From d63affc1542b6f07f01a15b884a64422c90efcaf Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 30 Jan 2023 16:16:21 -0500 Subject: [PATCH 1/2] re-synced notebooks --- notebooks/nmdc-schema-view-sandbox.ipynb | 2 +- notebooks/nmdc_sandbox.ipynb | 2 +- notebooks/split_sort_paste.ipynb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/notebooks/nmdc-schema-view-sandbox.ipynb b/notebooks/nmdc-schema-view-sandbox.ipynb index cec391bb07..dcee82b659 100644 --- a/notebooks/nmdc-schema-view-sandbox.ipynb +++ b/notebooks/nmdc-schema-view-sandbox.ipynb @@ -400,4 +400,4 @@ }, "nbformat": 4, "nbformat_minor": 5 -} \ No newline at end of file +} diff --git a/notebooks/nmdc_sandbox.ipynb b/notebooks/nmdc_sandbox.ipynb index 6875e4e2b6..2d6c0d2941 100644 --- a/notebooks/nmdc_sandbox.ipynb +++ b/notebooks/nmdc_sandbox.ipynb @@ -548,4 +548,4 @@ }, "nbformat": 4, "nbformat_minor": 0 -} \ No newline at end of file +} diff --git a/notebooks/split_sort_paste.ipynb b/notebooks/split_sort_paste.ipynb index 76d9d7740d..f6c8b750aa 100644 --- a/notebooks/split_sort_paste.ipynb +++ b/notebooks/split_sort_paste.ipynb @@ -80,4 +80,4 @@ }, "nbformat": 4, "nbformat_minor": 0 -} \ No newline at end of file +} From 5b90d887dc1f103e8f09edbaafe5eb62578534f0 Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Mon, 30 Jan 2023 16:53:04 -0500 Subject: [PATCH 2/2] removed rel_to_oxygen from Biosample; added elev and oxy_stat_samp usage --- src/data/output/Biosample-exhasutive.json | 533 ------------------- src/data/output/Biosample-exhasutive.ttl | 386 -------------- src/data/output/Biosample-exhasutive.yaml | 399 --------------- src/data/output/Biosample-minimal.json | 25 - src/data/output/Biosample-minimal.ttl | 24 - src/data/output/Biosample-minimal.yaml | 15 - src/data/output/README.md | 592 ---------------------- src/data/output/Study-exhaustive.json | 121 ----- src/data/output/Study-exhaustive.ttl | 85 ---- src/data/output/Study-exhaustive.yaml | 96 ---- src/data/output/Study-minimal.json | 4 - src/data/output/Study-minimal.ttl | 4 - src/data/output/Study-minimal.yaml | 1 - src/schema/mixs.yaml | 8 +- src/schema/nmdc.yaml | 13 +- 15 files changed, 16 insertions(+), 2290 deletions(-) delete mode 100644 src/data/output/Biosample-exhasutive.json delete mode 100644 src/data/output/Biosample-exhasutive.ttl delete mode 100644 src/data/output/Biosample-exhasutive.yaml delete mode 100644 src/data/output/Biosample-minimal.json delete mode 100644 src/data/output/Biosample-minimal.ttl delete mode 100644 src/data/output/Biosample-minimal.yaml delete mode 100644 src/data/output/Study-exhaustive.json delete mode 100644 src/data/output/Study-exhaustive.ttl delete mode 100644 src/data/output/Study-exhaustive.yaml delete mode 100644 src/data/output/Study-minimal.json delete mode 100644 src/data/output/Study-minimal.ttl delete mode 100644 src/data/output/Study-minimal.yaml diff --git a/src/data/output/Biosample-exhasutive.json b/src/data/output/Biosample-exhasutive.json deleted file mode 100644 index ee4a7738a0..0000000000 --- a/src/data/output/Biosample-exhasutive.json +++ /dev/null @@ -1,533 +0,0 @@ -{ - "id": "nmdc:bsm-99-dtTMNb", - "name": "Sample Exhaustive Biosample instance. Although all of these values should pass validation, that does not mean that any Biosample of any type would necessarily have this particular combination of values.", - "description": "unconstrained text", - "alternative_identifiers": [ - "any_string", - "seriously_anything" - ], - "part_of": [ - "nmdc:unconstrained_study_identifier_string1_needs_pattern_materialization_what_about_referential_integrity", - "nmdc:unconstrained_study_identifier_string2" - ], - "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, - "collected_from": "nmdc:unconstrained_site_identifier_string", - "type": "nmdc:Biosample. change this to require a class name or an enumeration", - "img_identifiers": [ - "any string 1", - "any string 2" - ], - "samp_name": "see also name", - "biosample_categories": [ - "LTER", - "FICUS" - ], - "gold_biosample_identifiers": [ - "GOLD:Gb123456789", - "GOLD:Gb" - ], - "insdc_biosample_identifiers": [ - "biosample:SAMN123456789", - "biosample:SAMN000" - ], - "emsl_biosample_identifiers": [ - "any_string", - "seriously_anything" - ], - "igsn_biosample_identifiers": [ - "any:curie_1", - "any:curie_2" - ], - "agrochem_addition": { - "has_raw_value": "lime;1 kg/acre;2022-11-16T16:05:42+0000" - }, - "alkalinity": { - "has_raw_value": "50 milligram per liter" - }, - "alkalinity_method": { - "has_raw_value": "https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity" - }, - "alkyl_diethers": { - "has_raw_value": "0.005 mole per liter" - }, - "alt": { - "has_raw_value": "100 meter" - }, - "al_sat": { - "has_raw_value": "0.1 mg/kg" - }, - "al_sat_meth": { - "has_raw_value": "https://journaljeai.com/index.php/JEAI/article/view/583" - }, - "aminopept_act": { - "has_raw_value": "0.269 mole per liter per hour" - }, - "ammonium": { - "has_raw_value": "1.5 milligram per liter" - }, - "annual_precpt": { - "has_raw_value": "0.5 milligram per liter" - }, - "annual_temp": { - "has_raw_value": "12.5 degree Celsius" - }, - "bacteria_carb_prod": { - "has_raw_value": "2.53 microgram per liter per hour" - }, - "bishomohopanol": { - "has_raw_value": "14 microgram per liter" - }, - "bromide": { - "has_raw_value": "0.05 parts per million" - }, - "calcium": { - "has_raw_value": "0.2 micromole per liter" - }, - "carb_nitro_ratio": { - "has_raw_value": "0.417361111" - }, - "chem_administration": { - "has_raw_value": "agar [CHEBI:2509];2018-05-11T20:00Z" - }, - "chloride": { - "has_raw_value": "5000 milligram per liter" - }, - "chlorophyll": { - "has_raw_value": "5 milligram per cubic meter" - }, - "collection_date": { - "has_raw_value": "2023-01-16T16:05:42+0000" - }, - "cur_land_use": { - "has_raw_value": "conifers" - }, - "cur_vegetation": { - "has_raw_value": "MIxS doesn't provide any guidance more specific than \"text\"" - }, - "cur_vegetation_meth": { - "has_raw_value": "https://link.springer.com/article/10.1023/A:1011975321668" - }, - "crop_rotation": { - "has_raw_value": "yes;R2/2017-01-01/2018-12-31/P6M" - }, - "density": { - "has_raw_value": "1000 kilogram per cubic meter" - }, - "depth": { - "has_raw_value": "1.5 to 2.5 meters (that may not be the pattern the submission schema expects). Extractions below require external migration logic.", - "has_unit": "meter", - "has_numeric_value": 2.0, - "has_minimum_numeric_value": 1.5, - "has_maximum_numeric_value": 2.5 - }, - "diss_carb_dioxide": { - "has_raw_value": "5 milligram per liter" - }, - "diss_hydrogen": { - "has_raw_value": "0.3 micromole per liter" - }, - "diss_inorg_carb": { - "has_raw_value": "2059 micromole per kilogram" - }, - "diss_inorg_phosp": { - "has_raw_value": "56.5 micromole per liter" - }, - "diss_org_carb": { - "has_raw_value": "197 micromole per liter" - }, - "diss_org_nitro": { - "has_raw_value": "0.05 micromole per liter" - }, - "diss_oxygen": { - "has_raw_value": "175 micromole per kilogram" - }, - "drainage_class": { - "has_raw_value": "well" - }, - "elev": { - "has_raw_value": "100 meter" - }, - "env_package": { - "has_raw_value": "unconstrained text. should require the name of a MIxS EnvironmentalPackage class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM!" - }, - "extreme_event": "2023-01-15", - "fao_class": { - "has_raw_value": "Fluvisol" - }, - "fire": "2000-11 to 2000-12", - "flooding": "2000-01-15", - "geo_loc_name": { - "has_raw_value": "USA: Maryland, Bethesda" - }, - "glucosidase_act": { - "has_raw_value": "5 mol per liter per hour" - }, - "heavy_metals": [ - { - "has_raw_value": "mercury;0.09 micrograms per gram" - }, - { - "has_raw_value": "arsenic;0.09 micrograms per gram" - } - ], - "heavy_metals_meth": [ - { - "has_raw_value": "https://link.springer.com/article/10.1007/s42452-019-1578-x" - } - ], - "lat_lon": { - "has_raw_value": "50.586825 6.408977", - "latitude": 50.586825, - "longitude": 6.408977 - }, - "link_addit_analys": { - "has_raw_value": "https://pubmed.ncbi.nlm.nih.gov/2315679/" - }, - "link_class_info": { - "has_raw_value": "https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf" - }, - "link_climate_info": { - "has_raw_value": "https://www.int-res.com/abstracts/cr/v14/n3/p161-173/" - }, - "local_class": { - "has_raw_value": "jicama soil" - }, - "local_class_meth": { - "has_raw_value": "https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083" - }, - "magnesium": { - "has_raw_value": "52.8 micromole per kilogram" - }, - "mean_frict_vel": { - "has_raw_value": "0.5 meter per second" - }, - "mean_peak_frict_vel": { - "has_raw_value": "1 meter per second" - }, - "misc_param": { - "has_raw_value": "Bicarbonate ion concentration;2075 micromole per kilogram" - }, - "n_alkanes": { - "has_raw_value": "n-hexadecane;100 milligram per liter" - }, - "nitrate": { - "has_raw_value": "65 micromole per liter" - }, - "nitrite": { - "has_raw_value": "0.5 micromole per liter" - }, - "org_matter": { - "has_raw_value": "1.75 milligram per cubic meter" - }, - "org_nitro": { - "has_raw_value": "4 micromole per liter" - }, - "organism_count": { - "has_raw_value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - }, - "oxy_stat_samp": { - "has_raw_value": "aerobic. change implementation from text value to string with enumerated range" - }, - "part_org_carb": { - "has_raw_value": "1.92 micromole per liter" - }, - "perturbation": { - "has_raw_value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" - }, - "petroleum_hydrocarb": { - "has_raw_value": "0.05 micromole per liter" - }, - "ph": { - "has_raw_value": "7.5" - }, - "ph_meth": { - "has_raw_value": "https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf" - }, - "phaeopigments": { - "has_raw_value": "2.5 milligram per cubic meter" - }, - "phosplipid_fatt_acid": { - "has_raw_value": "2.98 milligram per liter" - }, - "pool_dna_extracts": { - "has_raw_value": "yes, 5" - }, - "potassium": { - "has_raw_value": "463 milligram per liter" - }, - "pressure": { - "has_raw_value": "50 atmosphere" - }, - "profile_position": { - "has_raw_value": "summit. change validation to enumeration" - }, - "redox_potential": { - "has_raw_value": "300 millivolt" - }, - "salinity": { - "has_raw_value": "25 