air_temp_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.al_sat = Slot(uri=MIXS['0000607'], name="al_sat", curie=MIXS.curie('0000607'), - model_uri=DEFAULT_.al_sat, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.al_sat_meth = Slot(uri=MIXS['0000324'], name="al_sat_meth", curie=MIXS.curie('0000324'), - model_uri=DEFAULT_.al_sat_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.alkalinity = Slot(uri=MIXS['0000421'], name="alkalinity", curie=MIXS.curie('0000421'), - model_uri=DEFAULT_.alkalinity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.alkalinity_method = Slot(uri=MIXS['0000298'], name="alkalinity_method", curie=MIXS.curie('0000298'), - model_uri=DEFAULT_.alkalinity_method, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.alkyl_diethers = Slot(uri=MIXS['0000490'], name="alkyl_diethers", curie=MIXS.curie('0000490'), - model_uri=DEFAULT_.alkyl_diethers, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.alt = Slot(uri=MIXS['0000094'], name="alt", curie=MIXS.curie('0000094'), - model_uri=DEFAULT_.alt, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.environment_field = Slot(uri=DEFAULT_.environment_field, name="environment field", curie=DEFAULT_.curie('environment_field'), - model_uri=DEFAULT_.environment_field, domain=None, range=Optional[str]) - -slots.aminopept_act = Slot(uri=MIXS['0000172'], name="aminopept_act", curie=MIXS.curie('0000172'), - model_uri=DEFAULT_.aminopept_act, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ammonium = Slot(uri=MIXS['0000427'], name="ammonium", curie=MIXS.curie('0000427'), - model_uri=DEFAULT_.ammonium, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.amount_light = Slot(uri=MIXS['0000140'], name="amount_light", curie=MIXS.curie('0000140'), - model_uri=DEFAULT_.amount_light, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ances_data = Slot(uri=MIXS['0000247'], name="ances_data", curie=MIXS.curie('0000247'), - model_uri=DEFAULT_.ances_data, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.annual_precpt = Slot(uri=MIXS['0000644'], name="annual_precpt", curie=MIXS.curie('0000644'), - model_uri=DEFAULT_.annual_precpt, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.annual_temp = Slot(uri=MIXS['0000642'], name="annual_temp", curie=MIXS.curie('0000642'), - model_uri=DEFAULT_.annual_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.antibiotic_regm = Slot(uri=MIXS['0000553'], name="antibiotic_regm", curie=MIXS.curie('0000553'), - model_uri=DEFAULT_.antibiotic_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.api = Slot(uri=MIXS['0000157'], name="api", curie=MIXS.curie('0000157'), - model_uri=DEFAULT_.api, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.arch_struc = Slot(uri=MIXS['0000774'], name="arch_struc", curie=MIXS.curie('0000774'), - model_uri=DEFAULT_.arch_struc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.aromatics_pc = Slot(uri=MIXS['0000133'], name="aromatics_pc", curie=MIXS.curie('0000133'), - model_uri=DEFAULT_.aromatics_pc, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.asphaltenes_pc = Slot(uri=MIXS['0000135'], name="asphaltenes_pc", curie=MIXS.curie('0000135'), - model_uri=DEFAULT_.asphaltenes_pc, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.atmospheric_data = Slot(uri=MIXS['0001097'], name="atmospheric_data", curie=MIXS.curie('0001097'), - model_uri=DEFAULT_.atmospheric_data, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.avg_dew_point = Slot(uri=MIXS['0000141'], name="avg_dew_point", curie=MIXS.curie('0000141'), - model_uri=DEFAULT_.avg_dew_point, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.avg_occup = Slot(uri=MIXS['0000775'], name="avg_occup", curie=MIXS.curie('0000775'), - model_uri=DEFAULT_.avg_occup, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.avg_temp = Slot(uri=MIXS['0000142'], name="avg_temp", curie=MIXS.curie('0000142'), - model_uri=DEFAULT_.avg_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.bac_prod = Slot(uri=MIXS['0000683'], name="bac_prod", curie=MIXS.curie('0000683'), - model_uri=DEFAULT_.bac_prod, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.bac_resp = Slot(uri=MIXS['0000684'], name="bac_resp", curie=MIXS.curie('0000684'), - model_uri=DEFAULT_.bac_resp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.bacteria_carb_prod = Slot(uri=MIXS['0000173'], name="bacteria_carb_prod", curie=MIXS.curie('0000173'), - model_uri=DEFAULT_.bacteria_carb_prod, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.barometric_press = Slot(uri=MIXS['0000096'], name="barometric_press", curie=MIXS.curie('0000096'), - model_uri=DEFAULT_.barometric_press, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.basin = Slot(uri=MIXS['0000290'], name="basin", curie=MIXS.curie('0000290'), - model_uri=DEFAULT_.basin, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.bathroom_count = Slot(uri=MIXS['0000776'], name="bathroom_count", curie=MIXS.curie('0000776'), - model_uri=DEFAULT_.bathroom_count, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.bedroom_count = Slot(uri=MIXS['0000777'], name="bedroom_count", curie=MIXS.curie('0000777'), - model_uri=DEFAULT_.bedroom_count, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.benzene = Slot(uri=MIXS['0000153'], name="benzene", curie=MIXS.curie('0000153'), - model_uri=DEFAULT_.benzene, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.biochem_oxygen_dem = Slot(uri=MIXS['0000653'], name="biochem_oxygen_dem", curie=MIXS.curie('0000653'), - model_uri=DEFAULT_.biochem_oxygen_dem, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.biocide = Slot(uri=MIXS['0001011'], name="biocide", curie=MIXS.curie('0001011'), - model_uri=DEFAULT_.biocide, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.biocide_admin_method = Slot(uri=MIXS['0000456'], name="biocide_admin_method", curie=MIXS.curie('0000456'), - model_uri=DEFAULT_.biocide_admin_method, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.biol_stat = Slot(uri=MIXS['0000858'], name="biol_stat", curie=MIXS.curie('0000858'), - model_uri=DEFAULT_.biol_stat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.biomass = Slot(uri=MIXS['0000174'], name="biomass", curie=MIXS.curie('0000174'), - model_uri=DEFAULT_.biomass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.biotic_regm = Slot(uri=MIXS['0001038'], name="biotic_regm", curie=MIXS.curie('0001038'), - model_uri=DEFAULT_.biotic_regm, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.biotic_relationship = Slot(uri=MIXS['0000028'], name="biotic_relationship", curie=MIXS.curie('0000028'), - model_uri=DEFAULT_.biotic_relationship, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.nucleic_acid_sequence_source_field = Slot(uri=DEFAULT_.nucleic_acid_sequence_source_field, name="nucleic acid sequence source field", curie=DEFAULT_.curie('nucleic_acid_sequence_source_field'), - model_uri=DEFAULT_.nucleic_acid_sequence_source_field, domain=None, range=Optional[str]) - -slots.bishomohopanol = Slot(uri=MIXS['0000175'], name="bishomohopanol", curie=MIXS.curie('0000175'), - model_uri=DEFAULT_.bishomohopanol, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.blood_press_diast = Slot(uri=MIXS['0000258'], name="blood_press_diast", curie=MIXS.curie('0000258'), - model_uri=DEFAULT_.blood_press_diast, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.blood_press_syst = Slot(uri=MIXS['0000259'], name="blood_press_syst", curie=MIXS.curie('0000259'), - model_uri=DEFAULT_.blood_press_syst, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.bromide = Slot(uri=MIXS['0000176'], name="bromide", curie=MIXS.curie('0000176'), - model_uri=DEFAULT_.bromide, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.build_docs = Slot(uri=MIXS['0000787'], name="build_docs", curie=MIXS.curie('0000787'), - model_uri=DEFAULT_.build_docs, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.build_occup_type = Slot(uri=MIXS['0000761'], name="build_occup_type", curie=MIXS.curie('0000761'), - model_uri=DEFAULT_.build_occup_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.building_setting = Slot(uri=MIXS['0000768'], name="building_setting", curie=MIXS.curie('0000768'), - model_uri=DEFAULT_.building_setting, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.built_struc_age = Slot(uri=MIXS['0000145'], name="built_struc_age", curie=MIXS.curie('0000145'), - model_uri=DEFAULT_.built_struc_age, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.built_struc_set = Slot(uri=MIXS['0000778'], name="built_struc_set", curie=MIXS.curie('0000778'), - model_uri=DEFAULT_.built_struc_set, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.built_struc_type = Slot(uri=MIXS['0000721'], name="built_struc_type", curie=MIXS.curie('0000721'), - model_uri=DEFAULT_.built_struc_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.calcium = Slot(uri=MIXS['0000432'], name="calcium", curie=MIXS.curie('0000432'), - model_uri=DEFAULT_.calcium, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.carb_dioxide = Slot(uri=MIXS['0000097'], name="carb_dioxide", curie=MIXS.curie('0000097'), - model_uri=DEFAULT_.carb_dioxide, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.carb_monoxide = Slot(uri=MIXS['0000098'], name="carb_monoxide", curie=MIXS.curie('0000098'), - model_uri=DEFAULT_.carb_monoxide, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.carb_nitro_ratio = Slot(uri=MIXS['0000310'], name="carb_nitro_ratio", curie=MIXS.curie('0000310'), - model_uri=DEFAULT_.carb_nitro_ratio, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ceil_area = Slot(uri=MIXS['0000148'], name="ceil_area", curie=MIXS.curie('0000148'), - model_uri=DEFAULT_.ceil_area, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ceil_cond = Slot(uri=MIXS['0000779'], name="ceil_cond", curie=MIXS.curie('0000779'), - model_uri=DEFAULT_.ceil_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ceil_finish_mat = Slot(uri=MIXS['0000780'], name="ceil_finish_mat", curie=MIXS.curie('0000780'), - model_uri=DEFAULT_.ceil_finish_mat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ceil_struc = Slot(uri=MIXS['0000782'], name="ceil_struc", curie=MIXS.curie('0000782'), - model_uri=DEFAULT_.ceil_struc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ceil_texture = Slot(uri=MIXS['0000783'], name="ceil_texture", curie=MIXS.curie('0000783'), - model_uri=DEFAULT_.ceil_texture, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ceil_thermal_mass = Slot(uri=MIXS['0000143'], name="ceil_thermal_mass", curie=MIXS.curie('0000143'), - model_uri=DEFAULT_.ceil_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ceil_type = Slot(uri=MIXS['0000784'], name="ceil_type", curie=MIXS.curie('0000784'), - model_uri=DEFAULT_.ceil_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ceil_water_mold = Slot(uri=MIXS['0000781'], name="ceil_water_mold", curie=MIXS.curie('0000781'), - model_uri=DEFAULT_.ceil_water_mold, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.chem_administration = Slot(uri=MIXS['0000751'], name="chem_administration", curie=MIXS.curie('0000751'), - model_uri=DEFAULT_.chem_administration, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.chem_mutagen = Slot(uri=MIXS['0000555'], name="chem_mutagen", curie=MIXS.curie('0000555'), - model_uri=DEFAULT_.chem_mutagen, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.chem_oxygen_dem = Slot(uri=MIXS['0000656'], name="chem_oxygen_dem", curie=MIXS.curie('0000656'), - model_uri=DEFAULT_.chem_oxygen_dem, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.chem_treat_method = Slot(uri=MIXS['0000457'], name="chem_treat_method", curie=MIXS.curie('0000457'), - model_uri=DEFAULT_.chem_treat_method, domain=None, range=Optional[str]) - -slots.chem_treatment = Slot(uri=MIXS['0001012'], name="chem_treatment", curie=MIXS.curie('0001012'), - model_uri=DEFAULT_.chem_treatment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.chimera_check = Slot(uri=MIXS['0000052'], name="chimera_check", curie=MIXS.curie('0000052'), - model_uri=DEFAULT_.chimera_check, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sequencing_field = Slot(uri=DEFAULT_.sequencing_field, name="sequencing field", curie=DEFAULT_.curie('sequencing_field'), - model_uri=DEFAULT_.sequencing_field, domain=None, range=Optional[str]) - -slots.chloride = Slot(uri=MIXS['0000429'], name="chloride", curie=MIXS.curie('0000429'), - model_uri=DEFAULT_.chloride, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.chlorophyll = Slot(uri=MIXS['0000177'], name="chlorophyll", curie=MIXS.curie('0000177'), - model_uri=DEFAULT_.chlorophyll, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.climate_environment = Slot(uri=MIXS['0001040'], name="climate_environment", curie=MIXS.curie('0001040'), - model_uri=DEFAULT_.climate_environment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.collection_date = Slot(uri=MIXS['0000011'], name="collection_date", curie=MIXS.curie('0000011'), - model_uri=DEFAULT_.collection_date, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.conduc = Slot(uri=MIXS['0000692'], name="conduc", curie=MIXS.curie('0000692'), - model_uri=DEFAULT_.conduc, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.cool_syst_id = Slot(uri=MIXS['0000785'], name="cool_syst_id", curie=MIXS.curie('0000785'), - model_uri=DEFAULT_.cool_syst_id, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.crop_rotation = Slot(uri=MIXS['0000318'], name="crop_rotation", curie=MIXS.curie('0000318'), - model_uri=DEFAULT_.crop_rotation, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.cult_root_med = Slot(uri=MIXS['0001041'], name="cult_root_med", curie=MIXS.curie('0001041'), - model_uri=DEFAULT_.cult_root_med, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.cur_land_use = Slot(uri=MIXS['0001080'], name="cur_land_use", curie=MIXS.curie('0001080'), - model_uri=DEFAULT_.cur_land_use, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.cur_vegetation = Slot(uri=MIXS['0000312'], name="cur_vegetation", curie=MIXS.curie('0000312'), - model_uri=DEFAULT_.cur_vegetation, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.cur_vegetation_meth = Slot(uri=MIXS['0000314'], name="cur_vegetation_meth", curie=MIXS.curie('0000314'), - model_uri=DEFAULT_.cur_vegetation_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.date_last_rain = Slot(uri=MIXS['0000786'], name="date_last_rain", curie=MIXS.curie('0000786'), - model_uri=DEFAULT_.date_last_rain, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.density = Slot(uri=MIXS['0000435'], name="density", curie=MIXS.curie('0000435'), - model_uri=DEFAULT_.density, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.depos_env = Slot(uri=MIXS['0000992'], name="depos_env", curie=MIXS.curie('0000992'), - model_uri=DEFAULT_.depos_env, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.depth = Slot(uri=MIXS['0000018'], name="depth", curie=MIXS.curie('0000018'), - model_uri=DEFAULT_.depth, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.dew_point = Slot(uri=MIXS['0000129'], name="dew_point", curie=MIXS.curie('0000129'), - model_uri=DEFAULT_.dew_point, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diether_lipids = Slot(uri=MIXS['0000178'], name="diether_lipids", curie=MIXS.curie('0000178'), - model_uri=DEFAULT_.diether_lipids, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_carb_dioxide = Slot(uri=MIXS['0000436'], name="diss_carb_dioxide", curie=MIXS.curie('0000436'), - model_uri=DEFAULT_.diss_carb_dioxide, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_hydrogen = Slot(uri=MIXS['0000179'], name="diss_hydrogen", curie=MIXS.curie('0000179'), - model_uri=DEFAULT_.diss_hydrogen, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_inorg_carb = Slot(uri=MIXS['0000434'], name="diss_inorg_carb", curie=MIXS.curie('0000434'), - model_uri=DEFAULT_.diss_inorg_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_inorg_nitro = Slot(uri=MIXS['0000698'], name="diss_inorg_nitro", curie=MIXS.curie('0000698'), - model_uri=DEFAULT_.diss_inorg_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_inorg_phosp = Slot(uri=MIXS['0000106'], name="diss_inorg_phosp", curie=MIXS.curie('0000106'), - model_uri=DEFAULT_.diss_inorg_phosp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_iron = Slot(uri=MIXS['0000139'], name="diss_iron", curie=MIXS.curie('0000139'), - model_uri=DEFAULT_.diss_iron, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_org_carb = Slot(uri=MIXS['0000433'], name="diss_org_carb", curie=MIXS.curie('0000433'), - model_uri=DEFAULT_.diss_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_org_nitro = Slot(uri=MIXS['0000162'], name="diss_org_nitro", curie=MIXS.curie('0000162'), - model_uri=DEFAULT_.diss_org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_oxygen = Slot(uri=MIXS['0000119'], name="diss_oxygen", curie=MIXS.curie('0000119'), - model_uri=DEFAULT_.diss_oxygen, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.diss_oxygen_fluid = Slot(uri=MIXS['0000438'], name="diss_oxygen_fluid", curie=MIXS.curie('0000438'), - model_uri=DEFAULT_.diss_oxygen_fluid, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.door_comp_type = Slot(uri=MIXS['0000795'], name="door_comp_type", curie=MIXS.curie('0000795'), - model_uri=DEFAULT_.door_comp_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_cond = Slot(uri=MIXS['0000788'], name="door_cond", curie=MIXS.curie('0000788'), - model_uri=DEFAULT_.door_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_direct = Slot(uri=MIXS['0000789'], name="door_direct", curie=MIXS.curie('0000789'), - model_uri=DEFAULT_.door_direct, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_loc = Slot(uri=MIXS['0000790'], name="door_loc", curie=MIXS.curie('0000790'), - model_uri=DEFAULT_.door_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_mat = Slot(uri=MIXS['0000791'], name="door_mat", curie=MIXS.curie('0000791'), - model_uri=DEFAULT_.door_mat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_move = Slot(uri=MIXS['0000792'], name="door_move", curie=MIXS.curie('0000792'), - model_uri=DEFAULT_.door_move, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_size = Slot(uri=MIXS['0000158'], name="door_size", curie=MIXS.curie('0000158'), - model_uri=DEFAULT_.door_size, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.door_type = Slot(uri=MIXS['0000794'], name="door_type", curie=MIXS.curie('0000794'), - model_uri=DEFAULT_.door_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_type_metal = Slot(uri=MIXS['0000796'], name="door_type_metal", curie=MIXS.curie('0000796'), - model_uri=DEFAULT_.door_type_metal, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_type_wood = Slot(uri=MIXS['0000797'], name="door_type_wood", curie=MIXS.curie('0000797'), - model_uri=DEFAULT_.door_type_wood, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.door_water_mold = Slot(uri=MIXS['0000793'], name="door_water_mold", curie=MIXS.curie('0000793'), - model_uri=DEFAULT_.door_water_mold, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.down_par = Slot(uri=MIXS['0000703'], name="down_par", curie=MIXS.curie('0000703'), - model_uri=DEFAULT_.down_par, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.drainage_class = Slot(uri=MIXS['0001085'], name="drainage_class", curie=MIXS.curie('0001085'), - model_uri=DEFAULT_.drainage_class, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.drawings = Slot(uri=MIXS['0000798'], name="drawings", curie=MIXS.curie('0000798'), - model_uri=DEFAULT_.drawings, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.efficiency_percent = Slot(uri=MIXS['0000657'], name="efficiency_percent", curie=MIXS.curie('0000657'), - model_uri=DEFAULT_.efficiency_percent, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.elev = Slot(uri=MIXS['0000093'], name="elev", curie=MIXS.curie('0000093'), - model_uri=DEFAULT_.elev, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.elevator = Slot(uri=MIXS['0000799'], name="elevator", curie=MIXS.curie('0000799'), - model_uri=DEFAULT_.elevator, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.emulsions = Slot(uri=MIXS['0000660'], name="emulsions", curie=MIXS.curie('0000660'), - model_uri=DEFAULT_.emulsions, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.env_broad_scale = Slot(uri=MIXS['0000012'], name="env_broad_scale", curie=MIXS.curie('0000012'), - model_uri=DEFAULT_.env_broad_scale, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.env_local_scale = Slot(uri=MIXS['0000013'], name="env_local_scale", curie=MIXS.curie('0000013'), - model_uri=DEFAULT_.env_local_scale, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.env_medium = Slot(uri=MIXS['0000014'], name="env_medium", curie=MIXS.curie('0000014'), - model_uri=DEFAULT_.env_medium, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.escalator = Slot(uri=MIXS['0000800'], name="escalator", curie=MIXS.curie('0000800'), - model_uri=DEFAULT_.escalator, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ethylbenzene = Slot(uri=MIXS['0000155'], name="ethylbenzene", curie=MIXS.curie('0000155'), - model_uri=DEFAULT_.ethylbenzene, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.exp_duct = Slot(uri=MIXS['0000144'], name="exp_duct", curie=MIXS.curie('0000144'), - model_uri=DEFAULT_.exp_duct, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.exp_pipe = Slot(uri=MIXS['0000220'], name="exp_pipe", curie=MIXS.curie('0000220'), - model_uri=DEFAULT_.exp_pipe, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.experimental_factor = Slot(uri=MIXS['0000008'], name="experimental_factor", curie=MIXS.curie('0000008'), - model_uri=DEFAULT_.experimental_factor, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.investigation_field = Slot(uri=DEFAULT_.investigation_field, name="investigation field", curie=DEFAULT_.curie('investigation_field'), - model_uri=DEFAULT_.investigation_field, domain=None, range=Optional[str]) - -slots.ext_door = Slot(uri=MIXS['0000170'], name="ext_door", curie=MIXS.curie('0000170'), - model_uri=DEFAULT_.ext_door, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ext_wall_orient = Slot(uri=MIXS['0000817'], name="ext_wall_orient", curie=MIXS.curie('0000817'), - model_uri=DEFAULT_.ext_wall_orient, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ext_window_orient = Slot(uri=MIXS['0000818'], name="ext_window_orient", curie=MIXS.curie('0000818'), - model_uri=DEFAULT_.ext_window_orient, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.extreme_event = Slot(uri=MIXS['0000320'], name="extreme_event", curie=MIXS.curie('0000320'), - model_uri=DEFAULT_.extreme_event, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.fao_class = Slot(uri=MIXS['0001083'], name="fao_class", curie=MIXS.curie('0001083'), - model_uri=DEFAULT_.fao_class, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.fertilizer_regm = Slot(uri=MIXS['0000556'], name="fertilizer_regm", curie=MIXS.curie('0000556'), - model_uri=DEFAULT_.fertilizer_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.field = Slot(uri=MIXS['0000291'], name="field", curie=MIXS.curie('0000291'), - model_uri=DEFAULT_.field, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.filter_type = Slot(uri=MIXS['0000765'], name="filter_type", curie=MIXS.curie('0000765'), - model_uri=DEFAULT_.filter_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.fire = Slot(uri=MIXS['0001086'], name="fire", curie=MIXS.curie('0001086'), - model_uri=DEFAULT_.fire, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.fireplace_type = Slot(uri=MIXS['0000802'], name="fireplace_type", curie=MIXS.curie('0000802'), - model_uri=DEFAULT_.fireplace_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.flooding = Slot(uri=MIXS['0000319'], name="flooding", curie=MIXS.curie('0000319'), - model_uri=DEFAULT_.flooding, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.floor_age = Slot(uri=MIXS['0000164'], name="floor_age", curie=MIXS.curie('0000164'), - model_uri=DEFAULT_.floor_age, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.floor_area = Slot(uri=MIXS['0000165'], name="floor_area", curie=MIXS.curie('0000165'), - model_uri=DEFAULT_.floor_area, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.floor_cond = Slot(uri=MIXS['0000803'], name="floor_cond", curie=MIXS.curie('0000803'), - model_uri=DEFAULT_.floor_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.floor_count = Slot(uri=MIXS['0000225'], name="floor_count", curie=MIXS.curie('0000225'), - model_uri=DEFAULT_.floor_count, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.floor_finish_mat = Slot(uri=MIXS['0000804'], name="floor_finish_mat", curie=MIXS.curie('0000804'), - model_uri=DEFAULT_.floor_finish_mat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.floor_struc = Slot(uri=MIXS['0000806'], name="floor_struc", curie=MIXS.curie('0000806'), - model_uri=DEFAULT_.floor_struc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.floor_thermal_mass = Slot(uri=MIXS['0000166'], name="floor_thermal_mass", curie=MIXS.curie('0000166'), - model_uri=DEFAULT_.floor_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.floor_water_mold = Slot(uri=MIXS['0000805'], name="floor_water_mold", curie=MIXS.curie('0000805'), - model_uri=DEFAULT_.floor_water_mold, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.fluor = Slot(uri=MIXS['0000704'], name="fluor", curie=MIXS.curie('0000704'), - model_uri=DEFAULT_.fluor, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.freq_clean = Slot(uri=MIXS['0000226'], name="freq_clean", curie=MIXS.curie('0000226'), - model_uri=DEFAULT_.freq_clean, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.freq_cook = Slot(uri=MIXS['0000227'], name="freq_cook", curie=MIXS.curie('0000227'), - model_uri=DEFAULT_.freq_cook, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.fungicide_regm = Slot(uri=MIXS['0000557'], name="fungicide_regm", curie=MIXS.curie('0000557'), - model_uri=DEFAULT_.fungicide_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.furniture = Slot(uri=MIXS['0000807'], name="furniture", curie=MIXS.curie('0000807'), - model_uri=DEFAULT_.furniture, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.gaseous_environment = Slot(uri=MIXS['0000558'], name="gaseous_environment", curie=MIXS.curie('0000558'), - model_uri=DEFAULT_.gaseous_environment, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.gaseous_substances = Slot(uri=MIXS['0000661'], name="gaseous_substances", curie=MIXS.curie('0000661'), - model_uri=DEFAULT_.gaseous_substances, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.gender_restroom = Slot(uri=MIXS['0000808'], name="gender_restroom", curie=MIXS.curie('0000808'), - model_uri=DEFAULT_.gender_restroom, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.genetic_mod = Slot(uri=MIXS['0000859'], name="genetic_mod", curie=MIXS.curie('0000859'), - model_uri=DEFAULT_.genetic_mod, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.geo_loc_name = Slot(uri=MIXS['0000010'], name="geo_loc_name", curie=MIXS.curie('0000010'), - model_uri=DEFAULT_.geo_loc_name, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.glucosidase_act = Slot(uri=MIXS['0000137'], name="glucosidase_act", curie=MIXS.curie('0000137'), - model_uri=DEFAULT_.glucosidase_act, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.gravidity = Slot(uri=MIXS['0000875'], name="gravidity", curie=MIXS.curie('0000875'), - model_uri=DEFAULT_.gravidity, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.gravity = Slot(uri=MIXS['0000559'], name="gravity", curie=MIXS.curie('0000559'), - model_uri=DEFAULT_.gravity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.growth_facil = Slot(uri=MIXS['0001043'], name="growth_facil", curie=MIXS.curie('0001043'), - model_uri=DEFAULT_.growth_facil, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.growth_habit = Slot(uri=MIXS['0001044'], name="growth_habit", curie=MIXS.curie('0001044'), - model_uri=DEFAULT_.growth_habit, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.growth_hormone_regm = Slot(uri=MIXS['0000560'], name="growth_hormone_regm", curie=MIXS.curie('0000560'), - model_uri=DEFAULT_.growth_hormone_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.hall_count = Slot(uri=MIXS['0000228'], name="hall_count", curie=MIXS.curie('0000228'), - model_uri=DEFAULT_.hall_count, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.handidness = Slot(uri=MIXS['0000809'], name="handidness", curie=MIXS.curie('0000809'), - model_uri=DEFAULT_.handidness, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.hc_produced = Slot(uri=MIXS['0000989'], name="hc_produced", curie=MIXS.curie('0000989'), - model_uri=DEFAULT_.hc_produced, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.hcr = Slot(uri=MIXS['0000988'], name="hcr", curie=MIXS.curie('0000988'), - model_uri=DEFAULT_.hcr, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.hcr_fw_salinity = Slot(uri=MIXS['0000406'], name="hcr_fw_salinity", curie=MIXS.curie('0000406'), - model_uri=DEFAULT_.hcr_fw_salinity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.hcr_geol_age = Slot(uri=MIXS['0000993'], name="hcr_geol_age", curie=MIXS.curie('0000993'), - model_uri=DEFAULT_.hcr_geol_age, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.hcr_pressure = Slot(uri=MIXS['0000395'], name="hcr_pressure", curie=MIXS.curie('0000395'), - model_uri=DEFAULT_.hcr_pressure, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.hcr_temp = Slot(uri=MIXS['0000393'], name="hcr_temp", curie=MIXS.curie('0000393'), - model_uri=DEFAULT_.hcr_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.heat_cool_type = Slot(uri=MIXS['0000766'], name="heat_cool_type", curie=MIXS.curie('0000766'), - model_uri=DEFAULT_.heat_cool_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.heat_deliv_loc = Slot(uri=MIXS['0000810'], name="heat_deliv_loc", curie=MIXS.curie('0000810'), - model_uri=DEFAULT_.heat_deliv_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.heat_sys_deliv_meth = Slot(uri=MIXS['0000812'], name="heat_sys_deliv_meth", curie=MIXS.curie('0000812'), - model_uri=DEFAULT_.heat_sys_deliv_meth, domain=None, range=Optional[str]) - -slots.heat_system_id = Slot(uri=MIXS['0000833'], name="heat_system_id", curie=MIXS.curie('0000833'), - model_uri=DEFAULT_.heat_system_id, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.heavy_metals = Slot(uri=MIXS['0000652'], name="heavy_metals", curie=MIXS.curie('0000652'), - model_uri=DEFAULT_.heavy_metals, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.heavy_metals_meth = Slot(uri=MIXS['0000343'], name="heavy_metals_meth", curie=MIXS.curie('0000343'), - model_uri=DEFAULT_.heavy_metals_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.height_carper_fiber = Slot(uri=MIXS['0000167'], name="height_carper_fiber", curie=MIXS.curie('0000167'), - model_uri=DEFAULT_.height_carper_fiber, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.herbicide_regm = Slot(uri=MIXS['0000561'], name="herbicide_regm", curie=MIXS.curie('0000561'), - model_uri=DEFAULT_.herbicide_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.horizon = Slot(uri=MIXS['0001082'], name="horizon", curie=MIXS.curie('0001082'), - model_uri=DEFAULT_.horizon, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.horizon_meth = Slot(uri=MIXS['0000321'], name="horizon_meth", curie=MIXS.curie('0000321'), - model_uri=DEFAULT_.horizon_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_age = Slot(uri=MIXS['0000255'], name="host_age", curie=MIXS.curie('0000255'), - model_uri=DEFAULT_.host_age, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.host_body_habitat = Slot(uri=MIXS['0000866'], name="host_body_habitat", curie=MIXS.curie('0000866'), - model_uri=DEFAULT_.host_body_habitat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_body_product = Slot(uri=MIXS['0000888'], name="host_body_product", curie=MIXS.curie('0000888'), - model_uri=DEFAULT_.host_body_product, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.host_body_site = Slot(uri=MIXS['0000867'], name="host_body_site", curie=MIXS.curie('0000867'), - model_uri=DEFAULT_.host_body_site, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.host_body_temp = Slot(uri=MIXS['0000274'], name="host_body_temp", curie=MIXS.curie('0000274'), - model_uri=DEFAULT_.host_body_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.host_color = Slot(uri=MIXS['0000260'], name="host_color", curie=MIXS.curie('0000260'), - model_uri=DEFAULT_.host_color, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_common_name = Slot(uri=MIXS['0000248'], name="host_common_name", curie=MIXS.curie('0000248'), - model_uri=DEFAULT_.host_common_name, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_diet = Slot(uri=MIXS['0000869'], name="host_diet", curie=MIXS.curie('0000869'), - model_uri=DEFAULT_.host_diet, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_dry_mass = Slot(uri=MIXS['0000257'], name="host_dry_mass", curie=MIXS.curie('0000257'), - model_uri=DEFAULT_.host_dry_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.host_family_relation = Slot(uri=MIXS['0000872'], name="host_family_relation", curie=MIXS.curie('0000872'), - model_uri=DEFAULT_.host_family_relation, domain=None, range=Optional[Union[str, List[str]]]) - -slots.host_genotype = Slot(uri=MIXS['0000365'], name="host_genotype", curie=MIXS.curie('0000365'), - model_uri=DEFAULT_.host_genotype, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_growth_cond = Slot(uri=MIXS['0000871'], name="host_growth_cond", curie=MIXS.curie('0000871'), - model_uri=DEFAULT_.host_growth_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_height = Slot(uri=MIXS['0000264'], name="host_height", curie=MIXS.curie('0000264'), - model_uri=DEFAULT_.host_height, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.host_last_meal = Slot(uri=MIXS['0000870'], name="host_last_meal", curie=MIXS.curie('0000870'), - model_uri=DEFAULT_.host_last_meal, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_length = Slot(uri=MIXS['0000256'], name="host_length", curie=MIXS.curie('0000256'), - model_uri=DEFAULT_.host_length, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.host_life_stage = Slot(uri=MIXS['0000251'], name="host_life_stage", curie=MIXS.curie('0000251'), - model_uri=DEFAULT_.host_life_stage, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_phenotype = Slot(uri=MIXS['0000874'], name="host_phenotype", curie=MIXS.curie('0000874'), - model_uri=DEFAULT_.host_phenotype, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.host_sex = Slot(uri=MIXS['0000811'], name="host_sex", curie=MIXS.curie('0000811'), - model_uri=DEFAULT_.host_sex, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_shape = Slot(uri=MIXS['0000261'], name="host_shape", curie=MIXS.curie('0000261'), - model_uri=DEFAULT_.host_shape, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_subject_id = Slot(uri=MIXS['0000861'], name="host_subject_id", curie=MIXS.curie('0000861'), - model_uri=DEFAULT_.host_subject_id, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_subspecf_genlin = Slot(uri=MIXS['0001318'], name="host_subspecf_genlin", curie=MIXS.curie('0001318'), - model_uri=DEFAULT_.host_subspecf_genlin, domain=None, range=Optional[Union[str, List[str]]]) - -slots.host_substrate = Slot(uri=MIXS['0000252'], name="host_substrate", curie=MIXS.curie('0000252'), - model_uri=DEFAULT_.host_substrate, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_symbiont = Slot(uri=MIXS['0001298'], name="host_symbiont", curie=MIXS.curie('0001298'), - model_uri=DEFAULT_.host_symbiont, domain=None, range=Optional[Union[str, List[str]]]) - -slots.host_taxid = Slot(uri=MIXS['0000250'], name="host_taxid", curie=MIXS.curie('0000250'), - model_uri=DEFAULT_.host_taxid, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.host_tot_mass = Slot(uri=MIXS['0000263'], name="host_tot_mass", curie=MIXS.curie('0000263'), - model_uri=DEFAULT_.host_tot_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.host_wet_mass = Slot(uri=MIXS['0000567'], name="host_wet_mass", curie=MIXS.curie('0000567'), - model_uri=DEFAULT_.host_wet_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.humidity = Slot(uri=MIXS['0000100'], name="humidity", curie=MIXS.curie('0000100'), - model_uri=DEFAULT_.humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.humidity_regm = Slot(uri=MIXS['0000568'], name="humidity_regm", curie=MIXS.curie('0000568'), - model_uri=DEFAULT_.humidity_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.indoor_space = Slot(uri=MIXS['0000763'], name="indoor_space", curie=MIXS.curie('0000763'), - model_uri=DEFAULT_.indoor_space, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.indoor_surf = Slot(uri=MIXS['0000764'], name="indoor_surf", curie=MIXS.curie('0000764'), - model_uri=DEFAULT_.indoor_surf, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.indust_eff_percent = Slot(uri=MIXS['0000662'], name="indust_eff_percent", curie=MIXS.curie('0000662'), - model_uri=DEFAULT_.indust_eff_percent, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.inorg_particles = Slot(uri=MIXS['0000664'], name="inorg_particles", curie=MIXS.curie('0000664'), - model_uri=DEFAULT_.inorg_particles, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.inside_lux = Slot(uri=MIXS['0000168'], name="inside_lux", curie=MIXS.curie('0000168'), - model_uri=DEFAULT_.inside_lux, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.int_wall_cond = Slot(uri=MIXS['0000813'], name="int_wall_cond", curie=MIXS.curie('0000813'), - model_uri=DEFAULT_.int_wall_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.iw_bt_date_well = Slot(uri=MIXS['0001010'], name="iw_bt_date_well", curie=MIXS.curie('0001010'), - model_uri=DEFAULT_.iw_bt_date_well, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.iwf = Slot(uri=MIXS['0000455'], name="iwf", curie=MIXS.curie('0000455'), - model_uri=DEFAULT_.iwf, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.last_clean = Slot(uri=MIXS['0000814'], name="last_clean", curie=MIXS.curie('0000814'), - model_uri=DEFAULT_.last_clean, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.lat_lon = Slot(uri=MIXS['0000009'], name="lat_lon", curie=MIXS.curie('0000009'), - model_uri=DEFAULT_.lat_lon, domain=None, range=Optional[Union[dict, GeolocationValue]]) - -slots.light_intensity = Slot(uri=MIXS['0000706'], name="light_intensity", curie=MIXS.curie('0000706'), - model_uri=DEFAULT_.light_intensity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.light_regm = Slot(uri=MIXS['0000569'], name="light_regm", curie=MIXS.curie('0000569'), - model_uri=DEFAULT_.light_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.light_type = Slot(uri=MIXS['0000769'], name="light_type", curie=MIXS.curie('0000769'), - model_uri=DEFAULT_.light_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.link_addit_analys = Slot(uri=MIXS['0000340'], name="link_addit_analys", curie=MIXS.curie('0000340'), - model_uri=DEFAULT_.link_addit_analys, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.link_class_info = Slot(uri=MIXS['0000329'], name="link_class_info", curie=MIXS.curie('0000329'), - model_uri=DEFAULT_.link_class_info, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.link_climate_info = Slot(uri=MIXS['0000328'], name="link_climate_info", curie=MIXS.curie('0000328'), - model_uri=DEFAULT_.link_climate_info, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.lithology = Slot(uri=MIXS['0000990'], name="lithology", curie=MIXS.curie('0000990'), - model_uri=DEFAULT_.lithology, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.local_class = Slot(uri=MIXS['0000330'], name="local_class", curie=MIXS.curie('0000330'), - model_uri=DEFAULT_.local_class, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.local_class_meth = Slot(uri=MIXS['0000331'], name="local_class_meth", curie=MIXS.curie('0000331'), - model_uri=DEFAULT_.local_class_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.magnesium = Slot(uri=MIXS['0000431'], name="magnesium", curie=MIXS.curie('0000431'), - model_uri=DEFAULT_.magnesium, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.max_occup = Slot(uri=MIXS['0000229'], name="max_occup", curie=MIXS.curie('0000229'), - model_uri=DEFAULT_.max_occup, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.mean_frict_vel = Slot(uri=MIXS['0000498'], name="mean_frict_vel", curie=MIXS.curie('0000498'), - model_uri=DEFAULT_.mean_frict_vel, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.mean_peak_frict_vel = Slot(uri=MIXS['0000502'], name="mean_peak_frict_vel", curie=MIXS.curie('0000502'), - model_uri=DEFAULT_.mean_peak_frict_vel, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.mech_struc = Slot(uri=MIXS['0000815'], name="mech_struc", curie=MIXS.curie('0000815'), - model_uri=DEFAULT_.mech_struc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.mechanical_damage = Slot(uri=MIXS['0001052'], name="mechanical_damage", curie=MIXS.curie('0001052'), - model_uri=DEFAULT_.mechanical_damage, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.methane = Slot(uri=MIXS['0000101'], name="methane", curie=MIXS.curie('0000101'), - model_uri=DEFAULT_.methane, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.micro_biomass_meth = Slot(uri=MIXS['0000339'], name="micro_biomass_meth", curie=MIXS.curie('0000339'), - model_uri=DEFAULT_.micro_biomass_meth, domain=None, range=Optional[str]) - -slots.microbial_biomass = Slot(uri=MIXS['0000650'], name="microbial_biomass", curie=MIXS.curie('0000650'), - model_uri=DEFAULT_.microbial_biomass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.microbial_biomass_meth = Slot(uri=MIXS['0000339'], name="microbial_biomass_meth", curie=MIXS.curie('0000339'), - model_uri=DEFAULT_.microbial_biomass_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.mineral_nutr_regm = Slot(uri=MIXS['0000570'], name="mineral_nutr_regm", curie=MIXS.curie('0000570'), - model_uri=DEFAULT_.mineral_nutr_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.misc_param = Slot(uri=MIXS['0000752'], name="misc_param", curie=MIXS.curie('0000752'), - model_uri=DEFAULT_.misc_param, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.n_alkanes = Slot(uri=MIXS['0000503'], name="n_alkanes", curie=MIXS.curie('0000503'), - model_uri=DEFAULT_.n_alkanes, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.nitrate = Slot(uri=MIXS['0000425'], name="nitrate", curie=MIXS.curie('0000425'), - model_uri=DEFAULT_.nitrate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.nitrite = Slot(uri=MIXS['0000426'], name="nitrite", curie=MIXS.curie('0000426'), - model_uri=DEFAULT_.nitrite, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.nitro = Slot(uri=MIXS['0000504'], name="nitro", curie=MIXS.curie('0000504'), - model_uri=DEFAULT_.nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.non_min_nutr_regm = Slot(uri=MIXS['0000571'], name="non_min_nutr_regm", curie=MIXS.curie('0000571'), - model_uri=DEFAULT_.non_min_nutr_regm, domain=None, range=Optional[Union[str, List[str]]]) - -slots.nucl_acid_amp = Slot(uri=MIXS['0000038'], name="nucl_acid_amp", curie=MIXS.curie('0000038'), - model_uri=DEFAULT_.nucl_acid_amp, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.nucl_acid_ext = Slot(uri=MIXS['0000037'], name="nucl_acid_ext", curie=MIXS.curie('0000037'), - model_uri=DEFAULT_.nucl_acid_ext, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.number_pets = Slot(uri=MIXS['0000231'], name="number_pets", curie=MIXS.curie('0000231'), - model_uri=DEFAULT_.number_pets, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.number_plants = Slot(uri=MIXS['0000230'], name="number_plants", curie=MIXS.curie('0000230'), - model_uri=DEFAULT_.number_plants, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.number_resident = Slot(uri=MIXS['0000232'], name="number_resident", curie=MIXS.curie('0000232'), - model_uri=DEFAULT_.number_resident, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.occup_density_samp = Slot(uri=MIXS['0000217'], name="occup_density_samp", curie=MIXS.curie('0000217'), - model_uri=DEFAULT_.occup_density_samp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.occup_document = Slot(uri=MIXS['0000816'], name="occup_document", curie=MIXS.curie('0000816'), - model_uri=DEFAULT_.occup_document, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.occup_samp = Slot(uri=MIXS['0000772'], name="occup_samp", curie=MIXS.curie('0000772'), - model_uri=DEFAULT_.occup_samp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.org_carb = Slot(uri=MIXS['0000508'], name="org_carb", curie=MIXS.curie('0000508'), - model_uri=DEFAULT_.org_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.org_count_qpcr_info = Slot(uri=MIXS['0000099'], name="org_count_qpcr_info", curie=MIXS.curie('0000099'), - model_uri=DEFAULT_.org_count_qpcr_info, domain=None, range=Optional[str]) - -slots.org_matter = Slot(uri=MIXS['0000204'], name="org_matter", curie=MIXS.curie('0000204'), - model_uri=DEFAULT_.org_matter, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.org_nitro = Slot(uri=MIXS['0000205'], name="org_nitro", curie=MIXS.curie('0000205'), - model_uri=DEFAULT_.org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.org_particles = Slot(uri=MIXS['0000665'], name="org_particles", curie=MIXS.curie('0000665'), - model_uri=DEFAULT_.org_particles, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.organism_count = Slot(uri=MIXS['0000103'], name="organism_count", curie=MIXS.curie('0000103'), - model_uri=DEFAULT_.organism_count, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.owc_tvdss = Slot(uri=MIXS['0000405'], name="owc_tvdss", curie=MIXS.curie('0000405'), - model_uri=DEFAULT_.owc_tvdss, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.oxy_stat_samp = Slot(uri=MIXS['0000753'], name="oxy_stat_samp", curie=MIXS.curie('0000753'), - model_uri=DEFAULT_.oxy_stat_samp, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.oxygen = Slot(uri=MIXS['0000104'], name="oxygen", curie=MIXS.curie('0000104'), - model_uri=DEFAULT_.oxygen, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.part_org_carb = Slot(uri=MIXS['0000515'], name="part_org_carb", curie=MIXS.curie('0000515'), - model_uri=DEFAULT_.part_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.part_org_nitro = Slot(uri=MIXS['0000719'], name="part_org_nitro", curie=MIXS.curie('0000719'), - model_uri=DEFAULT_.part_org_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.particle_class = Slot(uri=MIXS['0000206'], name="particle_class", curie=MIXS.curie('0000206'), - model_uri=DEFAULT_.particle_class, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.pcr_cond = Slot(uri=MIXS['0000049'], name="pcr_cond", curie=MIXS.curie('0000049'), - model_uri=DEFAULT_.pcr_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.pcr_primers = Slot(uri=MIXS['0000046'], name="pcr_primers", curie=MIXS.curie('0000046'), - model_uri=DEFAULT_.pcr_primers, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.permeability = Slot(uri=MIXS['0000404'], name="permeability", curie=MIXS.curie('0000404'), - model_uri=DEFAULT_.permeability, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.perturbation = Slot(uri=MIXS['0000754'], name="perturbation", curie=MIXS.curie('0000754'), - model_uri=DEFAULT_.perturbation, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.pesticide_regm = Slot(uri=MIXS['0000573'], name="pesticide_regm", curie=MIXS.curie('0000573'), - model_uri=DEFAULT_.pesticide_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.petroleum_hydrocarb = Slot(uri=MIXS['0000516'], name="petroleum_hydrocarb", curie=MIXS.curie('0000516'), - model_uri=DEFAULT_.petroleum_hydrocarb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ph = Slot(uri=MIXS['0001001'], name="ph", curie=MIXS.curie('0001001'), - model_uri=DEFAULT_.ph, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ph_meth = Slot(uri=MIXS['0001106'], name="ph_meth", curie=MIXS.curie('0001106'), - model_uri=DEFAULT_.ph_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.ph_regm = Slot(uri=MIXS['0001056'], name="ph_regm", curie=MIXS.curie('0001056'), - model_uri=DEFAULT_.ph_regm, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.phaeopigments = Slot(uri=MIXS['0000180'], name="phaeopigments", curie=MIXS.curie('0000180'), - model_uri=DEFAULT_.phaeopigments, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.phosphate = Slot(uri=MIXS['0000505'], name="phosphate", curie=MIXS.curie('0000505'), - model_uri=DEFAULT_.phosphate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.phosplipid_fatt_acid = Slot(uri=MIXS['0000181'], name="phosplipid_fatt_acid", curie=MIXS.curie('0000181'), - model_uri=DEFAULT_.phosplipid_fatt_acid, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.photon_flux = Slot(uri=MIXS['0000725'], name="photon_flux", curie=MIXS.curie('0000725'), - model_uri=DEFAULT_.photon_flux, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.plant_growth_med = Slot(uri=MIXS['0001057'], name="plant_growth_med", curie=MIXS.curie('0001057'), - model_uri=DEFAULT_.plant_growth_med, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.plant_product = Slot(uri=MIXS['0001058'], name="plant_product", curie=MIXS.curie('0001058'), - model_uri=DEFAULT_.plant_product, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.plant_sex = Slot(uri=MIXS['0001059'], name="plant_sex", curie=MIXS.curie('0001059'), - model_uri=DEFAULT_.plant_sex, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.plant_struc = Slot(uri=MIXS['0001060'], name="plant_struc", curie=MIXS.curie('0001060'), - model_uri=DEFAULT_.plant_struc, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.pollutants = Slot(uri=MIXS['0000107'], name="pollutants", curie=MIXS.curie('0000107'), - model_uri=DEFAULT_.pollutants, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.pool_dna_extracts = Slot(uri=MIXS['0000325'], name="pool_dna_extracts", curie=MIXS.curie('0000325'), - model_uri=DEFAULT_.pool_dna_extracts, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.porosity = Slot(uri=MIXS['0000211'], name="porosity", curie=MIXS.curie('0000211'), - model_uri=DEFAULT_.porosity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.potassium = Slot(uri=MIXS['0000430'], name="potassium", curie=MIXS.curie('0000430'), - model_uri=DEFAULT_.potassium, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.pour_point = Slot(uri=MIXS['0000127'], name="pour_point", curie=MIXS.curie('0000127'), - model_uri=DEFAULT_.pour_point, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.pre_treatment = Slot(uri=MIXS['0000348'], name="pre_treatment", curie=MIXS.curie('0000348'), - model_uri=DEFAULT_.pre_treatment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.pres_animal_insect = Slot(uri=MIXS['0000819'], name="pres_animal_insect", curie=MIXS.curie('0000819'), - model_uri=DEFAULT_.pres_animal_insect, domain=None, range=Optional[str], - pattern=re.compile(r'^(cat|dog|rodent|snake|other);\d+$')) - -slots.pressure = Slot(uri=MIXS['0000412'], name="pressure", curie=MIXS.curie('0000412'), - model_uri=DEFAULT_.pressure, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.prev_land_use_meth = Slot(uri=MIXS['0000316'], name="prev_land_use_meth", curie=MIXS.curie('0000316'), - model_uri=DEFAULT_.prev_land_use_meth, domain=None, range=Optional[str]) - -slots.previous_land_use = Slot(uri=MIXS['0000315'], name="previous_land_use", curie=MIXS.curie('0000315'), - model_uri=DEFAULT_.previous_land_use, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.previous_land_use_meth = Slot(uri=MIXS['0000316'], name="previous_land_use_meth", curie=MIXS.curie('0000316'), - model_uri=DEFAULT_.previous_land_use_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.primary_prod = Slot(uri=MIXS['0000728'], name="primary_prod", curie=MIXS.curie('0000728'), - model_uri=DEFAULT_.primary_prod, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.primary_treatment = Slot(uri=MIXS['0000349'], name="primary_treatment", curie=MIXS.curie('0000349'), - model_uri=DEFAULT_.primary_treatment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.prod_rate = Slot(uri=MIXS['0000452'], name="prod_rate", curie=MIXS.curie('0000452'), - model_uri=DEFAULT_.prod_rate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.prod_start_date = Slot(uri=MIXS['0001008'], name="prod_start_date", curie=MIXS.curie('0001008'), - model_uri=DEFAULT_.prod_start_date, domain=None, range=Optional[Union[dict, TimestampValue]]) - -slots.profile_position = Slot(uri=MIXS['0001084'], name="profile_position", curie=MIXS.curie('0001084'), - model_uri=DEFAULT_.profile_position, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.quad_pos = Slot(uri=MIXS['0000820'], name="quad_pos", curie=MIXS.curie('0000820'), - model_uri=DEFAULT_.quad_pos, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.radiation_regm = Slot(uri=MIXS['0000575'], name="radiation_regm", curie=MIXS.curie('0000575'), - model_uri=DEFAULT_.radiation_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.rainfall_regm = Slot(uri=MIXS['0000576'], name="rainfall_regm", curie=MIXS.curie('0000576'), - model_uri=DEFAULT_.rainfall_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.reactor_type = Slot(uri=MIXS['0000350'], name="reactor_type", curie=MIXS.curie('0000350'), - model_uri=DEFAULT_.reactor_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.redox_potential = Slot(uri=MIXS['0000182'], name="redox_potential", curie=MIXS.curie('0000182'), - model_uri=DEFAULT_.redox_potential, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.rel_air_humidity = Slot(uri=MIXS['0000121'], name="rel_air_humidity", curie=MIXS.curie('0000121'), - model_uri=DEFAULT_.rel_air_humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.rel_humidity_out = Slot(uri=MIXS['0000188'], name="rel_humidity_out", curie=MIXS.curie('0000188'), - model_uri=DEFAULT_.rel_humidity_out, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.rel_samp_loc = Slot(uri=MIXS['0000821'], name="rel_samp_loc", curie=MIXS.curie('0000821'), - model_uri=DEFAULT_.rel_samp_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.rel_to_oxygen = Slot(uri=MIXS['0000015'], name="rel_to_oxygen", curie=MIXS.curie('0000015'), - model_uri=DEFAULT_.rel_to_oxygen, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.reservoir = Slot(uri=MIXS['0000303'], name="reservoir", curie=MIXS.curie('0000303'), - model_uri=DEFAULT_.reservoir, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.resins_pc = Slot(uri=MIXS['0000134'], name="resins_pc", curie=MIXS.curie('0000134'), - model_uri=DEFAULT_.resins_pc, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.room_air_exch_rate = Slot(uri=MIXS['0000169'], name="room_air_exch_rate", curie=MIXS.curie('0000169'), - model_uri=DEFAULT_.room_air_exch_rate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.room_architec_elem = Slot(uri=MIXS['0000233'], name="room_architec_elem", curie=MIXS.curie('0000233'), - model_uri=DEFAULT_.room_architec_elem, domain=None, range=Optional[str]) - -slots.room_condt = Slot(uri=MIXS['0000822'], name="room_condt", curie=MIXS.curie('0000822'), - model_uri=DEFAULT_.room_condt, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_connected = Slot(uri=MIXS['0000826'], name="room_connected", curie=MIXS.curie('0000826'), - model_uri=DEFAULT_.room_connected, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_count = Slot(uri=MIXS['0000234'], name="room_count", curie=MIXS.curie('0000234'), - model_uri=DEFAULT_.room_count, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_dim = Slot(uri=MIXS['0000192'], name="room_dim", curie=MIXS.curie('0000192'), - model_uri=DEFAULT_.room_dim, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.room_door_dist = Slot(uri=MIXS['0000193'], name="room_door_dist", curie=MIXS.curie('0000193'), - model_uri=DEFAULT_.room_door_dist, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.room_door_share = Slot(uri=MIXS['0000242'], name="room_door_share", curie=MIXS.curie('0000242'), - model_uri=DEFAULT_.room_door_share, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_hallway = Slot(uri=MIXS['0000238'], name="room_hallway", curie=MIXS.curie('0000238'), - model_uri=DEFAULT_.room_hallway, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_loc = Slot(uri=MIXS['0000823'], name="room_loc", curie=MIXS.curie('0000823'), - model_uri=DEFAULT_.room_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_moist_dam_hist = Slot(uri=MIXS['0000235'], name="room_moist_dam_hist", curie=MIXS.curie('0000235'), - model_uri=DEFAULT_.room_moist_dam_hist, domain=None, range=Optional[int]) - -slots.room_net_area = Slot(uri=MIXS['0000194'], name="room_net_area", curie=MIXS.curie('0000194'), - model_uri=DEFAULT_.room_net_area, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.room_occup = Slot(uri=MIXS['0000236'], name="room_occup", curie=MIXS.curie('0000236'), - model_uri=DEFAULT_.room_occup, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.room_samp_pos = Slot(uri=MIXS['0000824'], name="room_samp_pos", curie=MIXS.curie('0000824'), - model_uri=DEFAULT_.room_samp_pos, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_type = Slot(uri=MIXS['0000825'], name="room_type", curie=MIXS.curie('0000825'), - model_uri=DEFAULT_.room_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_vol = Slot(uri=MIXS['0000195'], name="room_vol", curie=MIXS.curie('0000195'), - model_uri=DEFAULT_.room_vol, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.room_wall_share = Slot(uri=MIXS['0000243'], name="room_wall_share", curie=MIXS.curie('0000243'), - model_uri=DEFAULT_.room_wall_share, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.room_window_count = Slot(uri=MIXS['0000237'], name="room_window_count", curie=MIXS.curie('0000237'), - model_uri=DEFAULT_.room_window_count, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.root_cond = Slot(uri=MIXS['0001061'], name="root_cond", curie=MIXS.curie('0001061'), - model_uri=DEFAULT_.root_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.root_med_carbon = Slot(uri=MIXS['0000577'], name="root_med_carbon", curie=MIXS.curie('0000577'), - model_uri=DEFAULT_.root_med_carbon, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.root_med_macronutr = Slot(uri=MIXS['0000578'], name="root_med_macronutr", curie=MIXS.curie('0000578'), - model_uri=DEFAULT_.root_med_macronutr, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.root_med_micronutr = Slot(uri=MIXS['0000579'], name="root_med_micronutr", curie=MIXS.curie('0000579'), - model_uri=DEFAULT_.root_med_micronutr, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.root_med_ph = Slot(uri=MIXS['0001062'], name="root_med_ph", curie=MIXS.curie('0001062'), - model_uri=DEFAULT_.root_med_ph, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.root_med_regl = Slot(uri=MIXS['0000581'], name="root_med_regl", curie=MIXS.curie('0000581'), - model_uri=DEFAULT_.root_med_regl, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.root_med_solid = Slot(uri=MIXS['0001063'], name="root_med_solid", curie=MIXS.curie('0001063'), - model_uri=DEFAULT_.root_med_solid, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.root_med_suppl = Slot(uri=MIXS['0000580'], name="root_med_suppl", curie=MIXS.curie('0000580'), - model_uri=DEFAULT_.root_med_suppl, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.salinity = Slot(uri=MIXS['0000183'], name="salinity", curie=MIXS.curie('0000183'), - model_uri=DEFAULT_.salinity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.salinity_meth = Slot(uri=MIXS['0000341'], name="salinity_meth", curie=MIXS.curie('0000341'), - model_uri=DEFAULT_.salinity_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.salt_regm = Slot(uri=MIXS['0000582'], name="salt_regm", curie=MIXS.curie('0000582'), - model_uri=DEFAULT_.salt_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_capt_status = Slot(uri=MIXS['0000860'], name="samp_capt_status", curie=MIXS.curie('0000860'), - model_uri=DEFAULT_.samp_capt_status, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_collec_device = Slot(uri=MIXS['0000002'], name="samp_collec_device", curie=MIXS.curie('0000002'), - model_uri=DEFAULT_.samp_collec_device, domain=None, range=Optional[str]) - -slots.samp_collec_method = Slot(uri=MIXS['0001225'], name="samp_collec_method", curie=MIXS.curie('0001225'), - model_uri=DEFAULT_.samp_collec_method, domain=None, range=Optional[str]) - -slots.samp_collect_device = Slot(uri=MIXS['0000002'], name="samp_collect_device", curie=MIXS.curie('0000002'), - model_uri=DEFAULT_.samp_collect_device, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_collect_point = Slot(uri=MIXS['0001015'], name="samp_collect_point", curie=MIXS.curie('0001015'), - model_uri=DEFAULT_.samp_collect_point, domain=None, range=Optional[Union[str, "SampCollectPointEnum"]]) - -slots.samp_dis_stage = Slot(uri=MIXS['0000249'], name="samp_dis_stage", curie=MIXS.curie('0000249'), - model_uri=DEFAULT_.samp_dis_stage, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_floor = Slot(uri=MIXS['0000828'], name="samp_floor", curie=MIXS.curie('0000828'), - model_uri=DEFAULT_.samp_floor, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_loc_corr_rate = Slot(uri=MIXS['0000136'], name="samp_loc_corr_rate", curie=MIXS.curie('0000136'), - model_uri=DEFAULT_.samp_loc_corr_rate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_mat_process = Slot(uri=MIXS['0000016'], name="samp_mat_process", curie=MIXS.curie('0000016'), - model_uri=DEFAULT_.samp_mat_process, domain=None, range=Optional[Union[dict, ControlledTermValue]]) - -slots.samp_md = Slot(uri=MIXS['0000413'], name="samp_md", curie=MIXS.curie('0000413'), - model_uri=DEFAULT_.samp_md, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_name = Slot(uri=MIXS['0001107'], name="samp_name", curie=MIXS.curie('0001107'), - model_uri=DEFAULT_.samp_name, domain=None, range=Optional[str]) - -slots.samp_preserv = Slot(uri=MIXS['0000463'], name="samp_preserv", curie=MIXS.curie('0000463'), - model_uri=DEFAULT_.samp_preserv, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_room_id = Slot(uri=MIXS['0000244'], name="samp_room_id", curie=MIXS.curie('0000244'), - model_uri=DEFAULT_.samp_room_id, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_size = Slot(uri=MIXS['0000001'], name="samp_size", curie=MIXS.curie('0000001'), - model_uri=DEFAULT_.samp_size, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_sort_meth = Slot(uri=MIXS['0000216'], name="samp_sort_meth", curie=MIXS.curie('0000216'), - model_uri=DEFAULT_.samp_sort_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_store_dur = Slot(uri=MIXS['0000116'], name="samp_store_dur", curie=MIXS.curie('0000116'), - model_uri=DEFAULT_.samp_store_dur, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_store_loc = Slot(uri=MIXS['0000755'], name="samp_store_loc", curie=MIXS.curie('0000755'), - model_uri=DEFAULT_.samp_store_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_store_temp = Slot(uri=MIXS['0000110'], name="samp_store_temp", curie=MIXS.curie('0000110'), - model_uri=DEFAULT_.samp_store_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_subtype = Slot(uri=MIXS['0000999'], name="samp_subtype", curie=MIXS.curie('0000999'), - model_uri=DEFAULT_.samp_subtype, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_time_out = Slot(uri=MIXS['0000196'], name="samp_time_out", curie=MIXS.curie('0000196'), - model_uri=DEFAULT_.samp_time_out, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_transport_cond = Slot(uri=MIXS['0000410'], name="samp_transport_cond", curie=MIXS.curie('0000410'), - model_uri=DEFAULT_.samp_transport_cond, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_tvdss = Slot(uri=MIXS['0000409'], name="samp_tvdss", curie=MIXS.curie('0000409'), - model_uri=DEFAULT_.samp_tvdss, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_type = Slot(uri=MIXS['0000998'], name="samp_type", curie=MIXS.curie('0000998'), - model_uri=DEFAULT_.samp_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_vol_we_dna_ext = Slot(uri=MIXS['0000111'], name="samp_vol_we_dna_ext", curie=MIXS.curie('0000111'), - model_uri=DEFAULT_.samp_vol_we_dna_ext, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.samp_weather = Slot(uri=MIXS['0000827'], name="samp_weather", curie=MIXS.curie('0000827'), - model_uri=DEFAULT_.samp_weather, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.samp_well_name = Slot(uri=MIXS['0000296'], name="samp_well_name", curie=MIXS.curie('0000296'), - model_uri=DEFAULT_.samp_well_name, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.saturates_pc = Slot(uri=MIXS['0000131'], name="saturates_pc", curie=MIXS.curie('0000131'), - model_uri=DEFAULT_.saturates_pc, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.season = Slot(uri=MIXS['0000829'], name="season", curie=MIXS.curie('0000829'), - model_uri=DEFAULT_.season, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.season_environment = Slot(uri=MIXS['0001068'], name="season_environment", curie=MIXS.curie('0001068'), - model_uri=DEFAULT_.season_environment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.season_precpt = Slot(uri=MIXS['0000645'], name="season_precpt", curie=MIXS.curie('0000645'), - model_uri=DEFAULT_.season_precpt, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.season_temp = Slot(uri=MIXS['0000643'], name="season_temp", curie=MIXS.curie('0000643'), - model_uri=DEFAULT_.season_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.season_use = Slot(uri=MIXS['0000830'], name="season_use", curie=MIXS.curie('0000830'), - model_uri=DEFAULT_.season_use, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.secondary_treatment = Slot(uri=MIXS['0000351'], name="secondary_treatment", curie=MIXS.curie('0000351'), - model_uri=DEFAULT_.secondary_treatment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sediment_type = Slot(uri=MIXS['0001078'], name="sediment_type", curie=MIXS.curie('0001078'), - model_uri=DEFAULT_.sediment_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.seq_meth = Slot(uri=MIXS['0000050'], name="seq_meth", curie=MIXS.curie('0000050'), - model_uri=DEFAULT_.seq_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.seq_quality_check = Slot(uri=MIXS['0000051'], name="seq_quality_check", curie=MIXS.curie('0000051'), - model_uri=DEFAULT_.seq_quality_check, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sewage_type = Slot(uri=MIXS['0000215'], name="sewage_type", curie=MIXS.curie('0000215'), - model_uri=DEFAULT_.sewage_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.shad_dev_water_mold = Slot(uri=MIXS['0000834'], name="shad_dev_water_mold", curie=MIXS.curie('0000834'), - model_uri=DEFAULT_.shad_dev_water_mold, domain=None, range=Optional[str]) - -slots.shading_device_cond = Slot(uri=MIXS['0000831'], name="shading_device_cond", curie=MIXS.curie('0000831'), - model_uri=DEFAULT_.shading_device_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.shading_device_loc = Slot(uri=MIXS['0000832'], name="shading_device_loc", curie=MIXS.curie('0000832'), - model_uri=DEFAULT_.shading_device_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.shading_device_mat = Slot(uri=MIXS['0000245'], name="shading_device_mat", curie=MIXS.curie('0000245'), - model_uri=DEFAULT_.shading_device_mat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.shading_device_type = Slot(uri=MIXS['0000835'], name="shading_device_type", curie=MIXS.curie('0000835'), - model_uri=DEFAULT_.shading_device_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sieving = Slot(uri=MIXS['0000322'], name="sieving", curie=MIXS.curie('0000322'), - model_uri=DEFAULT_.sieving, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.silicate = Slot(uri=MIXS['0000184'], name="silicate", curie=MIXS.curie('0000184'), - model_uri=DEFAULT_.silicate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.size_frac = Slot(uri=MIXS['0000017'], name="size_frac", curie=MIXS.curie('0000017'), - model_uri=DEFAULT_.size_frac, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.size_frac_low = Slot(uri=MIXS['0000735'], name="size_frac_low", curie=MIXS.curie('0000735'), - model_uri=DEFAULT_.size_frac_low, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.size_frac_up = Slot(uri=MIXS['0000736'], name="size_frac_up", curie=MIXS.curie('0000736'), - model_uri=DEFAULT_.size_frac_up, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.slope_aspect = Slot(uri=MIXS['0000647'], name="slope_aspect", curie=MIXS.curie('0000647'), - model_uri=DEFAULT_.slope_aspect, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.slope_gradient = Slot(uri=MIXS['0000646'], name="slope_gradient", curie=MIXS.curie('0000646'), - model_uri=DEFAULT_.slope_gradient, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.sludge_retent_time = Slot(uri=MIXS['0000669'], name="sludge_retent_time", curie=MIXS.curie('0000669'), - model_uri=DEFAULT_.sludge_retent_time, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.sodium = Slot(uri=MIXS['0000428'], name="sodium", curie=MIXS.curie('0000428'), - model_uri=DEFAULT_.sodium, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.soil_horizon = Slot(uri=MIXS['0001082'], name="soil_horizon", curie=MIXS.curie('0001082'), - model_uri=DEFAULT_.soil_horizon, domain=None, range=Optional[Union[str, "SoilHorizonEnum"]]) - -slots.soil_text_measure = Slot(uri=MIXS['0000335'], name="soil_text_measure", curie=MIXS.curie('0000335'), - model_uri=DEFAULT_.soil_text_measure, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.soil_texture_meth = Slot(uri=MIXS['0000336'], name="soil_texture_meth", curie=MIXS.curie('0000336'), - model_uri=DEFAULT_.soil_texture_meth, domain=None, range=Optional[str]) - -slots.soil_type = Slot(uri=MIXS['0000332'], name="soil_type", curie=MIXS.curie('0000332'), - model_uri=DEFAULT_.soil_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.soil_type_meth = Slot(uri=MIXS['0000334'], name="soil_type_meth", curie=MIXS.curie('0000334'), - model_uri=DEFAULT_.soil_type_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.solar_irradiance = Slot(uri=MIXS['0000112'], name="solar_irradiance", curie=MIXS.curie('0000112'), - model_uri=DEFAULT_.solar_irradiance, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.soluble_inorg_mat = Slot(uri=MIXS['0000672'], name="soluble_inorg_mat", curie=MIXS.curie('0000672'), - model_uri=DEFAULT_.soluble_inorg_mat, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.soluble_org_mat = Slot(uri=MIXS['0000673'], name="soluble_org_mat", curie=MIXS.curie('0000673'), - model_uri=DEFAULT_.soluble_org_mat, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.soluble_react_phosp = Slot(uri=MIXS['0000738'], name="soluble_react_phosp", curie=MIXS.curie('0000738'), - model_uri=DEFAULT_.soluble_react_phosp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.source_mat_id = Slot(uri=MIXS['0000026'], name="source_mat_id", curie=MIXS.curie('0000026'), - model_uri=DEFAULT_.source_mat_id, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.space_typ_state = Slot(uri=MIXS['0000770'], name="space_typ_state", curie=MIXS.curie('0000770'), - model_uri=DEFAULT_.space_typ_state, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.specific = Slot(uri=MIXS['0000836'], name="specific", curie=MIXS.curie('0000836'), - model_uri=DEFAULT_.specific, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.specific_humidity = Slot(uri=MIXS['0000214'], name="specific_humidity", curie=MIXS.curie('0000214'), - model_uri=DEFAULT_.specific_humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.sr_dep_env = Slot(uri=MIXS['0000996'], name="sr_dep_env", curie=MIXS.curie('0000996'), - model_uri=DEFAULT_.sr_dep_env, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sr_geol_age = Slot(uri=MIXS['0000997'], name="sr_geol_age", curie=MIXS.curie('0000997'), - model_uri=DEFAULT_.sr_geol_age, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sr_kerog_type = Slot(uri=MIXS['0000994'], name="sr_kerog_type", curie=MIXS.curie('0000994'), - model_uri=DEFAULT_.sr_kerog_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sr_lithology = Slot(uri=MIXS['0000995'], name="sr_lithology", curie=MIXS.curie('0000995'), - model_uri=DEFAULT_.sr_lithology, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.standing_water_regm = Slot(uri=MIXS['0001069'], name="standing_water_regm", curie=MIXS.curie('0001069'), - model_uri=DEFAULT_.standing_water_regm, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.store_cond = Slot(uri=MIXS['0000327'], name="store_cond", curie=MIXS.curie('0000327'), - model_uri=DEFAULT_.store_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.substructure_type = Slot(uri=MIXS['0000767'], name="substructure_type", curie=MIXS.curie('0000767'), - model_uri=DEFAULT_.substructure_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.sulfate = Slot(uri=MIXS['0000423'], name="sulfate", curie=MIXS.curie('0000423'), - model_uri=DEFAULT_.sulfate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.sulfate_fw = Slot(uri=MIXS['0000407'], name="sulfate_fw", curie=MIXS.curie('0000407'), - model_uri=DEFAULT_.sulfate_fw, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.sulfide = Slot(uri=MIXS['0000424'], name="sulfide", curie=MIXS.curie('0000424'), - model_uri=DEFAULT_.sulfide, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.surf_air_cont = Slot(uri=MIXS['0000759'], name="surf_air_cont", curie=MIXS.curie('0000759'), - model_uri=DEFAULT_.surf_air_cont, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.surf_humidity = Slot(uri=MIXS['0000123'], name="surf_humidity", curie=MIXS.curie('0000123'), - model_uri=DEFAULT_.surf_humidity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.surf_material = Slot(uri=MIXS['0000758'], name="surf_material", curie=MIXS.curie('0000758'), - model_uri=DEFAULT_.surf_material, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.surf_moisture = Slot(uri=MIXS['0000128'], name="surf_moisture", curie=MIXS.curie('0000128'), - model_uri=DEFAULT_.surf_moisture, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.surf_moisture_ph = Slot(uri=MIXS['0000760'], name="surf_moisture_ph", curie=MIXS.curie('0000760'), - model_uri=DEFAULT_.surf_moisture_ph, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.surf_temp = Slot(uri=MIXS['0000125'], name="surf_temp", curie=MIXS.curie('0000125'), - model_uri=DEFAULT_.surf_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.suspend_part_matter = Slot(uri=MIXS['0000741'], name="suspend_part_matter", curie=MIXS.curie('0000741'), - model_uri=DEFAULT_.suspend_part_matter, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.suspend_solids = Slot(uri=MIXS['0000150'], name="suspend_solids", curie=MIXS.curie('0000150'), - model_uri=DEFAULT_.suspend_solids, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tan = Slot(uri=MIXS['0000120'], name="tan", curie=MIXS.curie('0000120'), - model_uri=DEFAULT_.tan, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.target_gene = Slot(uri=MIXS['0000044'], name="target_gene", curie=MIXS.curie('0000044'), - model_uri=DEFAULT_.target_gene, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.target_subfragment = Slot(uri=MIXS['0000045'], name="target_subfragment", curie=MIXS.curie('0000045'), - model_uri=DEFAULT_.target_subfragment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.temp = Slot(uri=MIXS['0000113'], name="temp", curie=MIXS.curie('0000113'), - model_uri=DEFAULT_.temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.temp_out = Slot(uri=MIXS['0000197'], name="temp_out", curie=MIXS.curie('0000197'), - model_uri=DEFAULT_.temp_out, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tertiary_treatment = Slot(uri=MIXS['0000352'], name="tertiary_treatment", curie=MIXS.curie('0000352'), - model_uri=DEFAULT_.tertiary_treatment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.texture = Slot(uri=MIXS['0000335'], name="texture", curie=MIXS.curie('0000335'), - model_uri=DEFAULT_.texture, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.texture_meth = Slot(uri=MIXS['0000336'], name="texture_meth", curie=MIXS.curie('0000336'), - model_uri=DEFAULT_.texture_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.tidal_stage = Slot(uri=MIXS['0000750'], name="tidal_stage", curie=MIXS.curie('0000750'), - model_uri=DEFAULT_.tidal_stage, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.tillage = Slot(uri=MIXS['0001081'], name="tillage", curie=MIXS.curie('0001081'), - model_uri=DEFAULT_.tillage, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.tiss_cult_growth_med = Slot(uri=MIXS['0001070'], name="tiss_cult_growth_med", curie=MIXS.curie('0001070'), - model_uri=DEFAULT_.tiss_cult_growth_med, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.toluene = Slot(uri=MIXS['0000154'], name="toluene", curie=MIXS.curie('0000154'), - model_uri=DEFAULT_.toluene, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_carb = Slot(uri=MIXS['0000525'], name="tot_carb", curie=MIXS.curie('0000525'), - model_uri=DEFAULT_.tot_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_depth_water_col = Slot(uri=MIXS['0000634'], name="tot_depth_water_col", curie=MIXS.curie('0000634'), - model_uri=DEFAULT_.tot_depth_water_col, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_diss_nitro = Slot(uri=MIXS['0000744'], name="tot_diss_nitro", curie=MIXS.curie('0000744'), - model_uri=DEFAULT_.tot_diss_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_inorg_nitro = Slot(uri=MIXS['0000745'], name="tot_inorg_nitro", curie=MIXS.curie('0000745'), - model_uri=DEFAULT_.tot_inorg_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_iron = Slot(uri=MIXS['0000105'], name="tot_iron", curie=MIXS.curie('0000105'), - model_uri=DEFAULT_.tot_iron, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_nitro = Slot(uri=MIXS['0000102'], name="tot_nitro", curie=MIXS.curie('0000102'), - model_uri=DEFAULT_.tot_nitro, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_nitro_cont_meth = Slot(uri=MIXS['0000338'], name="tot_nitro_cont_meth", curie=MIXS.curie('0000338'), - model_uri=DEFAULT_.tot_nitro_cont_meth, domain=None, range=Optional[str]) - -slots.tot_nitro_content = Slot(uri=MIXS['0000530'], name="tot_nitro_content", curie=MIXS.curie('0000530'), - model_uri=DEFAULT_.tot_nitro_content, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_org_c_meth = Slot(uri=MIXS['0000337'], name="tot_org_c_meth", curie=MIXS.curie('0000337'), - model_uri=DEFAULT_.tot_org_c_meth, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.tot_org_carb = Slot(uri=MIXS['0000533'], name="tot_org_carb", curie=MIXS.curie('0000533'), - model_uri=DEFAULT_.tot_org_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_part_carb = Slot(uri=MIXS['0000747'], name="tot_part_carb", curie=MIXS.curie('0000747'), - model_uri=DEFAULT_.tot_part_carb, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_phosp = Slot(uri=MIXS['0000117'], name="tot_phosp", curie=MIXS.curie('0000117'), - model_uri=DEFAULT_.tot_phosp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_phosphate = Slot(uri=MIXS['0000689'], name="tot_phosphate", curie=MIXS.curie('0000689'), - model_uri=DEFAULT_.tot_phosphate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tot_sulfur = Slot(uri=MIXS['0000419'], name="tot_sulfur", curie=MIXS.curie('0000419'), - model_uri=DEFAULT_.tot_sulfur, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.train_line = Slot(uri=MIXS['0000837'], name="train_line", curie=MIXS.curie('0000837'), - model_uri=DEFAULT_.train_line, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.train_stat_loc = Slot(uri=MIXS['0000838'], name="train_stat_loc", curie=MIXS.curie('0000838'), - model_uri=DEFAULT_.train_stat_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.train_stop_loc = Slot(uri=MIXS['0000839'], name="train_stop_loc", curie=MIXS.curie('0000839'), - model_uri=DEFAULT_.train_stop_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.turbidity = Slot(uri=MIXS['0000191'], name="turbidity", curie=MIXS.curie('0000191'), - model_uri=DEFAULT_.turbidity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tvdss_of_hcr_press = Slot(uri=MIXS['0000397'], name="tvdss_of_hcr_press", curie=MIXS.curie('0000397'), - model_uri=DEFAULT_.tvdss_of_hcr_press, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.tvdss_of_hcr_temp = Slot(uri=MIXS['0000394'], name="tvdss_of_hcr_temp", curie=MIXS.curie('0000394'), - model_uri=DEFAULT_.tvdss_of_hcr_temp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.typ_occup_density = Slot(uri=MIXS['0000771'], name="typ_occup_density", curie=MIXS.curie('0000771'), - model_uri=DEFAULT_.typ_occup_density, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ventilation_rate = Slot(uri=MIXS['0000114'], name="ventilation_rate", curie=MIXS.curie('0000114'), - model_uri=DEFAULT_.ventilation_rate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.ventilation_type = Slot(uri=MIXS['0000756'], name="ventilation_type", curie=MIXS.curie('0000756'), - model_uri=DEFAULT_.ventilation_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.vfa = Slot(uri=MIXS['0000152'], name="vfa", curie=MIXS.curie('0000152'), - model_uri=DEFAULT_.vfa, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.vfa_fw = Slot(uri=MIXS['0000408'], name="vfa_fw", curie=MIXS.curie('0000408'), - model_uri=DEFAULT_.vfa_fw, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.vis_media = Slot(uri=MIXS['0000840'], name="vis_media", curie=MIXS.curie('0000840'), - model_uri=DEFAULT_.vis_media, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.viscosity = Slot(uri=MIXS['0000126'], name="viscosity", curie=MIXS.curie('0000126'), - model_uri=DEFAULT_.viscosity, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.volatile_org_comp = Slot(uri=MIXS['0000115'], name="volatile_org_comp", curie=MIXS.curie('0000115'), - model_uri=DEFAULT_.volatile_org_comp, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.wall_area = Slot(uri=MIXS['0000198'], name="wall_area", curie=MIXS.curie('0000198'), - model_uri=DEFAULT_.wall_area, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.wall_const_type = Slot(uri=MIXS['0000841'], name="wall_const_type", curie=MIXS.curie('0000841'), - model_uri=DEFAULT_.wall_const_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wall_finish_mat = Slot(uri=MIXS['0000842'], name="wall_finish_mat", curie=MIXS.curie('0000842'), - model_uri=DEFAULT_.wall_finish_mat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wall_height = Slot(uri=MIXS['0000221'], name="wall_height", curie=MIXS.curie('0000221'), - model_uri=DEFAULT_.wall_height, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.wall_loc = Slot(uri=MIXS['0000843'], name="wall_loc", curie=MIXS.curie('0000843'), - model_uri=DEFAULT_.wall_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wall_surf_treatment = Slot(uri=MIXS['0000845'], name="wall_surf_treatment", curie=MIXS.curie('0000845'), - model_uri=DEFAULT_.wall_surf_treatment, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wall_texture = Slot(uri=MIXS['0000846'], name="wall_texture", curie=MIXS.curie('0000846'), - model_uri=DEFAULT_.wall_texture, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wall_thermal_mass = Slot(uri=MIXS['0000222'], name="wall_thermal_mass", curie=MIXS.curie('0000222'), - model_uri=DEFAULT_.wall_thermal_mass, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.wall_water_mold = Slot(uri=MIXS['0000844'], name="wall_water_mold", curie=MIXS.curie('0000844'), - model_uri=DEFAULT_.wall_water_mold, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wastewater_type = Slot(uri=MIXS['0000353'], name="wastewater_type", curie=MIXS.curie('0000353'), - model_uri=DEFAULT_.wastewater_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.water_cont_soil_meth = Slot(uri=MIXS['0000323'], name="water_cont_soil_meth", curie=MIXS.curie('0000323'), - model_uri=DEFAULT_.water_cont_soil_meth, domain=None, range=Optional[str]) - -slots.water_content = Slot(uri=MIXS['0000185'], name="water_content", curie=MIXS.curie('0000185'), - model_uri=DEFAULT_.water_content, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.water_current = Slot(uri=MIXS['0000203'], name="water_current", curie=MIXS.curie('0000203'), - model_uri=DEFAULT_.water_current, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.water_cut = Slot(uri=MIXS['0000454'], name="water_cut", curie=MIXS.curie('0000454'), - model_uri=DEFAULT_.water_cut, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.water_feat_size = Slot(uri=MIXS['0000223'], name="water_feat_size", curie=MIXS.curie('0000223'), - model_uri=DEFAULT_.water_feat_size, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.water_feat_type = Slot(uri=MIXS['0000847'], name="water_feat_type", curie=MIXS.curie('0000847'), - model_uri=DEFAULT_.water_feat_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.water_prod_rate = Slot(uri=MIXS['0000453'], name="water_prod_rate", curie=MIXS.curie('0000453'), - model_uri=DEFAULT_.water_prod_rate, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.water_temp_regm = Slot(uri=MIXS['0000590'], name="water_temp_regm", curie=MIXS.curie('0000590'), - model_uri=DEFAULT_.water_temp_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.watering_regm = Slot(uri=MIXS['0000591'], name="watering_regm", curie=MIXS.curie('0000591'), - model_uri=DEFAULT_.watering_regm, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.weekday = Slot(uri=MIXS['0000848'], name="weekday", curie=MIXS.curie('0000848'), - model_uri=DEFAULT_.weekday, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.win = Slot(uri=MIXS['0000297'], name="win", curie=MIXS.curie('0000297'), - model_uri=DEFAULT_.win, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wind_direction = Slot(uri=MIXS['0000757'], name="wind_direction", curie=MIXS.curie('0000757'), - model_uri=DEFAULT_.wind_direction, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.wind_speed = Slot(uri=MIXS['0000118'], name="wind_speed", curie=MIXS.curie('0000118'), - model_uri=DEFAULT_.wind_speed, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.window_cond = Slot(uri=MIXS['0000849'], name="window_cond", curie=MIXS.curie('0000849'), - model_uri=DEFAULT_.window_cond, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_cover = Slot(uri=MIXS['0000850'], name="window_cover", curie=MIXS.curie('0000850'), - model_uri=DEFAULT_.window_cover, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_horiz_pos = Slot(uri=MIXS['0000851'], name="window_horiz_pos", curie=MIXS.curie('0000851'), - model_uri=DEFAULT_.window_horiz_pos, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_loc = Slot(uri=MIXS['0000852'], name="window_loc", curie=MIXS.curie('0000852'), - model_uri=DEFAULT_.window_loc, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_mat = Slot(uri=MIXS['0000853'], name="window_mat", curie=MIXS.curie('0000853'), - model_uri=DEFAULT_.window_mat, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_open_freq = Slot(uri=MIXS['0000246'], name="window_open_freq", curie=MIXS.curie('0000246'), - model_uri=DEFAULT_.window_open_freq, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_size = Slot(uri=MIXS['0000224'], name="window_size", curie=MIXS.curie('0000224'), - model_uri=DEFAULT_.window_size, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.window_status = Slot(uri=MIXS['0000855'], name="window_status", curie=MIXS.curie('0000855'), - model_uri=DEFAULT_.window_status, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_type = Slot(uri=MIXS['0000856'], name="window_type", curie=MIXS.curie('0000856'), - model_uri=DEFAULT_.window_type, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_vert_pos = Slot(uri=MIXS['0000857'], name="window_vert_pos", curie=MIXS.curie('0000857'), - model_uri=DEFAULT_.window_vert_pos, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.window_water_mold = Slot(uri=MIXS['0000854'], name="window_water_mold", curie=MIXS.curie('0000854'), - model_uri=DEFAULT_.window_water_mold, domain=None, range=Optional[Union[dict, TextValue]]) - -slots.xylene = Slot(uri=MIXS['0000156'], name="xylene", curie=MIXS.curie('0000156'), - model_uri=DEFAULT_.xylene, domain=None, range=Optional[Union[dict, QuantityValue]]) - -slots.env_package = Slot(uri=DEFAULT_.env_package, name="env_package", curie=DEFAULT_.curie('env_package'), - model_uri=DEFAULT_.env_package, domain=None, range=Optional[Union[dict, TextValue]], mappings = [MIXS.env_package], - pattern=re.compile(r'[air|built environment|host\-associated|human\-associated|human\-skin|human\-oral|human\-gut|human\-vaginal|hydrocarbon resources\-cores|hydrocarbon resources\-fluids\/swabs|microbial mat\/biofilm|misc environment|plant\-associated|sediment|soil|wastewater\/sludge|water]')) - -slots.language = Slot(uri=NMDC.language, name="language", curie=NMDC.curie('language'), - model_uri=DEFAULT_.language, domain=None, range=Optional[str]) - -slots.attribute = Slot(uri=NMDC.attribute, name="attribute", curie=NMDC.curie('attribute'), - model_uri=DEFAULT_.attribute, domain=None, range=Optional[str]) - -slots.has_raw_value = Slot(uri=NMDC.has_raw_value, name="has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.has_raw_value, domain=AttributeValue, range=Optional[str]) - -slots.has_unit = Slot(uri=NMDC.has_unit, name="has unit", curie=NMDC.curie('has_unit'), - model_uri=DEFAULT_.has_unit, domain=None, range=Optional[str], mappings = [QUD.unit, SCHEMA.unitCode]) - -slots.has_numeric_value = Slot(uri=NMDC.has_numeric_value, name="has numeric value", curie=NMDC.curie('has_numeric_value'), - model_uri=DEFAULT_.has_numeric_value, domain=None, range=Optional[float], mappings = [QUD.quantityValue, SCHEMA.value]) - -slots.has_minimum_numeric_value = Slot(uri=NMDC.has_minimum_numeric_value, name="has minimum numeric value", curie=NMDC.curie('has_minimum_numeric_value'), - model_uri=DEFAULT_.has_minimum_numeric_value, domain=None, range=Optional[float]) - -slots.has_maximum_numeric_value = Slot(uri=NMDC.has_maximum_numeric_value, name="has maximum numeric value", curie=NMDC.curie('has_maximum_numeric_value'), - model_uri=DEFAULT_.has_maximum_numeric_value, domain=None, range=Optional[float]) - -slots.has_boolean_value = Slot(uri=NMDC.has_boolean_value, name="has boolean value", curie=NMDC.curie('has_boolean_value'), - model_uri=DEFAULT_.has_boolean_value, domain=None, range=Optional[Union[bool, Bool]]) - -slots.latitude = Slot(uri=WGS.lat, name="latitude", curie=WGS.curie('lat'), - model_uri=DEFAULT_.latitude, domain=GeolocationValue, range=Optional[float], mappings = [SCHEMA.latitude]) - -slots.longitude = Slot(uri=WGS.long, name="longitude", curie=WGS.curie('long'), - model_uri=DEFAULT_.longitude, domain=GeolocationValue, range=Optional[float], mappings = [SCHEMA.longitude]) - -slots.term = Slot(uri=RDF.type, name="term", curie=RDF.curie('type'), - model_uri=DEFAULT_.term, domain=ControlledTermValue, range=Optional[Union[dict, OntologyClass]]) - -slots.orcid = Slot(uri=NMDC.orcid, name="orcid", curie=NMDC.curie('orcid'), - model_uri=DEFAULT_.orcid, domain=PersonValue, range=Optional[str]) - -slots.email = Slot(uri=SCHEMA.email, name="email", curie=SCHEMA.curie('email'), - model_uri=DEFAULT_.email, domain=None, range=Optional[str]) - -slots.alternate_emails = Slot(uri=NMDC.alternate_emails, name="alternate emails", curie=NMDC.curie('alternate_emails'), - model_uri=DEFAULT_.alternate_emails, domain=None, range=Optional[str]) - -slots.profile_image_url = Slot(uri=NMDC.profile_image_url, name="profile image url", curie=NMDC.curie('profile_image_url'), - model_uri=DEFAULT_.profile_image_url, domain=PersonValue, range=Optional[str]) - -slots.has_input = Slot(uri=NMDC.has_input, name="has input", curie=NMDC.curie('has_input'), - model_uri=DEFAULT_.has_input, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) - -slots.has_output = Slot(uri=NMDC.has_output, name="has output", curie=NMDC.curie('has_output'), - model_uri=DEFAULT_.has_output, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) - -slots.part_of = Slot(uri=DCTERMS.isPartOf, name="part of", curie=DCTERMS.curie('isPartOf'), - model_uri=DEFAULT_.part_of, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) - -slots.execution_resource = Slot(uri=NMDC.execution_resource, name="execution resource", curie=NMDC.curie('execution_resource'), - model_uri=DEFAULT_.execution_resource, domain=None, range=Optional[str]) - -slots.url = Slot(uri=NMDC.url, name="url", curie=NMDC.curie('url'), - model_uri=DEFAULT_.url, domain=None, range=Optional[str]) - -slots.display_order = Slot(uri=NMDC.display_order, name="display order", curie=NMDC.curie('display_order'), - model_uri=DEFAULT_.display_order, domain=None, range=Optional[str]) - -slots.git_url = Slot(uri=NMDC.git_url, name="git url", curie=NMDC.curie('git_url'), - model_uri=DEFAULT_.git_url, domain=None, range=Optional[str]) - -slots.file_size_bytes = Slot(uri=NMDC.file_size_bytes, name="file size bytes", curie=NMDC.curie('file_size_bytes'), - model_uri=DEFAULT_.file_size_bytes, domain=None, range=Optional[int]) - -slots.md5_checksum = Slot(uri=NMDC.md5_checksum, name="md5 checksum", curie=NMDC.curie('md5_checksum'), - model_uri=DEFAULT_.md5_checksum, domain=None, range=Optional[str]) - -slots.abstract = Slot(uri=NMDC.abstract, name="abstract", curie=NMDC.curie('abstract'), - model_uri=DEFAULT_.abstract, domain=None, range=Optional[str]) - -slots.keywords = Slot(uri=NMDC.keywords, name="keywords", curie=NMDC.curie('keywords'), - model_uri=DEFAULT_.keywords, domain=None, range=Optional[Union[str, List[str]]], mappings = [DCTERMS.subject]) - -slots.objective = Slot(uri=NMDC.objective, name="objective", curie=NMDC.curie('objective'), - model_uri=DEFAULT_.objective, domain=None, range=Optional[str], mappings = [SIO["000337"]]) - -slots.websites = Slot(uri=NMDC.websites, name="websites", curie=NMDC.curie('websites'), - model_uri=DEFAULT_.websites, domain=None, range=Optional[Union[str, List[str]]]) - -slots.publications = Slot(uri=NMDC.publications, name="publications", curie=NMDC.curie('publications'), - model_uri=DEFAULT_.publications, domain=None, range=Optional[Union[str, List[str]]]) - -slots.id = Slot(uri=NMDC.id, name="id", curie=NMDC.curie('id'), - model_uri=DEFAULT_.id, domain=None, range=URIRef) - -slots.name = Slot(uri=NMDC.name, name="name", curie=NMDC.curie('name'), - model_uri=DEFAULT_.name, domain=None, range=Optional[str]) - -slots.description = Slot(uri=DCTERMS.description, name="description", curie=DCTERMS.curie('description'), - model_uri=DEFAULT_.description, domain=None, range=Optional[str]) - -slots.type = Slot(uri=NMDC.type, name="type", curie=NMDC.curie('type'), - model_uri=DEFAULT_.type, domain=None, range=Optional[str]) - -slots.title = Slot(uri=NMDC.title, name="title", curie=NMDC.curie('title'), - model_uri=DEFAULT_.title, domain=None, range=Optional[str]) - -slots.alternative_titles = Slot(uri=NMDC.alternative_titles, name="alternative titles", curie=NMDC.curie('alternative_titles'), - model_uri=DEFAULT_.alternative_titles, domain=None, range=Optional[Union[str, List[str]]]) - -slots.alternative_names = Slot(uri=NMDC.alternative_names, name="alternative names", curie=NMDC.curie('alternative_names'), - model_uri=DEFAULT_.alternative_names, domain=None, range=Optional[Union[str, List[str]]]) - -slots.alternative_descriptions = Slot(uri=NMDC.alternative_descriptions, name="alternative descriptions", curie=NMDC.curie('alternative_descriptions'), - model_uri=DEFAULT_.alternative_descriptions, domain=None, range=Optional[Union[str, List[str]]]) - -slots.alternative_identifiers = Slot(uri=NMDC.alternative_identifiers, name="alternative identifiers", curie=NMDC.curie('alternative_identifiers'), - model_uri=DEFAULT_.alternative_identifiers, domain=None, range=Optional[Union[str, List[str]]]) - -slots.started_at_time = Slot(uri=NMDC.started_at_time, name="started at time", curie=NMDC.curie('started_at_time'), - model_uri=DEFAULT_.started_at_time, domain=None, range=Optional[Union[str, XSDDateTime]], mappings = [PROV.startedAtTime], - pattern=re.compile(r'^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$')) - -slots.ended_at_time = Slot(uri=NMDC.ended_at_time, name="ended at time", curie=NMDC.curie('ended_at_time'), - model_uri=DEFAULT_.ended_at_time, domain=None, range=Optional[Union[str, XSDDateTime]], mappings = [PROV.endedAtTime], - pattern=re.compile(r'^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$')) - -slots.was_informed_by = Slot(uri=NMDC.was_informed_by, name="was informed by", curie=NMDC.curie('was_informed_by'), - model_uri=DEFAULT_.was_informed_by, domain=None, range=Optional[Union[str, ActivityId]], mappings = [PROV.wasInformedBy]) - -slots.was_associated_with = Slot(uri=NMDC.was_associated_with, name="was associated with", curie=NMDC.curie('was_associated_with'), - model_uri=DEFAULT_.was_associated_with, domain=None, range=Optional[Union[dict, Agent]], mappings = [PROV.wasAssociatedWith]) - -slots.acted_on_behalf_of = Slot(uri=NMDC.acted_on_behalf_of, name="acted on behalf of", curie=NMDC.curie('acted_on_behalf_of'), - model_uri=DEFAULT_.acted_on_behalf_of, domain=None, range=Optional[Union[dict, Agent]], mappings = [PROV.actedOnBehalfOf]) - -slots.was_generated_by = Slot(uri=NMDC.was_generated_by, name="was generated by", curie=NMDC.curie('was_generated_by'), - model_uri=DEFAULT_.was_generated_by, domain=None, range=Optional[Union[str, ActivityId]], mappings = [PROV.wasGeneratedBy]) - -slots.used = Slot(uri=NMDC.used, name="used", curie=NMDC.curie('used'), - model_uri=DEFAULT_.used, domain=Activity, range=Optional[str], mappings = [PROV.used]) - -slots.mAGBin__bin_name = Slot(uri=DEFAULT_.bin_name, name="mAGBin__bin_name", curie=DEFAULT_.curie('bin_name'), - model_uri=DEFAULT_.mAGBin__bin_name, domain=None, range=Optional[str]) - -slots.mAGBin__number_of_contig = Slot(uri=DEFAULT_.number_of_contig, name="mAGBin__number_of_contig", curie=DEFAULT_.curie('number_of_contig'), - model_uri=DEFAULT_.mAGBin__number_of_contig, domain=None, range=Optional[int]) - -slots.mAGBin__completeness = Slot(uri=DEFAULT_.completeness, name="mAGBin__completeness", curie=DEFAULT_.curie('completeness'), - model_uri=DEFAULT_.mAGBin__completeness, domain=None, range=Optional[float]) - -slots.mAGBin__contamination = Slot(uri=DEFAULT_.contamination, name="mAGBin__contamination", curie=DEFAULT_.curie('contamination'), - model_uri=DEFAULT_.mAGBin__contamination, domain=None, range=Optional[float]) - -slots.mAGBin__gene_count = Slot(uri=DEFAULT_.gene_count, name="mAGBin__gene_count", curie=DEFAULT_.curie('gene_count'), - model_uri=DEFAULT_.mAGBin__gene_count, domain=None, range=Optional[int]) - -slots.mAGBin__bin_quality = Slot(uri=DEFAULT_.bin_quality, name="mAGBin__bin_quality", curie=DEFAULT_.curie('bin_quality'), - model_uri=DEFAULT_.mAGBin__bin_quality, domain=None, range=Optional[str]) - -slots.mAGBin__num_16s = Slot(uri=DEFAULT_.num_16s, name="mAGBin__num_16s", curie=DEFAULT_.curie('num_16s'), - model_uri=DEFAULT_.mAGBin__num_16s, domain=None, range=Optional[int]) - -slots.mAGBin__num_5s = Slot(uri=DEFAULT_.num_5s, name="mAGBin__num_5s", curie=DEFAULT_.curie('num_5s'), - model_uri=DEFAULT_.mAGBin__num_5s, domain=None, range=Optional[int]) - -slots.mAGBin__num_23s = Slot(uri=DEFAULT_.num_23s, name="mAGBin__num_23s", curie=DEFAULT_.curie('num_23s'), - model_uri=DEFAULT_.mAGBin__num_23s, domain=None, range=Optional[int]) - -slots.mAGBin__num_tRNA = Slot(uri=DEFAULT_.num_tRNA, name="mAGBin__num_tRNA", curie=DEFAULT_.curie('num_tRNA'), - model_uri=DEFAULT_.mAGBin__num_tRNA, domain=None, range=Optional[int]) - -slots.mAGBin__gtdbtk_domain = Slot(uri=DEFAULT_.gtdbtk_domain, name="mAGBin__gtdbtk_domain", curie=DEFAULT_.curie('gtdbtk_domain'), - model_uri=DEFAULT_.mAGBin__gtdbtk_domain, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_phylum = Slot(uri=DEFAULT_.gtdbtk_phylum, name="mAGBin__gtdbtk_phylum", curie=DEFAULT_.curie('gtdbtk_phylum'), - model_uri=DEFAULT_.mAGBin__gtdbtk_phylum, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_class = Slot(uri=DEFAULT_.gtdbtk_class, name="mAGBin__gtdbtk_class", curie=DEFAULT_.curie('gtdbtk_class'), - model_uri=DEFAULT_.mAGBin__gtdbtk_class, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_order = Slot(uri=DEFAULT_.gtdbtk_order, name="mAGBin__gtdbtk_order", curie=DEFAULT_.curie('gtdbtk_order'), - model_uri=DEFAULT_.mAGBin__gtdbtk_order, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_family = Slot(uri=DEFAULT_.gtdbtk_family, name="mAGBin__gtdbtk_family", curie=DEFAULT_.curie('gtdbtk_family'), - model_uri=DEFAULT_.mAGBin__gtdbtk_family, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_genus = Slot(uri=DEFAULT_.gtdbtk_genus, name="mAGBin__gtdbtk_genus", curie=DEFAULT_.curie('gtdbtk_genus'), - model_uri=DEFAULT_.mAGBin__gtdbtk_genus, domain=None, range=Optional[str]) - -slots.mAGBin__gtdbtk_species = Slot(uri=DEFAULT_.gtdbtk_species, name="mAGBin__gtdbtk_species", curie=DEFAULT_.curie('gtdbtk_species'), - model_uri=DEFAULT_.mAGBin__gtdbtk_species, domain=None, range=Optional[str]) - -slots.metabolite_quantified = Slot(uri=DEFAULT_.metabolite_quantified, name="metabolite quantified", curie=DEFAULT_.curie('metabolite_quantified'), - model_uri=DEFAULT_.metabolite_quantified, domain=None, range=Optional[Union[str, ChemicalEntityId]]) - -slots.highest_similarity_score = Slot(uri=DEFAULT_.highest_similarity_score, name="highest similarity score", curie=DEFAULT_.curie('highest_similarity_score'), - model_uri=DEFAULT_.highest_similarity_score, domain=None, range=Optional[float]) - -slots.peptide_sequence = Slot(uri=DEFAULT_.peptide_sequence, name="peptide sequence", curie=DEFAULT_.curie('peptide_sequence'), - model_uri=DEFAULT_.peptide_sequence, domain=None, range=Optional[str]) - -slots.best_protein = Slot(uri=DEFAULT_.best_protein, name="best protein", curie=DEFAULT_.curie('best_protein'), - model_uri=DEFAULT_.best_protein, domain=None, range=Optional[Union[str, GeneProductId]]) - -slots.all_proteins = Slot(uri=DEFAULT_.all_proteins, name="all proteins", curie=DEFAULT_.curie('all_proteins'), - model_uri=DEFAULT_.all_proteins, domain=None, range=Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]]) - -slots.min_q_value = Slot(uri=DEFAULT_.min_q_value, name="min_q_value", curie=DEFAULT_.curie('min_q_value'), - model_uri=DEFAULT_.min_q_value, domain=None, range=Optional[float]) - -slots.peptide_spectral_count = Slot(uri=DEFAULT_.peptide_spectral_count, name="peptide_spectral_count", curie=DEFAULT_.curie('peptide_spectral_count'), - model_uri=DEFAULT_.peptide_spectral_count, domain=None, range=Optional[int]) - -slots.peptide_sum_masic_abundance = Slot(uri=DEFAULT_.peptide_sum_masic_abundance, name="peptide_sum_masic_abundance", curie=DEFAULT_.curie('peptide_sum_masic_abundance'), - model_uri=DEFAULT_.peptide_sum_masic_abundance, domain=None, range=Optional[int]) - -slots.peptide_sequence_count = Slot(uri=DEFAULT_.peptide_sequence_count, name="peptide_sequence_count", curie=DEFAULT_.curie('peptide_sequence_count'), - model_uri=DEFAULT_.peptide_sequence_count, domain=None, range=Optional[int]) - -slots.protein_spectral_count = Slot(uri=DEFAULT_.protein_spectral_count, name="protein_spectral_count", curie=DEFAULT_.curie('protein_spectral_count'), - model_uri=DEFAULT_.protein_spectral_count, domain=None, range=Optional[int]) - -slots.protein_sum_masic_abundance = Slot(uri=DEFAULT_.protein_sum_masic_abundance, name="protein_sum_masic_abundance", curie=DEFAULT_.curie('protein_sum_masic_abundance'), - model_uri=DEFAULT_.protein_sum_masic_abundance, domain=None, range=Optional[int]) - -slots.inchi = Slot(uri=DEFAULT_.inchi, name="inchi", curie=DEFAULT_.curie('inchi'), - model_uri=DEFAULT_.inchi, domain=None, range=Optional[str]) - -slots.inchi_key = Slot(uri=DEFAULT_.inchi_key, name="inchi key", curie=DEFAULT_.curie('inchi_key'), - model_uri=DEFAULT_.inchi_key, domain=None, range=Optional[str]) - -slots.smiles = Slot(uri=DEFAULT_.smiles, name="smiles", curie=DEFAULT_.curie('smiles'), - model_uri=DEFAULT_.smiles, domain=None, range=Optional[Union[str, List[str]]]) - -slots.chemical_formula = Slot(uri=DEFAULT_.chemical_formula, name="chemical formula", curie=DEFAULT_.curie('chemical_formula'), - model_uri=DEFAULT_.chemical_formula, domain=None, range=Optional[str]) - -slots.attribute_value_type = Slot(uri=NMDC.type, name="attribute value_type", curie=NMDC.curie('type'), - model_uri=DEFAULT_.attribute_value_type, domain=AttributeValue, range=Optional[str]) - -slots.quantity_value_has_raw_value = Slot(uri=NMDC.has_raw_value, name="quantity value_has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.quantity_value_has_raw_value, domain=QuantityValue, range=Optional[str]) - -slots.quantity_value_has_unit = Slot(uri=NMDC.has_unit, name="quantity value_has unit", curie=NMDC.curie('has_unit'), - model_uri=DEFAULT_.quantity_value_has_unit, domain=QuantityValue, range=Optional[str], mappings = [QUD.unit, SCHEMA.unitCode]) - -slots.quantity_value_has_numeric_value = Slot(uri=NMDC.has_numeric_value, name="quantity value_has numeric value", curie=NMDC.curie('has_numeric_value'), - model_uri=DEFAULT_.quantity_value_has_numeric_value, domain=QuantityValue, range=Optional[float], mappings = [QUD.quantityValue, SCHEMA.value]) - -slots.person_value_orcid = Slot(uri=NMDC.orcid, name="person value_orcid", curie=NMDC.curie('orcid'), - model_uri=DEFAULT_.person_value_orcid, domain=PersonValue, range=Optional[str]) - -slots.person_value_email = Slot(uri=SCHEMA.email, name="person value_email", curie=SCHEMA.curie('email'), - model_uri=DEFAULT_.person_value_email, domain=PersonValue, range=Optional[str]) - -slots.person_value_has_raw_value = Slot(uri=NMDC.has_raw_value, name="person value_has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.person_value_has_raw_value, domain=PersonValue, range=Optional[str]) - -slots.person_value_name = Slot(uri=NMDC.name, name="person value_name", curie=NMDC.curie('name'), - model_uri=DEFAULT_.person_value_name, domain=PersonValue, range=Optional[str]) - -slots.person_id = Slot(uri=NMDC.id, name="person_id", curie=NMDC.curie('id'), - model_uri=DEFAULT_.person_id, domain=Person, range=Union[str, PersonId]) - -slots.metabolite_quantification_metabolite_quantified = Slot(uri=DEFAULT_.metabolite_quantified, name="metabolite quantification_metabolite quantified", curie=DEFAULT_.curie('metabolite_quantified'), - model_uri=DEFAULT_.metabolite_quantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) - -slots.metabolite_quantification_highest_similarity_score = Slot(uri=DEFAULT_.highest_similarity_score, name="metabolite quantification_highest similarity score", curie=DEFAULT_.curie('highest_similarity_score'), - model_uri=DEFAULT_.metabolite_quantification_highest_similarity_score, domain=MetaboliteQuantification, range=Optional[float]) - -slots.peptide_quantification_peptide_sequence = Slot(uri=DEFAULT_.peptide_sequence, name="peptide quantification_peptide sequence", curie=DEFAULT_.curie('peptide_sequence'), - model_uri=DEFAULT_.peptide_quantification_peptide_sequence, domain=PeptideQuantification, range=Optional[str]) - -slots.peptide_quantification_best_protein = Slot(uri=DEFAULT_.best_protein, name="peptide quantification_best protein", curie=DEFAULT_.curie('best_protein'), - model_uri=DEFAULT_.peptide_quantification_best_protein, domain=PeptideQuantification, range=Optional[Union[str, GeneProductId]]) - -slots.peptide_quantification_all_proteins = Slot(uri=DEFAULT_.all_proteins, name="peptide quantification_all proteins", curie=DEFAULT_.curie('all_proteins'), - model_uri=DEFAULT_.peptide_quantification_all_proteins, domain=PeptideQuantification, range=Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]]) - -slots.peptide_quantification_min_q_value = Slot(uri=DEFAULT_.min_q_value, name="peptide quantification_min_q_value", curie=DEFAULT_.curie('min_q_value'), - model_uri=DEFAULT_.peptide_quantification_min_q_value, domain=PeptideQuantification, range=Optional[float]) - -slots.peptide_quantification_peptide_spectral_count = Slot(uri=DEFAULT_.peptide_spectral_count, name="peptide quantification_peptide_spectral_count", curie=DEFAULT_.curie('peptide_spectral_count'), - model_uri=DEFAULT_.peptide_quantification_peptide_spectral_count, domain=PeptideQuantification, range=Optional[int]) - -slots.peptide_quantification_peptide_sum_masic_abundance = Slot(uri=DEFAULT_.peptide_sum_masic_abundance, name="peptide quantification_peptide_sum_masic_abundance", curie=DEFAULT_.curie('peptide_sum_masic_abundance'), - model_uri=DEFAULT_.peptide_quantification_peptide_sum_masic_abundance, domain=PeptideQuantification, range=Optional[int]) - -slots.protein_quantification_best_protein = Slot(uri=DEFAULT_.best_protein, name="protein quantification_best protein", curie=DEFAULT_.curie('best_protein'), - model_uri=DEFAULT_.protein_quantification_best_protein, domain=ProteinQuantification, range=Optional[Union[str, GeneProductId]]) - -slots.protein_quantification_all_proteins = Slot(uri=DEFAULT_.all_proteins, name="protein quantification_all proteins", curie=DEFAULT_.curie('all_proteins'), - model_uri=DEFAULT_.protein_quantification_all_proteins, domain=ProteinQuantification, range=Optional[Union[Union[str, GeneProductId], List[Union[str, GeneProductId]]]]) - -slots.protein_quantification_peptide_sequence_count = Slot(uri=DEFAULT_.peptide_sequence_count, name="protein quantification_peptide_sequence_count", curie=DEFAULT_.curie('peptide_sequence_count'), - model_uri=DEFAULT_.protein_quantification_peptide_sequence_count, domain=ProteinQuantification, range=Optional[int]) - -slots.protein_quantification_protein_spectral_count = Slot(uri=DEFAULT_.protein_spectral_count, name="protein quantification_protein_spectral_count", curie=DEFAULT_.curie('protein_spectral_count'), - model_uri=DEFAULT_.protein_quantification_protein_spectral_count, domain=ProteinQuantification, range=Optional[int]) - -slots.protein_quantification_protein_sum_masic_abundance = Slot(uri=DEFAULT_.protein_sum_masic_abundance, name="protein quantification_protein_sum_masic_abundance", curie=DEFAULT_.curie('protein_sum_masic_abundance'), - model_uri=DEFAULT_.protein_quantification_protein_sum_masic_abundance, domain=ProteinQuantification, range=Optional[int]) - -slots.chemical_entity_inchi = Slot(uri=DEFAULT_.inchi, name="chemical entity_inchi", curie=DEFAULT_.curie('inchi'), - model_uri=DEFAULT_.chemical_entity_inchi, domain=ChemicalEntity, range=Optional[str]) - -slots.chemical_entity_inchi_key = Slot(uri=DEFAULT_.inchi_key, name="chemical entity_inchi key", curie=DEFAULT_.curie('inchi_key'), - model_uri=DEFAULT_.chemical_entity_inchi_key, domain=ChemicalEntity, range=Optional[str]) - -slots.chemical_entity_smiles = Slot(uri=DEFAULT_.smiles, name="chemical entity_smiles", curie=DEFAULT_.curie('smiles'), - model_uri=DEFAULT_.chemical_entity_smiles, domain=ChemicalEntity, range=Optional[Union[str, List[str]]]) - -slots.chemical_entity_chemical_formula = Slot(uri=DEFAULT_.chemical_formula, name="chemical entity_chemical formula", curie=DEFAULT_.curie('chemical_formula'), - model_uri=DEFAULT_.chemical_entity_chemical_formula, domain=ChemicalEntity, range=Optional[str]) - -slots.geolocation_value_has_raw_value = Slot(uri=NMDC.has_raw_value, name="geolocation value_has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=DEFAULT_.geolocation_value_has_raw_value, domain=GeolocationValue, range=Optional[str]) diff --git a/python/nmdc.py b/python/nmdc.py index 6f80137795..85464f8111 100644 --- a/python/nmdc.py +++ b/python/nmdc.py @@ -1,5 +1,5 @@ # Auto generated from nmdc.