diff --git a/assets/yq-for-mixs_subset_modified.txt b/assets/yq-for-mixs_subset_modified.txt new file mode 100644 index 0000000000..e194b4de38 --- /dev/null +++ b/assets/yq-for-mixs_subset_modified.txt @@ -0,0 +1,154 @@ +'.slots.agrochem_addition.range |= "TextValue"' +'.slots.air_temp_regm.range |= "TextValue"' +'.slots.antibiotic_regm.range |= "TextValue"' +'.slots.aromatics_pc.range |= "TextValue"' +'.slots.asphaltenes_pc.range |= "TextValue"' +'.slots.atmospheric_data.range |= "TextValue"' +'.slots.avg_occup.range |= "TextValue"' +'.slots.bathroom_count.range |= "TextValue"' +'.slots.bedroom_count.range |= "TextValue"' +'.slots.biocide_admin_method.range |= "TextValue"' +'.slots.biomass.range |= "TextValue"' +'.slots.chem_administration.range |= "ControlledTermValue"' +'.slots.chem_mutagen.range |= "TextValue"' +'.slots.chem_treat_method.range |= "string"' +'.slots.collection_date.range |= "TimestampValue"' +'.slots.cool_syst_id.range |= "TextValue"' +'.slots.date_last_rain.range |= "TimestampValue"' +'.slots.diether_lipids.range |= "TextValue"' +'.slots.elevator.range |= "TextValue"' +'.slots.emulsions.range |= "TextValue"' +'.slots.env_broad_scale.range |= "ControlledIdentifiedTermValue"' +'.slots.env_local_scale.range |= "ControlledIdentifiedTermValue"' +'.slots.env_medium.range |= "ControlledIdentifiedTermValue"' +'.slots.escalator.range |= "TextValue"' +'.slots.exp_pipe.range |= "QuantityValue"' +'.slots.experimental_factor.range |= "ControlledTermValue"' +'.slots.ext_door.range |= "TextValue"' +'.slots.extreme_event.range |= "TimestampValue"' +'.slots.fertilizer_regm.range |= "TextValue"' +'.slots.fire.range |= "TimestampValue"' +'.slots.flooding.range |= "TimestampValue"' +'.slots.floor_count.range |= "TextValue"' +'.slots.freq_clean.range |= "QuantityValue"' +'.slots.freq_cook.range |= "QuantityValue"' +'.slots.fungicide_regm.range |= "TextValue"' +'.slots.gaseous_environment.range |= "TextValue"' +'.slots.gaseous_substances.range |= "TextValue"' +'.slots.gravity.range |= "TextValue"' +'.slots.growth_facil.range |= "ControlledTermValue"' +'.slots.growth_hormone_regm.range |= "TextValue"' +'.slots.hall_count.range |= "TextValue"' +'.slots.hall_count.range |= "TextValue"' +'.slots.hcr_pressure.range |= "TextValue"' +'.slots.hcr_temp.range |= "TextValue"' +'.slots.heat_sys_deliv_meth.range |= "string"' +'.slots.heat_system_id.range |= "TextValue"' +'.slots.heavy_metals.range |= "TextValue"' +'.slots.herbicide_regm.range |= "TextValue"' +'.slots.host_body_product.range |= "ControlledTermValue"' +'.slots.host_body_site.range |= "ControlledTermValue"' +'.slots.host_family_relation.range |= "string"' +'.slots.host_phenotype.range |= "ControlledTermValue"' +'.slots.host_subspecf_genlin.range |= "string"' +'.slots.host_symbiont.range |= "string"' +'.slots.humidity_regm.range |= "TextValue"' +'.slots.inorg_particles.range |= "TextValue"' +'.slots.iw_bt_date_well.range |= "TimestampValue"' +'.slots.last_clean.range |= "TimestampValue"' +'.slots.lat_lon.range |= "GeolocationValue"' +'.slots.light_regm.range |= "TextValue"' +'.slots.max_occup.range |= "QuantityValue"' +'.slots.micro_biomass_meth.range |= "string"' +'.slots.mineral_nutr_regm.range |= "TextValue"' +'.slots.misc_param.range |= "TextValue"' +'.slots.n_alkanes.range |= "TextValue"' +'.slots.non_min_nutr_regm.range |= "string"' +'.slots.number_pets.range |= "QuantityValue"' +'.slots.number_plants.range |= "QuantityValue"' +'.slots.number_resident.range |= "QuantityValue"' +'.slots.occup_density_samp.range |= "QuantityValue"' +'.slots.occup_samp.range |= "QuantityValue"' +'.slots.org_count_qpcr_info.range |= "string"' +'.slots.org_particles.range |= "TextValue"' +'.slots.organism_count.range |= "QuantityValue"' +'.slots.particle_class.range |= "TextValue"' +'.slots.permeability.range |= "TextValue"' +'.slots.pesticide_regm.range |= "TextValue"' +'.slots.phaeopigments.range |= "TextValue"' +'.slots.phosplipid_fatt_acid.range |= "TextValue"' +'.slots.plant_growth_med.range |= "ControlledTermValue"' +'.slots.plant_struc.range |= "ControlledTermValue"' +'.slots.pollutants.range |= "TextValue"' +'.slots.porosity.range |= "TextValue"' +'.slots.pres_animal_insect.range |= "string"' +'.slots.prev_land_use_meth.range |= "string"' +'.slots.prod_start_date.range |= "TimestampValue"' +'.slots.radiation_regm.range |= "TextValue"' +'.slots.rainfall_regm.range |= "TextValue"' +'.slots.resins_pc.range |= "TextValue"' +'.slots.room_architec_elem.range |= "string"' +'.slots.room_count.range |= "TextValue"' +'.slots.room_dim.range |= "TextValue"' +'.slots.room_door_dist.range |= "TextValue"' +'.slots.room_net_area.range |= "TextValue"' +'.slots.room_occup.range |= "QuantityValue"' +'.slots.room_vol.range |= "TextValue"' +'.slots.root_med_carbon.range |= "TextValue"' +'.slots.root_med_macronutr.range |= "TextValue"' +'.slots.root_med_micronutr.range |= "TextValue"' +'.slots.root_med_ph.range |= "QuantityValue"' +'.slots.root_med_regl.range |= "TextValue"' +'.slots.root_med_suppl.range |= "TextValue"' +'.slots.salt_regm.range |= "TextValue"' +'.slots.samp_collec_device.range |= "string"' +'.slots.samp_collec_method.range |= "string"' +'.slots.samp_loc_corr_rate.range |= "TextValue"' +'.slots.samp_mat_process.range |= "ControlledTermValue"' +'.slots.samp_md.range |= "QuantityValue"' +'.slots.samp_name.range |= "string"' +'.slots.samp_preserv.range |= "TextValue"' +'.slots.samp_room_id.range |= "TextValue"' +'.slots.samp_time_out.range |= "TextValue"' +'.slots.samp_transport_cond.range |= "TextValue"' +'.slots.samp_tvdss.range |= "TextValue"' +'.slots.saturates_pc.range |= "TextValue"' +'.slots.shad_dev_water_mold.range |= "string"' +'.slots.sieving.range |= "TextValue"' +'.slots.size_frac.range |= "TextValue"' +'.slots.soil_texture_meth.range |= "string"' +'.slots.soluble_inorg_mat.range |= "TextValue"' +'.slots.soluble_org_mat.range |= "TextValue"' +'.slots.suspend_solids.range |= "TextValue"' +'.slots.tot_nitro_cont_meth.range |= "string"' +'.slots.viscosity.range |= "TextValue"' +'.slots.volatile_org_comp.range |= "TextValue"' +'.slots.water_cont_soil_meth.range |= "string"' +'.slots.water_temp_regm.range |= "TextValue"' +'.slots.watering_regm.range |= "TextValue"' +'.slots.window_open_freq.range |= "TextValue"' +'.slots.window_size.range |= "TextValue"' + +'del(.classes)' +'del(.enums.[].name)' +'del(.enums.[].permissible_values.[].text)' +'del(.slots.[].name)' +'del(.slots.add_recov_method.pattern)' +'del(.subsets.[].name)' + +'.id |= "https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml"' + +# update host_taxid and samp_taxon_id. may want to flatten to a string or URIORCURIE eventually +'del(.slots.host_taxid.examples)' +'del(.slots.host_taxid.string_serialization)' +'del(.slots.samp_taxon_id.examples)' +'del(.slots.samp_taxon_id.string_serialization)' + +'.slots.host_taxid.comments |= ["Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value"]' +'.slots.host_taxid.range = "ControlledIdentifiedTermValue"' +'.slots.samp_taxon_id.comments |= ["coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value"]' +'.slots.samp_taxon_id.range = "ControlledIdentifiedTermValue"' + + +# add "M horizon" to soil_horizon_enum +'.enums.soil_horizon_enum.permissible_values.["M horizon"] = {}' diff --git a/assets/yq-for-nmdc_schema_accepting_legacy_ids.txt b/assets/yq-for-nmdc_schema_accepting_legacy_ids.txt new file mode 100644 index 0000000000..8442bd8f16 --- /dev/null +++ b/assets/yq-for-nmdc_schema_accepting_legacy_ids.txt @@ -0,0 +1,38 @@ +# probably should have made a list of classes and then looped over a parameterized version of this +# could also assert that the range is string +'(.classes[] | select(.name == "Biosample") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "Biosample") | .slot_usage.part_of.pattern) = ".*"' +'(.classes[] | select(.name == "Biosample") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "DataObject") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "DataObject") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "MagsAnalysisActivity") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "MagsAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "MetabolomicsAnalysisActivity") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "MetabolomicsAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "MetagenomeAnnotationActivity") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "MetagenomeAnnotationActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "MetagenomeAssembly") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "MetagenomeAssembly") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "MetagenomeSequencingActivity") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "MetagenomeSequencingActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "MetaproteomicsAnalysisActivity") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "MetaproteomicsAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "MetatranscriptomeActivity") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "MetatranscriptomeActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "MetatranscriptomeAnnotationActivity") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "MetatranscriptomeAnnotationActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "MetatranscriptomeAssembly") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "MetatranscriptomeAssembly") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "NomAnalysisActivity") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "NomAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.part_of.pattern) = ".*"' +'(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.has_input.pattern) = ".*"' +'(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.has_output.pattern) = ".*"' +'(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "ReadBasedTaxonomyAnalysisActivity") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "ReadBasedTaxonomyAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "ReadQcAnalysisActivity") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "ReadQcAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' +'(.classes[] | select(.name == "Study") | .slot_usage.id.pattern) = ".*"' +'(.classes[] | select(.name == "Study") | .slot_usage.id.structured_pattern.syntax) = ".*"' diff --git a/poetry.lock b/poetry.lock index cf8bca201a..3cc1a7cb9e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -101,19 +101,22 @@ files = [ [[package]] name = "beautifulsoup4" -version = "4.12.2" +version = "4.12.3" description = "Screen-scraping library" optional = false python-versions = ">=3.6.0" files = [ - {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"}, - {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"}, + {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"}, + {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"}, ] [package.dependencies] soupsieve = ">1.2" [package.extras] +cchardet = ["cchardet"] +chardet = ["chardet"] +charset-normalizer = ["charset-normalizer"] html5lib = ["html5lib"] lxml = ["lxml"] @@ -411,13 +414,13 @@ files = [ [[package]] name = "curies" -version = "0.7.4" +version = "0.7.6" description = "Idiomatic conversion between URIs and compact URIs (CURIEs)." optional = false python-versions = ">=3.8" files = [ - {file = "curies-0.7.4-py3-none-any.whl", hash = "sha256:478f1818345988933d8bc6060f80a985401331f856ff8cf9bd98fa00d178ad39"}, - {file = "curies-0.7.4.tar.gz", hash = "sha256:d3aaf16644b26ac2605ff83c565ec7df0ba0b5f7425516047666e609ec5fb718"}, + {file = "curies-0.7.6-py3-none-any.whl", hash = "sha256:3307e757e47ed4384edb705c73cad40ad5e688e2dea263a60e6a5e5a6c33105d"}, + {file = "curies-0.7.6.tar.gz", hash = "sha256:f86da3539cee349249f5b64db99651053649551920b9fe945c150719c8b9b40e"}, ] [package.dependencies] @@ -477,22 +480,23 @@ files = [ [[package]] name = "dnspython" -version = "2.4.2" +version = "2.5.0" description = "DNS toolkit" optional = false -python-versions = ">=3.8,<4.0" +python-versions = ">=3.8" files = [ - {file = "dnspython-2.4.2-py3-none-any.whl", hash = "sha256:57c6fbaaeaaf39c891292012060beb141791735dbb4004798328fc2c467402d8"}, - {file = "dnspython-2.4.2.tar.gz", hash = "sha256:8dcfae8c7460a2f84b4072e26f1c9f4101ca20c071649cb7c34e8b6a93d58984"}, + {file = "dnspython-2.5.0-py3-none-any.whl", hash = "sha256:6facdf76b73c742ccf2d07add296f178e629da60be23ce4b0a9c927b1e02c3a6"}, + {file = "dnspython-2.5.0.tar.gz", hash = "sha256:a0034815a59ba9ae888946be7ccca8f7c157b286f8455b379c692efb51022a15"}, ] [package.extras] -dnssec = ["cryptography (>=2.6,<42.0)"] -doh = ["h2 (>=4.1.0)", "httpcore (>=0.17.3)", "httpx (>=0.24.1)"] +dev = ["black (>=23.1.0)", "coverage (>=7.0)", "flake8 (>=5.0.3)", "mypy (>=1.0.1)", "pylint (>=2.7)", "pytest (>=6.2.5)", "pytest-cov (>=3.0.0)", "sphinx (>=7.0.0)", "twine (>=4.0.0)", "wheel (>=0.41.0)"] +dnssec = ["cryptography (>=41)"] +doh = ["h2 (>=4.1.0)", "httpcore (>=0.17.3)", "httpx (>=0.25.1)"] doq = ["aioquic (>=0.9.20)"] -idna = ["idna (>=2.1,<4.0)"] -trio = ["trio (>=0.14,<0.23)"] -wmi = ["wmi (>=1.5.1,<2.0.0)"] +idna = ["idna (>=2.1)"] +trio = ["trio (>=0.14)"] +wmi = ["wmi (>=1.5.1)"] [[package]] name = "editorconfig" @@ -740,13 +744,13 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"] [[package]] name = "google-api-python-client" -version = "2.113.0" +version = "2.114.0" description = "Google API Client Library for Python" optional = false python-versions = ">=3.7" files = [ - {file = "google-api-python-client-2.113.0.tar.gz", hash = "sha256:bcffbc8ffbad631f699cf85aa91993f3dc03060b234ca9e6e2f9135028bd9b52"}, - {file = "google_api_python_client-2.113.0-py2.py3-none-any.whl", hash = "sha256:25659d488df6c8a69615b2a510af0e63b4c47ab2cb87d71c1e13b28715906e27"}, + {file = "google-api-python-client-2.114.0.tar.gz", hash = "sha256:e041bbbf60e682261281e9d64b4660035f04db1cccba19d1d68eebc24d1465ed"}, + {file = "google_api_python_client-2.114.0-py2.py3-none-any.whl", hash = "sha256:690e0bb67d70ff6dea4e8a5d3738639c105a478ac35da153d3b2a384064e9e1a"}, ] [package.dependencies] @@ -1220,13 +1224,13 @@ files = [ [[package]] name = "jsonschema" -version = "4.20.0" +version = "4.21.1" description = "An implementation of JSON Schema validation for Python" optional = false python-versions = ">=3.8" files = [ - {file = "jsonschema-4.20.0-py3-none-any.whl", hash = "sha256:ed6231f0429ecf966f5bc8dfef245998220549cbbcf140f913b7464c52c3b6b3"}, - {file = "jsonschema-4.20.0.tar.gz", hash = "sha256:4f614fd46d8d61258610998997743ec5492a648b33cf478c1ddc23ed4598a5fa"}, + {file = "jsonschema-4.21.1-py3-none-any.whl", hash = "sha256:7996507afae316306f9e2290407761157c6f78002dcf7419acb99822143d1c6f"}, + {file = "jsonschema-4.21.1.tar.gz", hash = "sha256:85727c00279f5fa6bedbe6238d2aa6403bedd8b4864ab11207d07df3cc1b2ee5"}, ] [package.dependencies] @@ -1312,13 +1316,13 @@ regex = ["regex"] [[package]] name = "linkml" -version = "1.6.8" +version = "1.6.9" description = "Linked Open Data Modeling Language" optional = false python-versions = ">=3.8.1,<4.0.0" files = [ - {file = "linkml-1.6.8-py3-none-any.whl", hash = "sha256:4fd8fc28b3c374100155923906094c84b165488fd40f3c2deac7b3d5b7ff7f9e"}, - {file = "linkml-1.6.8.tar.gz", hash = "sha256:dd1a75e5a258b02fc88cbc55063b79023799e0c1127321e736fab182a28dc758"}, + {file = "linkml-1.6.9-py3-none-any.whl", hash = "sha256:694c1bc91f8b5b78d9ba9f9a38f72095e25fbeacf072139571cffa1671b8556b"}, + {file = "linkml-1.6.9.tar.gz", hash = "sha256:5b9c30e2b415d04f73186753b5416fbb12a6f85ac2a73dd97a542ea1836b661b"}, ] [package.dependencies] @@ -1521,71 +1525,71 @@ testing = ["coverage", "pyyaml"] [[package]] name = "markupsafe" -version = "2.1.3" +version = "2.1.4" description = "Safely add untrusted strings to HTML/XML markup." optional = false python-versions = ">=3.7" files = [ - {file = "MarkupSafe-2.1.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:cd0f502fe016460680cd20aaa5a76d241d6f35a1c3350c474bac1273803893fa"}, - {file = "MarkupSafe-2.1.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e09031c87a1e51556fdcb46e5bd4f59dfb743061cf93c4d6831bf894f125eb57"}, - {file = "MarkupSafe-2.1.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:68e78619a61ecf91e76aa3e6e8e33fc4894a2bebe93410754bd28fce0a8a4f9f"}, - {file = "MarkupSafe-2.1.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:65c1a9bcdadc6c28eecee2c119465aebff8f7a584dd719facdd9e825ec61ab52"}, - {file = "MarkupSafe-2.1.3-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = 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"re-assert (>=1.1)", "time-machine (>=2.13)", "wheel (>=0.42)"] [[package]] name = "tqdm" diff --git a/project.Makefile b/project.Makefile index fbb2868463..e8d4274909 100644 --- a/project.Makefile +++ b/project.Makefile @@ -87,168 +87,16 @@ local/mixs_regen/mixs_subset.yaml: local/mixs_regen/import_slots_regardless_gen. --config_tsv $< \ --yaml_output $@ -local/mixs_regen/mixs_subset_modified.yaml: local/mixs_regen/mixs_subset.yaml +local/mixs_regen/mixs_subset_modified.yaml: local/mixs_regen/mixs_subset.yaml assets/yq-for-mixs_subset_modified.txt # switching to TextValue may not add any value. the other range changes do improve the structure of the data. # ironically changing back to strings for the submission-schema, data harmonizer, submission portal etc. # may switch source of truth to the MIxS 6.2.2 release candidate - sed 's/quantity value/QuantityValue/' $< > $@ + sed 's/quantity value/QuantityValue/' $(word 1, $^) > $@ sed -i.bak 's/range: string/range: TextValue/' $@ sed -i.bak 's/range: text value/range: TextValue/' $@ - yq -i '.slots.agrochem_addition.range |= "TextValue"' $@ - yq -i '.slots.air_temp_regm.range |= "TextValue"' $@ - yq -i '.slots.antibiotic_regm.range |= "TextValue"' $@ - yq -i '.slots.aromatics_pc.range |= "TextValue"' $@ - yq -i '.slots.asphaltenes_pc.range |= "TextValue"' $@ - yq -i '.slots.atmospheric_data.range |= "TextValue"' $@ - yq -i '.slots.avg_occup.range |= "TextValue"' $@ - yq -i '.slots.bathroom_count.range |= "TextValue"' $@ - yq -i '.slots.bedroom_count.range |= "TextValue"' $@ - yq -i '.slots.biocide_admin_method.range |= "TextValue"' $@ - yq -i '.slots.biomass.range |= "TextValue"' $@ - yq -i '.slots.chem_administration.range |= "ControlledTermValue"' $@ - yq -i '.slots.chem_mutagen.range |= "TextValue"' $@ - yq -i '.slots.chem_treat_method.range |= "string"' $@ - yq -i '.slots.collection_date.range |= "TimestampValue"' $@ - yq -i '.slots.cool_syst_id.range |= "TextValue"' $@ - yq -i '.slots.date_last_rain.range |= "TimestampValue"' $@ - yq -i '.slots.diether_lipids.range |= "TextValue"' $@ - yq -i '.slots.elevator.range |= "TextValue"' $@ - yq -i '.slots.emulsions.range |= "TextValue"' $@ - yq -i '.slots.env_broad_scale.range |= "ControlledIdentifiedTermValue"' $@ - yq -i '.slots.env_local_scale.range |= "ControlledIdentifiedTermValue"' $@ - yq -i '.slots.env_medium.range |= "ControlledIdentifiedTermValue"' $@ - yq -i '.slots.escalator.range |= "TextValue"' $@ - yq -i '.slots.exp_pipe.range |= "QuantityValue"' $@ - yq -i '.slots.experimental_factor.range |= "ControlledTermValue"' $@ - yq -i '.slots.ext_door.range |= "TextValue"' $@ - yq -i '.slots.extreme_event.range |= "TimestampValue"' $@ - yq -i '.slots.fertilizer_regm.range |= "TextValue"' $@ - yq -i '.slots.fire.range |= "TimestampValue"' $@ - yq -i '.slots.flooding.range |= "TimestampValue"' $@ - yq -i '.slots.floor_count.range |= "TextValue"' $@ - yq -i '.slots.freq_clean.range |= "QuantityValue"' $@ - yq -i '.slots.freq_cook.range |= 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"TimestampValue"' $@ - yq -i '.slots.radiation_regm.range |= "TextValue"' $@ - yq -i '.slots.rainfall_regm.range |= "TextValue"' $@ - yq -i '.slots.resins_pc.range |= "TextValue"' $@ - yq -i '.slots.room_architec_elem.range |= "string"' $@ - yq -i '.slots.room_count.range |= "TextValue"' $@ - yq -i '.slots.room_dim.range |= "TextValue"' $@ - yq -i '.slots.room_door_dist.range |= "TextValue"' $@ - yq -i '.slots.room_net_area.range |= "TextValue"' $@ - yq -i '.slots.room_occup.range |= "QuantityValue"' $@ - yq -i '.slots.room_vol.range |= "TextValue"' $@ - yq -i '.slots.root_med_carbon.range |= "TextValue"' $@ - yq -i '.slots.root_med_macronutr.range |= "TextValue"' $@ - yq -i '.slots.root_med_micronutr.range |= "TextValue"' $@ - yq -i '.slots.root_med_ph.range |= "QuantityValue"' $@ - yq -i '.slots.root_med_regl.range |= "TextValue"' $@ - yq -i '.slots.root_med_suppl.range |= "TextValue"' $@ - yq -i '.slots.salt_regm.range |= "TextValue"' $@ - yq -i '.slots.samp_collec_device.range |= "string"' $@ - yq -i '.slots.samp_collec_method.range |= "string"' $@ - yq -i '.slots.samp_loc_corr_rate.range |= "TextValue"' $@ - yq -i '.slots.samp_mat_process.range |= "ControlledTermValue"' $@ - yq -i '.slots.samp_md.range |= "QuantityValue"' $@ - yq -i '.slots.samp_name.range |= "string"' $@ - yq -i '.slots.samp_preserv.range |= "TextValue"' $@ - yq -i '.slots.samp_room_id.range |= "TextValue"' $@ - yq -i '.slots.samp_time_out.range |= "TextValue"' $@ - yq -i '.slots.samp_transport_cond.range |= "TextValue"' $@ - yq -i '.slots.samp_tvdss.range |= "TextValue"' $@ - yq -i '.slots.saturates_pc.range |= "TextValue"' $@ - yq -i '.slots.shad_dev_water_mold.range |= "string"' $@ - yq -i '.slots.sieving.range |= "TextValue"' $@ - yq -i '.slots.size_frac.range |= "TextValue"' $@ - yq -i '.slots.soil_texture_meth.range |= "string"' $@ - yq -i '.slots.soluble_inorg_mat.range |= "TextValue"' $@ - yq -i '.slots.soluble_org_mat.range |= "TextValue"' $@ - yq -i '.slots.suspend_solids.range |= "TextValue"' $@ - yq -i '.slots.tot_nitro_cont_meth.range |= "string"' $@ - yq -i '.slots.viscosity.range |= "TextValue"' $@ - yq -i '.slots.volatile_org_comp.range |= "TextValue"' $@ - yq -i '.slots.water_cont_soil_meth.range |= "string"' $@ - yq -i '.slots.water_temp_regm.range |= "TextValue"' $@ - yq -i '.slots.watering_regm.range |= "TextValue"' $@ - yq -i '.slots.window_open_freq.range |= "TextValue"' $@ - yq -i '.slots.window_size.range |= "TextValue"' $@ - - yq -i 'del(.classes)' $@ - yq -i 'del(.enums.