practical salinity unit" - }, - "salinity_meth": { - "has_raw_value": "PMID:22895776" - }, - "samp_mat_process": { - "has_raw_value": "filtering of seawater" - }, - "samp_store_dur": { - "has_raw_value": "P1Y6M" - }, - "samp_store_loc": { - "has_raw_value": "Freezer no:5" - }, - "samp_taxon_id": "soil metagenome [NCBItaxon:410658] but no validation applied yet", - "samp_store_temp": { - "has_raw_value": "-80 degree Celsius" - }, - "samp_vol_we_dna_ext": { - "has_raw_value": "1500 milliliter" - }, - "season_temp": { - "has_raw_value": "18 degree Celsius" - }, - "season_precpt": { - "has_raw_value": "75 millimeters" - }, - "sieving": { - "has_raw_value": "MIxS does not provide an example" - }, - "size_frac_low": { - "has_raw_value": "0.2 micrometer" - }, - "size_frac_up": { - "has_raw_value": "20 micrometer" - }, - "slope_gradient": { - "has_raw_value": "MIxS does not provide an example" - }, - "slope_aspect": { - "has_raw_value": "MIxS does not provide an example" - }, - "sodium": { - "has_raw_value": "10.5 milligram per liter" - }, - "soil_type": { - "has_raw_value": "plinthosol [ENVO:00002250]" - }, - "soil_type_meth": { - "has_raw_value": "Frederick series" - }, - "store_cond": { - "has_raw_value": "-20 degree Celsius freezer;P2Y10D" - }, - "sulfate": { - "has_raw_value": "5 micromole per liter" - }, - "sulfide": { - "has_raw_value": "2 micromole per liter" - }, - "temp": { - "has_raw_value": "25 degree Celsius" - }, - "tillage": { - "has_raw_value": "chisel. change validation to enumeration" - }, - "tidal_stage": { - "has_raw_value": "high tide. change validation to enumeration" - }, - "tot_carb": { - "has_raw_value": "MIxS does not provide an example" - }, - "tot_depth_water_col": { - "has_raw_value": "500 meter" - }, - "tot_diss_nitro": { - "has_raw_value": "40 microgram per liter" - }, - "tot_org_carb": { - "has_raw_value": "2%" - }, - "tot_org_c_meth": { - "has_raw_value": "https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf" - }, - "tot_nitro_content": { - "has_raw_value": "35 milligrams Nitrogen per kilogram of soil" - }, - "tot_nitro_cont_meth": "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00", - "tot_phosp": { - "has_raw_value": "0.03 milligram per liter" - }, - "water_content": [ - "MIxS doesn't provide an example 1", - "MIxS doesn't provide an example 2" - ], - "water_cont_soil_meth": "MIxS doesn't provide an example", - "ecosystem": "unconstrained text. should be validated against the controlled vocabulary, by the sample's environmental package. would also be nice to align the CV with MIxS environmental triads", - "ecosystem_category": "unconstrained text", - "ecosystem_type": "unconstrained text", - "ecosystem_subtype": "unconstrained text", - "specific_ecosystem": "unconstrained text", - "add_date": "2021-03-31", - "community": "no_example_from_mixs", - "habitat": "unconstrained text", - "host_name": "snail is an example value, but unconstrained text is accepted at this point", - "location": "unconstrained text. should we even keep this slot? check if it ahs been used in MongoDB.", - "mod_date": "2023-01-25", - "ncbi_taxonomy_name": "soil metagenome", - "proport_woa_temperature": "no example from MIxS", - "salinity_category": "halotolerant is an example from the schema, but MIxS doesn't provide this slot any more", - "sample_collection_site": "unconstrained text", - "soluble_iron_micromol": "MIxS doesn't provide an example", - "subsurface_depth": { - "has_raw_value": "MIxS does not provide an example" - }, - "air_temp_regm": { - "has_raw_value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - }, - "biotic_regm": { - "has_raw_value": "sample inoculated with Rhizobium spp. Culture" - }, - "biotic_relationship": { - "has_raw_value": "MIxS suggest enum [free living|parasite|commensal|symbiont] but not currently enforced here" - }, - "climate_environment": { - "has_raw_value": "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - }, - "experimental_factor": { - "has_raw_value": "unconstrained text, unlike the MIxS environmental triad" - }, - "gaseous_environment": { - "has_raw_value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - }, - "growth_facil": { - "has_raw_value": "Growth chamber [CO_715:0000189]" - }, - "humidity_regm": { - "has_raw_value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - }, - "light_regm": { - "has_raw_value": "incandescent light;10 lux;450 nanometer" - }, - "phosphate": { - "has_raw_value": "0.7 micromole per liter" - }, - "rel_to_oxygen": { - "has_raw_value": "aerobe. change validation to enumeration" - }, - "samp_collec_method": "swabbing", - "samp_size": { - "has_raw_value": "5 liters" - }, - "source_mat_id": { - "has_raw_value": "MPI012345" - }, - "watering_regm": { - "has_raw_value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - }, - "dna_absorb1": "2.02", - "dna_absorb2": "2.02", - "dna_collect_site": "untreated pond water", - "dna_concentration": "100", - "dna_cont_type": "plate", - "dna_cont_well": "C2", - "dna_container_id": "Pond_MT_041618", - "dna_dnase": "yes", - "dna_isolate_meth": "phenol/chloroform extraction", - "dna_organisms": "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)", - "dna_project_contact": "John Jones", - "dna_samp_id": "187654", - "dna_sample_format": "10 mM Tris-HCl", - "dna_sample_name": "JGI_pond_041618", - "dna_seq_project": "1191234", - "dna_seq_project_pi": "Jane Johnson", - "dna_seq_project_name": "JGI Pond metagenomics", - "dna_volume": "25", - "proposal_dna": "504000", - "dnase_rna": "yes", - "proposal_rna": "504000", - "rna_absorb1": "2.02", - "rna_absorb2": "2.02", - "rna_collect_site": "untreated pond water", - "rna_concentration": "100", - "rna_cont_type": "plate", - "rna_cont_well": "C2", - "rna_container_id": "Pond_MT_041618", - "rna_isolate_meth": "phenol/chloroform extraction", - "rna_organisms": "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)", - "rna_project_contact": "John Jones", - "rna_samp_id": "187654", - "rna_sample_format": "10 mM Tris-HCl", - "rna_sample_name": "JGI_pond_041618", - "rna_seq_project": "1191234", - "rna_seq_project_pi": "Jane Johnson", - "rna_seq_project_name": "JGI Pond metagenomics", - "rna_volume": "25", - "collection_date_inc": "2023-01-29", - "collection_time": "05:42+0000", - "collection_time_inc": "13:42+0000", - "experimental_factor_other": "unconstrained text, but presumably expects 'term label [term id]'", - "filter_method": "Basix PES, 13-100-106 FisherSci is an example value, but unconstrained text is accepted at this point", - "isotope_exposure": "13C glucose", - "micro_biomass_c_meth": "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12", - "micro_biomass_n_meth": "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12", - "microbial_biomass_c": "0.05 ug C/g dry soil", - "microbial_biomass_n": "0.05 ug N/g dry soil", - "non_microb_biomass": "insect 0.23 ug; plant 1g", - "non_microb_biomass_method": "https://doi.org/10.1038/s41467-021-26181-3", - "org_nitro_method": "https://doi.org/10.1016/0038-0717(85)90144-0", - "other_treatment": "unconstrained text", - "start_date_inc": "2023-01-27", - "start_time_inc": "13:42+0000", - "project_id": "no example from MIxS", - "replicate_number": "1", - "sample_shipped": "15 g", - "sample_type": "water_extract_soil", - "technical_reps": "2", - "analysis_type": [ - "metabolomics", - "metagenomics" - ], - "sample_link": [ - "IGSN:DSJ0284", - "any:curie" - ], - "zinc": { - "has_raw_value": "2.5 mg/kg" - }, - "manganese": { - "has_raw_value": "24.7 mg/kg" - }, - "ammonium_nitrogen": { - "has_raw_value": "0.5 milligram per liter" - }, - "nitrate_nitrogen": { - "has_raw_value": "0.29 mg/kg" - }, - "nitrite_nitrogen": { - "has_raw_value": "1.2 mg/kg" - }, - "lbc_thirty": { - "has_raw_value": "543 mg/kg" - }, - "lbceq": { - "has_raw_value": "1575 mg/kg" - }, - "@type": "Biosample" -} \ No newline at end of file diff --git a/src/data/output/Biosample-exhasutive.ttl b/src/data/output/Biosample-exhasutive.ttl deleted file mode 100644 index 73aa804125..0000000000 --- a/src/data/output/Biosample-exhasutive.ttl +++ /dev/null @@ -1,386 +0,0 @@ -@prefix ENVO: . -@prefix dcterms: . -@prefix mixs: . -@prefix nmdc: . -@prefix wgs84: . -@prefix xsd: . - -nmdc:bsm-99-dtTMNb a nmdc:Biosample ; - dcterms:description "unconstrained text" ; - dcterms:isPartOf nmdc:unconstrained_study_identifier_string1_needs_pattern_materialization_what_about_referential_integrity, - nmdc:unconstrained_study_identifier_string2 ; - mixs:0000001 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "5 liters" ] ; - mixs:0000008 [ a nmdc:ControlledTermValue ; - nmdc:has_raw_value "unconstrained text, unlike the MIxS environmental triad" ] ; - mixs:0000009 [ a nmdc:GeolocationValue ; - wgs84:lat 50.586825 ; - wgs84:long 6.408977 ; - nmdc:has_raw_value "50.586825 6.408977" ] ; - mixs:0000010 [ a nmdc:TextValue ; - nmdc:has_raw_value "USA: Maryland, Bethesda" ] ; - mixs:0000011 [ a nmdc:TimestampValue ; - nmdc:has_raw_value "2023-01-16T16:05:42+0000" ] ; - mixs:0000012 [ a nmdc:ControlledIdentifiedTermValue ; - nmdc:has_raw_value "ENVO:00002030" ; - nmdc:term ENVO:00002030 ] ; - mixs:0000013 [ a nmdc:ControlledIdentifiedTermValue ; - nmdc:has_raw_value "ENVO:00002169" ; - nmdc:term ENVO:00002169 ] ; - mixs:0000014 [ a nmdc:ControlledIdentifiedTermValue ; - nmdc:has_raw_value "ENVO:00005792" ; - nmdc:term ENVO:00005792 ] ; - mixs:0000015 [ a nmdc:TextValue ; - nmdc:has_raw_value "aerobe. change validation to enumeration" ] ; - mixs:0000016 [ a nmdc:ControlledTermValue ; - nmdc:has_raw_value "filtering of seawater" ] ; - mixs:0000018 [ a nmdc:QuantityValue ; - nmdc:has_maximum_numeric_value "2.5"^^xsd:float ; - nmdc:has_minimum_numeric_value "1.5"^^xsd:float ; - nmdc:has_numeric_value 2e+00 ; - nmdc:has_raw_value "1.5 to 2.5 meters (that may not be the pattern the submission schema expects). Extractions below require external migration logic." ; - nmdc:has_unit "meter" ] ; - mixs:0000026 [ a nmdc:TextValue ; - nmdc:has_raw_value "MPI012345" ] ; - mixs:0000028 [ a nmdc:TextValue ; - nmdc:has_raw_value "MIxS suggest enum [free living|parasite|commensal|symbiont] but not currently enforced here" ] ; - mixs:0000093 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "100 