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:11 +# Generation date: 2023-01-20T13:17:08 # Schema: NMDC # # id: https://microbiomedata/schema @@ -971,15 +971,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class Biosample(MaterialEntity): """ @@ -1982,11 +1973,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -8266,7 +8252,8 @@ class slots: model_uri=NMDC.dna_cont_type, domain=None, range=Optional[Union[str, "DnaContTypeEnum"]]) slots.dna_cont_well = Slot(uri=NMDC.dna_cont_well, name="dna_cont_well", curie=NMDC.curie('dna_cont_well'), - model_uri=NMDC.dna_cont_well, domain=None, range=Optional[str]) + model_uri=NMDC.dna_cont_well, domain=None, range=Optional[str], + pattern=re.compile(r'^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$')) slots.dna_container_id = Slot(uri=NMDC.dna_container_id, name="dna_container_id", curie=NMDC.curie('dna_container_id'), model_uri=NMDC.dna_container_id, domain=None, range=Optional[str]) @@ -8329,7 +8316,8 @@ class slots: model_uri=NMDC.rna_cont_type, domain=None, range=Optional[Union[str, "RnaContTypeEnum"]]) slots.rna_cont_well = Slot(uri=NMDC.rna_cont_well, name="rna_cont_well", curie=NMDC.curie('rna_cont_well'), - model_uri=NMDC.rna_cont_well, domain=None, range=Optional[str]) + model_uri=NMDC.rna_cont_well, domain=None, range=Optional[str], + pattern=re.compile(r'^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$')) slots.rna_container_id = Slot(uri=NMDC.rna_container_id, name="rna_container_id", curie=NMDC.curie('rna_container_id'), model_uri=NMDC.rna_container_id, domain=None, range=Optional[str]) @@ -8702,21 +8690,33 @@ class slots: slots.Database_metatranscriptome_activity_set = Slot(uri=NMDC.metatranscriptome_activity_set, name="Database_metatranscriptome_activity_set", curie=NMDC.curie('metatranscriptome_activity_set'), model_uri=NMDC.Database_metatranscriptome_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]]) +slots.FieldResearchSite_id = Slot(uri=NMDC.id, name="FieldResearchSite_id", curie=NMDC.curie('id'), + model_uri=NMDC.FieldResearchSite_id, domain=FieldResearchSite, range=Union[str, FieldResearchSiteId], + pattern=re.compile(r'^nmdc:frsite')) + slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) slots.CollectingBiosamplesFromSite_has_outputs = Slot(uri=NMDC.has_outputs, name="CollectingBiosamplesFromSite_has_outputs", curie=NMDC.curie('has_outputs'), model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) +slots.CollectingBiosamplesFromSite_id = Slot(uri=NMDC.id, name="CollectingBiosamplesFromSite_id", curie=NMDC.curie('id'), + model_uri=NMDC.CollectingBiosamplesFromSite_id, domain=CollectingBiosamplesFromSite, range=Union[str, CollectingBiosamplesFromSiteId], + pattern=re.compile(r'^nmdc:clsite')) + slots.DataObject_name = Slot(uri=NMDC.name, name="DataObject_name", curie=NMDC.curie('name'), model_uri=NMDC.DataObject_name, domain=DataObject, range=str) slots.DataObject_description = Slot(uri=DCTERMS.description, name="DataObject_description", curie=DCTERMS.curie('description'), model_uri=NMDC.DataObject_description, domain=DataObject, range=str) +slots.DataObject_id = Slot(uri=NMDC.id, name="DataObject_id", curie=NMDC.curie('id'), + model_uri=NMDC.DataObject_id, domain=DataObject, range=Union[str, DataObjectId], + pattern=re.compile(r'^nmdc:dobj')) + slots.Biosample_id = Slot(uri=NMDC.id, name="Biosample_id", curie=NMDC.curie('id'), model_uri=NMDC.Biosample_id, domain=Biosample, range=Union[str, BiosampleId], - pattern=re.compile(r'^nmdc:')) + pattern=re.compile(r'^nmdc:bsm')) slots.Biosample_gold_biosample_identifiers = Slot(uri=NMDC.gold_biosample_identifiers, name="Biosample_gold_biosample_identifiers", curie=NMDC.curie('gold_biosample_identifiers'), model_uri=NMDC.Biosample_gold_biosample_identifiers, domain=Biosample, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]], @@ -8747,7 +8747,8 @@ class slots: model_uri=NMDC.Biosample_extreme_event, domain=Biosample, range=Optional[str]) slots.Study_id = Slot(uri=NMDC.id, name="Study_id", curie=NMDC.curie('id'), - model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId]) + model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId], + pattern=re.compile(r'^nmdc:sty')) slots.Study_doi = Slot(uri=NMDC.doi, name="Study_doi", curie=NMDC.curie('doi'), model_uri=NMDC.Study_doi, domain=Study, range=Optional[Union[dict, "AttributeValue"]]) @@ -8784,13 +8785,15 @@ class slots: model_uri=NMDC.Study_emsl_proposal_doi, domain=Study, range=Optional[str]) slots.BiosampleProcessing_id = Slot(uri=NMDC.id, name="BiosampleProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId]) + model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId], + pattern=re.compile(r'^nmdc:bsmprc')) slots.BiosampleProcessing_has_input = Slot(uri=NMDC.has_input, name="BiosampleProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.BiosampleProcessing_has_input, domain=BiosampleProcessing, range=Optional[Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]]) slots.OmicsProcessing_id = Slot(uri=NMDC.id, name="OmicsProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId]) + model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId], + pattern=re.compile(r'^nmdc:omprc')) slots.OmicsProcessing_has_input = Slot(uri=NMDC.has_input, name="OmicsProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.OmicsProcessing_has_input, domain=OmicsProcessing, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) @@ -8865,6 +8868,14 @@ class slots: slots.FunctionalAnnotation_was_generated_by = Slot(uri=NMDC.was_generated_by, name="FunctionalAnnotation_was_generated_by", curie=NMDC.curie('was_generated_by'), model_uri=NMDC.FunctionalAnnotation_was_generated_by, domain=FunctionalAnnotation, range=Optional[Union[str, MetagenomeAnnotationActivityId]], mappings = [PROV.wasGeneratedBy]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -8892,6 +8903,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -8949,12 +8964,20 @@ class slots: slots.GeolocationValue_has_raw_value = Slot(uri=NMDC.has_raw_value, name="GeolocationValue_has_raw_value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) + slots.DissolvingActivity_material_input = Slot(uri=NMDC.material_input, name="DissolvingActivity_material_input", curie=NMDC.curie('material_input'), model_uri=NMDC.DissolvingActivity_material_input, domain=DissolvingActivity, range=Optional[Union[str, MaterialSampleId]]) slots.DissolvingActivity_material_output = Slot(uri=NMDC.material_output, name="DissolvingActivity_material_output", curie=NMDC.curie('material_output'), model_uri=NMDC.DissolvingActivity_material_output, domain=DissolvingActivity, range=Optional[Union[str, MaterialSampleId]]) +slots.MaterialSample_id = Slot(uri=NMDC.id, name="MaterialSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.MaterialSample_id, domain=MaterialSample, range=Union[str, MaterialSampleId], + pattern=re.compile(r'^nmdc:matsm')) + slots.MaterialSamplingActivity_amount_collected = Slot(uri=NMDC.amount_collected, name="MaterialSamplingActivity_amount_collected", curie=NMDC.curie('amount_collected'), model_uri=NMDC.MaterialSamplingActivity_amount_collected, domain=MaterialSamplingActivity, range=Optional[Union[dict, QuantityValue]]) @@ -9008,6 +9031,34 @@ class slots: slots.WorkflowExecutionActivity_type = Slot(uri=NMDC.type, name="WorkflowExecutionActivity_type", curie=NMDC.curie('type'), model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) +slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], + pattern=re.compile(r'^nmdc:wf')) + +slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmgas')) + +slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmtas')) + +slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmgan')) + +slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmtan')) + +slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], + pattern=re.compile(r'^nmdc:wfmt')) + +slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmag')) + slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -9020,6 +9071,14 @@ class slots: slots.ReadQcAnalysisActivity_has_output = Slot(uri=NMDC.has_output, name="ReadQcAnalysisActivity_has_output", curie=NMDC.curie('has_output'), model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) +slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrqc')) + +slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrbt')) + slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9029,14 +9088,26 @@ class slots: slots.MetabolomicsAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="MetabolomicsAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) +slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmb')) + slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.MetaproteomicsAnalysisActivity_has_peptide_quantifications = Slot(uri=NMDC.has_peptide_quantifications, name="MetaproteomicsAnalysisActivity_has_peptide_quantifications", curie=NMDC.curie('has_peptide_quantifications'), model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, PeptideQuantification], List[Union[dict, PeptideQuantification]]]]) +slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmp')) + slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.NomAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="NomAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) + +slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfnom')) diff --git a/python/portal/README.md b/python/portal/README.md new file mode 100644 index 0000000000..7d21cb294d --- /dev/null +++ b/python/portal/README.md @@ -0,0 +1,3 @@ +# Python + +Do not edit the files in here - these are autogenerated from the schema. See the Makefile for details. diff --git a/python/portal/emsl.py b/python/portal/emsl.py index e11ba5ed86..1db5f20016 100644 --- a/python/portal/emsl.py +++ b/python/portal/emsl.py @@ -1,5 +1,5 @@ # Auto generated from emsl.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:32 +# Generation date: 2023-01-20T13:16:50 # Schema: emsl # # id: https://microbiomedata/schema/emsl diff --git a/python/portal/jgi_metagenomics.py b/python/portal/jgi_metagenomics.py index 60ad0bbc33..af90352a48 100644 --- a/python/portal/jgi_metagenomics.py +++ b/python/portal/jgi_metagenomics.py @@ -1,5 +1,5 @@ # Auto generated from jgi_metagenomics.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:34 +# Generation date: 2023-01-20T13:16:43 # Schema: jgi_metagenomics # # id: https://microbiomedata/schema/jgi_metagenomics @@ -110,7 +110,8 @@ class slots: model_uri=NMDC.dna_cont_type, domain=None, range=Optional[Union[str, "DnaContTypeEnum"]]) slots.dna_cont_well = Slot(uri=NMDC.dna_cont_well, name="dna_cont_well", curie=NMDC.curie('dna_cont_well'), - model_uri=NMDC.dna_cont_well, domain=None, range=Optional[str]) + model_uri=NMDC.dna_cont_well, domain=None, range=Optional[str], + pattern=re.compile(r'^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$')) slots.dna_container_id = Slot(uri=NMDC.dna_container_id, name="dna_container_id", curie=NMDC.curie('dna_container_id'), model_uri=NMDC.dna_container_id, domain=None, range=Optional[str]) diff --git a/python/portal/jgi_metatranscriptomics.py b/python/portal/jgi_metatranscriptomics.py index 9962947cc3..041abf35ac 100644 --- a/python/portal/jgi_metatranscriptomics.py +++ b/python/portal/jgi_metatranscriptomics.py @@ -1,5 +1,5 @@ # Auto generated from jgi_metatranscriptomics.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:28 +# Generation date: 2023-01-20T13:16:46 # Schema: jgi_metatranscriptomics # # id: https://microbiomedata/schema/jgi_metatranscriptomics @@ -116,7 +116,8 @@ class slots: model_uri=NMDC.rna_cont_type, domain=None, range=Optional[Union[str, "RnaContTypeEnum"]]) slots.rna_cont_well = Slot(uri=NMDC.rna_cont_well, name="rna_cont_well", curie=NMDC.curie('rna_cont_well'), - model_uri=NMDC.rna_cont_well, domain=None, range=Optional[str]) + model_uri=NMDC.rna_cont_well, domain=None, range=Optional[str], + pattern=re.compile(r'^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$')) slots.rna_container_id = Slot(uri=NMDC.rna_container_id, name="rna_container_id", curie=NMDC.curie('rna_container_id'), model_uri=NMDC.rna_container_id, domain=None, range=Optional[str]) diff --git a/python/portal/mixs_inspired.py b/python/portal/mixs_inspired.py index 908400f411..f04a3cf25a 100644 --- a/python/portal/mixs_inspired.py +++ b/python/portal/mixs_inspired.py @@ -1,5 +1,5 @@ # Auto generated from mixs_inspired.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:29 +# Generation date: 2023-01-20T13:16:44 # Schema: mixs_inspired # # id: https://microbiomedata/schema/mixs_inspired diff --git a/python/portal/sample_id.py b/python/portal/sample_id.py index 939978fe80..c136a01774 100644 --- a/python/portal/sample_id.py +++ b/python/portal/sample_id.py @@ -1,5 +1,5 @@ # Auto generated from sample_id.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:31 +# Generation date: 2023-01-20T13:16:48 # Schema: sample_id # # id: https://microbiomedata/schema/sample_id diff --git a/python/prov.py b/python/prov.py index 10232a9005..0a3d86016c 100644 --- a/python/prov.py +++ b/python/prov.py @@ -1,5 +1,5 @@ # Auto generated from prov.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:20 +# Generation date: 2023-01-20T13:17:03 # Schema: NMDC-PROV # # id: https://microbiomedata/schema/prov @@ -258,15 +258,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -322,11 +313,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, Agent]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -1234,6 +1220,18 @@ class slots: slots.magBin__gtdbtk_species = Slot(uri=NMDC.gtdbtk_species, name="magBin__gtdbtk_species", curie=NMDC.curie('gtdbtk_species'), model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) + +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1261,6 +1259,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) diff --git a/python/sample_prep.py b/python/sample_prep.py index 88f55268bb..b09c3dfc82 100644 --- a/python/sample_prep.py +++ b/python/sample_prep.py @@ -1,5 +1,5 @@ # Auto generated from sample_prep.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:05 +# Generation date: 2023-01-20T13:16:34 # Schema: sample_prep # # id: https://microbiomedata/schema/sample_prep @@ -71,9 +71,7 @@ BIOLINK = CurieNamespace('biolink', 'https://w3id.org/biolink/vocab/') DCTERMS = CurieNamespace('dcterms', 'http://purl.org/dc/terms/') GTPO = CurieNamespace('gtpo', 'https://unknown.to.linter.org/') -INSDC_SRS = CurieNamespace('insdc_srs', 'https://unknown.to.linter.org/') LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -MGNIFY = CurieNamespace('mgnify', 'https://unknown.to.linter.org/') MIXS = CurieNamespace('mixs', 'https://w3id.org/mixs/') NMDC = CurieNamespace('nmdc', 'https://w3id.org/nmdc/') PROV = CurieNamespace('prov', 'http://www.w3.org/ns/prov#') @@ -1025,15 +1023,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class Biosample(MaterialEntity): """ @@ -2036,11 +2025,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, "Agent"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -8327,7 +8311,8 @@ class slots: model_uri=NMDC.dna_cont_type, domain=None, range=Optional[Union[str, "DnaContTypeEnum"]]) slots.dna_cont_well = Slot(uri=NMDC.dna_cont_well, name="dna_cont_well", curie=NMDC.curie('dna_cont_well'), - model_uri=NMDC.dna_cont_well, domain=None, range=Optional[str]) + model_uri=NMDC.dna_cont_well, domain=None, range=Optional[str], + pattern=re.compile(r'^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$')) slots.dna_container_id = Slot(uri=NMDC.dna_container_id, name="dna_container_id", curie=NMDC.curie('dna_container_id'), model_uri=NMDC.dna_container_id, domain=None, range=Optional[str]) @@ -8390,7 +8375,8 @@ class slots: model_uri=NMDC.rna_cont_type, domain=None, range=Optional[Union[str, "RnaContTypeEnum"]]) slots.rna_cont_well = Slot(uri=NMDC.rna_cont_well, name="rna_cont_well", curie=NMDC.curie('rna_cont_well'), - model_uri=NMDC.rna_cont_well, domain=None, range=Optional[str]) + model_uri=NMDC.rna_cont_well, domain=None, range=Optional[str], + pattern=re.compile(r'^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$')) slots.rna_container_id = Slot(uri=NMDC.rna_container_id, name="rna_container_id", curie=NMDC.curie('rna_container_id'), model_uri=NMDC.rna_container_id, domain=None, range=Optional[str]) @@ -8691,6 +8677,10 @@ class slots: slots.DissolvingActivity_material_output = Slot(uri=NMDC.material_output, name="DissolvingActivity_material_output", curie=NMDC.curie('material_output'), model_uri=NMDC.DissolvingActivity_material_output, domain=DissolvingActivity, range=Optional[Union[str, MaterialSampleId]]) +slots.MaterialSample_id = Slot(uri=NMDC.id, name="MaterialSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.MaterialSample_id, domain=MaterialSample, range=Union[str, MaterialSampleId], + pattern=re.compile(r'^nmdc:matsm')) + slots.MaterialSamplingActivity_amount_collected = Slot(uri=NMDC.amount_collected, name="MaterialSamplingActivity_amount_collected", curie=NMDC.curie('amount_collected'), model_uri=NMDC.MaterialSamplingActivity_amount_collected, domain=MaterialSamplingActivity, range=Optional[Union[dict, "QuantityValue"]]) @@ -8724,21 +8714,33 @@ class slots: slots.Database_metatranscriptome_activity_set = Slot(uri=NMDC.metatranscriptome_activity_set, name="Database_metatranscriptome_activity_set", curie=NMDC.curie('metatranscriptome_activity_set'), model_uri=NMDC.Database_metatranscriptome_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]]) +slots.FieldResearchSite_id = Slot(uri=NMDC.id, name="FieldResearchSite_id", curie=NMDC.curie('id'), + model_uri=NMDC.FieldResearchSite_id, domain=FieldResearchSite, range=Union[str, FieldResearchSiteId], + pattern=re.compile(r'^nmdc:frsite')) + slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) slots.CollectingBiosamplesFromSite_has_outputs = Slot(uri=NMDC.has_outputs, name="CollectingBiosamplesFromSite_has_outputs", curie=NMDC.curie('has_outputs'), model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) +slots.CollectingBiosamplesFromSite_id = Slot(uri=NMDC.id, name="CollectingBiosamplesFromSite_id", curie=NMDC.curie('id'), + model_uri=NMDC.CollectingBiosamplesFromSite_id, domain=CollectingBiosamplesFromSite, range=Union[str, CollectingBiosamplesFromSiteId], + pattern=re.compile(r'^nmdc:clsite')) + slots.DataObject_name = Slot(uri=NMDC.name, name="DataObject_name", curie=NMDC.curie('name'), model_uri=NMDC.DataObject_name, domain=DataObject, range=str) slots.DataObject_description = Slot(uri=DCTERMS.description, name="DataObject_description", curie=DCTERMS.curie('description'), model_uri=NMDC.DataObject_description, domain=DataObject, range=str) +slots.DataObject_id = Slot(uri=NMDC.id, name="DataObject_id", curie=NMDC.curie('id'), + model_uri=NMDC.DataObject_id, domain=DataObject, range=Union[str, DataObjectId], + pattern=re.compile(r'^nmdc:dobj')) + slots.Biosample_id = Slot(uri=NMDC.id, name="Biosample_id", curie=NMDC.curie('id'), model_uri=NMDC.Biosample_id, domain=Biosample, range=Union[str, BiosampleId], - pattern=re.compile(r'^nmdc:')) + pattern=re.compile(r'^nmdc:bsm')) slots.Biosample_gold_biosample_identifiers = Slot(uri=NMDC.gold_biosample_identifiers, name="Biosample_gold_biosample_identifiers", curie=NMDC.curie('gold_biosample_identifiers'), model_uri=NMDC.Biosample_gold_biosample_identifiers, domain=Biosample, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]], @@ -8769,7 +8771,8 @@ class slots: model_uri=NMDC.Biosample_extreme_event, domain=Biosample, range=Optional[str]) slots.Study_id = Slot(uri=NMDC.id, name="Study_id", curie=NMDC.curie('id'), - model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId]) + model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId], + pattern=re.compile(r'^nmdc:sty')) slots.Study_doi = Slot(uri=NMDC.doi, name="Study_doi", curie=NMDC.curie('doi'), model_uri=NMDC.Study_doi, domain=Study, range=Optional[Union[dict, "AttributeValue"]]) @@ -8806,17 +8809,27 @@ class slots: model_uri=NMDC.Study_emsl_proposal_doi, domain=Study, range=Optional[str]) slots.BiosampleProcessing_id = Slot(uri=NMDC.id, name="BiosampleProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId]) + model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId], + pattern=re.compile(r'^nmdc:bsmprc')) slots.BiosampleProcessing_has_input = Slot(uri=NMDC.has_input, name="BiosampleProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.BiosampleProcessing_has_input, domain=BiosampleProcessing, range=Optional[Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]]) slots.OmicsProcessing_id = Slot(uri=NMDC.id, name="OmicsProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId]) + model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId], + pattern=re.compile(r'^nmdc:omprc')) slots.OmicsProcessing_has_input = Slot(uri=NMDC.has_input, name="OmicsProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.OmicsProcessing_has_input, domain=OmicsProcessing, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -8844,6 +8857,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -8971,6 +8988,10 @@ class slots: slots.FunctionalAnnotation_was_generated_by = Slot(uri=NMDC.was_generated_by, name="FunctionalAnnotation_was_generated_by", curie=NMDC.curie('was_generated_by'), model_uri=NMDC.FunctionalAnnotation_was_generated_by, domain=FunctionalAnnotation, range=Optional[Union[str, MetagenomeAnnotationActivityId]], mappings = [PROV.wasGeneratedBy]) +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) + slots.WorkflowExecutionActivity_was_associated_with = Slot(uri=NMDC.was_associated_with, name="WorkflowExecutionActivity_was_associated_with", curie=NMDC.curie('was_associated_with'), model_uri=NMDC.WorkflowExecutionActivity_was_associated_with, domain=WorkflowExecutionActivity, range=Optional[Union[str, WorkflowExecutionActivityId]], mappings = [PROV.wasAssociatedWith]) @@ -9000,6 +9021,34 @@ class slots: slots.WorkflowExecutionActivity_type = Slot(uri=NMDC.type, name="WorkflowExecutionActivity_type", curie=NMDC.curie('type'), model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) +slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], + pattern=re.compile(r'^nmdc:wf')) + +slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmgas')) + +slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmtas')) + +slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmgan')) + +slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmtan')) + +slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], + pattern=re.compile(r'^nmdc:wfmt')) + +slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmag')) + slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -9012,6 +9061,14 @@ class slots: slots.ReadQcAnalysisActivity_has_output = Slot(uri=NMDC.has_output, name="ReadQcAnalysisActivity_has_output", curie=NMDC.curie('has_output'), model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) +slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrqc')) + +slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrbt')) + slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9021,14 +9078,26 @@ class slots: slots.MetabolomicsAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="MetabolomicsAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) +slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmb')) + slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.MetaproteomicsAnalysisActivity_has_peptide_quantifications = Slot(uri=NMDC.has_peptide_quantifications, name="MetaproteomicsAnalysisActivity_has_peptide_quantifications", curie=NMDC.curie('has_peptide_quantifications'), model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, PeptideQuantification], List[Union[dict, PeptideQuantification]]]]) +slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmp')) + slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.NomAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="NomAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) + +slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfnom')) diff --git a/python/workflow_execution_activity.py b/python/workflow_execution_activity.py index 0ca0547b61..b0dfd52910 100644 --- a/python/workflow_execution_activity.py +++ b/python/workflow_execution_activity.py @@ -1,5 +1,5 @@ # Auto generated from workflow_execution_activity.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-22T13:47:01 +# Generation date: 2023-01-20T13:17:01 # Schema: NMDC-Workflow-Execution # # id: https://microbiomedata/schema/workflow_execution_activity @@ -1076,15 +1076,6 @@ class MaterialEntity(NamedThing): id: Union[str, MaterialEntityId] = None - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MaterialEntityId): - self.id = MaterialEntityId(self.id) - - super().