[].name)' $@ - yq -i 'del(.enums.[].permissible_values.[].text)' $@ - yq -i 'del(.slots.[].name)' $@ - yq -i 'del(.slots.add_recov_method.pattern)' $@ - yq -i 'del(.subsets.[].name)' $@ - - yq -i '.id |= "https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml"' $@ - -# # update host_taxid and samp_taxon_id. may want to flatten to a string or URIORCURIE eventually - yq -i 'del(.slots.host_taxid.examples)' $@ - yq -i 'del(.slots.host_taxid.string_serialization)' $@ - yq -i 'del(.slots.samp_taxon_id.examples)' $@ - yq -i 'del(.slots.samp_taxon_id.string_serialization)' $@ - - yq -i '.slots.host_taxid.comments |= ["Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value"]' $@ - yq -i '.slots.host_taxid.range = "ControlledIdentifiedTermValue"' $@ - yq -i '.slots.samp_taxon_id.comments |= ["coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value"]' $@ - yq -i '.slots.samp_taxon_id.range = "ControlledIdentifiedTermValue"' $@ - - - # add "M horizon" to soil_horizon_enum - yq -i '.enums.soil_horizon_enum.permissible_values.["M horizon"] = {}' $@ + grep "^'" $(word 2, $^) | while IFS= read -r line ; do echo $$line ; eval yq -i $$line $@ ; done + # eval yq -i $$line $@ rm -rf local/mixs_regen/mixs_subset_modified.yaml.bak @@ -259,10 +107,7 @@ local/mixs_regen/mixs_subset_modified_inj_land_use.yaml: assets/other_mixs_yaml_ 'select(fileIndex==1).enums.cur_land_use_enum = select(fileIndex==0).enums.cur_land_use_enum | select(fileIndex==1)' \ $^ | cat > $@ -#mixs-deepdiff: src/schema/mixs.yaml -# mv src/schema/mixs.yaml.bak src/schema/mixs.bak.yaml -# $(RUN) deep diff src/schema/mixs.bak.yaml $^ -# mv src/schema/mixs.bak.yaml src/schema/mixs.yaml.bak +# will we ever want to use deepdiff to compare the MIxS schema between two verisons or forms? project/nmdc_schema_generated.yaml: $(SOURCE_SCHEMA_PATH) # the need for this may be eliminated by adding mandatory pattern materialization to gen-json-schema @@ -311,12 +156,10 @@ examples/output/Biosample-exhasutive-pretty-sorted.yaml: src/data/valid/Biosampl -i $< \ -o $@ -# # # # +### Illustrations of getting Neon data from third parties -local/envo.db: - $(RUN) semsql download envo -o $@ - -# # # # +#local/envo.db: +# $(RUN) semsql download envo -o $@ #local/nlcd_2019_land_cover_l48_20210604.xml: # curl -o $@ https://www.mrlc.gov/downloads/sciweb1/shared/mrlc/metadata/nlcd_2019_land_cover_l48_20210604.xml @@ -335,13 +178,12 @@ local/envo.db: #local/neon-soil-order-envo-mapping.tsv: # $(RUN) python nmdc_schema/neon-soil-order-envo-mapping.py -# # # # +### accepting-legacy-ids-all: accepting-legacy-ids-clean \ nmdc_schema/nmdc_schema_accepting_legacy_ids.schema.json nmdc_schema/nmdc_schema_accepting_legacy_ids.py -# --useuris / --metauris -nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml: src/schema/nmdc.yaml +nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml: src/schema/nmdc.yaml assets/yq-for-nmdc_schema_accepting_legacy_ids.txt $(RUN) gen-linkml \ --format yaml \ --mergeimports \ @@ -349,46 +191,9 @@ nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml: src/schema/nmdc.yaml --no-materialize-attributes \ --no-materialize-patterns \ --useuris \ - --output $@ $< - # probably should have made a list of classes and then looped over a parameterized version of this - # could also assert that the range is string - yq -i '(.classes[] | select(.name == "Biosample") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "Biosample") | .slot_usage.part_of.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "Biosample") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "DataObject") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "DataObject") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MagsAnalysisActivity") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MagsAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetabolomicsAnalysisActivity") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetabolomicsAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetagenomeAnnotationActivity") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetagenomeAnnotationActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetagenomeAssembly") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetagenomeAssembly") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetagenomeSequencingActivity") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetagenomeSequencingActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetaproteomicsAnalysisActivity") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetaproteomicsAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetatranscriptomeActivity") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetatranscriptomeActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetatranscriptomeAnnotationActivity") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetatranscriptomeAnnotationActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetatranscriptomeAssembly") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "MetatranscriptomeAssembly") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "NomAnalysisActivity") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "NomAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.part_of.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.has_input.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.has_output.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "OmicsProcessing") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "ReadBasedTaxonomyAnalysisActivity") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "ReadBasedTaxonomyAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "ReadQcAnalysisActivity") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "ReadQcAnalysisActivity") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ - yq -i '(.classes[] | select(.name == "Study") | .slot_usage.id.pattern) = ".*"' $@ - yq -i '(.classes[] | select(.name == "Study") | .slot_usage.id.structured_pattern.syntax) = ".*"' $@ + --output $@ $(word 1, $^) + grep "^'" $(word 2, $^) | while IFS= read -r line ; do echo $$line ; eval yq -i $$line $@ ; done $(RUN) gen-linkml \ --format yaml \ @@ -422,38 +227,17 @@ nmdc_schema/nmdc_schema_accepting_legacy_ids.py: nmdc_schema/nmdc_schema_accepti # todo: switch to API method for getting collection names and stats: https://api.microbiomedata.org/nmdcschema/collection_stats # partially implemented make-rdf: rdf-clean local/mongo_as_nmdc_database_validation.log local/mongo_as_nmdc_database_cuire_repaired.ttl - -# could also check --client-base-url https://api-napa.microbiomedata.org -# but separate validate-filtered-request-all is available for that now - -# todo also notes about large collections: functional_annotation_agg and metaproteomics_analysis_activity_set - -# --selected-collections data_object_set \ -# --selected-collections extraction_set \ -# --selected-collections field_research_site_set \ -# --selected-collections library_preparation_set \ -# --selected-collections mags_activity_set \ -# --selected-collections metabolomics_analysis_activity_set \ -# --selected-collections metagenome_annotation_activity_set \ -# --selected-collections metagenome_assembly_set \ -# --selected-collections metagenome_sequencing_activity_set \ -# --selected-collections metaproteomics_analysis_activity_set \ -# --selected-collections metatranscriptome_activity_set \ -# --selected-collections nom_analysis_activity_set \ -# --selected-collections omics_processing_set \ -# --selected-collections pooling_set \ -# --selected-collections processed_sample_set \ -# --selected-collections read_based_taxonomy_analysis_activity_set \ -# --selected-collections read_qc_analysis_activity_set \ +# todo also notes about huge functional_annotation_agg and large metaproteomics_analysis_activity_set ## can't handle empty selected-collections yet ## https://github.com/microbiomedata/nmdc-schema/issues/1485 # --selected-collections activity_set \ # --selected-collections collecting_biosamples_from_site_set \ # --selected-collections material_sample_set \ - # --selected-collections planned_process_set \ + # --selected-collections metap_gene_function_aggregation \ + # --selected-collections planned_process_set -# --selected-collections metap_gene_function_aggregation \ +## to ensure API only access: --skip-collection-check local/mongo_as_unvalidated_nmdc_database.yaml: date # 276.50 seconds on 2023-08-30 without functional_annotation_agg or metaproteomics_analysis_activity_set @@ -472,6 +256,7 @@ local/mongo_as_unvalidated_nmdc_database.yaml: --selected-collections data_object_set \ --selected-collections functional_annotation_agg \ --selected-collections study_set \ + --selected-collections data_object_set \ --selected-collections extraction_set \ --selected-collections field_research_site_set \ --selected-collections library_preparation_set \ @@ -480,7 +265,6 @@ local/mongo_as_unvalidated_nmdc_database.yaml: --selected-collections metagenome_annotation_activity_set \ --selected-collections metagenome_assembly_set \ --selected-collections metagenome_sequencing_activity_set \ - --selected-collections metaproteomics_analysis_activity_set \ --selected-collections metatranscriptome_activity_set \ --selected-collections nom_analysis_activity_set \ --selected-collections omics_processing_set \ @@ -489,8 +273,6 @@ local/mongo_as_unvalidated_nmdc_database.yaml: --selected-collections read_based_taxonomy_analysis_activity_set \ --selected-collections read_qc_analysis_activity_set -# --skip-collection-check - local/mongo_as_nmdc_database_rdf_safe.yaml: nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml local/mongo_as_unvalidated_nmdc_database.yaml date # 449.56 seconds on 2023-08-30 without functional_annotation_agg or metaproteomics_analysis_activity_set @@ -583,6 +365,18 @@ migration-doctests: migrator: $(RUN) create-migrator +.PHONY: filtered-status +filtered-status: + git status | grep -v 'project/' | grep -v 'nmdc_schema/.*yaml' | grep -v 'nmdc_schema/.*json' | \ + grep -v 'nmdc.py' | grep -v 'nmdc_schema_accepting_legacy_ids.py' + +local/biosample-slot-range-type-report.tsv: src/schema/nmdc.yaml + $(RUN) slot-range-type-reporter \ + --schema $< \ + --output $@ \ + --schema-class Biosample + +### example of preparing to validate napa squad data local/nmdc-schema-v8.0.0.yaml: curl -o $@ https://raw.githubusercontent.com/microbiomedata/nmdc-schema/v8.0.0/nmdc_schema/nmdc_materialized_patterns.yaml # need to remove lines like this (see_alsos whose values aren't legitimate URIs) @@ -601,7 +395,6 @@ local/nmdc-sty-11-aygzgv51.yaml: --output-file $@ ### FUSEKI ETC - .PHONY: thorough-docker-fuseki-cleanup-from-host thorough-docker-fuseki-cleanup-from-host: - docker compose down @@ -614,8 +407,7 @@ thorough-docker-fuseki-cleanup-from-host: docker-startup-from-host: docker compose up --build --detach -# manually: -# docker compose exec app bash +# manually: `docker compose exec app bash` .PHONY: create-nmdc-tdb2-from-app create-nmdc-tdb2-from-app: @@ -642,12 +434,11 @@ stop-nmdc-tdb2-from-app: curl http://fuseki:3030/$$/datasets \ --user 'admin:password' # false means offline -# Warning: 'get-study-related-records' is an entry point defined in pyproject.toml, but it's not installed as a script. You may get improper `sys.argv[0]`. -# The support to run uninstalled scripts will be removed in a future release. -# Run `poetry install` to resolve and get rid of this message. - .PHONY: build-schema-in-app build-schema-in-app: + # Warning: 'get-study-related-records' is an entry point defined in pyproject.toml, but it's not installed as a script. You may get improper `sys.argv[0]`. + # The support to run uninstalled scripts will be removed in a future release. + # Run `poetry install` to resolve and get rid of this message. poetry install make squeaky-clean all test @@ -710,15 +501,14 @@ restart-nmdc-tdb2-from-app: curl http://fuseki:3030/$$/datasets \ --user 'admin:password' - -# does with work in both the datasets offline and active states? +# does this with work in both the datasets offline and active states? local/nmdc-tdb2-graph-list.tsv: tdb2.tdbquery \ --loc=$(FD_ROOT)/nmdc-tdb2 \ --query=assets/sparql/tdb-graph-list.rq \ --results=TSV > $@ -### +### these docker container commands shouldn't be necessary any more due to stop-nmdc-tdb2-from-app and restart-nmdc-tdb2-from-app #.PHONY: fuseki-shutdown-from-host #fuseki-shutdown-from-host: @@ -732,16 +522,3 @@ local/nmdc-tdb2-graph-list.tsv: docker-compose-down-from-host: docker compose down -### - -.PHONY: filtered-status -filtered-status: - git status | grep -v 'project/' | grep -v 'nmdc_schema/.*yaml' | grep -v 'nmdc_schema/.*json' | \ - grep -v 'nmdc.py' | grep -v 'nmdc_schema_accepting_legacy_ids.py' - -local/biosample-slot-range-type-report.tsv: src/schema/nmdc.yaml - $(RUN) slot-range-type-reporter \ - --schema $< \ - --output $@ \ - --schema-class Biosample - diff --git a/project/jsonld/nmdc.context.jsonld b/project/jsonld/nmdc.context.jsonld index ac90930e2a..92ff357254 100644 --- a/project/jsonld/nmdc.context.jsonld +++ b/project/jsonld/nmdc.context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-12-15T16:21:56", + "generation_date": "2024-01-22T11:43:46", "source": "nmdc.yaml" }, "@context": { @@ -1309,6 +1309,9 @@ "@type": "@id", "@id": "prov:qualifiedAssociation" }, + "has_failure_categorization": { + "@type": "@id" + }, "has_input": { "@type": "@id" }, @@ -2192,6 +2195,30 @@ "protocol_link": { "@type": "@id" }, + "qc_failure_what": { + "@context": { + "@vocab": "@null", + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + } + }, + "qc_failure_where": { + "@context": { + "@vocab": "@null", + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + } + }, + "qc_status": { + "@context": { + "@vocab": "@null", + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + } + }, "quad_pos": { "@context": { "@vocab": "@null", @@ -2201,9 +2228,6 @@ }, "@id": "MIXS:0000820" }, - "quality_control_report": { - "@type": "@id" - }, "radiation_regm": { "@type": "@id", "@id": "MIXS:0000575" @@ -2851,14 +2875,6 @@ "meaning": "@id" } }, - "status": { - "@context": { - "@vocab": "@null", - "text": "skos:notation", - "description": "skos:prefLabel", - "meaning": "@id" - } - }, "stoichiometry": { "@type": "xsd:integer" }, diff --git a/project/jsonschema/nmdc.schema.json b/project/jsonschema/nmdc.schema.json index e2eaedc090..215620fe5e 100644 --- a/project/jsonschema/nmdc.schema.json +++ b/project/jsonschema/nmdc.schema.json @@ -1363,6 +1363,14 @@ "$ref": "#/$defs/QuantityValue", "description": "Percentage of industrial effluents received by wastewater treatment plant" }, + "infiltrations": { + "description": "The amount of time it takes to complete each infiltration activity", + "items": { + "pattern": "^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$", + "type": "string" + }, + "type": "array" + }, "inorg_particles": { "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", "items": { @@ -2859,6 +2867,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -2893,6 +2907,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -3123,6 +3145,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -3172,6 +3200,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -3217,6 +3253,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -3251,6 +3293,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -4058,6 +4108,12 @@ "extraction_target": { "$ref": "#/$defs/ExtractionTargetEnum" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4104,12 +4160,21 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, - "quality_control_report": { - "$ref": "#/$defs/QualityControlReport" + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" + }, + "volume": { + "$ref": "#/$defs/QuantityValue", + "description": "The volume of the solvent/solute being used, not the input." } }, "required": [ @@ -4132,6 +4197,51 @@ "title": "ExtractionTargetEnum", "type": "string" }, + "FailureCategorization": { + "additionalProperties": false, + "description": "", + "properties": { + "qc_failure_what": { + "$ref": "#/$defs/FailureWhatEnum", + "description": "Provides a summary about what caused a lab or workflow process to fail" + }, + "qc_failure_where": { + "$ref": "#/$defs/FailureWhereEnum", + "description": "Describes the nmdc schema class that corresonds to where the failure occurred. Most commonly this would be the same as Class that generated the results." + } + }, + "title": "FailureCategorization", + "type": "object" + }, + "FailureWhatEnum": { + "description": "The permitted values for describing where a failure occurred during processing in the lab during analysis workflows.", + "enum": [ + "low_read_count", + "malformed_data", + "assembly_size_too_small", + "no_valid_data_generated", + "other" + ], + "title": "FailureWhatEnum", + "type": "string" + }, + "FailureWhereEnum": { + "description": "The permitted values for describing where in the process, either a lab or analysis workflow step, the failure occurred.", + "enum": [ + "OmicsProcessing", + "Pooling", + "Extraction", + "LibraryPreparation", + "MetagenomeAssembly", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetagenomeAnnotationActivity" + ], + "title": "FailureWhereEnum", + "type": "string" + }, "FaoClassEnum": { "description": "", "enum": [ @@ -4369,6 +4479,12 @@ "description": "The type of conditioning applied to a filter, device, etc.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4407,6 +4523,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "separation_method": { "$ref": "#/$defs/SeparationMethodEnum", "description": "The method that was used to separate a substance from a solution or mixture." @@ -4533,12 +4657,19 @@ "type": "integer" }, "gene_function_id": { + "description": "The identifier for the gene function.", "type": "string" }, "metagenome_annotation_id": { + "description": "The identifier for the analysis activity (WorkflowExecutionActivity) that generated the functional annotation results.", "type": "string" } }, + "required": [ + "metagenome_annotation_id", + "gene_function_id", + "count" + ], "title": "FunctionalAnnotationAggMember", "type": "object" }, @@ -4926,6 +5057,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4969,6 +5106,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -5094,6 +5239,48 @@ }, "MagsAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", "properties": { "binned_contig_num": { @@ -5109,6 +5296,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5151,6 +5344,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_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)?)?)?)?$", "type": "string" @@ -5180,7 +5381,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5229,6 +5429,48 @@ }, "MetabolomicsAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -5245,6 +5487,12 @@ "description": "A reference to a file that holds calibration information.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5281,6 +5529,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5303,7 +5559,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5314,6 +5569,48 @@ }, "MetagenomeAnnotationActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", "properties": { "ended_at_time": { @@ -5334,6 +5631,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5364,6 +5667,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_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)?)?)?)?$", "type": "string" @@ -5387,7 +5698,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5397,6 +5707,48 @@ }, "MetagenomeAssembly": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", "properties": { "asm_score": { @@ -5461,6 +5813,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5503,6 +5861,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "scaf_bp": { "description": "Total size in bp of all scaffolds.", "type": "number" @@ -5574,7 +5940,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5584,6 +5949,48 @@ }, "MetagenomeSequencingActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.", "properties": { "ended_at_time": { @@ -5596,6 +6003,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5626,6 +6039,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5648,7 +6069,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5659,10 +6079,52 @@ }, "MetaproteomicsAnalysisActivity": { "additionalProperties": false, - "description": "", - "properties": { - "ended_at_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)?)