meter" ] ; - mixs:0000094 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "100 meter" ] ; - mixs:0000103 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "total prokaryotes;3.5e7 cells per milliliter;qPCR" ] ; - mixs:0000106 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "56.5 micromole per liter" ] ; - mixs:0000110 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "-80 degree Celsius" ] ; - mixs:0000111 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "1500 milliliter" ] ; - mixs:0000113 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "25 degree Celsius" ] ; - mixs:0000116 [ a nmdc:TextValue ; - nmdc:has_raw_value "P1Y6M" ] ; - mixs:0000117 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.03 milligram per liter" ] ; - mixs:0000119 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "175 micromole per kilogram" ] ; - mixs:0000137 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "5 mol per liter per hour" ] ; - mixs:0000162 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.05 micromole per liter" ] ; - mixs:0000172 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.269 mole per liter per hour" ] ; - mixs:0000173 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "2.53 microgram per liter per hour" ] ; - mixs:0000175 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "14 microgram per liter" ] ; - mixs:0000176 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.05 parts per million" ] ; - mixs:0000177 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "5 milligram per cubic meter" ] ; - mixs:0000179 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.3 micromole per liter" ] ; - mixs:0000180 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "2.5 milligram per cubic meter" ] ; - mixs:0000181 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "2.98 milligram per liter" ] ; - mixs:0000182 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "300 millivolt" ] ; - mixs:0000183 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "25 practical salinity unit" ] ; - mixs:0000185 "MIxS doesn't provide an example 1", - "MIxS doesn't provide an example 2" ; - mixs:0000204 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "1.75 milligram per cubic meter" ] ; - mixs:0000205 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "4 micromole per liter" ] ; - mixs:0000298 [ a nmdc:TextValue ; - nmdc:has_raw_value "https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity" ] ; - mixs:0000310 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.417361111" ] ; - mixs:0000312 [ a nmdc:TextValue ; - nmdc:has_raw_value "MIxS doesn't provide any guidance more specific than \"text\"" ] ; - mixs:0000314 [ a nmdc:TextValue ; - nmdc:has_raw_value "https://link.springer.com/article/10.1023/A:1011975321668" ] ; - mixs:0000318 [ a nmdc:TextValue ; - nmdc:has_raw_value "yes;R2/2017-01-01/2018-12-31/P6M" ] ; - mixs:0000319 "2000-01-15" ; - mixs:0000320 "2023-01-15" ; - mixs:0000322 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "MIxS does not provide an example" ] ; - mixs:0000323 "MIxS doesn't provide an example" ; - mixs:0000324 [ a nmdc:TextValue ; - nmdc:has_raw_value "https://journaljeai.com/index.php/JEAI/article/view/583" ] ; - mixs:0000325 [ a nmdc:TextValue ; - nmdc:has_raw_value "yes, 5" ] ; - mixs:0000327 [ a nmdc:TextValue ; - nmdc:has_raw_value "-20 degree Celsius freezer;P2Y10D" ] ; - mixs:0000328 [ a nmdc:TextValue ; - nmdc:has_raw_value "https://www.int-res.com/abstracts/cr/v14/n3/p161-173/" ] ; - mixs:0000329 [ a nmdc:TextValue ; - nmdc:has_raw_value "https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf" ] ; - mixs:0000330 [ a nmdc:TextValue ; - nmdc:has_raw_value "jicama soil" ] ; - mixs:0000331 [ a nmdc:TextValue ; - nmdc:has_raw_value "https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083" ] ; - mixs:0000332 [ a nmdc:TextValue ; - nmdc:has_raw_value "plinthosol [ENVO:00002250]" ] ; - mixs:0000334 [ a nmdc:TextValue ; - nmdc:has_raw_value "Frederick series" ] ; - mixs:0000337 [ a nmdc:TextValue ; - nmdc:has_raw_value "https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf" ] ; - mixs:0000338 "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00" ; - mixs:0000340 [ a nmdc:TextValue ; - nmdc:has_raw_value "https://pubmed.ncbi.nlm.nih.gov/2315679/" ] ; - mixs:0000341 [ a nmdc:TextValue ; - nmdc:has_raw_value "PMID:22895776" ] ; - mixs:0000343 [ a nmdc:TextValue ; - nmdc:has_raw_value "https://link.springer.com/article/10.1007/s42452-019-1578-x" ] ; - mixs:0000412 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "50 atmosphere" ] ; - mixs:0000421 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "50 milligram per liter" ] ; - mixs:0000423 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "5 micromole per liter" ] ; - mixs:0000424 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "2 micromole per liter" ] ; - mixs:0000425 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "65 micromole per liter" ] ; - mixs:0000426 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.5 micromole per liter" ] ; - mixs:0000427 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "1.5 milligram per liter" ] ; - mixs:0000428 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "10.5 milligram per liter" ] ; - mixs:0000429 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "5000 milligram per liter" ] ; - mixs:0000430 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "463 milligram per liter" ] ; - mixs:0000431 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "52.8 micromole per kilogram" ] ; - mixs:0000432 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.2 micromole per liter" ] ; - mixs:0000433 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "197 micromole per liter" ] ; - mixs:0000434 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "2059 micromole per kilogram" ] ; - mixs:0000435 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "1000 kilogram per cubic meter" ] ; - mixs:0000436 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "5 milligram per liter" ] ; - mixs:0000490 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.005 mole per liter" ] ; - mixs:0000498 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.5 meter per second" ] ; - mixs:0000502 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "1 meter per second" ] ; - mixs:0000503 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "n-hexadecane;100 milligram per liter" ] ; - mixs:0000505 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.7 micromole per liter" ] ; - mixs:0000515 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "1.92 micromole per liter" ] ; - mixs:0000516 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.05 micromole per liter" ] ; - mixs:0000525 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "MIxS does not provide an example" ] ; - mixs:0000530 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "35 milligrams Nitrogen per kilogram of soil" ] ; - mixs:0000533 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "2%" ] ; - mixs:0000551 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; - mixs:0000558 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; - mixs:0000568 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; - mixs:0000569 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "incandescent light;10 lux;450 nanometer" ] ; - mixs:0000591 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; - mixs:0000607 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.1 mg/kg" ] ; - mixs:0000634 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "500 meter" ] ; - mixs:0000639 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "lime;1 kg/acre;2022-11-16T16:05:42+0000" ] ; - mixs:0000642 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "12.5 degree Celsius" ] ; - mixs:0000643 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "18 degree Celsius" ] ; - mixs:0000644 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.5 milligram per liter" ] ; - mixs:0000645 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "75 millimeters" ] ; - mixs:0000646 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "MIxS does not provide an example" ] ; - mixs:0000647 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "MIxS does not provide an example" ] ; - mixs:0000652 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "arsenic;0.09 micrograms per gram" ], - [ a nmdc:QuantityValue ; - nmdc:has_raw_value "mercury;0.09 micrograms per gram" ] ; - mixs:0000735 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.2 micrometer" ] ; - mixs:0000736 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "20 micrometer" ] ; - mixs:0000744 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "40 microgram per liter" ] ; - mixs:0000750 [ a nmdc:TextValue ; - nmdc:has_raw_value "high tide. change validation to enumeration" ] ; - mixs:0000751 [ a nmdc:ControlledTermValue ; - nmdc:has_raw_value "agar [CHEBI:2509];2018-05-11T20:00Z" ] ; - mixs:0000752 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "Bicarbonate ion concentration;2075 micromole per kilogram" ] ; - mixs:0000753 [ a nmdc:TextValue ; - nmdc:has_raw_value "aerobic. change implementation from text value to string with enumerated range" ] ; - mixs:0000754 [ a nmdc:TextValue ; - nmdc:has_raw_value "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" ] ; - mixs:0000755 [ a nmdc:TextValue ; - nmdc:has_raw_value "Freezer no:5" ] ; - mixs:0001001 [ a nmdc:QuantityValue ; - nmdc:has_raw_value "7.5" ] ; - mixs:0001038 [ a nmdc:TextValue ; - nmdc:has_raw_value "sample inoculated with Rhizobium spp. Culture" ] ; - mixs:0001040 [ a nmdc:TextValue ; - nmdc:has_raw_value "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; - mixs:0001043 [ a nmdc:ControlledTermValue ; - nmdc:has_raw_value "Growth chamber [CO_715:0000189]" ] ; - mixs:0001080 [ a nmdc:TextValue ; - nmdc:has_raw_value "conifers" ] ; - mixs:0001081 [ a nmdc:TextValue ; - nmdc:has_raw_value "chisel. change validation to enumeration" ] ; - mixs:0001083 [ a nmdc:TextValue ; - nmdc:has_raw_value "Fluvisol" ] ; - mixs:0001084 [ a nmdc:TextValue ; - nmdc:has_raw_value "summit. change validation to enumeration" ] ; - mixs:0001085 [ a nmdc:TextValue ; - nmdc:has_raw_value "well" ] ; - mixs:0001086 "2000-11 to 2000-12" ; - mixs:0001106 [ a nmdc:TextValue ; - nmdc:has_raw_value "https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf" ] ; - mixs:0001107 "see also name" ; - mixs:0001225 "swabbing" ; - mixs:0001320 "soil metagenome [NCBItaxon:410658] but no validation applied yet" ; - nmdc:add_date "2021-03-31" ; - nmdc:alternative_identifiers "any_string", - "seriously_anything" ; - nmdc:ammonium_nitrogen [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.5 milligram per liter" ] ; - nmdc:analysis_type "metabolomics", - "metagenomics" ; - nmdc:biosample_categories "FICUS", - "LTER" ; - nmdc:collected_from nmdc:unconstrained_site_identifier_string ; - nmdc:collection_date_inc "2023-01-29" ; - nmdc:collection_time "05:42+0000" ; - nmdc:collection_time_inc "13:42+0000" ; - nmdc:community "no_example_from_mixs" ; - nmdc:dna_absorb1 "2.02" ; - nmdc:dna_absorb2 "2.02" ; - nmdc:dna_collect_site "untreated pond water" ; - nmdc:dna_concentration "100" ; - nmdc:dna_cont_type "plate" ; - nmdc:dna_cont_well "C2" ; - nmdc:dna_container_id "Pond_MT_041618" ; - nmdc:dna_dnase "yes" ; - nmdc:dna_isolate_meth "phenol/chloroform extraction" ; - nmdc:dna_organisms "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)" ; - nmdc:dna_project_contact "John Jones" ; - nmdc:dna_samp_id "187654" ; - nmdc:dna_sample_format "10 mM Tris-HCl" ; - nmdc:dna_sample_name "JGI_pond_041618" ; - nmdc:dna_seq_project "1191234" ; - nmdc:dna_seq_project_name "JGI Pond metagenomics" ; - nmdc:dna_seq_project_pi "Jane Johnson" ; - nmdc:dna_volume "25" ; - nmdc:dnase_rna "yes" ; - nmdc:ecosystem "unconstrained text. should be validated against the controlled vocabulary, by the sample's environmental package. would also be nice to align the CV with MIxS environmental triads" ; - nmdc:ecosystem_category "unconstrained text" ; - nmdc:ecosystem_subtype "unconstrained text" ; - nmdc:ecosystem_type "unconstrained text" ; - nmdc:embargoed true ; - nmdc:emsl_biosample_identifiers "any_string"^^xsd:anyURI, - "seriously_anything"^^xsd:anyURI ; - nmdc:env_package [ a nmdc:TextValue ; - nmdc:has_raw_value "unconstrained text. should require the name of a MIxS EnvironmentalPackage class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM!" ] ; - nmdc:experimental_factor_other "unconstrained text, but presumably expects 'term label [term id]'" ; - nmdc:filter_method "Basix PES, 13-100-106 FisherSci is an example value, but unconstrained text is accepted at this point" ; - nmdc:gold_biosample_identifiers "GOLD:Gb"^^xsd:anyURI, - "GOLD:Gb123456789"^^xsd:anyURI ; - nmdc:habitat "unconstrained text" ; - nmdc:host_name "snail is an example value, but unconstrained text is accepted at this point" ; - nmdc:igsn_biosample_identifiers "any:curie_1"^^xsd:anyURI, - "any:curie_2"^^xsd:anyURI ; - nmdc:img_identifiers "any string 1", - "any string 2" ; - nmdc:insdc_biosample_identifiers "biosample:SAMN000"^^xsd:anyURI, - "biosample:SAMN123456789"^^xsd:anyURI ; - nmdc:isotope_exposure "13C glucose" ; - nmdc:lbc_thirty [ a nmdc:QuantityValue ; - nmdc:has_raw_value "543 mg/kg" ] ; - nmdc:lbceq [ a nmdc:QuantityValue ; - nmdc:has_raw_value "1575 mg/kg" ] ; - nmdc:location "unconstrained text. should we even keep this slot? check if it ahs been used in MongoDB." ; - nmdc:manganese [ a nmdc:QuantityValue ; - nmdc:has_raw_value "24.7 mg/kg" ] ; - nmdc:micro_biomass_c_meth "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12" ; - nmdc:micro_biomass_n_meth "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12" ; - nmdc:microbial_biomass_c "0.05 ug C/g dry soil" ; - nmdc:microbial_biomass_n "0.05 ug N/g dry soil" ; - nmdc:mod_date "2023-01-25" ; - nmdc:name "Sample Exhaustive Biosample instance. Although all of these values should pass validation, that does not mean that any Biosample of any type would necessarily have this particular combination of values." ; - nmdc:ncbi_taxonomy_name "soil metagenome" ; - nmdc:nitrate_nitrogen [ a nmdc:QuantityValue ; - nmdc:has_raw_value "0.29 mg/kg" ] ; - nmdc:nitrite_nitrogen [ a nmdc:QuantityValue ; - nmdc:has_raw_value "1.2 mg/kg" ] ; - nmdc:non_microb_biomass "insect 0.23 ug; plant 1g" ; - nmdc:non_microb_biomass_method "https://doi.org/10.1038/s41467-021-26181-3" ; - nmdc:org_nitro_method "https://doi.org/10.1016/0038-0717(85)90144-0" ; - nmdc:other_treatment "unconstrained text" ; - nmdc:project_id "no example from MIxS" ; - nmdc:proport_woa_temperature "no example from MIxS" ; - nmdc:proposal_dna "504000" ; - nmdc:proposal_rna "504000" ; - nmdc:replicate_number "1" ; - nmdc:rna_absorb1 "2.02" ; - nmdc:rna_absorb2 "2.02" ; - nmdc:rna_collect_site "untreated pond water" ; - nmdc:rna_concentration "100" ; - nmdc:rna_cont_type "plate" ; - nmdc:rna_cont_well "C2" ; - nmdc:rna_container_id "Pond_MT_041618" ; - nmdc:rna_isolate_meth "phenol/chloroform extraction" ; - nmdc:rna_organisms "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)" ; - nmdc:rna_project_contact "John Jones" ; - nmdc:rna_samp_id "187654" ; - nmdc:rna_sample_format "10 mM Tris-HCl" ; - nmdc:rna_sample_name "JGI_pond_041618" ; - nmdc:rna_seq_project "1191234" ; - nmdc:rna_seq_project_name "JGI Pond metagenomics" ; - nmdc:rna_seq_project_pi "Jane Johnson" ; - nmdc:rna_volume "25" ; - nmdc:salinity_category "halotolerant is an example from the schema, but MIxS doesn't provide this slot any more" ; - nmdc:sample_collection_site "unconstrained text" ; - nmdc:sample_link "IGSN:DSJ0284", - "any:curie" ; - nmdc:sample_shipped "15 g" ; - nmdc:sample_type "water_extract_soil" ; - nmdc:soluble_iron_micromol "MIxS doesn't provide an example" ; - nmdc:specific_ecosystem "unconstrained text" ; - nmdc:start_date_inc "2023-01-27" ; - nmdc:start_time_inc "13:42+0000" ; - nmdc:subsurface_depth [ a nmdc:QuantityValue ; - nmdc:has_raw_value "MIxS does not provide an example" ] ; - nmdc:technical_reps "2" ; - nmdc:type "nmdc:Biosample. change this to require a class name or an enumeration" ; - nmdc:zinc [ a nmdc:QuantityValue ; - nmdc:has_raw_value "2.5 mg/kg" ] . - -ENVO:00002030 a nmdc:OntologyClass . - -ENVO:00002169 a nmdc:OntologyClass . - -ENVO:00005792 a nmdc:OntologyClass . - diff --git a/src/data/output/Biosample-exhasutive.yaml b/src/data/output/Biosample-exhasutive.yaml deleted file mode 100644 index 091367df36..0000000000 --- a/src/data/output/Biosample-exhasutive.yaml +++ /dev/null @@ -1,399 +0,0 @@ -id: nmdc:bsm-99-dtTMNb -name: Sample Exhaustive Biosample instance. Although all of these values should pass - validation, that does not mean that any Biosample of any type would necessarily - have this particular combination of values. -description: unconstrained text -alternative_identifiers: -- any_string -- seriously_anything -part_of: -- nmdc:unconstrained_study_identifier_string1_needs_pattern_materialization_what_about_referential_integrity -- nmdc:unconstrained_study_identifier_string2 -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 -collected_from: nmdc:unconstrained_site_identifier_string -type: nmdc:Biosample. change this to require a class name or an enumeration -img_identifiers: -- any string 1 -- any string 2 -samp_name: see also name -biosample_categories: -- LTER -- FICUS -gold_biosample_identifiers: -- GOLD:Gb123456789 -- GOLD:Gb -insdc_biosample_identifiers: -- biosample:SAMN123456789 -- biosample:SAMN000 -emsl_biosample_identifiers: -- any_string -- seriously_anything -igsn_biosample_identifiers: -- any:curie_1 -- any:curie_2 -agrochem_addition: - has_raw_value: lime;1 kg/acre;2022-11-16T16:05:42+0000 -alkalinity: - has_raw_value: 50 milligram per liter -alkalinity_method: - has_raw_value: https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity -alkyl_diethers: - has_raw_value: 0.005 mole per liter -alt: - has_raw_value: 100 meter -al_sat: - has_raw_value: 0.1 mg/kg -al_sat_meth: - has_raw_value: https://journaljeai.com/index.php/JEAI/article/view/583 -aminopept_act: - has_raw_value: 0.269 mole per liter per hour -ammonium: - has_raw_value: 1.5 milligram per liter -annual_precpt: - has_raw_value: 0.5 milligram per liter -annual_temp: - has_raw_value: 12.5 degree Celsius -bacteria_carb_prod: - has_raw_value: 2.53 microgram per liter per hour -bishomohopanol: - has_raw_value: 14 microgram per liter -bromide: - has_raw_value: 0.05 parts per million -calcium: - has_raw_value: 0.2 micromole per liter -carb_nitro_ratio: - has_raw_value: '0.417361111' -chem_administration: - has_raw_value: agar [CHEBI:2509];2018-05-11T20:00Z -chloride: - has_raw_value: 5000 milligram per liter -chlorophyll: - has_raw_value: 5 milligram per cubic meter -collection_date: - has_raw_value: 2023-01-16T16:05:42+0000 -cur_land_use: - has_raw_value: conifers -cur_vegetation: - has_raw_value: MIxS doesn't provide any guidance more specific than "text" -cur_vegetation_meth: - has_raw_value: https://link.springer.com/article/10.1023/A:1011975321668 -crop_rotation: - has_raw_value: yes;R2/2017-01-01/2018-12-31/P6M -density: - has_raw_value: 1000 kilogram per cubic meter -depth: - has_raw_value: 1.5 to 2.5 meters (that may not be the pattern the submission schema - expects). Extractions below require external migration logic. - has_unit: meter - has_numeric_value: 2.0 - has_minimum_numeric_value: 1.5 - has_maximum_numeric_value: 2.5 -diss_carb_dioxide: - has_raw_value: 5 milligram per liter -diss_hydrogen: - has_raw_value: 0.3 micromole per liter -diss_inorg_carb: - has_raw_value: 2059 micromole per kilogram -diss_inorg_phosp: - has_raw_value: 56.5 micromole per liter -diss_org_carb: - has_raw_value: 197 micromole per liter -diss_org_nitro: - has_raw_value: 0.05 micromole per liter -diss_oxygen: - has_raw_value: 175 micromole per kilogram -drainage_class: - has_raw_value: well -elev: - has_raw_value: 100 meter -env_package: - has_raw_value: unconstrained text. should require the name of a MIxS EnvironmentalPackage - class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM! -extreme_event: '2023-01-15' -fao_class: - has_raw_value: Fluvisol -fire: 2000-11 to 2000-12 -flooding: '2000-01-15' -geo_loc_name: - has_raw_value: 'USA: Maryland, Bethesda' -glucosidase_act: - has_raw_value: 5 mol per liter per hour -heavy_metals: -- has_raw_value: mercury;0.09 micrograms per gram -- has_raw_value: arsenic;0.09 micrograms per gram -heavy_metals_meth: -- has_raw_value: https://link.springer.com/article/10.1007/s42452-019-1578-x -lat_lon: - has_raw_value: 50.586825 6.408977 - latitude: 50.586825 - longitude: 6.408977 -link_addit_analys: - has_raw_value: https://pubmed.ncbi.nlm.nih.gov/2315679/ -link_class_info: - has_raw_value: https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf -link_climate_info: - has_raw_value: https://www.int-res.com/abstracts/cr/v14/n3/p161-173/ -local_class: - has_raw_value: jicama soil -local_class_meth: - has_raw_value: https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083 -magnesium: - has_raw_value: 52.8 micromole per kilogram -mean_frict_vel: - has_raw_value: 0.5 meter per second -mean_peak_frict_vel: - has_raw_value: 1 meter per second -misc_param: - has_raw_value: Bicarbonate ion concentration;2075 micromole per kilogram -n_alkanes: - has_raw_value: n-hexadecane;100 milligram per liter -nitrate: - has_raw_value: 65 micromole per liter -nitrite: - has_raw_value: 0.5 micromole per liter -org_matter: - has_raw_value: 1.75 milligram per cubic meter -org_nitro: - has_raw_value: 4 micromole per liter -organism_count: - has_raw_value: total prokaryotes;3.5e7 cells per milliliter;qPCR -oxy_stat_samp: - has_raw_value: aerobic. change implementation from text value to string with enumerated - range -part_org_carb: - has_raw_value: 1.92 micromole per liter -perturbation: - has_raw_value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M -petroleum_hydrocarb: - has_raw_value: 0.05 micromole per liter -ph: - has_raw_value: '7.5' -ph_meth: - has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf -phaeopigments: - has_raw_value: 2.5 milligram per cubic meter -phosplipid_fatt_acid: - has_raw_value: 2.98 milligram per liter -pool_dna_extracts: - has_raw_value: yes, 5 -potassium: - has_raw_value: 463 milligram per liter -pressure: - has_raw_value: 50 atmosphere -profile_position: - has_raw_value: summit. change validation to enumeration -redox_potential: - has_raw_value: 300 millivolt -salinity: - has_raw_value: 25 practical salinity unit -salinity_meth: - has_raw_value: PMID:22895776 -samp_mat_process: - has_raw_value: filtering of seawater -samp_store_dur: - has_raw_value: P1Y6M -samp_store_loc: - has_raw_value: Freezer no:5 -samp_taxon_id: soil metagenome [NCBItaxon:410658] but no validation applied yet -samp_store_temp: - has_raw_value: -80 degree Celsius -samp_vol_we_dna_ext: - has_raw_value: 1500 milliliter -season_temp: - has_raw_value: 18 degree Celsius -season_precpt: - has_raw_value: 75 millimeters -sieving: - has_raw_value: MIxS does not provide an example -size_frac_low: - has_raw_value: 0.2 micrometer -size_frac_up: - has_raw_value: 20 micrometer -slope_gradient: - has_raw_value: MIxS does not provide an example -slope_aspect: - has_raw_value: MIxS does not provide an example -sodium: - has_raw_value: 10.5 milligram per liter -soil_type: - has_raw_value: plinthosol [ENVO:00002250] -soil_type_meth: - has_raw_value: Frederick series -store_cond: - has_raw_value: -20 degree Celsius freezer;P2Y10D -sulfate: - has_raw_value: 5 micromole per liter -sulfide: - has_raw_value: 2 micromole per liter -temp: - has_raw_value: 25 degree Celsius -tillage: - has_raw_value: chisel. change validation to enumeration -tidal_stage: - has_raw_value: high tide. change validation to enumeration -tot_carb: - has_raw_value: MIxS does not provide an example -tot_depth_water_col: - has_raw_value: 500 meter -tot_diss_nitro: - has_raw_value: 40 microgram per liter -tot_org_carb: - has_raw_value: 2% -tot_org_c_meth: - has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf -tot_nitro_content: - has_raw_value: 35 milligrams Nitrogen per kilogram of soil -tot_nitro_cont_meth: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 -tot_phosp: - has_raw_value: 0.03 milligram per liter -water_content: -- MIxS doesn't provide an example 1 -- MIxS doesn't provide an example 2 -water_cont_soil_meth: MIxS doesn't provide an example -ecosystem: unconstrained text. should be validated against the controlled vocabulary, - by the sample's environmental package. would also be nice to align the CV with MIxS - environmental triads -ecosystem_category: unconstrained text -ecosystem_type: unconstrained text -ecosystem_subtype: unconstrained text -specific_ecosystem: unconstrained text -add_date: '2021-03-31' -community: no_example_from_mixs -habitat: unconstrained text -host_name: snail is an example value, but unconstrained text is accepted at this point -location: unconstrained text. should we even keep this slot? check if it ahs been - used in MongoDB. -mod_date: '2023-01-25' -ncbi_taxonomy_name: soil metagenome -proport_woa_temperature: no example from MIxS -salinity_category: halotolerant is an example from the schema, but MIxS doesn't provide - this slot any more -sample_collection_site: unconstrained text -soluble_iron_micromol: MIxS doesn't provide an example -subsurface_depth: - has_raw_value: MIxS does not provide an example -air_temp_regm: - has_raw_value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -biotic_regm: - has_raw_value: sample inoculated with Rhizobium spp. Culture -biotic_relationship: - has_raw_value: MIxS suggest enum [free living|parasite|commensal|symbiont] but not - currently enforced here -climate_environment: - has_raw_value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -experimental_factor: - has_raw_value: unconstrained text, unlike the MIxS environmental triad -gaseous_environment: - has_raw_value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -growth_facil: - has_raw_value: Growth chamber [CO_715:0000189] -humidity_regm: - has_raw_value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -light_regm: - has_raw_value: incandescent light;10 lux;450 nanometer -phosphate: - has_raw_value: 0.7 micromole per liter -rel_to_oxygen: - has_raw_value: aerobe. change validation to enumeration -samp_collec_method: swabbing -samp_size: - has_raw_value: 5 liters -source_mat_id: - has_raw_value: MPI012345 -watering_regm: - has_raw_value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -dna_absorb1: '2.02' -dna_absorb2: '2.02' -dna_collect_site: untreated pond water -dna_concentration: '100' -dna_cont_type: plate -dna_cont_well: C2 -dna_container_id: Pond_MT_041618 -dna_dnase: 'yes' -dna_isolate_meth: phenol/chloroform extraction -dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles - (1%) -dna_project_contact: John Jones -dna_samp_id: '187654' -dna_sample_format: 10 mM Tris-HCl -dna_sample_name: JGI_pond_041618 -dna_seq_project: '1191234' -dna_seq_project_pi: Jane Johnson -dna_seq_project_name: JGI Pond metagenomics -dna_volume: '25' -proposal_dna: '504000' -dnase_rna: 'yes' -proposal_rna: '504000' -rna_absorb1: '2.02' -rna_absorb2: '2.02' -rna_collect_site: untreated pond water -rna_concentration: '100' -rna_cont_type: plate -rna_cont_well: C2 -rna_container_id: Pond_MT_041618 -rna_isolate_meth: phenol/chloroform extraction -rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles - (1%) -rna_project_contact: John Jones -rna_samp_id: '187654' -rna_sample_format: 10 mM Tris-HCl -rna_sample_name: JGI_pond_041618 -rna_seq_project: '1191234' -rna_seq_project_pi: Jane Johnson -rna_seq_project_name: JGI Pond metagenomics -rna_volume: '25' -collection_date_inc: '2023-01-29' -collection_time: 05:42+0000 -collection_time_inc: 13:42+0000 -experimental_factor_other: unconstrained text, but presumably expects 'term label - [term id]' -filter_method: Basix PES, 13-100-106 FisherSci is an example value, but unconstrained - text is accepted at this point -isotope_exposure: 13C glucose -micro_biomass_c_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 -micro_biomass_n_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 -microbial_biomass_c: 0.05 ug C/g dry soil -microbial_biomass_n: 0.05 ug N/g dry soil -non_microb_biomass: insect 0.23 ug; plant 1g -non_microb_biomass_method: https://doi.org/10.1038/s41467-021-26181-3 -org_nitro_method: https://doi.org/10.1016/0038-0717(85)90144-0 -other_treatment: unconstrained text -start_date_inc: '2023-01-27' -start_time_inc: 13:42+0000 -project_id: no example from MIxS -replicate_number: '1' -sample_shipped: 15 g -sample_type: water_extract_soil -technical_reps: '2' -analysis_type: -- metabolomics -- metagenomics -sample_link: -- IGSN:DSJ0284 -- any:curie -zinc: - has_raw_value: 2.5 mg/kg -manganese: - has_raw_value: 24.7 mg/kg -ammonium_nitrogen: - has_raw_value: 0.5 milligram per liter -nitrate_nitrogen: - has_raw_value: 0.29 mg/kg -nitrite_nitrogen: - has_raw_value: 1.2 mg/kg -lbc_thirty: - has_raw_value: 543 mg/kg -lbceq: - has_raw_value: 1575 mg/kg diff --git a/src/data/output/Biosample-minimal.json b/src/data/output/Biosample-minimal.json deleted file mode 100644 index 0e4c4afac7..0000000000 --- a/src/data/output/Biosample-minimal.json +++ /dev/null @@ -1,25 +0,0 @@ -{ - "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" - } - }, - "@type": "Biosample" -} \ No newline at end of file diff --git a/src/data/output/Biosample-minimal.ttl b/src/data/output/Biosample-minimal.ttl deleted file mode 100644 index 377972faa3..0000000000 --- a/src/data/output/Biosample-minimal.ttl +++ /dev/null @@ -1,24 +0,0 @@ -@prefix ENVO: . -@prefix GOLD: . -@prefix dcterms: . -@prefix mixs: . -@prefix nmdc: . - -nmdc:bsm-99-dtTMNb a nmdc:Biosample ; - dcterms:isPartOf GOLD:Gs0110115 ; - mixs:0000012 [ a nmdc:ControlledIdentifiedTermValue ; - nmdc:has_raw_value "ENVO:00002030" ; - nmdc:term ENVO:00002030 ] ; - mixs:0000013 [ a nmdc:ControlledIdentifiedTermValue ; - nmdc:has_raw_value "ENVO:00002169" ; - nmdc:term ENVO:00002169 ] ; - mixs:0000014 [ a nmdc:ControlledIdentifiedTermValue ; - nmdc:has_raw_value "ENVO:00005792" ; - nmdc:term ENVO:00005792 ] . - -ENVO:00002030 a nmdc:OntologyClass . - -ENVO:00002169 a nmdc:OntologyClass . - -ENVO:00005792 a nmdc:OntologyClass . - diff --git a/src/data/output/Biosample-minimal.yaml b/src/data/output/Biosample-minimal.yaml deleted file mode 100644 index 349116e7b3..0000000000 --- a/src/data/output/Biosample-minimal.yaml +++ /dev/null @@ -1,15 +0,0 @@ -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/src/data/output/README.md