__post_init__(**kwargs) - - @dataclass class AnalyticalSample(MaterialEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -1140,11 +1131,6 @@ class PlannedProcess(NamedThing): participating_agent: Optional[Union[dict, Agent]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PlannedProcessId): - self.id = PlannedProcessId(self.id) - if not isinstance(self.has_inputs, list): self.has_inputs = [self.has_inputs] if self.has_inputs is not None else [] self.has_inputs = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_inputs] @@ -2291,6 +2277,34 @@ class slots: slots.WorkflowExecutionActivity_type = Slot(uri=NMDC.type, name="WorkflowExecutionActivity_type", curie=NMDC.curie('type'), model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) +slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], + pattern=re.compile(r'^nmdc:wf')) + +slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmgas')) + +slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], + pattern=re.compile(r'^nmdc:wfmtas')) + +slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmgan')) + +slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], + pattern=re.compile(r'^nmdc:wfmtan')) + +slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], + pattern=re.compile(r'^nmdc:wfmt')) + +slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmag')) + slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -2303,6 +2317,14 @@ class slots: slots.ReadQcAnalysisActivity_has_output = Slot(uri=NMDC.has_output, name="ReadQcAnalysisActivity_has_output", curie=NMDC.curie('has_output'), model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) +slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrqc')) + +slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfrbt')) + slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2312,18 +2334,42 @@ class slots: slots.MetabolomicsAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="MetabolomicsAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) +slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmb')) + slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.MetaproteomicsAnalysisActivity_has_peptide_quantifications = Slot(uri=NMDC.has_peptide_quantifications, name="MetaproteomicsAnalysisActivity_has_peptide_quantifications", curie=NMDC.curie('has_peptide_quantifications'), model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, "PeptideQuantification"], List[Union[dict, "PeptideQuantification"]]]]) +slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfmp')) + slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) slots.NomAnalysisActivity_has_calibration = Slot(uri=NMDC.has_calibration, name="NomAnalysisActivity_has_calibration", curie=NMDC.curie('has_calibration'), model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) +slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], + pattern=re.compile(r'^nmdc:wfnom')) + +slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], + pattern=re.compile(r'^nmdc:act')) + +slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], + pattern=re.compile(r'^nmdc:ansm')) + +slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], + pattern=re.compile(r'^nmdc:site')) + slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -2351,6 +2397,10 @@ class slots: slots.Person_id = Slot(uri=NMDC.id, name="Person_id", curie=NMDC.curie('id'), model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) +slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], + pattern=re.compile(r'^nmdc:inst')) + slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) From 6ea29e14221e44add6b12158230e2254e4bbe638 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Fri, 20 Jan 2023 15:27:52 -0500 Subject: [PATCH 58/60] #632 only structured_patterns --- Makefile | 1 + json/nmdc.linkml.json | 48 ------------ jsonld-context/nmdc.context.jsonld | 2 +- nmdc_schema/annotation.py | 50 +++++-------- nmdc_schema/basic_slots.py | 14 ++-- nmdc_schema/bioscales.py | 14 ++-- nmdc_schema/core.py | 14 ++-- nmdc_schema/external_identifiers.py | 14 ++-- nmdc_schema/mixs.py | 14 ++-- nmdc_schema/nmdc.py | 74 +++++++------------ nmdc_schema/nmdc.yaml | 16 ++-- nmdc_schema/prov.py | 14 ++-- nmdc_schema/sample_prep.py | 74 +++++++------------ nmdc_schema/workflow_execution_activity.py | 50 +++++-------- python/annotation.py | 50 +++++-------- python/basic_slots.py | 14 ++-- python/bioscales.py | 14 ++-- python/core.py | 14 ++-- python/external_identifiers.py | 14 ++-- python/mixs.py | 14 ++-- python/nmdc.py | 74 +++++++------------ python/portal/emsl.py | 2 +- python/portal/jgi_metagenomics.py | 2 +- python/portal/jgi_metatranscriptomics.py | 2 +- python/portal/mixs_inspired.py | 2 +- python/portal/sample_id.py | 2 +- python/prov.py | 14 ++-- python/sample_prep.py | 74 +++++++------------ python/workflow_execution_activity.py | 50 +++++-------- src/schema/core.yaml | 6 +- src/schema/nmdc.yaml | 16 ++-- src/schema/prov.yaml | 8 +- src/schema/sample_prep.yaml | 2 +- src/schema/workflow_execution_activity.yaml | 24 +++--- .../biosample_incomplete_napa_id.json | 54 ++++++++++++++ 35 files changed, 325 insertions(+), 526 deletions(-) create mode 100644 test/data/invalid_data/biosample_incomplete_napa_id.json diff --git a/Makefile b/Makefile index 46318f5c82..77b3d554e6 100644 --- a/Makefile +++ b/Makefile @@ -252,6 +252,7 @@ SCHEMA_TEST_EXAMPLES := \ study_test SCHEMA_TEST_EXAMPLES_INVALID := \ + biosample_incomplete_napa_id \ biosample_invalid_range \ biosample_mismatch_regex \ biosample_missing_required_field \ diff --git a/json/nmdc.linkml.json b/json/nmdc.linkml.json index 3c0f208cd4..6a3eced919 100644 --- a/json/nmdc.linkml.json +++ b/json/nmdc.linkml.json @@ -23469,7 +23469,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:frsite", "structured_pattern": { "syntax": "{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -23493,7 +23492,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:frsite", "structured_pattern": { "syntax": "{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -23585,7 +23583,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:clsite", "structured_pattern": { "syntax": "{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -23649,7 +23646,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:clsite", "structured_pattern": { "syntax": "{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -23756,7 +23752,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:dobj", "structured_pattern": { "syntax": "{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -23910,7 +23905,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:dobj", "structured_pattern": { "syntax": "{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -24239,7 +24233,6 @@ "NamedThing" ], "required": true, - "pattern": "^nmdc:bsm", "structured_pattern": { "syntax": "{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -24495,7 +24488,6 @@ ], "range": "string", "required": true, - "pattern": "^nmdc:bsm", "structured_pattern": { "syntax": "{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -31277,7 +31269,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:sty", "structured_pattern": { "syntax": "{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -31428,7 +31419,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:sty", "structured_pattern": { "syntax": "{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -31969,7 +31959,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:bsmprc", "structured_pattern": { "syntax": "{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -32020,7 +32009,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:bsmprc", "structured_pattern": { "syntax": "{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -32149,7 +32137,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:omprc", "structured_pattern": { "syntax": "{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -32750,7 +32737,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:omprc", "structured_pattern": { "syntax": "{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -33872,7 +33858,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:wf", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -34005,7 +33990,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:wf", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -34155,7 +34139,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:wfmgas", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -34683,7 +34666,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:wfmgas", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -34851,7 +34833,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:wfmtas", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -35409,7 +35390,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:wfmtas", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -35568,7 +35548,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:wfmgan", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -35817,7 +35796,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:wfmgan", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -35995,7 +35973,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:wfmtan", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -36283,7 +36260,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:wfmtan", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -36485,7 +36461,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:wfmt", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -36793,7 +36768,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:wfmt", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -37030,7 +37004,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:wfmag", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -37446,7 +37419,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:wfmag", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -37752,7 +37724,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:wfrqc", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -38143,7 +38114,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:wfrqc", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -38442,7 +38412,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:wfrbt", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -38886,7 +38855,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:wfrbt", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -39250,7 +39218,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:wfmb", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -39753,7 +39720,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:wfmb", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -40156,7 +40122,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:wfmp", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -40722,7 +40687,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:wfmp", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -41174,7 +41138,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:wfnom", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -41807,7 +41770,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:wfnom", "structured_pattern": { "syntax": "{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -42292,7 +42254,6 @@ "Activity", "NamedThing" ], - "pattern": "^nmdc:act", "structured_pattern": { "syntax": "{id_nmdc_prefix}:act-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -42336,7 +42297,6 @@ "NamedThing" ], "range": "string", - "pattern": "^nmdc:act", "structured_pattern": { "syntax": "{id_nmdc_prefix}:act-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -42927,7 +42887,6 @@ "NamedThing", "MaterialEntity" ], - "pattern": "^nmdc:ansm", "structured_pattern": { "syntax": "{id_nmdc_prefix}:ansm-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -42969,7 +42928,6 @@ "MaterialEntity" ], "range": "string", - "pattern": "^nmdc:ansm", "structured_pattern": { "syntax": "{id_nmdc_prefix}:ansm-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -43172,7 +43130,6 @@ "MaterialEntity", "AnalyticalSample" ], - "pattern": "^nmdc:site", "structured_pattern": { "syntax": "{id_nmdc_prefix}:site-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -43215,7 +43172,6 @@ "AnalyticalSample" ], "range": "string", - "pattern": "^nmdc:site", "structured_pattern": { "syntax": "{id_nmdc_prefix}:site-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -45116,7 +45072,6 @@ "EnvironmentalMaterialTerm", "Person" ], - "pattern": "^nmdc:inst", "structured_pattern": { "syntax": "{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -45164,7 +45119,6 @@ "Person" ], "range": "string", - "pattern": "^nmdc:inst", "structured_pattern": { "syntax": "{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -46918,7 +46872,6 @@ "ChemicalEntity", "GeneProduct" ], - "pattern": "^nmdc:matsm", "structured_pattern": { "syntax": "{id_nmdc_prefix}:matsm-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, @@ -46969,7 +46922,6 @@ "GeneProduct" ], "range": "string", - "pattern": "^nmdc:matsm", "structured_pattern": { "syntax": "{id_nmdc_prefix}:matsm-{id_shoulder}-{id_blade}{id_version}{id_locus}", "interpolated": true, diff --git a/jsonld-context/nmdc.context.jsonld b/jsonld-context/nmdc.context.jsonld index 941af6aa44..30d30031bf 100644 --- a/jsonld-context/nmdc.context.jsonld +++ b/jsonld-context/nmdc.context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-01-20T13:16:29", + "generation_date": "2023-01-20T15:23:06", "source": "nmdc.yaml" }, "@context": { diff --git a/nmdc_schema/annotation.py b/nmdc_schema/annotation.py index 1d35f0330d..f2fc0ad9c8 100644 --- a/nmdc_schema/annotation.py +++ b/nmdc_schema/annotation.py @@ -1,5 +1,5 @@ # Auto generated from annotation.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:52 +# Generation date: 2023-01-20T15:23:36 # Schema: NMDC-Annotation # # id: https://microbiomedata/schema/annotation @@ -2668,12 +2668,10 @@ class slots: model_uri=NMDC.FunctionalAnnotation_was_generated_by, domain=FunctionalAnnotation, range=Optional[Union[str, MetagenomeAnnotationActivityId]], mappings = [PROV.wasGeneratedBy]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -2703,8 +2701,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -2764,8 +2761,7 @@ class slots: model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) slots.WorkflowExecutionActivity_was_associated_with = Slot(uri=NMDC.was_associated_with, name="WorkflowExecutionActivity_was_associated_with", curie=NMDC.curie('was_associated_with'), model_uri=NMDC.WorkflowExecutionActivity_was_associated_with, domain=WorkflowExecutionActivity, range=Optional[Union[str, WorkflowExecutionActivityId]], mappings = [PROV.wasAssociatedWith]) @@ -2797,32 +2793,25 @@ class slots: model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], - pattern=re.compile(r'^nmdc:wf')) + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId]) slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmgas')) + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId]) slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmtas')) + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId]) slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmgan')) + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId]) slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmtan')) + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId]) slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], - pattern=re.compile(r'^nmdc:wfmt')) + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId]) slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmag')) + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId]) slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -2837,12 +2826,10 @@ class slots: model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrqc')) + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId]) slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrbt')) + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId]) slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2854,8 +2841,7 @@ class slots: model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmb')) + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId]) slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2864,8 +2850,7 @@ class slots: model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, PeptideQuantification], List[Union[dict, PeptideQuantification]]]]) slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmp')) + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId]) slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2874,5 +2859,4 @@ class slots: model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfnom')) + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId]) diff --git a/nmdc_schema/basic_slots.py b/nmdc_schema/basic_slots.py index 3caaf63148..8a574812dc 100644 --- a/nmdc_schema/basic_slots.py +++ b/nmdc_schema/basic_slots.py @@ -1,5 +1,5 @@ # Auto generated from basic_slots.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:40 +# Generation date: 2023-01-20T15:23:20 # Schema: NMDC-Basic-Slots # # id: https://microbiomedata/schema/basic_slots @@ -1223,12 +1223,10 @@ class slots: model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1258,8 +1256,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1319,5 +1316,4 @@ class slots: model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) diff --git a/nmdc_schema/bioscales.py b/nmdc_schema/bioscales.py index c096d0d0dc..d2af60bebb 100644 --- a/nmdc_schema/bioscales.py +++ b/nmdc_schema/bioscales.py @@ -1,5 +1,5 @@ # Auto generated from bioscales.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:17:05 +# Generation date: 2023-01-20T15:23:55 # Schema: NMDC-Bioscales # # id: https://microbiomedata/schema/bioscales @@ -1245,12 +1245,10 @@ class slots: model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1280,8 +1278,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1341,5 +1338,4 @@ class slots: model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) diff --git a/nmdc_schema/core.py b/nmdc_schema/core.py index b93015a04e..d8660fdeaf 100644 --- a/nmdc_schema/core.py +++ b/nmdc_schema/core.py @@ -1,5 +1,5 @@ # Auto generated from core.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:17:14 +# Generation date: 2023-01-20T15:24:05 # Schema: NMDC-Core # # id: https://microbiomedata/schema/core @@ -1224,12 +1224,10 @@ class slots: model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1259,8 +1257,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1320,5 +1317,4 @@ class slots: model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) diff --git a/nmdc_schema/external_identifiers.py b/nmdc_schema/external_identifiers.py index 1215e5e6da..b668665c04 100644 --- a/nmdc_schema/external_identifiers.py +++ b/nmdc_schema/external_identifiers.py @@ -1,5 +1,5 @@ # Auto generated from external_identifiers.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:54 +# Generation date: 2023-01-20T15:23:39 # Schema: external_identifiers # # id: https://microbiomedata/schema/external_identifiers @@ -1308,12 +1308,10 @@ class slots: model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1343,8 +1341,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1404,5 +1401,4 @@ class slots: model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) diff --git a/nmdc_schema/mixs.py b/nmdc_schema/mixs.py index 8fcb469f11..c7a0cfa8d1 100644 --- a/nmdc_schema/mixs.py +++ b/nmdc_schema/mixs.py @@ -1,5 +1,5 @@ # Auto generated from mixs.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:58 +# Generation date: 2023-01-20T15:23:45 # Schema: mixs-schema # # id: https://microbiomedata/schema/mixs @@ -4663,12 +4663,10 @@ class slots: model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -4698,8 +4696,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -4759,5 +4756,4 @@ class slots: model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) diff --git a/nmdc_schema/nmdc.py b/nmdc_schema/nmdc.py index 85464f8111..4f4607982b 100644 --- a/nmdc_schema/nmdc.py +++ b/nmdc_schema/nmdc.py @@ -1,5 +1,5 @@ # Auto generated from nmdc.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:17:08 +# Generation date: 2023-01-20T15:23:58 # Schema: NMDC # # id: https://microbiomedata/schema @@ -8691,8 +8691,7 @@ class slots: model_uri=NMDC.Database_metatranscriptome_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]]) slots.FieldResearchSite_id = Slot(uri=NMDC.id, name="FieldResearchSite_id", curie=NMDC.curie('id'), - model_uri=NMDC.FieldResearchSite_id, domain=FieldResearchSite, range=Union[str, FieldResearchSiteId], - pattern=re.compile(r'^nmdc:frsite')) + model_uri=NMDC.FieldResearchSite_id, domain=FieldResearchSite, range=Union[str, FieldResearchSiteId]) slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) @@ -8701,8 +8700,7 @@ class slots: model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) slots.CollectingBiosamplesFromSite_id = Slot(uri=NMDC.id, name="CollectingBiosamplesFromSite_id", curie=NMDC.curie('id'), - model_uri=NMDC.CollectingBiosamplesFromSite_id, domain=CollectingBiosamplesFromSite, range=Union[str, CollectingBiosamplesFromSiteId], - pattern=re.compile(r'^nmdc:clsite')) + model_uri=NMDC.CollectingBiosamplesFromSite_id, domain=CollectingBiosamplesFromSite, range=Union[str, CollectingBiosamplesFromSiteId]) slots.DataObject_name = Slot(uri=NMDC.name, name="DataObject_name", curie=NMDC.curie('name'), model_uri=NMDC.DataObject_name, domain=DataObject, range=str) @@ -8711,12 +8709,10 @@ class slots: model_uri=NMDC.DataObject_description, domain=DataObject, range=str) slots.DataObject_id = Slot(uri=NMDC.id, name="DataObject_id", curie=NMDC.curie('id'), - model_uri=NMDC.DataObject_id, domain=DataObject, range=Union[str, DataObjectId], - pattern=re.compile(r'^nmdc:dobj')) + model_uri=NMDC.DataObject_id, domain=DataObject, range=Union[str, DataObjectId]) slots.Biosample_id = Slot(uri=NMDC.id, name="Biosample_id", curie=NMDC.curie('id'), - model_uri=NMDC.Biosample_id, domain=Biosample, range=Union[str, BiosampleId], - pattern=re.compile(r'^nmdc:bsm')) + model_uri=NMDC.Biosample_id, domain=Biosample, range=Union[str, BiosampleId]) slots.Biosample_gold_biosample_identifiers = Slot(uri=NMDC.gold_biosample_identifiers, name="Biosample_gold_biosample_identifiers", curie=NMDC.curie('gold_biosample_identifiers'), model_uri=NMDC.Biosample_gold_biosample_identifiers, domain=Biosample, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]], @@ -8747,8 +8743,7 @@ class slots: model_uri=NMDC.Biosample_extreme_event, domain=Biosample, range=Optional[str]) slots.Study_id = Slot(uri=NMDC.id, name="Study_id", curie=NMDC.curie('id'), - model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId], - pattern=re.compile(r'^nmdc:sty')) + model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId]) slots.Study_doi = Slot(uri=NMDC.doi, name="Study_doi", curie=NMDC.curie('doi'), model_uri=NMDC.Study_doi, domain=Study, range=Optional[Union[dict, "AttributeValue"]]) @@ -8785,15 +8780,13 @@ class slots: model_uri=NMDC.Study_emsl_proposal_doi, domain=Study, range=Optional[str]) slots.BiosampleProcessing_id = Slot(uri=NMDC.id, name="BiosampleProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId], - pattern=re.compile(r'^nmdc:bsmprc')) + model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId]) slots.BiosampleProcessing_has_input = Slot(uri=NMDC.has_input, name="BiosampleProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.BiosampleProcessing_has_input, domain=BiosampleProcessing, range=Optional[Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]]) slots.OmicsProcessing_id = Slot(uri=NMDC.id, name="OmicsProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId], - pattern=re.compile(r'^nmdc:omprc')) + model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId]) slots.OmicsProcessing_has_input = Slot(uri=NMDC.has_input, name="OmicsProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.OmicsProcessing_has_input, domain=OmicsProcessing, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) @@ -8869,12 +8862,10 @@ class slots: model_uri=NMDC.FunctionalAnnotation_was_generated_by, domain=FunctionalAnnotation, range=Optional[Union[str, MetagenomeAnnotationActivityId]], mappings = [PROV.wasGeneratedBy]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -8904,8 +8895,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -8965,8 +8955,7 @@ class slots: model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) slots.DissolvingActivity_material_input = Slot(uri=NMDC.material_input, name="DissolvingActivity_material_input", curie=NMDC.curie('material_input'), model_uri=NMDC.DissolvingActivity_material_input, domain=DissolvingActivity, range=Optional[Union[str, MaterialSampleId]]) @@ -8975,8 +8964,7 @@ class slots: model_uri=NMDC.DissolvingActivity_material_output, domain=DissolvingActivity, range=Optional[Union[str, MaterialSampleId]]) slots.MaterialSample_id = Slot(uri=NMDC.id, name="MaterialSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.MaterialSample_id, domain=MaterialSample, range=Union[str, MaterialSampleId], - pattern=re.compile(r'^nmdc:matsm')) + model_uri=NMDC.MaterialSample_id, domain=MaterialSample, range=Union[str, MaterialSampleId]) slots.MaterialSamplingActivity_amount_collected = Slot(uri=NMDC.amount_collected, name="MaterialSamplingActivity_amount_collected", curie=NMDC.curie('amount_collected'), model_uri=NMDC.MaterialSamplingActivity_amount_collected, domain=MaterialSamplingActivity, range=Optional[Union[dict, QuantityValue]]) @@ -9032,32 +9020,25 @@ class slots: model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], - pattern=re.compile(r'^nmdc:wf')) + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId]) slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmgas')) + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId]) slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmtas')) + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId]) slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmgan')) + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId]) slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmtan')) + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId]) slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], - pattern=re.compile(r'^nmdc:wfmt')) + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId]) slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmag')) + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId]) slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -9072,12 +9053,10 @@ class slots: model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrqc')) + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId]) slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrbt')) + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId]) slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9089,8 +9068,7 @@ class slots: model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmb')) + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId]) slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9099,8 +9077,7 @@ class slots: model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, PeptideQuantification], List[Union[dict, PeptideQuantification]]]]) slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmp')) + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId]) slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9109,5 +9086,4 @@ class slots: model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfnom')) + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId]) diff --git a/nmdc_schema/nmdc.yaml b/nmdc_schema/nmdc.yaml index 21ed057b1f..af5843c96f 100644 --- a/nmdc_schema/nmdc.yaml +++ b/nmdc_schema/nmdc.yaml @@ -94,7 +94,7 @@ imports: settings: id_nmdc_prefix: "^(nmdc)" -# id_typecode: "([a-z]{1,6})" + # id_typecode: "([a-z]{1,6})" id_shoulder: "([0-9][a-z]{0,6}[0-9])" id_blade: "([A-Za-z0-9]{1,})" id_version: "(\\.