b/src/data/output/README.md index 1578e3480c..e69de29bb2 100644 --- a/src/data/output/README.md +++ b/src/data/output/README.md @@ -1,592 +0,0 @@ -## Biosample-embargoed -### Input -```yaml -embargoed: true -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 -id: nmdc:bsm-99-dtTMNb -part_of: -- gold:Gs0110115 - -``` -## Biosample-exhasutive -### Input -```yaml -add_date: '2021-03-31' -agrochem_addition: - has_raw_value: lime;1 kg/acre;2022-11-16T16:05:42+0000 -air_temp_regm: - has_raw_value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -al_sat: - has_raw_value: 0.1 mg/kg -al_sat_meth: - has_raw_value: https://journaljeai.com/index.php/JEAI/article/view/583 -alkalinity: - has_raw_value: 50 milligram per liter -alkalinity_method: - has_raw_value: https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity -alkyl_diethers: - has_raw_value: 0.005 mole per liter -alt: - has_raw_value: 100 meter -alternative_identifiers: -- any_string -- seriously_anything -aminopept_act: - has_raw_value: 0.269 mole per liter per hour -ammonium: - has_raw_value: 1.5 milligram per liter -ammonium_nitrogen: - has_raw_value: 0.5 milligram per liter -analysis_type: -- metabolomics -- metagenomics -annual_precpt: - has_raw_value: 0.5 milligram per liter -annual_temp: - has_raw_value: 12.5 degree Celsius -bacteria_carb_prod: - has_raw_value: 2.53 microgram per liter per hour -biosample_categories: -- LTER -- FICUS -biotic_regm: - has_raw_value: sample inoculated with Rhizobium spp. Culture -biotic_relationship: - has_raw_value: MIxS suggest enum [free living|parasite|commensal|symbiont] but not - currently enforced here -bishomohopanol: - has_raw_value: 14 microgram per liter -bromide: - has_raw_value: 0.05 parts per million -calcium: - has_raw_value: 0.2 micromole per liter -carb_nitro_ratio: - has_raw_value: '0.417361111' -chem_administration: - has_raw_value: agar [CHEBI:2509];2018-05-11T20:00Z -chloride: - has_raw_value: 5000 milligram per liter -chlorophyll: - has_raw_value: 5 milligram per cubic meter -climate_environment: - has_raw_value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -collected_from: nmdc:unconstrained_site_identifier_string -collection_date: - has_raw_value: 2023-01-16T16:05:42+0000 -collection_date_inc: '2023-01-29' -collection_time: 05:42+0000 -collection_time_inc: 13:42+0000 -community: no_example_from_mixs -crop_rotation: - has_raw_value: yes;R2/2017-01-01/2018-12-31/P6M -cur_land_use: - has_raw_value: conifers -cur_vegetation: - has_raw_value: MIxS doesn't provide any guidance more specific than "text" -cur_vegetation_meth: - has_raw_value: https://link.springer.com/article/10.1023/A:1011975321668 -density: - has_raw_value: 1000 kilogram per cubic meter -depth: - has_maximum_numeric_value: 2.5 - has_minimum_numeric_value: 1.5 - has_numeric_value: 2.0 - has_raw_value: 1.5 to 2.5 meters (that may not be the pattern the submission schema - expects). Extractions below require external migration logic. - has_unit: meter -description: unconstrained text -diss_carb_dioxide: - has_raw_value: 5 milligram per liter -diss_hydrogen: - has_raw_value: 0.3 micromole per liter -diss_inorg_carb: - has_raw_value: 2059 micromole per kilogram -diss_inorg_phosp: - has_raw_value: 56.5 micromole per liter -diss_org_carb: - has_raw_value: 197 micromole per liter -diss_org_nitro: - has_raw_value: 0.05 micromole per liter -diss_oxygen: - has_raw_value: 175 micromole per kilogram -dna_absorb1: '2.02' -dna_absorb2: '2.02' -dna_collect_site: untreated pond water -dna_concentration: '100' -dna_cont_type: plate -dna_cont_well: C2 -dna_container_id: Pond_MT_041618 -dna_dnase: 'yes' -dna_isolate_meth: phenol/chloroform extraction -dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles - (1%) -dna_project_contact: John Jones -dna_samp_id: '187654' -dna_sample_format: 10 mM Tris-HCl -dna_sample_name: JGI_pond_041618 -dna_seq_project: '1191234' -dna_seq_project_name: JGI Pond metagenomics -dna_seq_project_pi: Jane Johnson -dna_volume: '25' -dnase_rna: 'yes' -drainage_class: - has_raw_value: well -ecosystem: unconstrained text. should be validated against the controlled vocabulary, - by the sample's environmental package. would also be nice to align the CV with MIxS - environmental triads -ecosystem_category: unconstrained text -ecosystem_subtype: unconstrained text -ecosystem_type: unconstrained text -elev: - has_raw_value: 100 meter -embargoed: true -emsl_biosample_identifiers: -- any_string -- seriously_anything -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 -env_package: - has_raw_value: unconstrained text. should require the name of a MIxS EnvironmentalPackage - class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM! -experimental_factor: - has_raw_value: unconstrained text, unlike the MIxS environmental triad -experimental_factor_other: unconstrained text, but presumably expects 'term label - [term id]' -extreme_event: '2023-01-15' -fao_class: - has_raw_value: Fluvisol -filter_method: Basix PES, 13-100-106 FisherSci is an example value, but unconstrained - text is accepted at this point -fire: 2000-11 to 2000-12 -flooding: '2000-01-15' -gaseous_environment: - has_raw_value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -geo_loc_name: - has_raw_value: 'USA: Maryland, Bethesda' -glucosidase_act: - has_raw_value: 5 mol per liter per hour -gold_biosample_identifiers: -- GOLD:Gb123456789 -- GOLD:Gb -growth_facil: - has_raw_value: Growth chamber [CO_715:0000189] -habitat: unconstrained text -heavy_metals: -- has_raw_value: mercury;0.09 micrograms per gram -- has_raw_value: arsenic;0.09 micrograms per gram -heavy_metals_meth: -- has_raw_value: https://link.springer.com/article/10.1007/s42452-019-1578-x -host_name: snail is an example value, but unconstrained text is accepted at this point -humidity_regm: - has_raw_value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -id: nmdc:bsm-99-dtTMNb -igsn_biosample_identifiers: -- any:curie_1 -- any:curie_2 -img_identifiers: -- any string 1 -- any string 2 -insdc_biosample_identifiers: -- biosample:SAMN123456789 -- biosample:SAMN000 -isotope_exposure: 13C glucose -lat_lon: - has_raw_value: 50.586825 6.408977 - latitude: 50.586825 - longitude: 6.408977 -lbc_thirty: - has_raw_value: 543 mg/kg -lbceq: - has_raw_value: 1575 mg/kg -light_regm: - has_raw_value: incandescent light;10 lux;450 nanometer -link_addit_analys: - has_raw_value: https://pubmed.ncbi.nlm.nih.gov/2315679/ -link_class_info: - has_raw_value: https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf -link_climate_info: - has_raw_value: https://www.int-res.com/abstracts/cr/v14/n3/p161-173/ -local_class: - has_raw_value: jicama soil -local_class_meth: - has_raw_value: https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083 -location: unconstrained text. should we even keep this slot? check if it ahs been - used in MongoDB. -magnesium: - has_raw_value: 52.8 micromole per kilogram -manganese: - has_raw_value: 24.7 mg/kg -mean_frict_vel: - has_raw_value: 0.5 meter per second -mean_peak_frict_vel: - has_raw_value: 1 meter per second -micro_biomass_c_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 -micro_biomass_n_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 -microbial_biomass_c: 0.05 ug C/g dry soil -microbial_biomass_n: 0.05 ug N/g dry soil -misc_param: - has_raw_value: Bicarbonate ion concentration;2075 micromole per kilogram -mod_date: '2023-01-25' -n_alkanes: - has_raw_value: n-hexadecane;100 milligram per liter -name: Sample Exhaustive Biosample instance. Although all of these values should pass - validation, that does not mean that any Biosample of any type would necessarily - have this particular combination of values. -ncbi_taxonomy_name: soil metagenome -nitrate: - has_raw_value: 65 micromole per liter -nitrate_nitrogen: - has_raw_value: 0.29 mg/kg -nitrite: - has_raw_value: 0.5 micromole per liter -nitrite_nitrogen: - has_raw_value: 1.2 mg/kg -non_microb_biomass: insect 0.23 ug; plant 1g -non_microb_biomass_method: https://doi.org/10.1038/s41467-021-26181-3 -org_matter: - has_raw_value: 1.75 milligram per cubic meter -org_nitro: - has_raw_value: 4 micromole per liter -org_nitro_method: https://doi.org/10.1016/0038-0717(85)90144-0 -organism_count: - has_raw_value: total prokaryotes;3.5e7 cells per milliliter;qPCR -other_treatment: unconstrained text -oxy_stat_samp: - has_raw_value: aerobic. change implementation from text value to string with enumerated - range -part_of: -- nmdc:unconstrained_study_identifier_string1_needs_pattern_materialization_what_about_referential_integrity -- nmdc:unconstrained_study_identifier_string2 -part_org_carb: - has_raw_value: 1.92 micromole per liter -perturbation: - has_raw_value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M -petroleum_hydrocarb: - has_raw_value: 0.05 micromole per liter -ph: - has_raw_value: '7.5' -ph_meth: - has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf -phaeopigments: - has_raw_value: 2.5 milligram per cubic meter -phosphate: - has_raw_value: 0.7 micromole per liter -phosplipid_fatt_acid: - has_raw_value: 2.98 milligram per liter -pool_dna_extracts: - has_raw_value: yes, 5 -potassium: - has_raw_value: 463 milligram per liter -pressure: - has_raw_value: 50 atmosphere -profile_position: - has_raw_value: summit. change validation to enumeration -project_id: no example from MIxS -proport_woa_temperature: no example from MIxS -proposal_dna: '504000' -proposal_rna: '504000' -redox_potential: - has_raw_value: 300 millivolt -rel_to_oxygen: - has_raw_value: aerobe. change validation to enumeration -replicate_number: '1' -rna_absorb1: '2.02' -rna_absorb2: '2.02' -rna_collect_site: untreated pond water -rna_concentration: '100' -rna_cont_type: plate -rna_cont_well: C2 -rna_container_id: Pond_MT_041618 -rna_isolate_meth: phenol/chloroform extraction -rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles - (1%) -rna_project_contact: John Jones -rna_samp_id: '187654' -rna_sample_format: 10 mM Tris-HCl -rna_sample_name: JGI_pond_041618 -rna_seq_project: '1191234' -rna_seq_project_name: JGI Pond metagenomics -rna_seq_project_pi: Jane Johnson -rna_volume: '25' -salinity: - has_raw_value: 25 practical salinity unit -salinity_category: halotolerant is an example from the schema, but MIxS doesn't provide - this slot any more -salinity_meth: - has_raw_value: PMID:22895776 -samp_collec_method: swabbing -samp_mat_process: - has_raw_value: filtering of seawater -samp_name: see also name -samp_size: - has_raw_value: 5 liters -samp_store_dur: - has_raw_value: P1Y6M -samp_store_loc: - has_raw_value: Freezer no:5 -samp_store_temp: - has_raw_value: -80 degree Celsius -samp_taxon_id: soil metagenome [NCBItaxon:410658] but no validation applied yet -samp_vol_we_dna_ext: - has_raw_value: 1500 milliliter -sample_collection_site: unconstrained text -sample_link: -- IGSN:DSJ0284 -- any:curie -sample_shipped: 15 g -sample_type: water_extract_soil -season_precpt: - has_raw_value: 75 millimeters -season_temp: - has_raw_value: 18 degree Celsius -sieving: - has_raw_value: MIxS does not provide an example -size_frac_low: - has_raw_value: 0.2 micrometer -size_frac_up: - has_raw_value: 20 micrometer -slope_aspect: - has_raw_value: MIxS does not provide an example -slope_gradient: - has_raw_value: MIxS does not provide an example -sodium: - has_raw_value: 10.5 milligram per liter -soil_type: - has_raw_value: plinthosol [ENVO:00002250] -soil_type_meth: - has_raw_value: Frederick series -soluble_iron_micromol: MIxS doesn't provide an example -source_mat_id: - has_raw_value: MPI012345 -specific_ecosystem: unconstrained text -start_date_inc: '2023-01-27' -start_time_inc: 13:42+0000 -store_cond: - has_raw_value: -20 degree Celsius freezer;P2Y10D -subsurface_depth: - has_raw_value: MIxS does not provide an example -sulfate: - has_raw_value: 5 micromole per liter -sulfide: - has_raw_value: 2 micromole per liter -technical_reps: '2' -temp: - has_raw_value: 25 degree Celsius -tidal_stage: - has_raw_value: high tide. change validation to enumeration -tillage: - has_raw_value: chisel. change validation to enumeration -tot_carb: - has_raw_value: MIxS does not provide an example -tot_depth_water_col: - has_raw_value: 500 meter -tot_diss_nitro: - has_raw_value: 40 microgram per liter -tot_nitro_cont_meth: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 -tot_nitro_content: - has_raw_value: 35 milligrams Nitrogen per kilogram of soil -tot_org_c_meth: - has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf -tot_org_carb: - has_raw_value: 2% -tot_phosp: - has_raw_value: 0.03 milligram per liter -type: nmdc:Biosample. change this to require a class name or an enumeration -water_cont_soil_meth: MIxS doesn't provide an example -water_content: -- MIxS doesn't provide an example 1 -- MIxS doesn't provide an example 2 -watering_regm: - has_raw_value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -zinc: - has_raw_value: 2.5 mg/kg - -``` -## Study-minimal -### Input -```yaml -id: nmdc:sty-11-ab - -``` -## Study-exhaustive -### Input -```yaml -abstract: Nothing was studied. -alternative_descriptions: -- any string 1 -- any string 2 -alternative_identifiers: -- any string A1 -- any string A2 -alternative_names: -- any string 1 -- any string 2 -alternative_titles: -- any string 1 -- any string 2 -description: see also name, title, objective, various alternatives -doi: - has_raw_value: https://doi.org/10.1126/science.1058040 -ecosystem: unconstrained text. should be validated against the controlled vocabulary, - by the sample's environmental package. would also be nice to align the CV with MIxS - environmental triads -ecosystem_category: unconstrained text -ecosystem_subtype: unconstrained text -ecosystem_type: unconstrained text -emsl_proposal_doi: any string -emsl_proposal_identifier: any string EP1 -ess_dive_datasets: -- any string 1 -- any string 2 -funding_sources: -- any string 1 -- any string 2 -gold_study_identifiers: -- gold:any_string_1 -- gold:any_string_2 -has_credit_associations: -- applied_role: Funding acquisition - applied_roles: - - Supervision - - Conceptualization - applies_to_person: - email: jcventer@jcvi.org - has_raw_value: Craig Venter - name: J. Craig Venter - orcid: ORCID:0000-0002-7086-765X - profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg - was_generated_by: nmdc:any_string_1 - websites: - - https://www.jcvi.org/ - - https://www.jcvi.org/about/j-craig-venter - type: any string -- applied_roles: - - Investigation - - Supervision - applies_to_person: - name: Tanja Davidsen -id: nmdc:sty-11-ab -mgnify_project_identifiers: mgnify.proj:ABC123 -name: see also description, title, objective, various alternatives -objective: This record, an instance of class Study from the nmdc-schema was had authored, - so that the NMDC team would have at least one instance, using all slots, with a - mixture of reasonable values and minimally compliant values. -principal_investigator: - email: jcventer@jcvi.org - has_raw_value: Craig Venter - name: J. Craig Venter - orcid: ORCID:0000-0002-7086-765X - profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg - was_generated_by: nmdc:any_string_1 - websites: - - https://www.jcvi.org/ - - https://www.jcvi.org/about/j-craig-venter -publications: -- any string 1 -- any string 2 -related_identifiers: any string R1 -relevant_protocols: -- any string 1 -- any string 2 -specific_ecosystem: unconstrained text -study_image: -- description: Photo of Craig Venter Institute, Rockville, Maryland - display_order: '1' - has_raw_value: https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg - url: https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg - was_generated_by: nmdc:any_string_1 -- description: Photo of Craig Venter Institute, La Jolla, California - display_order: '2' - has_raw_value: https://today.ucsd.edu/news_uploads/140213ventor2.jpg - url: https://today.ucsd.edu/news_uploads/140213ventor2.jpg - was_generated_by: nmdc:any_string_1 -title: Sample Exhaustive Biosample instance. Although all of these values should pass - validation, that does not mean that any Biosample of any type would necessarily - have this particular combination of values. -type: any string -websites: -- https://w3id.org/nmdc -- https://w3id.org/linkml - -``` -## Biosample-minimal -### Input -```yaml -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 -id: nmdc:bsm-99-dtTMNb -part_of: -- gold:Gs0110115 - -``` -## Biosample-invalid-embargoed -### Input -```yaml -embargoed: 999 -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 -id: nmdc:bsm-99-dtTMNb -part_of: -- gold:Gs0110115 - -``` -## Biosample-missing-id -### Input -```yaml -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 -part_of: -- gold:Gs0110115 - -``` diff --git a/src/data/output/Study-exhaustive.json b/src/data/output/Study-exhaustive.json deleted file mode 100644 index 9d882fa6e6..0000000000 --- a/src/data/output/Study-exhaustive.json +++ /dev/null @@ -1,121 +0,0 @@ -{ - "id": "nmdc:sty-11-ab", - "name": "see also description, title, objective, various alternatives", - "description": "see also name, title, objective, various alternatives", - "alternative_identifiers": [ - "any string A1", - "any string A2" - ], - "related_identifiers": "any string R1", - "emsl_proposal_identifier": "any string EP1", - "emsl_proposal_doi": "any string", - "gold_study_identifiers": [ - "gold:any_string_1", - "gold:any_string_2" - ], - "mgnify_project_identifiers": "mgnify.proj:ABC123", - "ecosystem": "unconstrained text. should be validated against the controlled vocabulary, by the sample's environmental package. would also be nice to align the CV with MIxS environmental triads", - "ecosystem_category": "unconstrained text", - "ecosystem_type": "unconstrained text", - "ecosystem_subtype": "unconstrained text", - "specific_ecosystem": "unconstrained text", - "principal_investigator": { - "has_raw_value": "Craig Venter", - "was_generated_by": "nmdc:any_string_1", - "orcid": "ORCID:0000-0002-7086-765X", - "profile_image_url": "https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg", - "email": "jcventer@jcvi.org", - "name": "J. Craig Venter", - "websites": [ - "https://www.jcvi.org/", - "https://www.jcvi.org/about/j-craig-venter" - ] - }, - "doi": { - "has_raw_value": "https://doi.org/10.1126/science.1058040" - }, - "title": "Sample Exhaustive Biosample instance. Although all of these values should pass validation, that does not mean that any Biosample of any type would necessarily have this particular combination of values.", - "alternative_titles": [ - "any string 1", - "any string 2" - ], - "alternative_descriptions": [ - "any string 1", - "any string 2" - ], - "alternative_names": [ - "any string 1", - "any string 2" - ], - "abstract": "Nothing was studied.", - "objective": "This record, an instance of class Study from the nmdc-schema was had authored, so that the NMDC team would have at least one instance, using all slots, with a mixture of reasonable values and minimally compliant values.", - "websites": [ - "https://w3id.org/nmdc", - "https://w3id.org/linkml" - ], - "publications": [ - "any string 1", - "any string 2" - ], - "ess_dive_datasets": [ - "any string 1", - "any string 2" - ], - "type": "any string", - "relevant_protocols": [ - "any string 1", - "any string 2" - ], - "funding_sources": [ - "any string 1", - "any string 2" - ], - "has_credit_associations": [ - { - "applies_to_person": { - "has_raw_value": "Craig Venter", - "was_generated_by": "nmdc:any_string_1", - "orcid": "ORCID:0000-0002-7086-765X", - "profile_image_url": "https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg", - "email": "jcventer@jcvi.org", - "name": "J. Craig Venter", - "websites": [ - "https://www.jcvi.org/", - "https://www.jcvi.org/about/j-craig-venter" - ] - }, - "applied_roles": [ - "Supervision", - "Conceptualization" - ], - "applied_role": "Funding acquisition", - "type": "any string" - }, - { - "applies_to_person": { - "name": "Tanja Davidsen" - }, - "applied_roles": [ - "Investigation", - "Supervision" - ] - } - ], - "study_image": [ - { - "has_raw_value": "https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg", - "was_generated_by": "nmdc:any_string_1", - "url": "https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg", - "description": "Photo of Craig Venter Institute, Rockville, Maryland", - "display_order": "1" - }, - { - "has_raw_value": "https://today.ucsd.edu/news_uploads/140213ventor2.jpg", - "was_generated_by": "nmdc:any_string_1", - "url": "https://today.ucsd.edu/news_uploads/140213ventor2.jpg", - "description": "Photo