[A-Za-z0-9]{1,})*" @@ -175,7 +175,7 @@ classes: - "might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833" slot_usage: id: - pattern: '^nmdc:frsite' + # pattern: '^nmdc:frsite' structured_pattern: syntax: "{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -198,7 +198,7 @@ classes: range: Biosample required: true id: - pattern: '^nmdc:clsite' + # pattern: '^nmdc:clsite' structured_pattern: syntax: "{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -227,7 +227,7 @@ classes: description: required: true id: - pattern: '^nmdc:dobj' + # pattern: '^nmdc:dobj' structured_pattern: syntax: "{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -517,7 +517,7 @@ classes: id: description: An NMDC assigned unique identifier for a biosample submitted to NMDC. required: true - pattern: '^nmdc:bsm' + # pattern: '^nmdc:bsm' structured_pattern: syntax: "{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -622,7 +622,7 @@ classes: - study_image slot_usage: id: - pattern: '^nmdc:sty' + # pattern: '^nmdc:sty' structured_pattern: syntax: "{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -723,7 +723,7 @@ classes: - has_input slot_usage: id: - pattern: '^nmdc:bsmprc' + # pattern: '^nmdc:bsmprc' structured_pattern: syntax: "{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -775,7 +775,7 @@ classes: slot_usage: id: - pattern: '^nmdc:omprc' + # pattern: '^nmdc:omprc' structured_pattern: syntax: "{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true diff --git a/nmdc_schema/prov.py b/nmdc_schema/prov.py index 0a3d86016c..69f002e516 100644 --- a/nmdc_schema/prov.py +++ b/nmdc_schema/prov.py @@ -1,5 +1,5 @@ # Auto generated from prov.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:17:03 +# Generation date: 2023-01-20T15:23:51 # Schema: NMDC-PROV # # id: https://microbiomedata/schema/prov @@ -1221,16 +1221,13 @@ class slots: model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1260,8 +1257,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) diff --git a/nmdc_schema/sample_prep.py b/nmdc_schema/sample_prep.py index b09c3dfc82..a6bbdb2a7b 100644 --- a/nmdc_schema/sample_prep.py +++ b/nmdc_schema/sample_prep.py @@ -1,5 +1,5 @@ # Auto generated from sample_prep.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:34 +# Generation date: 2023-01-20T15:23:13 # Schema: sample_prep # # id: https://microbiomedata/schema/sample_prep @@ -8678,8 +8678,7 @@ class slots: model_uri=NMDC.DissolvingActivity_material_output, domain=DissolvingActivity, range=Optional[Union[str, MaterialSampleId]]) slots.MaterialSample_id = Slot(uri=NMDC.id, name="MaterialSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.MaterialSample_id, domain=MaterialSample, range=Union[str, MaterialSampleId], - pattern=re.compile(r'^nmdc:matsm')) + model_uri=NMDC.MaterialSample_id, domain=MaterialSample, range=Union[str, MaterialSampleId]) slots.MaterialSamplingActivity_amount_collected = Slot(uri=NMDC.amount_collected, name="MaterialSamplingActivity_amount_collected", curie=NMDC.curie('amount_collected'), model_uri=NMDC.MaterialSamplingActivity_amount_collected, domain=MaterialSamplingActivity, range=Optional[Union[dict, "QuantityValue"]]) @@ -8715,8 +8714,7 @@ class slots: model_uri=NMDC.Database_metatranscriptome_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]]) slots.FieldResearchSite_id = Slot(uri=NMDC.id, name="FieldResearchSite_id", curie=NMDC.curie('id'), - model_uri=NMDC.FieldResearchSite_id, domain=FieldResearchSite, range=Union[str, FieldResearchSiteId], - pattern=re.compile(r'^nmdc:frsite')) + model_uri=NMDC.FieldResearchSite_id, domain=FieldResearchSite, range=Union[str, FieldResearchSiteId]) slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) @@ -8725,8 +8723,7 @@ class slots: model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) slots.CollectingBiosamplesFromSite_id = Slot(uri=NMDC.id, name="CollectingBiosamplesFromSite_id", curie=NMDC.curie('id'), - model_uri=NMDC.CollectingBiosamplesFromSite_id, domain=CollectingBiosamplesFromSite, range=Union[str, CollectingBiosamplesFromSiteId], - pattern=re.compile(r'^nmdc:clsite')) + model_uri=NMDC.CollectingBiosamplesFromSite_id, domain=CollectingBiosamplesFromSite, range=Union[str, CollectingBiosamplesFromSiteId]) slots.DataObject_name = Slot(uri=NMDC.name, name="DataObject_name", curie=NMDC.curie('name'), model_uri=NMDC.DataObject_name, domain=DataObject, range=str) @@ -8735,12 +8732,10 @@ class slots: model_uri=NMDC.DataObject_description, domain=DataObject, range=str) slots.DataObject_id = Slot(uri=NMDC.id, name="DataObject_id", curie=NMDC.curie('id'), - model_uri=NMDC.DataObject_id, domain=DataObject, range=Union[str, DataObjectId], - pattern=re.compile(r'^nmdc:dobj')) + model_uri=NMDC.DataObject_id, domain=DataObject, range=Union[str, DataObjectId]) slots.Biosample_id = Slot(uri=NMDC.id, name="Biosample_id", curie=NMDC.curie('id'), - model_uri=NMDC.Biosample_id, domain=Biosample, range=Union[str, BiosampleId], - pattern=re.compile(r'^nmdc:bsm')) + model_uri=NMDC.Biosample_id, domain=Biosample, range=Union[str, BiosampleId]) slots.Biosample_gold_biosample_identifiers = Slot(uri=NMDC.gold_biosample_identifiers, name="Biosample_gold_biosample_identifiers", curie=NMDC.curie('gold_biosample_identifiers'), model_uri=NMDC.Biosample_gold_biosample_identifiers, domain=Biosample, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]], @@ -8771,8 +8766,7 @@ class slots: model_uri=NMDC.Biosample_extreme_event, domain=Biosample, range=Optional[str]) slots.Study_id = Slot(uri=NMDC.id, name="Study_id", curie=NMDC.curie('id'), - model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId], - pattern=re.compile(r'^nmdc:sty')) + model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId]) slots.Study_doi = Slot(uri=NMDC.doi, name="Study_doi", curie=NMDC.curie('doi'), model_uri=NMDC.Study_doi, domain=Study, range=Optional[Union[dict, "AttributeValue"]]) @@ -8809,26 +8803,22 @@ class slots: model_uri=NMDC.Study_emsl_proposal_doi, domain=Study, range=Optional[str]) slots.BiosampleProcessing_id = Slot(uri=NMDC.id, name="BiosampleProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId], - pattern=re.compile(r'^nmdc:bsmprc')) + model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId]) slots.BiosampleProcessing_has_input = Slot(uri=NMDC.has_input, name="BiosampleProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.BiosampleProcessing_has_input, domain=BiosampleProcessing, range=Optional[Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]]) slots.OmicsProcessing_id = Slot(uri=NMDC.id, name="OmicsProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId], - pattern=re.compile(r'^nmdc:omprc')) + model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId]) slots.OmicsProcessing_has_input = Slot(uri=NMDC.has_input, name="OmicsProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.OmicsProcessing_has_input, domain=OmicsProcessing, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -8858,8 +8848,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -8989,8 +8978,7 @@ class slots: model_uri=NMDC.FunctionalAnnotation_was_generated_by, domain=FunctionalAnnotation, range=Optional[Union[str, MetagenomeAnnotationActivityId]], mappings = [PROV.wasGeneratedBy]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) slots.WorkflowExecutionActivity_was_associated_with = Slot(uri=NMDC.was_associated_with, name="WorkflowExecutionActivity_was_associated_with", curie=NMDC.curie('was_associated_with'), model_uri=NMDC.WorkflowExecutionActivity_was_associated_with, domain=WorkflowExecutionActivity, range=Optional[Union[str, WorkflowExecutionActivityId]], mappings = [PROV.wasAssociatedWith]) @@ -9022,32 +9010,25 @@ class slots: model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], - pattern=re.compile(r'^nmdc:wf')) + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId]) slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmgas')) + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId]) slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmtas')) + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId]) slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmgan')) + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId]) slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmtan')) + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId]) slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], - pattern=re.compile(r'^nmdc:wfmt')) + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId]) slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmag')) + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId]) slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -9062,12 +9043,10 @@ class slots: model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrqc')) + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId]) slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrbt')) + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId]) slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9079,8 +9058,7 @@ class slots: model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmb')) + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId]) slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9089,8 +9067,7 @@ class slots: model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, PeptideQuantification], List[Union[dict, PeptideQuantification]]]]) slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmp')) + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId]) slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9099,5 +9076,4 @@ class slots: model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfnom')) + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId]) diff --git a/nmdc_schema/workflow_execution_activity.py b/nmdc_schema/workflow_execution_activity.py index b0dfd52910..ee679a73d0 100644 --- a/nmdc_schema/workflow_execution_activity.py +++ b/nmdc_schema/workflow_execution_activity.py @@ -1,5 +1,5 @@ # Auto generated from workflow_execution_activity.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:17:01 +# Generation date: 2023-01-20T15:23:49 # Schema: NMDC-Workflow-Execution # # id: https://microbiomedata/schema/workflow_execution_activity @@ -2278,32 +2278,25 @@ class slots: model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], - pattern=re.compile(r'^nmdc:wf')) + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId]) slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmgas')) + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId]) slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmtas')) + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId]) slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmgan')) + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId]) slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmtan')) + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId]) slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], - pattern=re.compile(r'^nmdc:wfmt')) + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId]) slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmag')) + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId]) slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -2318,12 +2311,10 @@ class slots: model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrqc')) + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId]) slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrbt')) + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId]) slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2335,8 +2326,7 @@ class slots: model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmb')) + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId]) slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2345,8 +2335,7 @@ class slots: model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, "PeptideQuantification"], List[Union[dict, "PeptideQuantification"]]]]) slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmp')) + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId]) slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2355,20 +2344,16 @@ class slots: model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfnom')) + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -2398,8 +2383,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) diff --git a/python/annotation.py b/python/annotation.py index 1d35f0330d..f2fc0ad9c8 100644 --- a/python/annotation.py +++ b/python/annotation.py @@ -1,5 +1,5 @@ # Auto generated from annotation.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:52 +# Generation date: 2023-01-20T15:23:36 # Schema: NMDC-Annotation # # id: https://microbiomedata/schema/annotation @@ -2668,12 +2668,10 @@ class slots: model_uri=NMDC.FunctionalAnnotation_was_generated_by, domain=FunctionalAnnotation, range=Optional[Union[str, MetagenomeAnnotationActivityId]], mappings = [PROV.wasGeneratedBy]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -2703,8 +2701,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -2764,8 +2761,7 @@ class slots: model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) slots.WorkflowExecutionActivity_was_associated_with = Slot(uri=NMDC.was_associated_with, name="WorkflowExecutionActivity_was_associated_with", curie=NMDC.curie('was_associated_with'), model_uri=NMDC.WorkflowExecutionActivity_was_associated_with, domain=WorkflowExecutionActivity, range=Optional[Union[str, WorkflowExecutionActivityId]], mappings = [PROV.wasAssociatedWith]) @@ -2797,32 +2793,25 @@ class slots: model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], - pattern=re.compile(r'^nmdc:wf')) + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId]) slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmgas')) + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId]) slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmtas')) + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId]) slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmgan')) + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId]) slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmtan')) + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId]) slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], - pattern=re.compile(r'^nmdc:wfmt')) + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId]) slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmag')) + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId]) slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -2837,12 +2826,10 @@ class slots: model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrqc')) + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId]) slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrbt')) + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId]) slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2854,8 +2841,7 @@ class slots: model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmb')) + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId]) slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2864,8 +2850,7 @@ class slots: model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, PeptideQuantification], List[Union[dict, PeptideQuantification]]]]) slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmp')) + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId]) slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2874,5 +2859,4 @@ class slots: model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfnom')) + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId]) diff --git a/python/basic_slots.py b/python/basic_slots.py index 3caaf63148..8a574812dc 100644 --- a/python/basic_slots.py +++ b/python/basic_slots.py @@ -1,5 +1,5 @@ # Auto generated from basic_slots.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:40 +# Generation date: 2023-01-20T15:23:20 # Schema: NMDC-Basic-Slots # # id: https://microbiomedata/schema/basic_slots @@ -1223,12 +1223,10 @@ class slots: model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1258,8 +1256,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1319,5 +1316,4 @@ class slots: model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) diff --git a/python/bioscales.py b/python/bioscales.py index c096d0d0dc..d2af60bebb 100644 --- a/python/bioscales.py +++ b/python/bioscales.py @@ -1,5 +1,5 @@ # Auto generated from bioscales.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:17:05 +# Generation date: 2023-01-20T15:23:55 # Schema: NMDC-Bioscales # # id: https://microbiomedata/schema/bioscales @@ -1245,12 +1245,10 @@ class slots: model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1280,8 +1278,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1341,5 +1338,4 @@ class slots: model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) diff --git a/python/core.py b/python/core.py index b93015a04e..d8660fdeaf 100644 --- a/python/core.py +++ b/python/core.py @@ -1,5 +1,5 @@ # Auto generated from core.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:17:14 +# Generation date: 2023-01-20T15:24:05 # Schema: NMDC-Core # # id: https://microbiomedata/schema/core @@ -1224,12 +1224,10 @@ class slots: model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1259,8 +1257,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1320,5 +1317,4 @@ class slots: model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) diff --git a/python/external_identifiers.py b/python/external_identifiers.py index 1215e5e6da..b668665c04 100644 --- a/python/external_identifiers.py +++ b/python/external_identifiers.py @@ -1,5 +1,5 @@ # Auto generated from external_identifiers.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:54 +# Generation date: 2023-01-20T15:23:39 # Schema: external_identifiers # # id: https://microbiomedata/schema/external_identifiers @@ -1308,12 +1308,10 @@ class slots: model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1343,8 +1341,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -1404,5 +1401,4 @@ class slots: model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) diff --git a/python/mixs.py b/python/mixs.py index 8fcb469f11..c7a0cfa8d1 100644 --- a/python/mixs.py +++ b/python/mixs.py @@ -1,5 +1,5 @@ # Auto generated from mixs.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:58 +# Generation date: 2023-01-20T15:23:45 # Schema: mixs-schema # # id: https://microbiomedata/schema/mixs @@ -4663,12 +4663,10 @@ class slots: model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -4698,8 +4696,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -4759,5 +4756,4 @@ class slots: model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) diff --git a/python/nmdc.py b/python/nmdc.py index 85464f8111..4f4607982b 100644 --- a/python/nmdc.py +++ b/python/nmdc.py @@ -1,5 +1,5 @@ # Auto generated from nmdc.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:17:08 +# Generation date: 2023-01-20T15:23:58 # Schema: NMDC # # id: https://microbiomedata/schema @@ -8691,8 +8691,7 @@ class slots: model_uri=NMDC.Database_metatranscriptome_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]]) slots.FieldResearchSite_id = Slot(uri=NMDC.id, name="FieldResearchSite_id", curie=NMDC.curie('id'), - model_uri=NMDC.FieldResearchSite_id, domain=FieldResearchSite, range=Union[str, FieldResearchSiteId], - pattern=re.compile(r'^nmdc:frsite')) + model_uri=NMDC.FieldResearchSite_id, domain=FieldResearchSite, range=Union[str, FieldResearchSiteId]) slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) @@ -8701,8 +8700,7 @@ class slots: model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) slots.CollectingBiosamplesFromSite_id = Slot(uri=NMDC.id, name="CollectingBiosamplesFromSite_id", curie=NMDC.curie('id'), - model_uri=NMDC.CollectingBiosamplesFromSite_id, domain=CollectingBiosamplesFromSite, range=Union[str, CollectingBiosamplesFromSiteId], - pattern=re.compile(r'^nmdc:clsite')) + model_uri=NMDC.CollectingBiosamplesFromSite_id, domain=CollectingBiosamplesFromSite, range=Union[str, CollectingBiosamplesFromSiteId]) slots.DataObject_name = Slot(uri=NMDC.name, name="DataObject_name", curie=NMDC.curie('name'), model_uri=NMDC.DataObject_name, domain=DataObject, range=str) @@ -8711,12 +8709,10 @@ class slots: model_uri=NMDC.DataObject_description, domain=DataObject, range=str) slots.DataObject_id = Slot(uri=NMDC.id, name="DataObject_id", curie=NMDC.curie('id'), - model_uri=NMDC.DataObject_id, domain=DataObject, range=Union[str, DataObjectId], - pattern=re.compile(r'^nmdc:dobj')) + model_uri=NMDC.DataObject_id, domain=DataObject, range=Union[str, DataObjectId]) slots.Biosample_id = Slot(uri=NMDC.id, name="Biosample_id", curie=NMDC.curie('id'), - model_uri=NMDC.Biosample_id, domain=Biosample, range=Union[str, BiosampleId], - pattern=re.compile(r'^nmdc:bsm')) + model_uri=NMDC.Biosample_id, domain=Biosample, range=Union[str, BiosampleId]) slots.Biosample_gold_biosample_identifiers = Slot(uri=NMDC.gold_biosample_identifiers, name="Biosample_gold_biosample_identifiers", curie=NMDC.curie('gold_biosample_identifiers'), model_uri=NMDC.Biosample_gold_biosample_identifiers, domain=Biosample, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]], @@ -8747,8 +8743,7 @@ class slots: model_uri=NMDC.Biosample_extreme_event, domain=Biosample, range=Optional[str]) slots.Study_id = Slot(uri=NMDC.id, name="Study_id", curie=NMDC.curie('id'), - model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId], - pattern=re.compile(r'^nmdc:sty')) + model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId]) slots.Study_doi = Slot(uri=NMDC.doi, name="Study_doi", curie=NMDC.curie('doi'), model_uri=NMDC.Study_doi, domain=Study, range=Optional[Union[dict, "AttributeValue"]]) @@ -8785,15 +8780,13 @@ class slots: model_uri=NMDC.Study_emsl_proposal_doi, domain=Study, range=Optional[str]) slots.BiosampleProcessing_id = Slot(uri=NMDC.id, name="BiosampleProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId], - pattern=re.compile(r'^nmdc:bsmprc')) + model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId]) slots.BiosampleProcessing_has_input = Slot(uri=NMDC.has_input, name="BiosampleProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.BiosampleProcessing_has_input, domain=BiosampleProcessing, range=Optional[Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]]) slots.OmicsProcessing_id = Slot(uri=NMDC.id, name="OmicsProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId], - pattern=re.compile(r'^nmdc:omprc')) + model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId]) slots.OmicsProcessing_has_input = Slot(uri=NMDC.has_input, name="OmicsProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.OmicsProcessing_has_input, domain=OmicsProcessing, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) @@ -8869,12 +8862,10 @@ class slots: model_uri=NMDC.FunctionalAnnotation_was_generated_by, domain=FunctionalAnnotation, range=Optional[Union[str, MetagenomeAnnotationActivityId]], mappings = [PROV.wasGeneratedBy]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -8904,8 +8895,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -8965,8 +8955,7 @@ class slots: model_uri=NMDC.GeolocationValue_has_raw_value, domain=GeolocationValue, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) slots.DissolvingActivity_material_input = Slot(uri=NMDC.material_input, name="DissolvingActivity_material_input", curie=NMDC.curie('material_input'), model_uri=NMDC.DissolvingActivity_material_input, domain=DissolvingActivity, range=Optional[Union[str, MaterialSampleId]]) @@ -8975,8 +8964,7 @@ class slots: model_uri=NMDC.DissolvingActivity_material_output, domain=DissolvingActivity, range=Optional[Union[str, MaterialSampleId]]) slots.MaterialSample_id = Slot(uri=NMDC.id, name="MaterialSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.MaterialSample_id, domain=MaterialSample, range=Union[str, MaterialSampleId], - pattern=re.compile(r'^nmdc:matsm')) + model_uri=NMDC.MaterialSample_id, domain=MaterialSample, range=Union[str, MaterialSampleId]) slots.MaterialSamplingActivity_amount_collected = Slot(uri=NMDC.amount_collected, name="MaterialSamplingActivity_amount_collected", curie=NMDC.curie('amount_collected'), model_uri=NMDC.MaterialSamplingActivity_amount_collected, domain=MaterialSamplingActivity, range=Optional[Union[dict, QuantityValue]]) @@ -9032,32 +9020,25 @@ class slots: model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], - pattern=re.compile(r'^nmdc:wf')) + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId]) slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmgas')) + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId]) slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmtas')) + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId]) slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmgan')) + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId]) slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmtan')) + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId]) slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], - pattern=re.compile(r'^nmdc:wfmt')) + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId]) slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmag')) + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId]) slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -9072,12 +9053,10 @@ class slots: model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrqc')) + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId]) slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrbt')) + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId]) slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9089,8 +9068,7 @@ class slots: model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmb')) + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId]) slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9099,8 +9077,7 @@ class slots: model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, PeptideQuantification], List[Union[dict, PeptideQuantification]]]]) slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmp')) + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId]) slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9109,5 +9086,4 @@ class slots: model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfnom')) + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId]) diff --git a/python/portal/emsl.py b/python/portal/emsl.py index 1db5f20016..bf38483d2c 100644 --- a/python/portal/emsl.py +++ b/python/portal/emsl.py @@ -1,5 +1,5 @@ # Auto generated from emsl.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:50 +# Generation date: 2023-01-20T15:23:33 # Schema: emsl # # id: https://microbiomedata/schema/emsl diff --git a/python/portal/jgi_metagenomics.py b/python/portal/jgi_metagenomics.py index af90352a48..090933299d 100644 --- a/python/portal/jgi_metagenomics.py +++ b/python/portal/jgi_metagenomics.py @@ -1,5 +1,5 @@ # Auto generated from jgi_metagenomics.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:43 +# Generation date: 2023-01-20T15:23:23 # Schema: jgi_metagenomics # # id: https://microbiomedata/schema/jgi_metagenomics diff --git a/python/portal/jgi_metatranscriptomics.py b/python/portal/jgi_metatranscriptomics.py index 041abf35ac..83b15b0537 100644 --- a/python/portal/jgi_metatranscriptomics.py +++ b/python/portal/jgi_metatranscriptomics.py @@ -1,5 +1,5 @@ # Auto generated from jgi_metatranscriptomics.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:46 +# Generation date: 2023-01-20T15:23:28 # Schema: jgi_metatranscriptomics # # id: https://microbiomedata/schema/jgi_metatranscriptomics diff --git a/python/portal/mixs_inspired.py b/python/portal/mixs_inspired.py index f04a3cf25a..2ab7db7040 100644 --- a/python/portal/mixs_inspired.py +++ b/python/portal/mixs_inspired.py @@ -1,5 +1,5 @@ # Auto generated from mixs_inspired.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:44 +# Generation date: 2023-01-20T15:23:25 # Schema: mixs_inspired # # id: https://microbiomedata/schema/mixs_inspired diff --git a/python/portal/sample_id.py b/python/portal/sample_id.py index c136a01774..d8d530cde5 100644 --- a/python/portal/sample_id.py +++ b/python/portal/sample_id.py @@ -1,5 +1,5 @@ # Auto generated from sample_id.