of Craig Venter Institute, La Jolla, California", - "display_order": "2" - } - ], - "@type": "Study" -} \ No newline at end of file diff --git a/src/data/output/Study-exhaustive.ttl b/src/data/output/Study-exhaustive.ttl deleted file mode 100644 index 7508c4de25..0000000000 --- a/src/data/output/Study-exhaustive.ttl +++ /dev/null @@ -1,85 +0,0 @@ -@prefix dcterms: . -@prefix nmdc: . -@prefix prov: . -@prefix schema: . -@prefix xsd: . - -nmdc:sty-11-ab a nmdc:Study ; - dcterms:description "see also name, title, objective, various alternatives" ; - prov:qualifiedAssociation [ a prov:Association ; - prov:agent [ a nmdc:PersonValue ; - schema:email "jcventer@jcvi.org" ; - nmdc:has_raw_value "Craig Venter" ; - nmdc:name "J. Craig Venter" ; - nmdc:orcid "ORCID:0000-0002-7086-765X" ; - nmdc:profile_image_url "https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg" ; - nmdc:was_generated_by nmdc:any_string_1 ; - nmdc:websites "https://www.jcvi.org/", - "https://www.jcvi.org/about/j-craig-venter" ] ; - prov:hadRole "Funding acquisition" ; - nmdc:applied_roles "Conceptualization", - "Supervision" ; - nmdc:type "any string" ], - [ a prov:Association ; - prov:agent [ a nmdc:PersonValue ; - nmdc:name "Tanja Davidsen" ] ; - nmdc:applied_roles "Investigation", - "Supervision" ] ; - nmdc:abstract "Nothing was studied." ; - nmdc:alternative_descriptions "any string 1", - "any string 2" ; - nmdc:alternative_identifiers "any string A1", - "any string A2" ; - nmdc:alternative_names "any string 1", - "any string 2" ; - nmdc:alternative_titles "any string 1", - "any string 2" ; - nmdc:doi [ a nmdc:AttributeValue ; - nmdc:has_raw_value "https://doi.org/10.1126/science.1058040" ] ; - nmdc:ecosystem "unconstrained text. should be validated against the controlled vocabulary, by the sample's environmental package. would also be nice to align the CV with MIxS environmental triads" ; - nmdc:ecosystem_category "unconstrained text" ; - nmdc:ecosystem_subtype "unconstrained text" ; - nmdc:ecosystem_type "unconstrained text" ; - nmdc:emsl_proposal_doi "any string" ; - nmdc:emsl_proposal_identifier "any string EP1" ; - nmdc:ess_dive_datasets "any string 1", - "any string 2" ; - nmdc:funding_sources "any string 1", - "any string 2" ; - nmdc:gold_study_identifiers "gold:any_string_1"^^xsd:anyURI, - "gold:any_string_2"^^xsd:anyURI ; - nmdc:mgnify_project_identifiers "mgnify.proj:ABC123" ; - nmdc:name "see also description, title, objective, various alternatives" ; - nmdc:objective "This record, an instance of class Study from the nmdc-schema was had authored, so that the NMDC team would have at least one instance, using all slots, with a mixture of reasonable values and minimally compliant values." ; - nmdc:principal_investigator [ a nmdc:PersonValue ; - schema:email "jcventer@jcvi.org" ; - nmdc:has_raw_value "Craig Venter" ; - nmdc:name "J. Craig Venter" ; - nmdc:orcid "ORCID:0000-0002-7086-765X" ; - nmdc:profile_image_url "https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg" ; - nmdc:was_generated_by nmdc:any_string_1 ; - nmdc:websites "https://www.jcvi.org/", - "https://www.jcvi.org/about/j-craig-venter" ] ; - nmdc:publications "any string 1", - "any string 2" ; - nmdc:related_identifiers "any string R1" ; - nmdc:relevant_protocols "any string 1", - "any string 2" ; - nmdc:specific_ecosystem "unconstrained text" ; - nmdc:study_image [ a nmdc:ImageValue ; - dcterms:description "Photo of Craig Venter Institute, La Jolla, California" ; - nmdc:display_order "2" ; - nmdc:has_raw_value "https://today.ucsd.edu/news_uploads/140213ventor2.jpg" ; - nmdc:url "https://today.ucsd.edu/news_uploads/140213ventor2.jpg" ; - nmdc:was_generated_by nmdc:any_string_1 ], - [ a nmdc:ImageValue ; - dcterms:description "Photo of Craig Venter Institute, Rockville, Maryland" ; - nmdc:display_order "1" ; - nmdc:has_raw_value "https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg" ; - nmdc:url "https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg" ; - nmdc:was_generated_by nmdc:any_string_1 ] ; - nmdc:title "Sample Exhaustive Biosample instance. Although all of these values should pass validation, that does not mean that any Biosample of any type would necessarily have this particular combination of values." ; - nmdc:type "any string" ; - nmdc:websites "https://w3id.org/linkml", - "https://w3id.org/nmdc" . - diff --git a/src/data/output/Study-exhaustive.yaml b/src/data/output/Study-exhaustive.yaml deleted file mode 100644 index 3c69ce818e..0000000000 --- a/src/data/output/Study-exhaustive.yaml +++ /dev/null @@ -1,96 +0,0 @@ -id: nmdc:sty-11-ab -name: see also description, title, objective, various alternatives -description: see also name, title, objective, various alternatives -alternative_identifiers: -- any string A1 -- any string A2 -related_identifiers: any string R1 -emsl_proposal_identifier: any string EP1 -emsl_proposal_doi: any string -gold_study_identifiers: -- gold:any_string_1 -- gold:any_string_2 -mgnify_project_identifiers: mgnify.proj:ABC123 -ecosystem: unconstrained text. should be validated against the controlled vocabulary, - by the sample's environmental package. would also be nice to align the CV with MIxS - environmental triads -ecosystem_category: unconstrained text -ecosystem_type: unconstrained text -ecosystem_subtype: unconstrained text -specific_ecosystem: unconstrained text -principal_investigator: - has_raw_value: Craig Venter - was_generated_by: nmdc:any_string_1 - orcid: ORCID:0000-0002-7086-765X - profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg - email: jcventer@jcvi.org - name: J. Craig Venter - websites: - - https://www.jcvi.org/ - - https://www.jcvi.org/about/j-craig-venter -doi: - has_raw_value: https://doi.org/10.1126/science.1058040 -title: Sample Exhaustive Biosample instance. Although all of these values should pass - validation, that does not mean that any Biosample of any type would necessarily - have this particular combination of values. -alternative_titles: -- any string 1 -- any string 2 -alternative_descriptions: -- any string 1 -- any string 2 -alternative_names: -- any string 1 -- any string 2 -abstract: Nothing was studied. -objective: This record, an instance of class Study from the nmdc-schema was had authored, - so that the NMDC team would have at least one instance, using all slots, with a - mixture of reasonable values and minimally compliant values. -websites: -- https://w3id.org/nmdc -- https://w3id.org/linkml -publications: -- any string 1 -- any string 2 -ess_dive_datasets: -- any string 1 -- any string 2 -type: any string -relevant_protocols: -- any string 1 -- any string 2 -funding_sources: -- any string 1 -- any string 2 -has_credit_associations: -- applies_to_person: - has_raw_value: Craig Venter - was_generated_by: nmdc:any_string_1 - orcid: ORCID:0000-0002-7086-765X - profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg - email: jcventer@jcvi.org - name: J. Craig Venter - websites: - - https://www.jcvi.org/ - - https://www.jcvi.org/about/j-craig-venter - applied_roles: - - Supervision - - Conceptualization - applied_role: Funding acquisition - type: any string -- applies_to_person: - name: Tanja Davidsen - applied_roles: - - Investigation - - Supervision -study_image: -- has_raw_value: https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg - was_generated_by: nmdc:any_string_1 - url: https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg - description: Photo of Craig Venter Institute, Rockville, Maryland - display_order: '1' -- has_raw_value: https://today.ucsd.edu/news_uploads/140213ventor2.jpg - was_generated_by: nmdc:any_string_1 - url: https://today.ucsd.edu/news_uploads/140213ventor2.jpg - description: Photo of Craig Venter Institute, La Jolla, California - display_order: '2' diff --git a/src/data/output/Study-minimal.json b/src/data/output/Study-minimal.json deleted file mode 100644 index 169ba49ba1..0000000000 --- a/src/data/output/Study-minimal.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "id": "nmdc:sty-11-ab", - "@type": "Study" -} \ No newline at end of file diff --git a/src/data/output/Study-minimal.ttl b/src/data/output/Study-minimal.ttl deleted file mode 100644 index ca41220f7a..0000000000 --- a/src/data/output/Study-minimal.ttl +++ /dev/null @@ -1,4 +0,0 @@ -@prefix nmdc: . - -nmdc:sty-11-ab a nmdc:Study . - diff --git a/src/data/output/Study-minimal.yaml b/src/data/output/Study-minimal.yaml deleted file mode 100644 index e474ba0226..0000000000 --- a/src/data/output/Study-minimal.yaml +++ /dev/null @@ -1 +0,0 @@ -id: nmdc:sty-11-ab diff --git a/src/schema/mixs.yaml b/src/schema/mixs.yaml index 8c4b2d9d73..73d08b82d3 100644 --- a/src/schema/mixs.yaml +++ b/src/schema/mixs.yaml @@ -1186,8 +1186,8 @@ enums: text: center of car under a seat: text: under a seat - rel_to_oxygen_enum: + rel_to_oxygen_enum: from_schema: http://w3id.org/mixs/terms permissible_values: aerobe: @@ -1204,8 +1204,8 @@ enums: text: obligate aerobe obligate anaerobe: text: obligate anaerobe - room_condt_enum: + room_condt_enum: from_schema: http://w3id.org/mixs/terms permissible_values: new: @@ -4904,8 +4904,8 @@ slots: slot_uri: mixs:0000657 multivalued: false range: QuantityValue - elev: + elev: aliases: - elevation annotations: @@ -4927,8 +4927,8 @@ slots: slot_uri: mixs:0000093 multivalued: false range: QuantityValue - elevator: + elevator: aliases: - elevator count annotations: diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index 679702a060..ce988f3889 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -453,7 +453,6 @@ classes: - light_regm # - micro_biomass_meth - phosphate - - rel_to_oxygen - samp_collec_method - samp_size # - soil_text_measure @@ -538,6 +537,18 @@ classes: - lbc_thirty - lbceq slot_usage: + elev: + title: elevation, meters + range: float + comments: + - All elevations must be reported in meters. Provide the numerical portion only. + examples: + value: 100 + oxy_stat_samp: + notes: + - this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration + range: rel_to_oxygen_enum + id: description: An NMDC assigned unique identifier for a biosample submitted to NMDC. required: true