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:48 +# Generation date: 2023-01-20T15:23:30 # Schema: sample_id # # id: https://microbiomedata/schema/sample_id diff --git a/python/prov.py b/python/prov.py index 0a3d86016c..69f002e516 100644 --- a/python/prov.py +++ b/python/prov.py @@ -1,5 +1,5 @@ # Auto generated from prov.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:17:03 +# Generation date: 2023-01-20T15:23:51 # Schema: NMDC-PROV # # id: https://microbiomedata/schema/prov @@ -1221,16 +1221,13 @@ class slots: model_uri=NMDC.magBin__gtdbtk_species, domain=None, range=Optional[str]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -1260,8 +1257,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) diff --git a/python/sample_prep.py b/python/sample_prep.py index b09c3dfc82..a6bbdb2a7b 100644 --- a/python/sample_prep.py +++ b/python/sample_prep.py @@ -1,5 +1,5 @@ # Auto generated from sample_prep.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:16:34 +# Generation date: 2023-01-20T15:23:13 # Schema: sample_prep # # id: https://microbiomedata/schema/sample_prep @@ -8678,8 +8678,7 @@ class slots: model_uri=NMDC.DissolvingActivity_material_output, domain=DissolvingActivity, range=Optional[Union[str, MaterialSampleId]]) slots.MaterialSample_id = Slot(uri=NMDC.id, name="MaterialSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.MaterialSample_id, domain=MaterialSample, range=Union[str, MaterialSampleId], - pattern=re.compile(r'^nmdc:matsm')) + model_uri=NMDC.MaterialSample_id, domain=MaterialSample, range=Union[str, MaterialSampleId]) slots.MaterialSamplingActivity_amount_collected = Slot(uri=NMDC.amount_collected, name="MaterialSamplingActivity_amount_collected", curie=NMDC.curie('amount_collected'), model_uri=NMDC.MaterialSamplingActivity_amount_collected, domain=MaterialSamplingActivity, range=Optional[Union[dict, "QuantityValue"]]) @@ -8715,8 +8714,7 @@ class slots: model_uri=NMDC.Database_metatranscriptome_activity_set, domain=Database, range=Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]]) slots.FieldResearchSite_id = Slot(uri=NMDC.id, name="FieldResearchSite_id", curie=NMDC.curie('id'), - model_uri=NMDC.FieldResearchSite_id, domain=FieldResearchSite, range=Union[str, FieldResearchSiteId], - pattern=re.compile(r'^nmdc:frsite')) + model_uri=NMDC.FieldResearchSite_id, domain=FieldResearchSite, range=Union[str, FieldResearchSiteId]) slots.CollectingBiosamplesFromSite_has_inputs = Slot(uri=NMDC.has_inputs, name="CollectingBiosamplesFromSite_has_inputs", curie=NMDC.curie('has_inputs'), model_uri=NMDC.CollectingBiosamplesFromSite_has_inputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, SiteId], List[Union[str, SiteId]]]) @@ -8725,8 +8723,7 @@ class slots: model_uri=NMDC.CollectingBiosamplesFromSite_has_outputs, domain=CollectingBiosamplesFromSite, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) slots.CollectingBiosamplesFromSite_id = Slot(uri=NMDC.id, name="CollectingBiosamplesFromSite_id", curie=NMDC.curie('id'), - model_uri=NMDC.CollectingBiosamplesFromSite_id, domain=CollectingBiosamplesFromSite, range=Union[str, CollectingBiosamplesFromSiteId], - pattern=re.compile(r'^nmdc:clsite')) + model_uri=NMDC.CollectingBiosamplesFromSite_id, domain=CollectingBiosamplesFromSite, range=Union[str, CollectingBiosamplesFromSiteId]) slots.DataObject_name = Slot(uri=NMDC.name, name="DataObject_name", curie=NMDC.curie('name'), model_uri=NMDC.DataObject_name, domain=DataObject, range=str) @@ -8735,12 +8732,10 @@ class slots: model_uri=NMDC.DataObject_description, domain=DataObject, range=str) slots.DataObject_id = Slot(uri=NMDC.id, name="DataObject_id", curie=NMDC.curie('id'), - model_uri=NMDC.DataObject_id, domain=DataObject, range=Union[str, DataObjectId], - pattern=re.compile(r'^nmdc:dobj')) + model_uri=NMDC.DataObject_id, domain=DataObject, range=Union[str, DataObjectId]) slots.Biosample_id = Slot(uri=NMDC.id, name="Biosample_id", curie=NMDC.curie('id'), - model_uri=NMDC.Biosample_id, domain=Biosample, range=Union[str, BiosampleId], - pattern=re.compile(r'^nmdc:bsm')) + model_uri=NMDC.Biosample_id, domain=Biosample, range=Union[str, BiosampleId]) slots.Biosample_gold_biosample_identifiers = Slot(uri=NMDC.gold_biosample_identifiers, name="Biosample_gold_biosample_identifiers", curie=NMDC.curie('gold_biosample_identifiers'), model_uri=NMDC.Biosample_gold_biosample_identifiers, domain=Biosample, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]], @@ -8771,8 +8766,7 @@ class slots: model_uri=NMDC.Biosample_extreme_event, domain=Biosample, range=Optional[str]) slots.Study_id = Slot(uri=NMDC.id, name="Study_id", curie=NMDC.curie('id'), - model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId], - pattern=re.compile(r'^nmdc:sty')) + model_uri=NMDC.Study_id, domain=Study, range=Union[str, StudyId]) slots.Study_doi = Slot(uri=NMDC.doi, name="Study_doi", curie=NMDC.curie('doi'), model_uri=NMDC.Study_doi, domain=Study, range=Optional[Union[dict, "AttributeValue"]]) @@ -8809,26 +8803,22 @@ class slots: model_uri=NMDC.Study_emsl_proposal_doi, domain=Study, range=Optional[str]) slots.BiosampleProcessing_id = Slot(uri=NMDC.id, name="BiosampleProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId], - pattern=re.compile(r'^nmdc:bsmprc')) + model_uri=NMDC.BiosampleProcessing_id, domain=BiosampleProcessing, range=Union[str, BiosampleProcessingId]) slots.BiosampleProcessing_has_input = Slot(uri=NMDC.has_input, name="BiosampleProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.BiosampleProcessing_has_input, domain=BiosampleProcessing, range=Optional[Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]]) slots.OmicsProcessing_id = Slot(uri=NMDC.id, name="OmicsProcessing_id", curie=NMDC.curie('id'), - model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId], - pattern=re.compile(r'^nmdc:omprc')) + model_uri=NMDC.OmicsProcessing_id, domain=OmicsProcessing, range=Union[str, OmicsProcessingId]) slots.OmicsProcessing_has_input = Slot(uri=NMDC.has_input, name="OmicsProcessing_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.OmicsProcessing_has_input, domain=OmicsProcessing, range=Union[Union[str, BiosampleId], List[Union[str, BiosampleId]]]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -8858,8 +8848,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) @@ -8989,8 +8978,7 @@ class slots: model_uri=NMDC.FunctionalAnnotation_was_generated_by, domain=FunctionalAnnotation, range=Optional[Union[str, MetagenomeAnnotationActivityId]], mappings = [PROV.wasGeneratedBy]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) slots.WorkflowExecutionActivity_was_associated_with = Slot(uri=NMDC.was_associated_with, name="WorkflowExecutionActivity_was_associated_with", curie=NMDC.curie('was_associated_with'), model_uri=NMDC.WorkflowExecutionActivity_was_associated_with, domain=WorkflowExecutionActivity, range=Optional[Union[str, WorkflowExecutionActivityId]], mappings = [PROV.wasAssociatedWith]) @@ -9022,32 +9010,25 @@ class slots: model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], - pattern=re.compile(r'^nmdc:wf')) + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId]) slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmgas')) + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId]) slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmtas')) + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId]) slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmgan')) + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId]) slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmtan')) + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId]) slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], - pattern=re.compile(r'^nmdc:wfmt')) + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId]) slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmag')) + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId]) slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -9062,12 +9043,10 @@ class slots: model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrqc')) + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId]) slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrbt')) + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId]) slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9079,8 +9058,7 @@ class slots: model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmb')) + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId]) slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9089,8 +9067,7 @@ class slots: model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, PeptideQuantification], List[Union[dict, PeptideQuantification]]]]) slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmp')) + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId]) slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -9099,5 +9076,4 @@ class slots: model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfnom')) + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId]) diff --git a/python/workflow_execution_activity.py b/python/workflow_execution_activity.py index b0dfd52910..ee679a73d0 100644 --- a/python/workflow_execution_activity.py +++ b/python/workflow_execution_activity.py @@ -1,5 +1,5 @@ # Auto generated from workflow_execution_activity.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-01-20T13:17:01 +# Generation date: 2023-01-20T15:23:49 # Schema: NMDC-Workflow-Execution # # id: https://microbiomedata/schema/workflow_execution_activity @@ -2278,32 +2278,25 @@ class slots: model_uri=NMDC.WorkflowExecutionActivity_type, domain=WorkflowExecutionActivity, range=Optional[str]) slots.WorkflowExecutionActivity_id = Slot(uri=NMDC.id, name="WorkflowExecutionActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId], - pattern=re.compile(r'^nmdc:wf')) + model_uri=NMDC.WorkflowExecutionActivity_id, domain=WorkflowExecutionActivity, range=Union[str, WorkflowExecutionActivityId]) slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmgas')) + model_uri=NMDC.MetagenomeAssembly_id, domain=MetagenomeAssembly, range=Union[str, MetagenomeAssemblyId]) slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId], - pattern=re.compile(r'^nmdc:wfmtas')) + model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId]) slots.MetagenomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetagenomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmgan')) + model_uri=NMDC.MetagenomeAnnotationActivity_id, domain=MetagenomeAnnotationActivity, range=Union[str, MetagenomeAnnotationActivityId]) slots.MetatranscriptomeAnnotationActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotationActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId], - pattern=re.compile(r'^nmdc:wfmtan')) + model_uri=NMDC.MetatranscriptomeAnnotationActivity_id, domain=MetatranscriptomeAnnotationActivity, range=Union[str, MetatranscriptomeAnnotationActivityId]) slots.MetatranscriptomeActivity_id = Slot(uri=NMDC.id, name="MetatranscriptomeActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId], - pattern=re.compile(r'^nmdc:wfmt')) + model_uri=NMDC.MetatranscriptomeActivity_id, domain=MetatranscriptomeActivity, range=Union[str, MetatranscriptomeActivityId]) slots.MagsAnalysisActivity_id = Slot(uri=NMDC.id, name="MagsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmag')) + model_uri=NMDC.MagsAnalysisActivity_id, domain=MagsAnalysisActivity, range=Union[str, MagsAnalysisActivityId]) slots.ReadQcAnalysisActivity_input_read_bases = Slot(uri=NMDC.input_read_bases, name="ReadQcAnalysisActivity_input_read_bases", curie=NMDC.curie('input_read_bases'), model_uri=NMDC.ReadQcAnalysisActivity_input_read_bases, domain=ReadQcAnalysisActivity, range=Optional[float]) @@ -2318,12 +2311,10 @@ class slots: model_uri=NMDC.ReadQcAnalysisActivity_has_output, domain=ReadQcAnalysisActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) slots.ReadQcAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadQcAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrqc')) + model_uri=NMDC.ReadQcAnalysisActivity_id, domain=ReadQcAnalysisActivity, range=Union[str, ReadQcAnalysisActivityId]) slots.ReadBasedTaxonomyAnalysisActivity_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfrbt')) + model_uri=NMDC.ReadBasedTaxonomyAnalysisActivity_id, domain=ReadBasedTaxonomyAnalysisActivity, range=Union[str, ReadBasedTaxonomyAnalysisActivityId]) slots.MetabolomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetabolomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetabolomicsAnalysisActivity_used, domain=MetabolomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2335,8 +2326,7 @@ class slots: model_uri=NMDC.MetabolomicsAnalysisActivity_has_calibration, domain=MetabolomicsAnalysisActivity, range=Optional[str]) slots.MetabolomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmb')) + model_uri=NMDC.MetabolomicsAnalysisActivity_id, domain=MetabolomicsAnalysisActivity, range=Union[str, MetabolomicsAnalysisActivityId]) slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2345,8 +2335,7 @@ class slots: model_uri=NMDC.MetaproteomicsAnalysisActivity_has_peptide_quantifications, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[Union[dict, "PeptideQuantification"], List[Union[dict, "PeptideQuantification"]]]]) slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfmp')) + model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId]) slots.NomAnalysisActivity_used = Slot(uri=NMDC.used, name="NomAnalysisActivity_used", curie=NMDC.curie('used'), model_uri=NMDC.NomAnalysisActivity_used, domain=NomAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) @@ -2355,20 +2344,16 @@ class slots: model_uri=NMDC.NomAnalysisActivity_has_calibration, domain=NomAnalysisActivity, range=Optional[str]) slots.NomAnalysisActivity_id = Slot(uri=NMDC.id, name="NomAnalysisActivity_id", curie=NMDC.curie('id'), - model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId], - pattern=re.compile(r'^nmdc:wfnom')) + model_uri=NMDC.NomAnalysisActivity_id, domain=NomAnalysisActivity, range=Union[str, NomAnalysisActivityId]) slots.Activity_id = Slot(uri=NMDC.id, name="Activity_id", curie=NMDC.curie('id'), - model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId], - pattern=re.compile(r'^nmdc:act')) + model_uri=NMDC.Activity_id, domain=Activity, range=Union[str, ActivityId]) slots.AnalyticalSample_id = Slot(uri=NMDC.id, name="AnalyticalSample_id", curie=NMDC.curie('id'), - model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId], - pattern=re.compile(r'^nmdc:ansm')) + model_uri=NMDC.AnalyticalSample_id, domain=AnalyticalSample, range=Union[str, AnalyticalSampleId]) slots.Site_id = Slot(uri=NMDC.id, name="Site_id", curie=NMDC.curie('id'), - model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId], - pattern=re.compile(r'^nmdc:site')) + model_uri=NMDC.Site_id, domain=Site, range=Union[str, SiteId]) slots.AttributeValue_type = Slot(uri=NMDC.type, name="AttributeValue_type", curie=NMDC.curie('type'), model_uri=NMDC.AttributeValue_type, domain=AttributeValue, range=Optional[str]) @@ -2398,8 +2383,7 @@ class slots: model_uri=NMDC.Person_id, domain=Person, range=Union[str, PersonId]) slots.Instrument_id = Slot(uri=NMDC.id, name="Instrument_id", curie=NMDC.curie('id'), - model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId], - pattern=re.compile(r'^nmdc:inst')) + model_uri=NMDC.Instrument_id, domain=Instrument, range=Union[str, InstrumentId]) slots.MetaboliteQuantification_metabolite_quantified = Slot(uri=NMDC.metabolite_quantified, name="MetaboliteQuantification_metabolite_quantified", curie=NMDC.curie('metabolite_quantified'), model_uri=NMDC.MetaboliteQuantification_metabolite_quantified, domain=MetaboliteQuantification, range=Optional[Union[str, ChemicalEntityId]]) diff --git a/src/schema/core.yaml b/src/schema/core.yaml index 74a62cd4b3..292a03bcd9 100644 --- a/src/schema/core.yaml +++ b/src/schema/core.yaml @@ -121,7 +121,7 @@ classes: title: Analytical Sample slot_usage: id: - pattern: '^nmdc:ansm' + # pattern: '^nmdc:ansm' structured_pattern: syntax: "{id_nmdc_prefix}:ansm-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -135,7 +135,7 @@ classes: - BCO sample collection site ? slot_usage: id: - pattern: '^nmdc:site' + # pattern: '^nmdc:site' structured_pattern: syntax: "{id_nmdc_prefix}:site-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -317,7 +317,7 @@ classes: - OBI:0000485 slot_usage: id: - pattern: '^nmdc:inst' + # pattern: '^nmdc:inst' structured_pattern: syntax: "{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 21ed057b1f..af5843c96f 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -94,7 +94,7 @@ imports: settings: id_nmdc_prefix: "^(nmdc)" -# id_typecode: "([a-z]{1,6})" + # id_typecode: "([a-z]{1,6})" id_shoulder: "([0-9][a-z]{0,6}[0-9])" id_blade: "([A-Za-z0-9]{1,})" id_version: "(\\.[A-Za-z0-9]{1,})*" @@ -175,7 +175,7 @@ classes: - "might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833" slot_usage: id: - pattern: '^nmdc:frsite' + # pattern: '^nmdc:frsite' structured_pattern: syntax: "{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -198,7 +198,7 @@ classes: range: Biosample required: true id: - pattern: '^nmdc:clsite' + # pattern: '^nmdc:clsite' structured_pattern: syntax: "{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -227,7 +227,7 @@ classes: description: required: true id: - pattern: '^nmdc:dobj' + # pattern: '^nmdc:dobj' structured_pattern: syntax: "{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -517,7 +517,7 @@ classes: id: description: An NMDC assigned unique identifier for a biosample submitted to NMDC. required: true - pattern: '^nmdc:bsm' + # pattern: '^nmdc:bsm' structured_pattern: syntax: "{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -622,7 +622,7 @@ classes: - study_image slot_usage: id: - pattern: '^nmdc:sty' + # pattern: '^nmdc:sty' structured_pattern: syntax: "{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -723,7 +723,7 @@ classes: - has_input slot_usage: id: - pattern: '^nmdc:bsmprc' + # pattern: '^nmdc:bsmprc' structured_pattern: syntax: "{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -775,7 +775,7 @@ classes: slot_usage: id: - pattern: '^nmdc:omprc' + # pattern: '^nmdc:omprc' structured_pattern: syntax: "{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true diff --git a/src/schema/prov.yaml b/src/schema/prov.yaml index 24470effd0..4549952ab2 100644 --- a/src/schema/prov.yaml +++ b/src/schema/prov.yaml @@ -9,7 +9,7 @@ prefixes: linkml: https://w3id.org/linkml/ nmdc: https://w3id.org/nmdc/ prov: http://www.w3.org/ns/prov# - + default_prefix: nmdc default_range: string @@ -38,14 +38,14 @@ classes: - prov:Activity slot_usage: id: - pattern: '^nmdc:act' + # pattern: '^nmdc:act' structured_pattern: todos: - remove the static pattern once the minter can generate ids that satisfy this structured_pattern and gen-linkml can expand the structured_pattern syntax: "{id_nmdc_prefix}:act-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true partial_match: false - + Agent: description: "a provence-generating agent" slots: @@ -53,7 +53,7 @@ classes: - was_informed_by mappings: - prov:Agent - + slots: started_at_time: diff --git a/src/schema/sample_prep.yaml b/src/schema/sample_prep.yaml index 48994809bc..6674decc09 100644 --- a/src/schema/sample_prep.yaml +++ b/src/schema/sample_prep.yaml @@ -271,7 +271,7 @@ classes: is_a: NamedThing slot_usage: id: - pattern: '^nmdc:matsm' + # pattern: '^nmdc:matsm' structured_pattern: syntax: "{id_nmdc_prefix}:matsm-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index b6db29eeaf..f1399d5c59 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -74,7 +74,7 @@ classes: required: true type: { } id: - pattern: '^nmdc:wf' + # pattern: '^nmdc:wf' structured_pattern: syntax: "{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -119,7 +119,7 @@ classes: - insdc_assembly_identifiers slot_usage: id: - pattern: '^nmdc:wfmgas' + # pattern: '^nmdc:wfmgas' structured_pattern: syntax: "{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -160,7 +160,7 @@ classes: - insdc_assembly_identifiers slot_usage: id: - pattern: '^nmdc:wfmtas' + # pattern: '^nmdc:wfmtas' structured_pattern: syntax: "{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -176,7 +176,7 @@ classes: - workflow subset slot_usage: id: - pattern: '^nmdc:wfmgan' + # pattern: '^nmdc:wfmgan' structured_pattern: syntax: "{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -191,7 +191,7 @@ classes: - workflow subset slot_usage: id: - pattern: '^nmdc:wfmtan' + # pattern: '^nmdc:wfmtan' structured_pattern: syntax: "{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -207,7 +207,7 @@ classes: - type slot_usage: id: - pattern: '^nmdc:wfmt' + # pattern: '^nmdc:wfmt' structured_pattern: syntax: "{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -230,7 +230,7 @@ classes: - mags_list slot_usage: id: - pattern: '^nmdc:wfmag' + # pattern: '^nmdc:wfmag' structured_pattern: syntax: "{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -263,7 +263,7 @@ classes: has_output: inlined: false id: - pattern: '^nmdc:wfrqc' + # pattern: '^nmdc:wfrqc' structured_pattern: syntax: "{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -279,7 +279,7 @@ classes: - type slot_usage: id: - pattern: '^nmdc:wfrbt' + # pattern: '^nmdc:wfrbt' structured_pattern: syntax: "{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -305,7 +305,7 @@ classes: description: >- TODO: Yuri to fill in id: - pattern: '^nmdc:wfmb' + # pattern: '^nmdc:wfmb' structured_pattern: syntax: "{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -327,7 +327,7 @@ classes: range: PeptideQuantification multivalued: true id: - pattern: '^nmdc:wfmp' + # pattern: '^nmdc:wfmp' structured_pattern: syntax: "{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true @@ -350,7 +350,7 @@ classes: description: >- A reference to a file that holds calibration information. id: - pattern: '^nmdc:wfnom' + # pattern: '^nmdc:wfnom' structured_pattern: syntax: "{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}{id_locus}" interpolated: true diff --git a/test/data/invalid_data/biosample_incomplete_napa_id.json b/test/data/invalid_data/biosample_incomplete_napa_id.json new file mode 100644 index 0000000000..6bbaaa91e3 --- /dev/null +++ b/test/data/invalid_data/biosample_incomplete_napa_id.json @@ -0,0 +1,54 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-", + "gold_biosample_identifiers": [ + "gold:Gb0101224" + ], + "name": "Lithgow State Coal Mine Calcium nutrients (early)", + "description": "Bulk Aqueous phase filtered water", + "type": "nmdc:Biosample", + "part_of": [ + "gold:Gs0110115" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "geo_loc_name": { + "has_raw_value": "Lithgow" + }, + "lat_lon": { + "has_raw_value": "-33.460524 150.168149", + "latitude": -33.460524, + "longitude": 150.168149 + }, + "ecosystem": "Environmental", + "ecosystem_category": "Aquatic", + "ecosystem_type": "Freshwater", + "ecosystem_subtype": "Groundwater", + "specific_ecosystem": "Coalbed water", + "add_date": "28-JUL-14 12.00.00.000000000 AM", + "community": "microbial communities", + "habitat": "Coalbed water", + "location": "from the Lithgow State Coal Mine, New South Wales, Australia", + "mod_date": "26-AUG-16 01.50.27.000000000 PM", + "ncbi_taxonomy_name": "coal metagenome", + "sample_collection_site": "Lithgow State Coal Mine" + } + ] +} \ No newline at end of file From bd55f003bb0f47f1e27f416e0e4a4ab762f0e137 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 23 Jan 2023 18:50:52 -0500 Subject: [PATCH 59/60] #639 embargoed slot on Biosample --- src/schema/nmdc.yaml | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 87ac91f6ef..8ef4b84d48 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -255,6 +255,7 @@ classes: Samples are associated with checklists, which define the fields used to annotate the samples. Samples are always associated with a taxon. slots: + - embargoed - collected_from - type - img_identifiers @@ -1007,6 +1008,17 @@ enums: slots: + embargoed: + description: >- + If true, the data are embargoed and not available for public access. + range: boolean + recommended: true + todos: + - make this required? + - first apply to Biosample + - try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata? + - applying to a Study may nto be granular enough + collected_from: description: The Site from which a Biosample was collected domain: Biosample From eb62cb0b917efebdc8396a9e6c22b91cc20efce8 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Tue, 24 Jan 2023 09:23:12 -0500 Subject: [PATCH 60/60] embargoed tests --- jsonschema/nmdc.schema.json | 8 +++++ ..._non_boolean_embargoed_biosample_test.json | 29 +++++++++++++++++++ test/data/minimal_valid_biosample_test.json | 28 ++++++++++++++++++ ...inimal_valid_embargoed_biosample_test.json | 29 +++++++++++++++++++ 4 files changed, 94 insertions(+) create mode 100644 test/data/invalid_data/minimal_non_boolean_embargoed_biosample_test.json create mode 100644 test/data/minimal_valid_biosample_test.json create mode 100644 test/data/minimal_valid_embargoed_biosample_test.json diff --git a/jsonschema/nmdc.schema.json b/jsonschema/nmdc.schema.json index 71442f7add..2b923745cc 100644 --- a/jsonschema/nmdc.schema.json +++ b/jsonschema/nmdc.schema.json @@ -433,6 +433,10 @@ "$ref": "#/$defs/QuantityValue", "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit." }, + "embargoed": { + "description": "If true, the data are embargoed and not available for public access.", + "type": "boolean" + }, "emsl_biosample_identifiers": { "description": "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.", "items": { @@ -880,6 +884,10 @@ "$ref": "#/$defs/QuantityValue", "description": "Temperature at which sample was stored, e.g. -80 degree Celsius" }, + "samp_taxon_id": { + "description": "NCBI taxon id of the sample. May be a single taxon or mixed taxa sample. Use 'synthetic metagenome' for mock community/positive controls, or 'blank sample' for negative controls.", + "type": "string" + }, "samp_vol_we_dna_ext": { "$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (mixs:0000001)." diff --git a/test/data/invalid_data/minimal_non_boolean_embargoed_biosample_test.json b/test/data/invalid_data/minimal_non_boolean_embargoed_biosample_test.json new file mode 100644 index 0000000000..31f6f039a2 --- /dev/null +++ b/test/data/invalid_data/minimal_non_boolean_embargoed_biosample_test.json @@ -0,0 +1,29 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "gold:Gs0110115" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "embargoed": 999 + } + ] +} diff --git a/test/data/minimal_valid_biosample_test.json b/test/data/minimal_valid_biosample_test.json new file mode 100644 index 0000000000..7c71174d4d --- /dev/null +++ b/test/data/minimal_valid_biosample_test.json @@ -0,0 +1,28 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "gold:Gs0110115" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + } + } + ] +} diff --git a/test/data/minimal_valid_embargoed_biosample_test.json b/test/data/minimal_valid_embargoed_biosample_test.json new file mode 100644 index 0000000000..df6ca07306 --- /dev/null +++ b/test/data/minimal_valid_embargoed_biosample_test.json @@ -0,0 +1,29 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "gold:Gs0110115" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "embargoed": true + } + ] +}