?)?)?$", + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], + "description": "", + "properties": { + "ended_at_time": { + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" }, "execution_resource": { @@ -5671,6 +6133,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5707,6 +6175,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_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)?)?)?)?$", "type": "string" @@ -5730,7 +6206,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5741,6 +6216,48 @@ }, "MetatranscriptomeActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", "properties": { "ended_at_time": { @@ -5753,6 +6270,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5783,6 +6306,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5806,7 +6337,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5816,6 +6346,48 @@ }, "MetatranscriptomeAnnotationActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -5836,6 +6408,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5866,6 +6444,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_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)?)?)?)?$", "type": "string" @@ -5889,7 +6475,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5899,6 +6484,48 @@ }, "MetatranscriptomeAssembly": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "asm_score": { @@ -5963,6 +6590,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6005,6 +6638,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "scaf_bp": { "description": "Total size in bp of all scaffolds.", "type": "number" @@ -6075,7 +6716,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -6114,6 +6754,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6156,6 +6802,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -6169,6 +6823,48 @@ }, "NomAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -6185,6 +6881,12 @@ "description": "A reference to a file that holds calibration information.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6215,6 +6917,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -6238,7 +6948,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -6300,6 +7009,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6390,6 +7105,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "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)." @@ -6701,6 +7424,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6738,6 +7467,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -6883,21 +7620,6 @@ "title": "QuadPosEnum", "type": "string" }, - "QualityControlReport": { - "additionalProperties": false, - "description": "", - "properties": { - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "status": { - "$ref": "#/$defs/StatusEnum" - } - }, - "title": "QualityControlReport", - "type": "object" - }, "QuantityValue": { "additionalProperties": false, "description": "A simple quantity, e.g. 2cm", @@ -7014,6 +7736,48 @@ }, "ReadBasedTaxonomyAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", "properties": { "ended_at_time": { @@ -7026,6 +7790,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7056,6 +7826,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_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)?)?)?)?$", "type": "string" @@ -7079,7 +7857,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -7089,6 +7866,48 @@ }, "ReadQcAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", "properties": { "ended_at_time": { @@ -7101,6 +7920,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7155,6 +7980,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -7178,7 +8011,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -7882,6 +8714,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7928,6 +8766,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -8297,6 +9143,48 @@ }, "WorkflowExecutionActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "Represents an instance of an execution of a particular workflow", "properties": { "ended_at_time": { @@ -8309,6 +9197,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -8339,6 +9233,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_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)?)?)?)?$", "type": "string" @@ -8361,7 +9263,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -8381,7 +9282,7 @@ } }, "$id": "https://w3id.org/nmdc/nmdc", - "$schema": "http://json-schema.org/draft-07/schema#", + "$schema": "https://json-schema.org/draft/2019-09/schema", "additionalProperties": true, "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. For MongoDB, the lists of objects that Database slots point to correspond to **collections**.", "metamodel_version": "1.7.0", diff --git a/project/nmdc_materialized_patterns.schema.json b/project/nmdc_materialized_patterns.schema.json index 66e1f03dfa..d40c53f6ce 100644 --- a/project/nmdc_materialized_patterns.schema.json +++ b/project/nmdc_materialized_patterns.schema.json @@ -1363,6 +1363,14 @@ "$ref": "#/$defs/QuantityValue", "description": "Percentage of industrial effluents received by wastewater treatment plant" }, + "infiltrations": { + "description": "The amount of time it takes to complete each infiltration activity", + "items": { + "pattern": "^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$", + "type": "string" + }, + "type": "array" + }, "inorg_particles": { "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", "items": { @@ -2859,6 +2867,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -2893,6 +2907,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -3123,6 +3145,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -3172,6 +3200,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -3217,6 +3253,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -3251,6 +3293,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -4058,6 +4108,12 @@ "extraction_target": { "$ref": "#/$defs/ExtractionTargetEnum" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4104,12 +4160,21 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, - "quality_control_report": { - "$ref": "#/$defs/QualityControlReport" + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" + }, + "volume": { + "$ref": "#/$defs/QuantityValue", + "description": "The volume of the solvent/solute being used, not the input." } }, "required": [ @@ -4132,6 +4197,51 @@ "title": "ExtractionTargetEnum", "type": "string" }, + "FailureCategorization": { + "additionalProperties": false, + "description": "", + "properties": { + "qc_failure_what": { + "$ref": "#/$defs/FailureWhatEnum", + "description": "Provides a summary about what caused a lab or workflow process to fail" + }, + "qc_failure_where": { + "$ref": "#/$defs/FailureWhereEnum", + "description": "Describes the nmdc schema class that corresonds to where the failure occurred. Most commonly this would be the same as Class that generated the results." + } + }, + "title": "FailureCategorization", + "type": "object" + }, + "FailureWhatEnum": { + "description": "The permitted values for describing where a failure occurred during processing in the lab during analysis workflows.", + "enum": [ + "low_read_count", + "malformed_data", + "assembly_size_too_small", + "no_valid_data_generated", + "other" + ], + "title": "FailureWhatEnum", + "type": "string" + }, + "FailureWhereEnum": { + "description": "The permitted values for describing where in the process, either a lab or analysis workflow step, the failure occurred.", + "enum": [ + "OmicsProcessing", + "Pooling", + "Extraction", + "LibraryPreparation", + "MetagenomeAssembly", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetagenomeAnnotationActivity" + ], + "title": "FailureWhereEnum", + "type": "string" + }, "FaoClassEnum": { "description": "", "enum": [ @@ -4369,6 +4479,12 @@ "description": "The type of conditioning applied to a filter, device, etc.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4407,6 +4523,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "separation_method": { "$ref": "#/$defs/SeparationMethodEnum", "description": "The method that was used to separate a substance from a solution or mixture." @@ -4533,12 +4657,19 @@ "type": "integer" }, "gene_function_id": { + "description": "The identifier for the gene function.", "type": "string" }, "metagenome_annotation_id": { + "description": "The identifier for the analysis activity (WorkflowExecutionActivity) that generated the functional annotation results.", "type": "string" } }, + "required": [ + "metagenome_annotation_id", + "gene_function_id", + "count" + ], "title": "FunctionalAnnotationAggMember", "type": "object" }, @@ -4926,6 +5057,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4969,6 +5106,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -5094,6 +5239,48 @@ }, "MagsAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", "properties": { "binned_contig_num": { @@ -5109,6 +5296,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5151,6 +5344,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5180,7 +5381,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5229,6 +5429,48 @@ }, "MetabolomicsAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -5245,6 +5487,12 @@ "description": "A reference to a file that holds calibration information.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5281,6 +5529,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_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)?)?)?)?$", "type": "string" @@ -5303,7 +5559,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5314,6 +5569,48 @@ }, "MetagenomeAnnotationActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", "properties": { "ended_at_time": { @@ -5334,6 +5631,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5364,6 +5667,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5387,7 +5698,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5397,6 +5707,48 @@ }, "MetagenomeAssembly": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", "properties": { "asm_score": { @@ -5461,6 +5813,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5503,6 +5861,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "scaf_bp": { "description": "Total size in bp of all scaffolds.", "type": "number" @@ -5574,7 +5940,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5584,6 +5949,48 @@ }, "MetagenomeSequencingActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.", "properties": { "ended_at_time": { @@ -5596,6 +6003,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5626,6 +6039,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_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)?)?)?)?$", "type": "string" @@ -5648,7 +6069,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5659,10 +6079,52 @@ }, "MetaproteomicsAnalysisActivity": { "additionalProperties": false, - "description": "", - "properties": { - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], + "description": "", + "properties": { + "ended_at_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)?)?)?)?$", "type": "string" }, "execution_resource": { @@ -5671,6 +6133,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5707,6 +6175,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5730,7 +6206,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5741,6 +6216,48 @@ }, "MetatranscriptomeActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", "properties": { "ended_at_time": { @@ -5753,6 +6270,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5783,6 +6306,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_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)?)?)?)?$", "type": "string" @@ -5806,7 +6337,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5816,6 +6346,48 @@ }, "MetatranscriptomeAnnotationActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -5836,6 +6408,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5866,6 +6444,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5889,7 +6475,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5899,6 +6484,48 @@ }, "MetatranscriptomeAssembly": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "asm_score": { @@ -5963,6 +6590,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6005,6 +6638,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "scaf_bp": { "description": "Total size in bp of all scaffolds.", "type": "number" @@ -6075,7 +6716,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -6114,6 +6754,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6156,6 +6802,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -6169,6 +6823,48 @@ }, "NomAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -6185,6 +6881,12 @@ "description": "A reference to a file that holds calibration information.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6215,6 +6917,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_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)?)?)?)?$", "type": "string" @@ -6238,7 +6948,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -6300,6 +7009,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6390,6 +7105,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "samp_vol_we_dna_ext": { "$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001)." @@ -6701,6 +7424,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6738,6 +7467,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -6883,21 +7620,6 @@ "title": "QuadPosEnum", "type": "string" }, - "QualityControlReport": { - "additionalProperties": false, - "description": "", - "properties": { - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "status": { - "$ref": "#/$defs/StatusEnum" - } - }, - "title": "QualityControlReport", - "type": "object" - }, "QuantityValue": { "additionalProperties": false, "description": "A simple quantity, e.g. 2cm", @@ -7014,6 +7736,48 @@ }, "ReadBasedTaxonomyAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", "properties": { "ended_at_time": { @@ -7026,6 +7790,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7056,6 +7826,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -7079,7 +7857,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -7089,6 +7866,48 @@ }, "ReadQcAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "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": { @@ -7101,6 +7920,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7155,6 +7980,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_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)?)?)?)?$", "type": "string" @@ -7178,7 +8011,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -7882,6 +8714,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7928,6 +8766,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -8297,6 +9143,48 @@ }, "WorkflowExecutionActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "Represents an instance of an execution of a particular workflow", "properties": { "ended_at_time": { @@ -8309,6 +9197,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -8339,6 +9233,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -8361,7 +9263,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -8381,7 +9282,7 @@ } }, "$id": "https://w3id.org/nmdc/nmdc", - "$schema": "http://json-schema.org/draft-07/schema#", + "$schema": "https://json-schema.org/draft/2019-09/schema", "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. For MongoDB, the lists of objects that Database slots point to correspond to **collections**.", "metamodel_version": "1.7.0", diff --git a/project/nmdc_materialized_patterns.yaml b/project/nmdc_materialized_patterns.yaml index 78d1aee127..abf3f76347 100644 --- a/project/nmdc_materialized_patterns.yaml +++ b/project/nmdc_materialized_patterns.yaml @@ -1276,6 +1276,73 @@ enums: text: V-bottom conical tube falcon tube: text: falcon tube + FailureWhatEnum: + name: FailureWhatEnum + description: The permitted values for describing where a failure occurred during + processing in the lab during analysis workflows. + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + low_read_count: + text: low_read_count + description: Number of output reads is not sufficient to continue to the next + analysis step. + malformed_data: + text: malformed_data + description: Workflow failure reading input or writing the output file(s). + assembly_size_too_small: + text: assembly_size_too_small + description: The size of the metagenome or metatranscriptome assembly is too + small to proceed to the next analysis workflow. + no_valid_data_generated: + text: no_valid_data_generated + description: A process ran but did not produce any output. Ie binning ran + but did not produce any medium or high quality bins. + other: + text: other + description: A lab process or analysis workflow has failed in a way that has + not been captured by the available values yet. Please use slot 'qc_comment' + to specify details. + FailureWhereEnum: + name: FailureWhereEnum + description: The permitted values for describing where in the process, either + a lab or analysis workflow step, the failure occurred. + comments: + - At Chris' recommendation permissible values for this enumeration are the same + as Class names. + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + OmicsProcessing: + text: OmicsProcessing + description: A failure has occurred in omics processing, a lab process. + Pooling: + text: Pooling + description: A failure has occurred in pooling, a lab process. + Extraction: + text: Extraction + description: A failure has occurred in extraction, a lab process. + LibraryPreparation: + text: LibraryPreparation + description: A failure has occurred in library preparation, a lab process. + MetagenomeAssembly: + text: MetagenomeAssembly + description: A failure has occurred in metagenome assembly, a workflow process. + MetatranscriptomeActivity: + text: MetatranscriptomeActivity + description: A failure has occurred in metatranscriptome analysis, a workflow + process. + MagsAnalysisActivity: + text: MagsAnalysisActivity + description: A failure has occurred in binning, a workflow process to generate + metagenome-assembled genomes (MAGS). + ReadQcAnalysisActivity: + text: ReadQcAnalysisActivity + description: A failure has occurred in read qc, a workflow process. + ReadBasedTaxonomyAnalysisActivity: + text: ReadBasedTaxonomyAnalysisActivity + description: A failure has occurred in reads based taxonomy, a workflow process. + MetagenomeAnnotationActivity: + text: MetagenomeAnnotationActivity + description: A failure has occurred in annotation, a workflow process. SeparationMethodEnum: name: SeparationMethodEnum description: The tool/substance used to separate or filter a solution or mixture. @@ -3534,6 +3601,11 @@ enums: high: text: high slots: + has_failure_categorization: + name: has_failure_categorization + from_schema: https://w3id.org/nmdc/nmdc + multivalued: true + range: FailureCategorization model: name: model from_schema: https://w3id.org/nmdc/nmdc @@ -3544,17 +3616,25 @@ slots: range: InstrumentVendorEnum metagenome_annotation_id: name: metagenome_annotation_id + description: The identifier for the analysis activity (WorkflowExecutionActivity) + that generated the functional annotation results. from_schema: https://w3id.org/nmdc/nmdc domain: FunctionalAnnotationAggMember range: WorkflowExecutionActivity + required: true gene_function_id: name: gene_function_id + description: The identifier for the gene function. + examples: + - value: KEGG.ORTHOLOGY:K00627 from_schema: https://w3id.org/nmdc/nmdc range: uriorcurie + required: true count: name: count from_schema: https://w3id.org/nmdc/nmdc range: integer + required: true functional_annotation_agg: name: functional_annotation_agg from_schema: https://w3id.org/nmdc/nmdc @@ -3599,10 +3679,12 @@ slots: sample_collection_month: name: sample_collection_month from_schema: https://w3id.org/nmdc/nmdc - status: - name: status + qc_status: + name: qc_status + description: Stores information about the result of a process (ie the process + of sequencing a library may have for qc_status of 'fail' if not enough data + was generated) from_schema: https://w3id.org/nmdc/nmdc - domain: QualityControlReport range: StatusEnum library_preparation_kit: name: library_preparation_kit @@ -3613,11 +3695,6 @@ slots: from_schema: https://w3id.org/nmdc/nmdc domain: Extraction range: ExtractionTargetEnum - quality_control_report: - name: quality_control_report - from_schema: https://w3id.org/nmdc/nmdc - domain: PlannedProcess - range: QualityControlReport pcr_cycles: name: pcr_cycles from_schema: https://w3id.org/nmdc/nmdc @@ -4460,6 +4537,21 @@ slots: description: The conductivity measurement was 0.017 millisiemens per centimeter. from_schema: https://w3id.org/nmdc/nmdc range: QuantityValue + infiltrations: + name: infiltrations + description: The amount of time it takes to complete each infiltration activity + examples: + - value: '[''00:01:32'', ''00:00:53'']' + from_schema: https://w3id.org/nmdc/nmdc + see_also: + - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1 + aliases: + - infiltration_1 + - infiltration_2 + multivalued: true + list_elements_ordered: true + range: string + pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$ filter_material: name: filter_material description: A porous material on which solid particles present in air or other @@ -5482,6 +5574,32 @@ slots: from_schema: https://w3id.org/nmdc/nmdc domain: ProcessedSample range: QuantityValue + qc_failure_what: + name: qc_failure_what + description: Provides a summary about what caused a lab or workflow process to + fail + comments: + - For example Low read count from a sequencer, malformed fastq files, etc) + from_schema: https://w3id.org/nmdc/nmdc + domain: FailureCategorization + range: FailureWhatEnum + qc_failure_where: + name: qc_failure_where + description: Describes the nmdc schema class that corresonds to where the failure + occurred. Most commonly this would be the same as Class that generated the results. + comments: + - If the assembly size was too small to proceed to annotation failure_where would + be MetagenomeAssembly. + from_schema: https://w3id.org/nmdc/nmdc + domain: FailureCategorization + range: FailureWhereEnum + qc_comment: + name: qc_comment + description: Slot to store additional comments about laboratory or workflow output. + For workflow output it may describe the particular workflow stage that failed. + (ie Failed at call-stage due to a malformed fastq file). + from_schema: https://w3id.org/nmdc/nmdc + range: string instrument_name: name: instrument_name description: The name of the instrument that was used for processing the sample. @@ -17898,6 +18016,12 @@ slots: is_a: gff_coordinate domain: GenomeFeature classes: + FailureCategorization: + name: FailureCategorization + from_schema: https://w3id.org/nmdc/nmdc + slots: + - qc_failure_what + - qc_failure_where FunctionalAnnotationAggMember: name: FunctionalAnnotationAggMember from_schema: https://w3id.org/nmdc/nmdc @@ -17916,6 +18040,8 @@ classes: aliases: - NMDC metadata object slots: + - planned_process_set + - functional_annotation_agg - activity_set - biosample_set - collecting_biosamples_from_site_set @@ -17978,7 +18104,7 @@ classes: - extraction_method - extraction_target - input_mass - - quality_control_report + - volume slot_usage: has_input: name: has_input @@ -18034,12 +18160,6 @@ classes: slots: - url - name - QualityControlReport: - name: QualityControlReport - from_schema: https://w3id.org/nmdc/nmdc - slots: - - status - - name LibraryPreparation: name: LibraryPreparation comments: @@ -18802,6 +18922,7 @@ classes: - analysis_type - sample_link - bulk_elect_conductivity + - infiltrations - zinc - manganese - ammonium_nitrogen @@ -19636,6 +19757,9 @@ classes: - part_of - type - version + - qc_status + - qc_comment + - has_failure_categorization slot_usage: started_at_time: name: started_at_time @@ -19649,9 +19773,6 @@ classes: has_input: name: has_input required: true - has_output: - name: has_output - required: true execution_resource: name: execution_resource required: true @@ -19665,6 +19786,31 @@ classes: structured_pattern: syntax: '{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true + rules: + - preconditions: + slot_conditions: + qc_status: + name: qc_status + equals_string: pass + postconditions: + slot_conditions: + has_output: + name: has_output + required: true + description: If qc_status has a value of pass, then the has_output slot is required. + title: qc_status_pass_has_output_required + - preconditions: + slot_conditions: + qc_status: + name: qc_status + value_presence: ABSENT + postconditions: + slot_conditions: + has_output: + name: has_output + required: true + description: If qc_status is not specified, then the has_output slot is required. + title: qc_status_pass_null_has_output_required MetagenomeAssembly: name: MetagenomeAssembly description: A workflow execution activity that converts sequencing reads into @@ -20037,6 +20183,9 @@ classes: - protocol_link - start_date - instrument_name + - qc_status + - qc_comment + - has_failure_categorization slot_usage: designated_class: name: designated_class diff --git a/project/nmdc_schema_generated.yaml b/project/nmdc_schema_generated.yaml index 78d1aee127..abf3f76347 100644 --- a/project/nmdc_schema_generated.yaml +++ b/project/nmdc_schema_generated.yaml @@ -1276,6 +1276,73 @@ enums: text: V-bottom conical tube falcon tube: text: falcon tube + FailureWhatEnum: + name: FailureWhatEnum + description: The permitted values for describing where a failure occurred during + processing in the lab during analysis workflows. + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + low_read_count: + text: low_read_count + description: Number of output reads is not sufficient to continue to the next + analysis step. + malformed_data: + text: malformed_data + description: Workflow failure reading input or writing the output file(s). + assembly_size_too_small: + text: assembly_size_too_small + description: The size of the metagenome or metatranscriptome assembly is too + small to proceed to the next analysis workflow. + no_valid_data_generated: + text: no_valid_data_generated + description: A process ran but did not produce any output. Ie binning ran + but did not produce any medium or high quality bins. + other: + text: other + description: A lab process or analysis workflow has failed in a way that has + not been captured by the available values yet. Please use slot 'qc_comment' + to specify details. + FailureWhereEnum: + name: FailureWhereEnum + description: The permitted values for describing where in the process, either + a lab or analysis workflow step, the failure occurred. + comments: + - At Chris' recommendation permissible values for this enumeration are the same + as Class names. + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + OmicsProcessing: + text: OmicsProcessing + description: A failure has occurred in omics processing, a lab process. + Pooling: + text: Pooling + description: A failure has occurred in pooling, a lab process. + Extraction: + text: Extraction + description: A failure has occurred in extraction, a lab process. + LibraryPreparation: + text: LibraryPreparation + description: A failure has occurred in library preparation, a lab process. + MetagenomeAssembly: + text: MetagenomeAssembly + description: A failure has occurred in metagenome assembly, a workflow process. + MetatranscriptomeActivity: + text: MetatranscriptomeActivity + description: A failure has occurred in metatranscriptome analysis, a workflow + process. + MagsAnalysisActivity: + text: MagsAnalysisActivity + description: A failure has occurred in binning, a workflow process to generate + metagenome-assembled genomes (MAGS). + ReadQcAnalysisActivity: + text: ReadQcAnalysisActivity + description: A failure has occurred in read qc, a workflow process. + ReadBasedTaxonomyAnalysisActivity: + text: ReadBasedTaxonomyAnalysisActivity + description: A failure has occurred in reads based taxonomy, a workflow process. + MetagenomeAnnotationActivity: + text: MetagenomeAnnotationActivity + description: A failure has occurred in annotation, a workflow process. SeparationMethodEnum: name: SeparationMethodEnum description: The tool/substance used to separate or filter a solution or mixture. @@ -3534,6 +3601,11 @@ enums: high: text: high slots: + has_failure_categorization: + name: has_failure_categorization + from_schema: https://w3id.org/nmdc/nmdc + multivalued: true + range: FailureCategorization model: name: model from_schema: https://w3id.org/nmdc/nmdc @@ -3544,17 +3616,25 @@ slots: range: InstrumentVendorEnum metagenome_annotation_id: name: metagenome_annotation_id + description: The identifier for the analysis activity (WorkflowExecutionActivity) + that generated the functional annotation results. from_schema: https://w3id.org/nmdc/nmdc domain: FunctionalAnnotationAggMember range: WorkflowExecutionActivity + required: true gene_function_id: name: gene_function_id + description: The identifier for the gene function. + examples: + - value: KEGG.ORTHOLOGY:K00627 from_schema: https://w3id.org/nmdc/nmdc range: uriorcurie + required: true count: name: count from_schema: https://w3id.org/nmdc/nmdc range: integer + required: true functional_annotation_agg: name: functional_annotation_agg from_schema: https://w3id.org/nmdc/nmdc @@ -3599,10 +3679,12 @@ slots: sample_collection_month: name: sample_collection_month from_schema: https://w3id.org/nmdc/nmdc - status: - name: status + qc_status: + name: qc_status + description: Stores information about the result of a process (ie the process + of sequencing a library may have for qc_status of 'fail' if not enough data + was generated) from_schema: https://w3id.org/nmdc/nmdc - domain: QualityControlReport range: StatusEnum library_preparation_kit: name: library_preparation_kit @@ -3613,11 +3695,6 @@ slots: from_schema: https://w3id.org/nmdc/nmdc domain: Extraction range: ExtractionTargetEnum - quality_control_report: - name: quality_control_report - from_schema: https://w3id.org/nmdc/nmdc - domain: PlannedProcess - range: QualityControlReport pcr_cycles: name: pcr_cycles from_schema: https://w3id.org/nmdc/nmdc @@ -4460,6 +4537,21 @@ slots: description: The conductivity measurement was 0.017 millisiemens per centimeter. from_schema: https://w3id.org/nmdc/nmdc range: QuantityValue + infiltrations: + name: infiltrations + description: The amount of time it takes to complete each infiltration activity + examples: + - value: '[''00:01:32'', ''00:00:53'']' + from_schema: https://w3id.org/nmdc/nmdc + see_also: + - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1 + aliases: + - infiltration_1 + - infiltration_2 + multivalued: true + list_elements_ordered: true + range: string + pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$ filter_material: name: filter_material description: A porous material on which solid particles present in air or other @@ -5482,6 +5574,32 @@ slots: from_schema: https://w3id.org/nmdc/nmdc domain: ProcessedSample range: QuantityValue + qc_failure_what: + name: qc_failure_what + description: Provides a summary about what caused a lab or workflow process to + fail + comments: + - For example Low read count from a sequencer, malformed fastq files, etc) + from_schema: https://w3id.org/nmdc/nmdc + domain: FailureCategorization + range: FailureWhatEnum + qc_failure_where: + name: qc_failure_where + description: Describes the nmdc schema class that corresonds to where the failure + occurred. Most commonly this would be the same as Class that generated the results. + comments: + - If the assembly size was too small to proceed to annotation failure_where would + be MetagenomeAssembly. + from_schema: https://w3id.org/nmdc/nmdc + domain: FailureCategorization + range: FailureWhereEnum + qc_comment: + name: qc_comment + description: Slot to store additional comments about laboratory or workflow output. + For workflow output it may describe the particular workflow stage that failed. + (ie Failed at call-stage due to a malformed fastq file). + from_schema: https://w3id.org/nmdc/nmdc + range: string instrument_name: name: instrument_name description: The name of the instrument that was used for processing the sample. @@ -17898,6 +18016,12 @@ slots: is_a: gff_coordinate domain: GenomeFeature classes: + FailureCategorization: + name: FailureCategorization + from_schema: https://w3id.org/nmdc/nmdc + slots: + - qc_failure_what + - qc_failure_where FunctionalAnnotationAggMember: name: FunctionalAnnotationAggMember from_schema: https://w3id.org/nmdc/nmdc @@ -17916,6 +18040,8 @@ classes: aliases: - NMDC metadata object slots: + - planned_process_set + - functional_annotation_agg - activity_set - biosample_set - collecting_biosamples_from_site_set @@ -17978,7 +18104,7 @@ classes: - extraction_method - extraction_target - input_mass - - quality_control_report + - volume slot_usage: has_input: name: has_input @@ -18034,12 +18160,6 @@ classes: slots: - url - name - QualityControlReport: - name: QualityControlReport - from_schema: https://w3id.org/nmdc/nmdc - slots: - - status - - name LibraryPreparation: name: LibraryPreparation comments: @@ -18802,6 +18922,7 @@ classes: - analysis_type - sample_link - bulk_elect_conductivity + - infiltrations - zinc - manganese - ammonium_nitrogen @@ -19636,6 +19757,9 @@ classes: - part_of - type - version + - qc_status + - qc_comment + - has_failure_categorization slot_usage: started_at_time: name: started_at_time @@ -19649,9 +19773,6 @@ classes: has_input: name: has_input required: true - has_output: - name: has_output - required: true execution_resource: name: execution_resource required: true @@ -19665,6 +19786,31 @@ classes: structured_pattern: syntax: '{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true + rules: + - preconditions: + slot_conditions: + qc_status: + name: qc_status + equals_string: pass + postconditions: + slot_conditions: + has_output: + name: has_output + required: true + description: If qc_status has a value of pass, then the has_output slot is required. + title: qc_status_pass_has_output_required + - preconditions: + slot_conditions: + qc_status: + name: qc_status + value_presence: ABSENT + postconditions: + slot_conditions: + has_output: + name: has_output + required: true + description: If qc_status is not specified, then the has_output slot is required. + title: qc_status_pass_null_has_output_required MetagenomeAssembly: name: MetagenomeAssembly description: A workflow execution activity that converts sequencing reads into @@ -20037,6 +20183,9 @@ classes: - protocol_link - start_date - instrument_name + - qc_status + - qc_comment + - has_failure_categorization slot_usage: designated_class: name: designated_class diff --git a/project/nmdc_schema_merged.yaml b/project/nmdc_schema_merged.yaml index ee119ab8a9..907eba8196 100644 --- a/project/nmdc_schema_merged.yaml +++ b/project/nmdc_schema_merged.yaml @@ -1276,6 +1276,73 @@ enums: text: V-bottom conical tube falcon tube: text: falcon tube + FailureWhatEnum: + name: FailureWhatEnum + description: The permitted values for describing where a failure occurred during + processing in the lab during analysis workflows. + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + low_read_count: + text: low_read_count + description: Number of output reads is not sufficient to continue to the next + analysis step. + malformed_data: + text: malformed_data + description: Workflow failure reading input or writing the output file(s). + assembly_size_too_small: + text: assembly_size_too_small + description: The size of the metagenome or metatranscriptome assembly is too + small to proceed to the next analysis workflow. + no_valid_data_generated: + text: no_valid_data_generated + description: A process ran but did not produce any output. Ie binning ran + but did not produce any medium or high quality bins. + other: + text: other + description: A lab process or analysis workflow has failed in a way that has + not been captured by the available values yet. Please use slot 'qc_comment' + to specify details. + FailureWhereEnum: + name: FailureWhereEnum + description: The permitted values for describing where in the process, either + a lab or analysis workflow step, the failure occurred. + comments: + - At Chris' recommendation permissible values for this enumeration are the same + as Class names. + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + OmicsProcessing: + text: OmicsProcessing + description: A failure has occurred in omics processing, a lab process. + Pooling: + text: Pooling + description: A failure has occurred in pooling, a lab process. + Extraction: + text: Extraction + description: A failure has occurred in extraction, a lab process. + LibraryPreparation: + text: LibraryPreparation + description: A failure has occurred in library preparation, a lab process. + MetagenomeAssembly: + text: MetagenomeAssembly + description: A failure has occurred in metagenome assembly, a workflow process. + MetatranscriptomeActivity: + text: MetatranscriptomeActivity + description: A failure has occurred in metatranscriptome analysis, a workflow + process. + MagsAnalysisActivity: + text: MagsAnalysisActivity + description: A failure has occurred in binning, a workflow process to generate + metagenome-assembled genomes (MAGS). + ReadQcAnalysisActivity: + text: ReadQcAnalysisActivity + description: A failure has occurred in read qc, a workflow process. + ReadBasedTaxonomyAnalysisActivity: + text: ReadBasedTaxonomyAnalysisActivity + description: A failure has occurred in reads based taxonomy, a workflow process. + MetagenomeAnnotationActivity: + text: MetagenomeAnnotationActivity + description: A failure has occurred in annotation, a workflow process. SeparationMethodEnum: name: SeparationMethodEnum description: The tool/substance used to separate or filter a solution or mixture. @@ -3534,6 +3601,11 @@ enums: high: text: high slots: + has_failure_categorization: + name: has_failure_categorization + from_schema: https://w3id.org/nmdc/nmdc + multivalued: true + range: FailureCategorization model: name: model from_schema: https://w3id.org/nmdc/nmdc @@ -3544,17 +3616,25 @@ slots: range: InstrumentVendorEnum metagenome_annotation_id: name: metagenome_annotation_id + description: The identifier for the analysis activity (WorkflowExecutionActivity) + that generated the functional annotation results. from_schema: https://w3id.org/nmdc/nmdc domain: FunctionalAnnotationAggMember range: WorkflowExecutionActivity + required: true gene_function_id: name: gene_function_id + description: The identifier for the gene function. + examples: + - value: KEGG.ORTHOLOGY:K00627 from_schema: https://w3id.org/nmdc/nmdc range: uriorcurie + required: true count: name: count from_schema: https://w3id.org/nmdc/nmdc range: integer + required: true functional_annotation_agg: name: functional_annotation_agg from_schema: https://w3id.org/nmdc/nmdc @@ -3599,10 +3679,12 @@ slots: sample_collection_month: name: sample_collection_month from_schema: https://w3id.org/nmdc/nmdc - status: - name: status + qc_status: + name: qc_status + description: Stores information about the result of a process (ie the process + of sequencing a library may have for qc_status of 'fail' if not enough data + was generated) from_schema: https://w3id.org/nmdc/nmdc - domain: QualityControlReport range: StatusEnum library_preparation_kit: name: library_preparation_kit @@ -3613,11 +3695,6 @@ slots: from_schema: https://w3id.org/nmdc/nmdc domain: Extraction range: ExtractionTargetEnum - quality_control_report: - name: quality_control_report - from_schema: https://w3id.org/nmdc/nmdc - domain: PlannedProcess - range: QualityControlReport pcr_cycles: name: pcr_cycles from_schema: https://w3id.org/nmdc/nmdc @@ -4460,6 +4537,21 @@ slots: description: The conductivity measurement was 0.017 millisiemens per centimeter. from_schema: https://w3id.org/nmdc/nmdc range: QuantityValue + infiltrations: + name: infiltrations + description: The amount of time it takes to complete each infiltration activity + examples: + - value: '[''00:01:32'', ''00:00:53'']' + from_schema: https://w3id.org/nmdc/nmdc + see_also: + - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1 + aliases: + - infiltration_1 + - infiltration_2 + multivalued: true + list_elements_ordered: true + range: string + pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$ filter_material: name: filter_material description: A porous material on which solid particles present in air or other @@ -5482,6 +5574,32 @@ slots: from_schema: https://w3id.org/nmdc/basic_slots domain: ProcessedSample range: QuantityValue + qc_failure_what: + name: qc_failure_what + description: Provides a summary about what caused a lab or workflow process to + fail + comments: + - For example Low read count from a sequencer, malformed fastq files, etc) + from_schema: https://w3id.org/nmdc/basic_slots + domain: FailureCategorization + range: FailureWhatEnum + qc_failure_where: + name: qc_failure_where + description: Describes the nmdc schema class that corresonds to where the failure + occurred. Most commonly this would be the same as Class that generated the results. + comments: + - If the assembly size was too small to proceed to annotation failure_where would + be MetagenomeAssembly. + from_schema: https://w3id.org/nmdc/basic_slots + domain: FailureCategorization + range: FailureWhereEnum + qc_comment: + name: qc_comment + description: Slot to store additional comments about laboratory or workflow output. + For workflow output it may describe the particular workflow stage that failed. + (ie Failed at call-stage due to a malformed fastq file). + from_schema: https://w3id.org/nmdc/basic_slots + range: string instrument_name: name: instrument_name description: The name of the instrument that was used for processing the sample. @@ -17898,6 +18016,12 @@ slots: is_a: gff_coordinate domain: GenomeFeature classes: + FailureCategorization: + name: FailureCategorization + from_schema: https://w3id.org/nmdc/nmdc + slots: + - qc_failure_what + - qc_failure_where FunctionalAnnotationAggMember: name: FunctionalAnnotationAggMember from_schema: https://w3id.org/nmdc/nmdc @@ -17916,6 +18040,8 @@ classes: aliases: - NMDC metadata object slots: + - planned_process_set + - functional_annotation_agg - activity_set - biosample_set - collecting_biosamples_from_site_set @@ -17977,7 +18103,7 @@ classes: - extraction_method - extraction_target - input_mass - - quality_control_report + - volume slot_usage: has_input: name: has_input @@ -18032,12 +18158,6 @@ classes: slots: - url - name - QualityControlReport: - name: QualityControlReport - from_schema: https://w3id.org/nmdc/nmdc - slots: - - status - - name LibraryPreparation: name: LibraryPreparation comments: @@ -18796,6 +18916,7 @@ classes: - analysis_type - sample_link - bulk_elect_conductivity + - infiltrations - zinc - manganese - ammonium_nitrogen @@ -19626,6 +19747,9 @@ classes: - part_of - type - version + - qc_status + - qc_comment + - has_failure_categorization slot_usage: started_at_time: name: started_at_time @@ -19639,9 +19763,6 @@ classes: has_input: name: has_input required: true - has_output: - name: has_output - required: true execution_resource: name: execution_resource required: true @@ -19654,6 +19775,31 @@ classes: structured_pattern: syntax: '{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true + rules: + - preconditions: + slot_conditions: + qc_status: + name: qc_status + equals_string: pass + postconditions: + slot_conditions: + has_output: + name: has_output + required: true + description: If qc_status has a value of pass, then the has_output slot is required. + title: qc_status_pass_has_output_required + - preconditions: + slot_conditions: + qc_status: + name: qc_status + value_presence: ABSENT + postconditions: + slot_conditions: + has_output: + name: has_output + required: true + description: If qc_status is not specified, then the has_output slot is required. + title: qc_status_pass_null_has_output_required MetagenomeAssembly: name: MetagenomeAssembly description: A workflow execution activity that converts sequencing reads into @@ -20011,6 +20157,9 @@ classes: - protocol_link - start_date - instrument_name + - qc_status + - qc_comment + - has_failure_categorization slot_usage: designated_class: name: designated_class diff --git a/project/owl/nmdc.owl.ttl b/project/owl/nmdc.owl.ttl index 3e0be21d1f..5034b84915 100644 --- a/project/owl/nmdc.owl.ttl +++ b/project/owl/nmdc.owl.ttl @@ -21,387 +21,19 @@ @prefix skos: . @prefix xsd: . - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "al_sat" ; - dcterms:title "extreme_unusual_properties/Al saturation" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "extreme_unusual_properties/Al saturation" ; - skos:definition "Aluminum saturation (esp. For tropical soils)" ; - skos:inScheme ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "percentage" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "al_sat_meth" ; - dcterms:title "extreme_unusual_properties/Al saturation method" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "extreme_unusual_properties/Al saturation method" ; - skos:definition "Reference or method used in determining Al saturation" ; - skos:inScheme ; - nmdc:expected_value "PMID,DOI or URL" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "annual_precpt" ; - dcterms:title "mean annual precipitation" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "mean annual precipitation" ; - skos:definition "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps." ; - skos:inScheme ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "millimeter" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "climate_environment" ; - dcterms:title "climate environment" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "climate environment" ; - skos:definition "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" ; - skos:inScheme ; - nmdc:expected_value "climate name;treatment interval and duration" ; - nmdc:occurrence "m" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "cur_vegetation_meth" ; - dcterms:title "current vegetation method" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "current vegetation method" ; - skos:definition "Reference or method used in vegetation classification" ; - skos:inScheme ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "env_broad_scale" ; - dcterms:title "broad-scale environmental context" ; - rdfs:range nmdc:ControlledIdentifiedTermValue ; - rdfs:subPropertyOf ; - skos:altLabel "broad-scale environmental context" ; - skos:definition "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" ; - skos:inScheme ; - nmdc:expected_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." . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "env_local_scale" ; - dcterms:title "local environmental context" ; - rdfs:range nmdc:ControlledIdentifiedTermValue ; - rdfs:subPropertyOf ; - skos:altLabel "local environmental context" ; - skos:definition "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." ; - skos:inScheme ; - nmdc:expected_value "Environmental entities having causal influences upon the entity at time of sampling." . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "env_medium" ; - dcterms:title "environmental medium" ; - rdfs:range nmdc:ControlledIdentifiedTermValue ; - rdfs:subPropertyOf ; - skos:altLabel "environmental medium" ; - skos:definition "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)." ; - skos:inScheme ; - nmdc:expected_value "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extreme_event" ; - dcterms:title "history/extreme events" ; - rdfs:range nmdc:TimestampValue ; - rdfs:subPropertyOf ; - skos:altLabel "history/extreme events" ; - skos:definition "Unusual physical events that may have affected microbial populations" ; - skos:inScheme ; - nmdc:expected_value "date" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "fire" ; - dcterms:title "history/fire" ; - rdfs:range nmdc:TimestampValue ; - rdfs:subPropertyOf ; - skos:altLabel "history/fire" ; - skos:definition "Historical and/or physical evidence of fire" ; - skos:inScheme ; - nmdc:expected_value "date" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "flooding" ; - dcterms:title "history/flooding" ; - rdfs:range nmdc:TimestampValue ; - rdfs:subPropertyOf ; - skos:altLabel "history/flooding" ; - skos:definition "Historical and/or physical evidence of flooding" ; - skos:inScheme ; - nmdc:expected_value "date" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gaseous_environment" ; - dcterms:title "gaseous environment" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "gaseous environment" ; - skos:definition "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" ; - skos:inScheme ; - nmdc:expected_value "gaseous compound name;gaseous compound amount;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "micromole per liter" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "heavy_metals" ; - dcterms:title "extreme_unusual_properties/heavy metals" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "extreme_unusual_properties/heavy metals" ; - skos:definition "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field." ; - skos:inScheme ; - nmdc:expected_value "heavy metal name;measurement value unit" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "microgram per gram" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "heavy_metals_meth" ; - dcterms:title "extreme_unusual_properties/heavy metals method" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "extreme_unusual_properties/heavy metals method" ; - skos:definition "Reference or method used in determining heavy metals" ; - skos:inScheme ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "oxy_stat_samp" ; - dcterms:title "oxygenation status of sample" ; - rdfs:range nmdc:OxyStatSampEnum ; - rdfs:subPropertyOf ; - skos:altLabel "oxygenation status of sample" ; - skos:definition "Oxygenation status of sample" ; - skos:inScheme ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ph_meth" ; - dcterms:title "pH method" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "pH method" ; - skos:definition "Reference or method used in determining ph" ; - skos:inScheme ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "salinity_meth" ; - dcterms:title "salinity method" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "salinity method" ; - skos:definition "Reference or method used in determining salinity" ; - skos:inScheme ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "season_precpt" ; - dcterms:title "mean seasonal precipitation" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "mean seasonal precipitation" ; - skos:definition "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps." ; - skos:inScheme ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "millimeter" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "sieving" ; - dcterms:title "composite design/sieving" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "composite design/sieving" ; - skos:definition "Collection design of pooled samples and/or sieve size and amount of sample sieved" ; - skos:inScheme ; - nmdc:expected_value "design name and/or size;amount" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "slope_aspect" ; - dcterms:title "slope aspect" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "slope aspect" ; - skos:definition "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." ; - skos:inScheme ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "degree" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "slope_gradient" ; - dcterms:title "slope gradient" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "slope gradient" ; - skos:definition "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" ; - skos:inScheme ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "percentage" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "source_mat_id" ; - dcterms:title "source material identifiers" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "source material identifiers" ; - skos:definition "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)." ; - skos:inScheme ; - nmdc:expected_value "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "tot_carb" ; - dcterms:title "total carbon" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "total carbon" ; - skos:definition "Total carbon content" ; - skos:inScheme ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "tot_nitro_cont_meth" ; - dcterms:title "total nitrogen content method" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf ; - skos:altLabel "total nitrogen content method" ; - skos:definition "Reference or method used in determining the total nitrogen" ; - skos:inScheme ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "tot_nitro_content" ; - dcterms:title "total nitrogen content" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "total nitrogen content" ; - skos:definition "Total nitrogen content of the sample" ; - skos:inScheme ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter, micromole per liter, milligram per liter" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "tot_org_c_meth" ; - dcterms:title "total organic carbon method" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "total organic carbon method" ; - skos:definition "Reference or method used in determining total organic carbon" ; - skos:inScheme ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "tot_org_carb" ; - dcterms:title "total organic carbon" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "total organic carbon" ; - skos:definition "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content" ; - skos:inScheme ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "gram Carbon per kilogram sample material" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "water_cont_soil_meth" ; - dcterms:title "water content method" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf ; - skos:altLabel "water content method" ; - skos:definition "Reference or method used in determining the water content of soil" ; - skos:inScheme ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "water_content" ; - dcterms:title "water content" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "water content" ; - skos:definition "Water content measurement" ; - skos:inScheme ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "gram per gram or cubic centimeter per cubic centimeter" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "watering_regm" ; - dcterms:title "watering regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "watering regimen" ; - skos:definition "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" ; - skos:inScheme ; - nmdc:expected_value "measurement value;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "milliliter, liter" . - nmdc:AnalyticalSample a owl:Class, linkml:ClassDefinition ; rdfs:label "AnalyticalSample" ; dcterms:title "Analytical Sample" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], nmdc:MaterialEntity ; skos:inScheme nmdc:core . @@ -409,13 +41,13 @@ nmdc:BooleanValue a owl:Class, linkml:ClassDefinition ; rdfs:label "BooleanValue" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:has_boolean_value ], [ a owl:Restriction ; owl:allValuesFrom linkml:Boolean ; owl:onProperty nmdc:has_boolean_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:has_boolean_value ], nmdc:AttributeValue ; skos:definition "A value that is a boolean" ; @@ -447,34 +79,34 @@ nmdc:MetatranscriptomeAnnotationActivity a owl:Class, linkml:ClassDefinition ; rdfs:label "MetatranscriptomeAnnotationActivity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gold_analysis_project_identifiers ], - [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^gold:Ga[0-9]+$" ] ) ] ; owl:onProperty nmdc:gold_analysis_project_identifiers ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:gold_analysis_project_identifiers ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:type ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:gold_analysis_project_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:type ], nmdc:WorkflowExecutionActivity ; skos:inScheme nmdc:workflow_execution_activity . @@ -482,268 +114,268 @@ nmdc:MetatranscriptomeAssembly a owl:Class, linkml:ClassDefinition ; rdfs:label "MetatranscriptomeAssembly" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_n90 ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_bp ], + owl:onProperty nmdc:insdc_assembly_identifiers ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_pct_gt50k ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:ctg_logsum ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:contig_bp ], + owl:onProperty nmdc:ctg_l50 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_logsum ], + owl:onProperty nmdc:num_aligned_reads ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_l90 ], + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_l50 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_powsum ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:num_input_reads ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_n_gt50k ], + owl:onProperty nmdc:ctg_n90 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaffolds ], + owl:onProperty nmdc:scaf_l_gt50k ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_logsum ], + owl:onProperty nmdc:ctg_n50 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_pct_gt50k ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:contigs ], + owl:onProperty nmdc:ctg_l90 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:num_input_reads ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_l50 ], + owl:onProperty nmdc:scaf_bp ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_powsum ], + owl:onProperty nmdc:ctg_l90 ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_n90 ], + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_n50 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_n50 ], + owl:onProperty nmdc:gap_pct ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:asm_score ], + owl:onProperty nmdc:ctg_n90 ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:ctg_l50 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_bp ], + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_l_gt50k ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$" ] ) ] ; owl:onProperty nmdc:insdc_assembly_identifiers ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:insdc_assembly_identifiers ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_n90 ], + owl:minCardinality 0 ; + owl:onProperty nmdc:contigs ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:asm_score ], + owl:onProperty nmdc:scaf_l90 ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaffolds ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_powsum ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:ctg_powsum ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:gc_avg ], + owl:onProperty nmdc:gc_std ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:gap_pct ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_pct_gt50k ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:contig_bp ], + owl:onProperty nmdc:gap_pct ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_n50 ], + owl:onProperty nmdc:ctg_powsum ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:gc_avg ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:asm_score ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_l50 ], + owl:onProperty nmdc:scaf_powsum ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_l90 ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_n90 ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:ctg_max ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_logsum ], + owl:onProperty nmdc:scaf_powsum ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_logsum ], + owl:onProperty nmdc:scaf_pct_gt50k ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_l90 ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:ctg_n50 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_max ], + owl:onProperty nmdc:ctg_l90 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:gap_pct ], + owl:onProperty nmdc:asm_score ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:scaf_l50 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_l90 ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:num_input_reads ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_max ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_n50 ], + owl:onProperty nmdc:scaf_n90 ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:scaf_l50 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_n_gt50k ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:gc_std ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:insdc_assembly_identifiers ], + owl:onProperty nmdc:scaf_bp ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gc_std ], + owl:onProperty nmdc:scaffolds ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:num_aligned_reads ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_logsum ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty nmdc:contigs ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_l50 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_l_gt50k ], + owl:onProperty nmdc:scaf_max ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaffolds ], + owl:onProperty nmdc:contig_bp ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_bp ], + owl:onProperty nmdc:scaf_n90 ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:ctg_powsum ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_l_gt50k ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:num_aligned_reads ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:scaffolds ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_max ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:gc_avg ], + owl:onProperty nmdc:num_input_reads ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:contig_bp ], + owl:onProperty nmdc:scaf_l90 ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_n90 ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:scaffolds ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_l_gt50k ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:num_aligned_reads ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_max ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty nmdc:asm_score ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_l_gt50k ], + owl:onProperty nmdc:scaf_n50 ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:ctg_n90 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_logsum ], + owl:onProperty nmdc:gc_avg ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_l90 ], + owl:onProperty nmdc:contig_bp ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:scaf_max ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_n50 ], + owl:onProperty nmdc:scaf_n_gt50k ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gap_pct ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:num_input_reads ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:num_aligned_reads ], + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_n_gt50k ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:num_input_reads ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:gc_avg ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_powsum ], + owl:onProperty nmdc:scaf_bp ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_l90 ], + owl:onProperty nmdc:ctg_max ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:gap_pct ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:ctg_logsum ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:contigs ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:ctg_n50 ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_pct_gt50k ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_max ], + owl:onProperty nmdc:scaf_n50 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_powsum ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_l90 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:contigs ], + owl:onProperty nmdc:gc_avg ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:gc_std ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty nmdc:insdc_assembly_identifiers ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:ctg_max ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_n_gt50k ], + owl:onProperty nmdc:scaf_logsum ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:ctg_logsum ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_logsum ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_n50 ], + owl:onProperty nmdc:scaf_logsum ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:scaf_n90 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:minCardinality 0 ; + owl:onProperty nmdc:gc_std ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_pct_gt50k ], + owl:onProperty nmdc:contig_bp ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:ctg_l50 ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:scaf_n_gt50k ], nmdc:WorkflowExecutionActivity ; skos:inScheme nmdc:workflow_execution_activity . @@ -760,11 +392,11 @@ nmdc:ProteinQuantification a owl:Class, linkml:ClassDefinition ; rdfs:label "ProteinQuantification" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 0 ; owl:onProperty nmdc:all_proteins ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:peptide_sequence_count ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:protein_sum_masic_abundance ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:protein_spectral_count ], @@ -772,35 +404,35 @@ nmdc:ProteinQuantification a owl:Class, owl:allValuesFrom linkml:Integer ; owl:onProperty nmdc:peptide_sequence_count ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:protein_spectral_count ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:protein_sum_masic_abundance ], + owl:allValuesFrom nmdc:GeneProduct ; + owl:onProperty nmdc:best_protein ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:protein_sum_masic_abundance ], + owl:minCardinality 0 ; + owl:onProperty nmdc:best_protein ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:peptide_sequence_count ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:best_protein ], + owl:allValuesFrom nmdc:GeneProduct ; + owl:onProperty nmdc:all_proteins ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:best_protein ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:protein_spectral_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:best_protein ], + owl:onProperty nmdc:protein_sum_masic_abundance ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:protein_sum_masic_abundance ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:protein_spectral_count ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:protein_sum_masic_abundance ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:best_protein ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:all_proteins ] ; + owl:onProperty nmdc:peptide_sequence_count ] ; skos:definition "This is used to link a metaproteomics analysis workflow to a specific protein" ; skos:inScheme nmdc:core . @@ -999,10 +631,10 @@ nmdc:Pathway a owl:Class, linkml:ClassDefinition ; rdfs:label "Pathway" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:Reaction ; + owl:minCardinality 1 ; owl:onProperty nmdc:has_part ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom nmdc:Reaction ; owl:onProperty nmdc:has_part ], nmdc:FunctionalAnnotationTerm ; skos:altLabel "biological process", @@ -1135,6 +767,19 @@ EFO:0001741 a owl:Class, nmdc:occurrence "m" ; nmdc:preferred_unit "micrograms per cubic meter" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "air_temp_regm" ; + dcterms:title "air temperature regimen" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "air temperature regimen" ; + skos:definition "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" ; + skos:inScheme ; + nmdc:expected_value "temperature value;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "meter" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "antibiotic_regm" ; @@ -1210,6 +855,18 @@ EFO:0001741 a owl:Class, nmdc:occurrence "m" ; nmdc:preferred_unit "milligram per liter" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "climate_environment" ; + dcterms:title "climate environment" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "climate environment" ; + skos:definition "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" ; + skos:inScheme ; + nmdc:expected_value "climate name;treatment interval and duration" ; + nmdc:occurrence "m" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "diether_lipids" ; @@ -1274,6 +931,19 @@ EFO:0001741 a owl:Class, nmdc:occurrence "m" ; nmdc:preferred_unit "gram, mole per liter, milligram per liter" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "gaseous_environment" ; + dcterms:title "gaseous environment" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "gaseous environment" ; + skos:definition "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" ; + skos:inScheme ; + nmdc:expected_value "gaseous compound name;gaseous compound amount;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "micromole per liter" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "gaseous_substances" ; @@ -1325,6 +995,31 @@ EFO:0001741 a owl:Class, nmdc:expected_value "enumeration" ; nmdc:occurrence "m" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "heavy_metals" ; + dcterms:title "extreme_unusual_properties/heavy metals" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "extreme_unusual_properties/heavy metals" ; + skos:definition "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field." ; + skos:inScheme ; + nmdc:expected_value "heavy metal name;measurement value unit" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "microgram per gram" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "heavy_metals_meth" ; + dcterms:title "extreme_unusual_properties/heavy metals method" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "extreme_unusual_properties/heavy metals method" ; + skos:definition "Reference or method used in determining heavy metals" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "herbicide_regm" ; @@ -1398,6 +1093,19 @@ EFO:0001741 a owl:Class, nmdc:expected_value "species name or common name" ; nmdc:occurrence "m" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "humidity_regm" ; + dcterms:title "humidity regimen" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "humidity regimen" ; + skos:definition "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" ; + skos:inScheme ; + nmdc:expected_value "humidity value;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram per cubic meter" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "inorg_particles" ; @@ -1764,6 +1472,19 @@ EFO:0001741 a owl:Class, nmdc:occurrence "m" ; nmdc:preferred_unit "microgram per cubic meter, parts per million, nanogram per liter" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "water_content" ; + dcterms:title "water content" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "water content" ; + skos:definition "Water content measurement" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "gram per gram or cubic centimeter per cubic centimeter" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "water_temp_regm" ; @@ -1777,6 +1498,19 @@ EFO:0001741 a owl:Class, nmdc:occurrence "m" ; nmdc:preferred_unit "degree Celsius" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "watering_regm" ; + dcterms:title "watering regimen" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "watering regimen" ; + skos:definition "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" ; + skos:inScheme ; + nmdc:expected_value "measurement value;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "milliliter, liter" . + a owl:Class, nmdc:AnalysisTypeEnum ; rdfs:label "metabolomics" ; @@ -3122,6 +2856,81 @@ EFO:0001741 a owl:Class, rdfs:label "protein" ; rdfs:subClassOf nmdc:ExtractionTargetEnum . + a owl:Class, + nmdc:FailureWhatEnum ; + rdfs:label "assembly_size_too_small" ; + rdfs:subClassOf nmdc:FailureWhatEnum . + + a owl:Class, + nmdc:FailureWhatEnum ; + rdfs:label "low_read_count" ; + rdfs:subClassOf nmdc:FailureWhatEnum . + + a owl:Class, + nmdc:FailureWhatEnum ; + rdfs:label "malformed_data" ; + rdfs:subClassOf nmdc:FailureWhatEnum . + + a owl:Class, + nmdc:FailureWhatEnum ; + rdfs:label "no_valid_data_generated" ; + rdfs:subClassOf nmdc:FailureWhatEnum . + + a owl:Class, + nmdc:FailureWhatEnum ; + rdfs:label "other" ; + rdfs:subClassOf nmdc:FailureWhatEnum . + + a owl:Class, + nmdc:FailureWhereEnum ; + rdfs:label "Extraction" ; + rdfs:subClassOf nmdc:FailureWhereEnum . + + a owl:Class, + nmdc:FailureWhereEnum ; + rdfs:label "LibraryPreparation" ; + rdfs:subClassOf nmdc:FailureWhereEnum . + + a owl:Class, + nmdc:FailureWhereEnum ; + rdfs:label "MagsAnalysisActivity" ; + rdfs:subClassOf nmdc:FailureWhereEnum . + + a owl:Class, + nmdc:FailureWhereEnum ; + rdfs:label "MetagenomeAnnotationActivity" ; + rdfs:subClassOf nmdc:FailureWhereEnum . + + a owl:Class, + nmdc:FailureWhereEnum ; + rdfs:label "MetagenomeAssembly" ; + rdfs:subClassOf nmdc:FailureWhereEnum . + + a owl:Class, + nmdc:FailureWhereEnum ; + rdfs:label "MetatranscriptomeActivity" ; + rdfs:subClassOf nmdc:FailureWhereEnum . + + a owl:Class, + nmdc:FailureWhereEnum ; + rdfs:label "OmicsProcessing" ; + rdfs:subClassOf nmdc:FailureWhereEnum . + + a owl:Class, + nmdc:FailureWhereEnum ; + rdfs:label "Pooling" ; + rdfs:subClassOf nmdc:FailureWhereEnum . + + a owl:Class, + nmdc:FailureWhereEnum ; + rdfs:label "ReadBasedTaxonomyAnalysisActivity" ; + rdfs:subClassOf nmdc:FailureWhereEnum . + + a owl:Class, + nmdc:FailureWhereEnum ; + rdfs:label "ReadQcAnalysisActivity" ; + rdfs:subClassOf nmdc:FailureWhereEnum . + a owl:Class, nmdc:FaoClassEnum ; rdfs:label "Acrisols" ; @@ -4466,277 +4275,277 @@ nmdc:MetagenomeAssembly a owl:Class, linkml:ClassDefinition ; rdfs:label "MetagenomeAssembly" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_powsum ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_n50 ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:scaffolds ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_l90 ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:ctg_l90 ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_n_gt50k ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:ctg_powsum ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:contigs ], + owl:onProperty nmdc:scaf_pct_gt50k ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_l90 ], + owl:onProperty nmdc:asm_score ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_n90 ], + owl:onProperty nmdc:num_input_reads ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:ctg_max ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:gap_pct ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_n_gt50k ], + owl:onProperty nmdc:scaffolds ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaffolds ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_bp ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_pct_gt50k ], + owl:onProperty nmdc:scaf_n_gt50k ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:num_aligned_reads ], + owl:onProperty nmdc:scaf_bp ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_n90 ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:scaf_n_gt50k ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:asm_score ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_l90 ], + owl:onProperty nmdc:scaf_l_gt50k ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gc_avg ], + owl:onProperty nmdc:num_aligned_reads ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_l90 ], + owl:onProperty nmdc:scaffolds ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_max ], + owl:onProperty nmdc:ctg_l90 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_l90 ], + owl:onProperty nmdc:num_input_reads ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_powsum ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_logsum ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:ctg_n90 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:ctg_l50 ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_n50 ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_logsum ], + owl:onProperty nmdc:contig_bp ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_n90 ], + owl:onProperty nmdc:scaf_max ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaffolds ], + owl:onProperty nmdc:scaf_logsum ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:gap_pct ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_max ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:contig_bp ], + owl:onProperty nmdc:scaf_l90 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_powsum ], + owl:minCardinality 0 ; + owl:onProperty nmdc:ctg_n90 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_l50 ], + owl:onProperty nmdc:scaf_n_gt50k ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:scaf_n50 ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_max ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:ctg_logsum ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:asm_score ], + owl:onProperty nmdc:scaf_logsum ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:ctg_n50 ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_max ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_powsum ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_pct_gt50k ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_l50 ], + owl:onProperty nmdc:insdc_assembly_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_bp ], + owl:minCardinality 0 ; + owl:onProperty nmdc:contigs ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_n50 ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:gc_std ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:onProperty nmdc:gc_avg ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:num_input_reads ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_l_gt50k ], + owl:onProperty nmdc:gap_pct ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:num_aligned_reads ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:contigs ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:insdc_assembly_identifiers ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:gc_std ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gc_std ], + owl:onProperty nmdc:ctg_logsum ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gc_std ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:ctg_max ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_max ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_l50 ], + owl:onProperty nmdc:ctg_powsum ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_logsum ], + owl:onProperty nmdc:num_aligned_reads ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_l_gt50k ], + owl:onProperty nmdc:ctg_n90 ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:scaf_powsum ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:contig_bp ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:num_input_reads ], + owl:onProperty nmdc:ctg_max ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:asm_score ], + owl:onProperty nmdc:scaf_l50 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_n90 ], + owl:onProperty nmdc:gc_avg ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_bp ], + owl:onProperty nmdc:gc_avg ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_l_gt50k ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:scaf_max ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:gc_avg ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:asm_score ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:contig_bp ], + owl:onProperty nmdc:num_aligned_reads ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; + owl:minCardinality 0 ; owl:onProperty nmdc:scaf_l50 ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_l50 ], + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_powsum ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:gc_std ], + owl:onProperty nmdc:scaf_n90 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:gap_pct ], + owl:onProperty nmdc:ctg_l50 ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:asm_score ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gap_pct ], + owl:onProperty nmdc:ctg_l90 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_n50 ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_n90 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:contigs ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_max ], + owl:minCardinality 0 ; + owl:onProperty nmdc:gc_std ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_pct_gt50k ], + owl:onProperty nmdc:scaf_l90 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_max ], + owl:onProperty nmdc:gap_pct ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_logsum ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:contig_bp ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_powsum ], + owl:onProperty nmdc:scaf_bp ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_powsum ], + owl:onProperty nmdc:scaf_l50 ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:insdc_assembly_identifiers ], + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_l_gt50k ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:num_aligned_reads ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:onProperty nmdc:scaf_n50 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_n_gt50k ], + owl:onProperty nmdc:ctg_l50 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_n90 ], + owl:onProperty nmdc:ctg_powsum ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:contig_bp ], + owl:onProperty nmdc:num_input_reads ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:gc_avg ], + owl:onProperty nmdc:scaf_l90 ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$" ] ) ] ; + owl:onProperty nmdc:insdc_assembly_identifiers ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:num_input_reads ], + owl:onProperty nmdc:ctg_logsum ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:scaf_n50 ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:scaf_l_gt50k ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaffolds ], + owl:onProperty nmdc:ctg_n50 ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:scaf_logsum ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:contigs ], + owl:onProperty nmdc:insdc_assembly_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_n90 ], + owl:onProperty nmdc:scaf_pct_gt50k ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_bp ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:ctg_n50 ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$" ] ) ] ; - owl:onProperty nmdc:insdc_assembly_identifiers ], + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_n90 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_logsum ], + owl:onProperty nmdc:scaf_pct_gt50k ], nmdc:WorkflowExecutionActivity ; skos:definition "A workflow execution activity that converts sequencing reads into an assembled metagenome." ; skos:inScheme nmdc:workflow_execution_activity ; @@ -4747,13 +4556,13 @@ nmdc:MetagenomeSequencingActivity a owl:Class, rdfs:label "MetagenomeSequencingActivity" ; dcterms:title "Metagenome sequencing activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:maxCardinality 1 ; owl:onProperty nmdc:id ], nmdc:WorkflowExecutionActivity ; skos:definition "Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data." ; @@ -4763,23 +4572,23 @@ nmdc:MetatranscriptomeActivity a owl:Class, linkml:ClassDefinition ; rdfs:label "MetatranscriptomeActivity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 0 ; owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], nmdc:WorkflowExecutionActivity ; skos:definition "A metatranscriptome activity that e.g. pools assembly and annotation activity." ; skos:inScheme nmdc:workflow_execution_activity . @@ -4790,19 +4599,19 @@ nmdc:MixingProcess a owl:Class, dcterms:contributor ORCID:0000-0002-8683-0050, ORCID:0009-0001-1555-1601 ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom [ owl:unionOf ( nmdc:Biosample nmdc:ProcessedSample ) ] ; owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty nmdc:duration ], [ a owl:Restriction ; - owl:allValuesFrom [ owl:unionOf ( nmdc:Biosample nmdc:ProcessedSample ) ] ; + owl:minCardinality 0 ; owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; + owl:maxCardinality 1 ; owl:onProperty nmdc:duration ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:duration ], [ a owl:Restriction ; owl:minCardinality 0 ; @@ -4822,32 +4631,32 @@ nmdc:NomAnalysisActivity a owl:Class, linkml:ClassDefinition ; rdfs:label "NomAnalysisActivity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:used ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:has_calibration ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:maxCardinality 1 ; owl:onProperty nmdc:has_calibration ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:used ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:used ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_calibration ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_calibration ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:used ], nmdc:WorkflowExecutionActivity ; skos:inScheme nmdc:workflow_execution_activity . @@ -4905,26 +4714,32 @@ nmdc:PeptideQuantification a owl:Class, linkml:ClassDefinition ; rdfs:label "PeptideQuantification" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:min_q_value ], + owl:allValuesFrom nmdc:GeneProduct ; + owl:onProperty nmdc:best_protein ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:peptide_sequence ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:peptide_spectral_count ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:peptide_sum_masic_abundance ], + owl:allValuesFrom nmdc:GeneProduct ; + owl:onProperty nmdc:all_proteins ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:peptide_sequence ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:GeneProduct ; - owl:onProperty nmdc:best_protein ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:peptide_spectral_count ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:min_q_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:peptide_sequence ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:peptide_sum_masic_abundance ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:peptide_sum_masic_abundance ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:min_q_value ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:peptide_spectral_count ], @@ -4932,29 +4747,23 @@ nmdc:PeptideQuantification a owl:Class, owl:minCardinality 0 ; owl:onProperty nmdc:best_protein ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:peptide_sum_masic_abundance ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:min_q_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:all_proteins ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:peptide_sequence ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:GeneProduct ; - owl:onProperty nmdc:all_proteins ], + owl:minCardinality 0 ; + owl:onProperty nmdc:peptide_sum_masic_abundance ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:best_protein ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:peptide_sum_masic_abundance ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:peptide_spectral_count ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:min_q_value ], + owl:minCardinality 0 ; + owl:onProperty nmdc:peptide_sequence ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:peptide_spectral_count ] ; + owl:minCardinality 0 ; + owl:onProperty nmdc:all_proteins ] ; skos:definition "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information" ; skos:inScheme nmdc:core . @@ -5177,23 +4986,23 @@ nmdc:Protocol a owl:Class, linkml:ClassDefinition ; rdfs:label "Protocol" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:name ], + [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:url ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:name ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:url ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:name ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:url ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:url ] ; + owl:onProperty nmdc:name ] ; skos:inScheme nmdc:nmdc . a owl:Class, @@ -5221,23 +5030,23 @@ nmdc:ReadBasedTaxonomyAnalysisActivity a owl:Class, rdfs:label "ReadBasedTaxonomyAnalysisActivity" ; dcterms:title "Read based analysis activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], nmdc:WorkflowExecutionActivity ; skos:definition "A workflow execution activity that performs taxonomy classification using sequencing reads" ; skos:inScheme nmdc:workflow_execution_activity . @@ -5247,86 +5056,86 @@ nmdc:ReadQcAnalysisActivity a owl:Class, rdfs:label "ReadQcAnalysisActivity" ; dcterms:title "Read quality control analysis activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; + owl:maxCardinality 1 ; owl:onProperty nmdc:input_base_count ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:input_read_bases ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:output_read_count ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:input_base_count ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:input_read_bases ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:maxCardinality 1 ; owl:onProperty nmdc:version ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:output_base_count ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:output_read_count ], + owl:onProperty nmdc:output_read_bases ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:input_read_bases ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:input_read_count ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:input_base_count ], + owl:onProperty nmdc:output_read_bases ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:input_base_count ], + owl:onProperty nmdc:input_read_count ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:maxCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:output_read_count ], + owl:minCardinality 0 ; + owl:onProperty nmdc:input_base_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:input_read_count ], + owl:onProperty nmdc:output_read_count ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:input_read_bases ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:version ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:input_read_count ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:output_base_count ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:input_read_bases ], + owl:minCardinality 0 ; + owl:onProperty nmdc:version ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:output_read_bases ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:output_read_bases ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:version ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:input_read_count ], + owl:onProperty nmdc:output_read_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:output_read_bases ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:output_base_count ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:output_base_count ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:input_read_bases ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:version ], nmdc:WorkflowExecutionActivity ; skos:definition "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" ; skos:inScheme nmdc:workflow_execution_activity . @@ -6021,14 +5830,14 @@ nmdc:Site a owl:Class, rdfs:label "Site" ; dcterms:title "Site" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], nmdc:MaterialEntity ; skos:inScheme nmdc:core ; skos:note "BCO sample collection site ?" . @@ -6406,62 +6215,62 @@ nmdc:SubSamplingProcess a owl:Class, ORCID:0009-0001-1555-1601, ORCID:0009-0008-4013-7737 ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:contained_in ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:temperature ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:container_size ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty nmdc:volume ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:mass ], + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:ContainerCategoryEnum ; owl:onProperty nmdc:contained_in ], [ a owl:Restriction ; owl:allValuesFrom [ owl:unionOf ( nmdc:Biosample nmdc:ProcessedSample ) ] ; owl:onProperty nmdc:has_input ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:mass ], + owl:onProperty nmdc:volume ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ContainerCategoryEnum ; - owl:onProperty nmdc:contained_in ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:temperature ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:container_size ], + owl:minCardinality 0 ; + owl:onProperty nmdc:contained_in ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:volume ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:container_size ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:mass ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:has_input ], + owl:onProperty nmdc:temperature ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:volume ], + owl:onProperty nmdc:mass ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; + owl:maxCardinality 1 ; owl:onProperty nmdc:container_size ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:mass ], + owl:minCardinality 0 ; + owl:onProperty nmdc:has_output ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; + owl:minCardinality 0 ; + owl:onProperty nmdc:container_size ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:temperature ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:mass ], [ a owl:Restriction ; owl:allValuesFrom nmdc:ProcessedSample ; owl:onProperty nmdc:has_output ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:temperature ], nmdc:PlannedProcess ; skos:definition """Separating a sample aliquot from the starting material for downstream activity. """ ; @@ -7315,6 +7124,19 @@ nmdc:has_solution_components a owl:ObjectProperty, skos:definition "Relationship from a Solution to one or more constituent solution components" ; skos:inScheme nmdc:nmdc . +nmdc:infiltrations a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "infiltrations" ; + rdfs:range [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$" ] ) ] ) ] ; + rdfs:seeAlso ; + skos:altLabel "infiltration_1", + "infiltration_2" ; + skos:definition "The amount of time it takes to complete each infiltration activity" ; + skos:inScheme nmdc:nmdc . + nmdc:left_participants a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "left_participants" ; @@ -7389,13 +7211,6 @@ nmdc:study_image a owl:ObjectProperty, skos:definition "Links a study to one or more images." ; skos:inScheme nmdc:nmdc . -nmdc:unit a owl:Class, - linkml:TypeDefinition ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onDataRange nmdc:unit ; - owl:onProperty linkml:topValue ; - owl:qualifiedCardinality 1 ] . - a owl:Class, nmdc:BiosampleCategoryEnum ; rdfs:label "NEON" ; @@ -7487,6 +7302,31 @@ nmdc:unit a owl:Class, nmdc:occurrence "1" ; nmdc:preferred_unit "degree Celsius" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "al_sat" ; + dcterms:title "extreme_unusual_properties/Al saturation" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "extreme_unusual_properties/Al saturation" ; + skos:definition "Aluminum saturation (esp. For tropical soils)" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "percentage" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "al_sat_meth" ; + dcterms:title "extreme_unusual_properties/Al saturation method" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "extreme_unusual_properties/Al saturation method" ; + skos:definition "Reference or method used in determining Al saturation" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or URL" ; + nmdc:occurrence "1" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "alkalinity" ; @@ -7581,11 +7421,24 @@ nmdc:unit a owl:Class, dcterms:title "ancestral data" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "ancestral data" ; - skos:definition "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)" ; + skos:altLabel "ancestral data" ; + skos:definition "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)" ; + skos:inScheme ; + nmdc:expected_value "free text" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "annual_precpt" ; + dcterms:title "mean annual precipitation" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "mean annual precipitation" ; + skos:definition "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps." ; skos:inScheme ; - nmdc:expected_value "free text" ; - nmdc:occurrence "1" . + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "millimeter" . a owl:ObjectProperty, linkml:SlotDefinition ; @@ -7840,6 +7693,29 @@ nmdc:unit a owl:Class, nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "biotic_regm" ; + dcterms:title "biotic regimen" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "biotic regimen" ; + skos:definition "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi." ; + skos:inScheme ; + nmdc:expected_value "free text" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "biotic_relationship" ; + dcterms:title "observed biotic relationship" ; + rdfs:range nmdc:BioticRelationshipEnum ; + rdfs:subPropertyOf ; + skos:altLabel "observed biotic relationship" ; + skos:definition "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" ; + skos:inScheme ; + nmdc:expected_value "enumeration" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "bishomohopanol" ; @@ -8238,16 +8114,16 @@ nmdc:unit a owl:Class, nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "cur_vegetation" ; - dcterms:title "current vegetation" ; + rdfs:label "cur_vegetation_meth" ; + dcterms:title "current vegetation method" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "current vegetation" ; - skos:definition "Vegetation classification from one or more standard classification systems, or agricultural crop" ; + skos:altLabel "current vegetation method" ; + skos:definition "Reference or method used in vegetation classification" ; skos:inScheme ; - nmdc:expected_value "current vegetation type" ; + nmdc:expected_value "PMID,DOI or url" ; nmdc:occurrence "1" . a owl:ObjectProperty, @@ -8624,17 +8500,6 @@ nmdc:unit a owl:Class, nmdc:occurrence "1" ; nmdc:preferred_unit "micromole per liter" . - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "elev" ; - dcterms:title "elevation" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "elevation" ; - skos:definition "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." ; - skos:inScheme ; - nmdc:expected_value "measurement value" . - a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "elevator" ; @@ -8647,6 +8512,39 @@ nmdc:unit a owl:Class, nmdc:expected_value "value" ; nmdc:occurrence "1" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "env_broad_scale" ; + dcterms:title "broad-scale environmental context" ; + rdfs:range nmdc:ControlledIdentifiedTermValue ; + rdfs:subPropertyOf ; + skos:altLabel "broad-scale environmental context" ; + skos:definition "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" ; + skos:inScheme ; + nmdc:expected_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." . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "env_local_scale" ; + dcterms:title "local environmental context" ; + rdfs:range nmdc:ControlledIdentifiedTermValue ; + rdfs:subPropertyOf ; + skos:altLabel "local environmental context" ; + skos:definition "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." ; + skos:inScheme ; + nmdc:expected_value "Environmental entities having causal influences upon the entity at time of sampling." . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "env_medium" ; + dcterms:title "environmental medium" ; + rdfs:range nmdc:ControlledIdentifiedTermValue ; + rdfs:subPropertyOf ; + skos:altLabel "environmental medium" ; + skos:definition "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)." ; + skos:inScheme ; + nmdc:expected_value "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "escalator" ; @@ -8697,6 +8595,17 @@ nmdc:unit a owl:Class, nmdc:expected_value "measurement value" ; nmdc:occurrence "1" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "experimental_factor" ; + dcterms:title "experimental factor" ; + rdfs:range nmdc:ControlledTermValue ; + rdfs:subPropertyOf ; + skos:altLabel "experimental factor" ; + skos:definition "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" ; + skos:inScheme ; + nmdc:expected_value "text or EFO and/or OBI" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "ext_door" ; @@ -8733,6 +8642,18 @@ nmdc:unit a owl:Class, nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "extreme_event" ; + dcterms:title "history/extreme events" ; + rdfs:range nmdc:TimestampValue ; + rdfs:subPropertyOf ; + skos:altLabel "history/extreme events" ; + skos:definition "Unusual physical events that may have affected microbial populations" ; + skos:inScheme ; + nmdc:expected_value "date" ; + nmdc:occurrence "1" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "fao_class" ; @@ -8757,6 +8678,18 @@ nmdc:unit a owl:Class, nmdc:expected_value "name" ; nmdc:occurrence "1" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "fire" ; + dcterms:title "history/fire" ; + rdfs:range nmdc:TimestampValue ; + rdfs:subPropertyOf ; + skos:altLabel "history/fire" ; + skos:definition "Historical and/or physical evidence of fire" ; + skos:inScheme ; + nmdc:expected_value "date" ; + nmdc:occurrence "1" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "fireplace_type" ; @@ -8769,6 +8702,18 @@ nmdc:unit a owl:Class, nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "flooding" ; + dcterms:title "history/flooding" ; + rdfs:range nmdc:TimestampValue ; + rdfs:subPropertyOf ; + skos:altLabel "history/flooding" ; + skos:definition "Historical and/or physical evidence of flooding" ; + skos:inScheme ; + nmdc:expected_value "date" ; + nmdc:occurrence "1" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "floor_age" ; @@ -8966,6 +8911,18 @@ nmdc:unit a owl:Class, nmdc:expected_value "gravidity status;timestamp" ; nmdc:occurrence "1" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "growth_facil" ; + dcterms:title "growth facility" ; + rdfs:range nmdc:ControlledTermValue ; + rdfs:subPropertyOf ; + skos:altLabel "growth facility" ; + skos:definition "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" ; + skos:inScheme ; + nmdc:expected_value "free text or CO" ; + nmdc:occurrence "1" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "growth_habit" ; @@ -9387,6 +9344,19 @@ nmdc:unit a owl:Class, nmdc:expected_value "substrate name" ; nmdc:occurrence "1" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "host_taxid" ; + dcterms:title "host taxid" ; + rdfs:range nmdc:ControlledIdentifiedTermValue ; + rdfs:subPropertyOf ; + skos:altLabel "host taxid" ; + skos:definition "NCBI taxon id of the host, e.g. 9606" ; + skos:inScheme ; + skos:note "Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value" ; + nmdc:expected_value "NCBI taxon identifier" ; + nmdc:occurrence "1" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "host_tot_mass" ; @@ -9525,17 +9495,6 @@ nmdc:unit a owl:Class, nmdc:expected_value "timestamp" ; nmdc:occurrence "1" . - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "lat_lon" ; - dcterms:title "geographic location (latitude and longitude)" ; - rdfs:range nmdc:GeolocationValue ; - rdfs:subPropertyOf ; - skos:altLabel "geographic location (latitude and longitude)" ; - skos:definition "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system" ; - skos:inScheme ; - nmdc:expected_value "decimal degrees, limit to 8 decimal points" . - a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "light_intensity" ; @@ -9549,6 +9508,19 @@ nmdc:unit a owl:Class, nmdc:occurrence "1" ; nmdc:preferred_unit "lux" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "light_regm" ; + dcterms:title "light regimen" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "light regimen" ; + skos:definition "Information about treatment(s) involving exposure to light, including both light intensity and quality." ; + skos:inScheme ; + nmdc:expected_value "exposure type;light intensity;light quality" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "lux; micrometer, nanometer, angstrom" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "link_addit_analys" ; @@ -9886,6 +9858,18 @@ nmdc:unit a owl:Class, nmdc:occurrence "1" ; nmdc:preferred_unit "meter" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "oxy_stat_samp" ; + dcterms:title "oxygenation status of sample" ; + rdfs:range nmdc:OxyStatSampEnum ; + rdfs:subPropertyOf ; + skos:altLabel "oxygenation status of sample" ; + skos:definition "Oxygenation status of sample" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "oxygen" ; @@ -9963,6 +9947,31 @@ nmdc:unit a owl:Class, nmdc:expected_value "measurement value" ; nmdc:occurrence "1" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "ph_meth" ; + dcterms:title "pH method" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "pH method" ; + skos:definition "Reference or method used in determining ph" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "phosphate" ; + dcterms:title "phosphate" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "phosphate" ; + skos:definition "Concentration of phosphate" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "photon_flux" ; @@ -10636,6 +10645,18 @@ nmdc:unit a owl:Class, nmdc:occurrence "1" ; nmdc:preferred_unit "practical salinity unit, percentage" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "salinity_meth" ; + dcterms:title "salinity method" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "salinity method" ; + skos:definition "Reference or method used in determining salinity" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "samp_capt_status" ; @@ -10659,6 +10680,17 @@ nmdc:unit a owl:Class, skos:inScheme ; nmdc:expected_value "device name" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "samp_collec_method" ; + dcterms:title "sample collection method" ; + rdfs:range linkml:String ; + rdfs:subPropertyOf ; + skos:altLabel "sample collection method" ; + skos:definition "The method employed for collecting the sample." ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI,url , or text" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "samp_collect_point" ; @@ -10754,8 +10786,20 @@ nmdc:unit a owl:Class, skos:altLabel "sampling room ID or name" ; skos:definition "Sampling room number. This ID should be consistent with the designations on the building floor plans" ; skos:inScheme ; - nmdc:expected_value "value" ; - nmdc:occurrence "1" . + nmdc:expected_value "value" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "samp_size" ; + dcterms:title "amount or size of sample collected" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "amount or size of sample collected" ; + skos:definition "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected." ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:preferred_unit "millliter, gram, milligram, liter" . a owl:ObjectProperty, linkml:SlotDefinition ; @@ -10918,6 +10962,19 @@ nmdc:unit a owl:Class, nmdc:expected_value "NCIT:C94729" ; nmdc:occurrence "1" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "season_precpt" ; + dcterms:title "mean seasonal precipitation" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "mean seasonal precipitation" ; + skos:definition "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps." ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "millimeter" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "season_temp" ; @@ -11039,6 +11096,18 @@ nmdc:unit a owl:Class, nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "sieving" ; + dcterms:title "composite design/sieving" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "composite design/sieving" ; + skos:definition "Collection design of pooled samples and/or sieve size and amount of sample sieved" ; + skos:inScheme ; + nmdc:expected_value "design name and/or size;amount" ; + nmdc:occurrence "1" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "silicate" ; @@ -11089,6 +11158,32 @@ nmdc:unit a owl:Class, nmdc:occurrence "1" ; nmdc:preferred_unit "micrometer" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "slope_aspect" ; + dcterms:title "slope aspect" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "slope aspect" ; + skos:definition "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." ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "degree" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "slope_gradient" ; + dcterms:title "slope gradient" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "slope gradient" ; + skos:definition "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" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "percentage" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "sludge_retent_time" ; @@ -11189,6 +11284,17 @@ nmdc:unit a owl:Class, nmdc:occurrence "1" ; nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "source_mat_id" ; + dcterms:title "source material identifiers" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "source material identifiers" ; + skos:definition "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)." ; + skos:inScheme ; + nmdc:expected_value "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "space_typ_state" ; @@ -11488,6 +11594,19 @@ nmdc:unit a owl:Class, nmdc:occurrence "1" ; nmdc:preferred_unit "milligram per liter, parts per million" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "tot_carb" ; + dcterms:title "total carbon" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "total carbon" ; + skos:definition "Total carbon content" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "microgram per liter" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "tot_depth_water_col" ; @@ -11553,6 +11672,56 @@ nmdc:unit a owl:Class, nmdc:occurrence "1" ; nmdc:preferred_unit "microgram per liter, micromole per liter, milligram per liter" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "tot_nitro_cont_meth" ; + dcterms:title "total nitrogen content method" ; + rdfs:range linkml:String ; + rdfs:subPropertyOf ; + skos:altLabel "total nitrogen content method" ; + skos:definition "Reference or method used in determining the total nitrogen" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "tot_nitro_content" ; + dcterms:title "total nitrogen content" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "total nitrogen content" ; + skos:definition "Total nitrogen content of the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "microgram per liter, micromole per liter, milligram per liter" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "tot_org_c_meth" ; + dcterms:title "total organic carbon method" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "total organic carbon method" ; + skos:definition "Reference or method used in determining total organic carbon" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "tot_org_carb" ; + dcterms:title "total organic carbon" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "total organic carbon" ; + skos:definition "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "gram Carbon per kilogram sample material" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "tot_part_carb" ; @@ -11891,6 +12060,18 @@ nmdc:unit a owl:Class, nmdc:expected_value "wastewater type name" ; nmdc:occurrence "1" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "water_cont_soil_meth" ; + dcterms:title "water content method" ; + rdfs:range linkml:String ; + rdfs:subPropertyOf ; + skos:altLabel "water content method" ; + skos:definition "Reference or method used in determining the water content of soil" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . + a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "water_current" ; @@ -12154,31 +12335,31 @@ nmdc:FunctionalAnnotationAggMember a owl:Class, linkml:ClassDefinition ; rdfs:label "FunctionalAnnotationAggMember" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:count ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:gene_function_id ], - [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty nmdc:gene_function_id ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:metagenome_annotation_id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:count ], + owl:onProperty nmdc:gene_function_id ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty nmdc:count ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty nmdc:gene_function_id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:WorkflowExecutionActivity ; owl:onProperty nmdc:metagenome_annotation_id ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; owl:onProperty nmdc:count ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WorkflowExecutionActivity ; + owl:minCardinality 1 ; + owl:onProperty nmdc:count ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty nmdc:metagenome_annotation_id ] ; skos:inScheme nmdc:nmdc . @@ -12195,32 +12376,32 @@ nmdc:ImageValue a owl:Class, linkml:ClassDefinition ; rdfs:label "ImageValue" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:description ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:display_order ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:url ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:description ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; owl:onProperty nmdc:display_order ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:maxCardinality 1 ; owl:onProperty nmdc:description ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:url ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:description ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:display_order ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:url ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:description ], nmdc:AttributeValue ; skos:definition "An attribute value representing an image." ; skos:inScheme nmdc:core . @@ -12230,74 +12411,74 @@ nmdc:MagsAnalysisActivity a owl:Class, rdfs:label "MagsAnalysisActivity" ; dcterms:title "Metagenome-Assembled Genome analysis activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:unbinned_contig_num ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:too_short_contig_num ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:low_depth_contig_num ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:too_short_contig_num ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:input_contig_num ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:input_contig_num ], + owl:onProperty nmdc:low_depth_contig_num ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:binned_contig_num ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:too_short_contig_num ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:unbinned_contig_num ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:input_contig_num ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:type ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:binned_contig_num ], [ a owl:Restriction ; owl:allValuesFrom nmdc:MagBin ; owl:onProperty nmdc:mags_list ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:unbinned_contig_num ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:onProperty nmdc:too_short_contig_num ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:mags_list ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:low_depth_contig_num ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:unbinned_contig_num ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:binned_contig_num ], + owl:minCardinality 0 ; + owl:onProperty nmdc:input_contig_num ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:too_short_contig_num ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:unbinned_contig_num ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:binned_contig_num ], + owl:onProperty nmdc:low_depth_contig_num ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:low_depth_contig_num ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:input_contig_num ], + owl:onProperty nmdc:binned_contig_num ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:low_depth_contig_num ], + owl:onProperty nmdc:unbinned_contig_num ], nmdc:WorkflowExecutionActivity ; skos:definition "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes" ; skos:inScheme nmdc:workflow_execution_activity . @@ -12306,19 +12487,22 @@ nmdc:MetaboliteQuantification a owl:Class, linkml:ClassDefinition ; rdfs:label "MetaboliteQuantification" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:alternative_identifiers ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:metabolite_quantified ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:highest_similarity_score ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:highest_similarity_score ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ChemicalEntity ; + owl:onProperty nmdc:metabolite_quantified ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:highest_similarity_score ], + owl:onProperty nmdc:alternative_identifiers ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:metabolite_quantified ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ChemicalEntity ; + owl:maxCardinality 1 ; owl:onProperty nmdc:metabolite_quantified ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; @@ -12327,10 +12511,7 @@ nmdc:MetaboliteQuantification a owl:Class, owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; owl:onProperty nmdc:alternative_identifiers ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:metabolite_quantified ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:highest_similarity_score ] ; skos:definition "This is used to link a metabolomics analysis workflow to a specific metabolite" ; skos:inScheme nmdc:core . @@ -12339,8 +12520,14 @@ nmdc:MetabolomicsAnalysisActivity a owl:Class, linkml:ClassDefinition ; rdfs:label "MetabolomicsAnalysisActivity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:has_calibration ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:has_calibration ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:has_metabolite_quantifications ], @@ -12348,19 +12535,13 @@ nmdc:MetabolomicsAnalysisActivity a owl:Class, owl:allValuesFrom linkml:String ; owl:onProperty nmdc:has_calibration ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:allValuesFrom nmdc:MetaboliteQuantification ; + owl:onProperty nmdc:has_metabolite_quantifications ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:has_calibration ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetaboliteQuantification ; - owl:onProperty nmdc:has_metabolite_quantifications ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty nmdc:id ], nmdc:WorkflowExecutionActivity ; skos:inScheme nmdc:workflow_execution_activity . @@ -12371,32 +12552,32 @@ nmdc:MetagenomeAnnotationActivity a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:gold_analysis_project_identifiers ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^gold:Ga[0-9]+$" ] ) ] ; + owl:onProperty nmdc:gold_analysis_project_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:gold_analysis_project_identifiers ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^gold:Ga[0-9]+$" ] ) ] ; + owl:minCardinality 0 ; owl:onProperty nmdc:gold_analysis_project_identifiers ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:gold_analysis_project_identifiers ], + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:type ], nmdc:WorkflowExecutionActivity ; skos:definition "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs" ; skos:inScheme nmdc:workflow_execution_activity . @@ -12405,54 +12586,31 @@ nmdc:MetaproteomicsAnalysisActivity a owl:Class, linkml:ClassDefinition ; rdfs:label "MetaproteomicsAnalysisActivity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:used ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:has_peptide_quantifications ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:PeptideQuantification ; - owl:onProperty nmdc:has_peptide_quantifications ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:used ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:used ], - nmdc:WorkflowExecutionActivity ; - skos:inScheme nmdc:workflow_execution_activity . - -nmdc:QualityControlReport a owl:Class, - linkml:ClassDefinition ; - rdfs:label "QualityControlReport" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:status ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:name ], + owl:onProperty nmdc:used ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:StatusEnum ; - owl:onProperty nmdc:status ], + owl:allValuesFrom nmdc:PeptideQuantification ; + owl:onProperty nmdc:has_peptide_quantifications ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:status ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:name ] ; - skos:inScheme nmdc:nmdc . + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:used ], + nmdc:WorkflowExecutionActivity ; + skos:inScheme nmdc:workflow_execution_activity . nmdc:activity_set a owl:ObjectProperty, linkml:SlotDefinition ; @@ -12463,6 +12621,20 @@ nmdc:activity_set a owl:ObjectProperty, skos:definition "This property links a database object to the set of workflow activities." ; skos:inScheme nmdc:nmdc . +nmdc:ammonium_nitrogen a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "ammonium_nitrogen" ; + dcterms:title "ammonium nitrogen" ; + rdfs:range nmdc:QuantityValue ; + rdfs:seeAlso ; + skos:altLabel "NH4-N", + "ammonium_nitrogen" ; + skos:definition "Concentration of ammonium nitrogen in the sample" ; + skos:inScheme nmdc:nmdc ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "mg/kg" . + nmdc:analysis_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "analysis_identifiers" ; @@ -12655,13 +12827,6 @@ nmdc:data_object_type a owl:ObjectProperty, skos:definition "The type of file represented by the data object." ; skos:inScheme nmdc:nmdc . -nmdc:decimal_degree a owl:Class, - linkml:TypeDefinition ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onDataRange nmdc:decimal_degree ; - owl:onProperty linkml:topValue ; - owl:qualifiedCardinality 1 ] . - nmdc:direction a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "direction" ; @@ -13035,6 +13200,7 @@ nmdc:gene_function_id a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "gene_function_id" ; rdfs:range linkml:Uriorcurie ; + skos:definition "The identifier for the gene function." ; skos:inScheme nmdc:nmdc . nmdc:genome_feature_set a owl:ObjectProperty, @@ -13398,6 +13564,38 @@ nmdc:latitude a owl:ObjectProperty, skos:inScheme nmdc:core ; skos:mappingRelation . +nmdc:lbc_thirty a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "lbc_thirty" ; + dcterms:title "lime buffer capacity (at 30 minutes)" ; + rdfs:range nmdc:QuantityValue ; + rdfs:seeAlso , + ; + skos:altLabel "lbc30", + "lbc_thirty", + "lime buffer capacity (at 30 minutes)" ; + skos:definition "lime buffer capacity, determined after 30 minute incubation" ; + skos:inScheme nmdc:nmdc ; + skos:note "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "ppm CaCO3/pH" . + +nmdc:lbceq a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "lbceq" ; + dcterms:title "lime buffer capacity (after 5 day incubation)" ; + rdfs:range nmdc:QuantityValue ; + rdfs:seeAlso ; + skos:altLabel "lbceq", + "lime buffer capacity (at 5-day equilibrium)" ; + skos:definition "lime buffer capacity, determined at equilibrium after 5 day incubation" ; + skos:inScheme nmdc:nmdc ; + skos:note "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "ppm CaCO3/pH" . + nmdc:library_preparation_kit a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "library_preparation_kit" ; @@ -13452,6 +13650,19 @@ nmdc:mags_activity_set a owl:ObjectProperty, skos:definition "This property links a database object to the set of MAGs analysis activities." ; skos:inScheme nmdc:nmdc . +nmdc:manganese a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "manganese" ; + dcterms:title "manganese" ; + rdfs:range nmdc:QuantityValue ; + rdfs:seeAlso ; + skos:altLabel "manganese" ; + skos:definition "Concentration of manganese in the sample" ; + skos:inScheme nmdc:nmdc ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "mg/kg (ppm)" . + nmdc:mass a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "mass" ; @@ -13506,6 +13717,7 @@ nmdc:metagenome_annotation_id a owl:ObjectProperty, rdfs:label "metagenome_annotation_id" ; rdfs:domain nmdc:FunctionalAnnotationAggMember ; rdfs:range nmdc:WorkflowExecutionActivity ; + skos:definition "The identifier for the analysis activity (WorkflowExecutionActivity) that generated the functional annotation results." ; skos:inScheme nmdc:nmdc . nmdc:metagenome_assembly_set a owl:ObjectProperty, @@ -13631,6 +13843,35 @@ nmdc:neon_study_identifiers a owl:ObjectProperty, nmdc:study_identifiers ; skos:inScheme nmdc:external_identifiers . +nmdc:nitrate_nitrogen a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "nitrate_nitrogen" ; + dcterms:title "nitrate_nitrogen" ; + rdfs:range nmdc:QuantityValue ; + rdfs:seeAlso ; + skos:altLabel "NO3-N", + "nitrate_nitrogen" ; + skos:definition "Concentration of nitrate nitrogen in the sample" ; + skos:inScheme nmdc:nmdc ; + skos:note "often below some specified limit of detection" ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "mg/kg" . + +nmdc:nitrite_nitrogen a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "nitrite_nitrogen" ; + dcterms:title "nitrite_nitrogen" ; + rdfs:range nmdc:QuantityValue ; + rdfs:seeAlso ; + skos:altLabel "NO2-N", + "nitrite_nitrogen" ; + skos:definition "Concentration of nitrite nitrogen in the sample" ; + skos:inScheme nmdc:nmdc ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "mg/kg" . + nmdc:nom_analysis_activity_set a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "nom_analysis_activity_set" ; @@ -13908,12 +14149,23 @@ nmdc:protocol_link a owl:ObjectProperty, rdfs:range nmdc:Protocol ; skos:inScheme nmdc:basic_slots . -nmdc:quality_control_report a owl:ObjectProperty, +nmdc:qc_failure_what a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "quality_control_report" ; - rdfs:domain nmdc:PlannedProcess ; - rdfs:range nmdc:QualityControlReport ; - skos:inScheme nmdc:nmdc . + rdfs:label "qc_failure_what" ; + rdfs:domain nmdc:FailureCategorization ; + rdfs:range nmdc:FailureWhatEnum ; + skos:definition "Provides a summary about what caused a lab or workflow process to fail" ; + skos:inScheme nmdc:basic_slots ; + skos:note "For example Low read count from a sequencer, malformed fastq files, etc)" . + +nmdc:qc_failure_where a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "qc_failure_where" ; + rdfs:domain nmdc:FailureCategorization ; + rdfs:range nmdc:FailureWhereEnum ; + skos:definition "Describes the nmdc schema class that corresonds to where the failure occurred. Most commonly this would be the same as Class that generated the results." ; + skos:inScheme nmdc:basic_slots ; + skos:note "If the assembly size was too small to proceed to annotation failure_where would be MetagenomeAssembly." . nmdc:read_based_taxonomy_analysis_activity_set a owl:ObjectProperty, linkml:SlotDefinition ; @@ -14205,13 +14457,6 @@ nmdc:stationary_phase a owl:ObjectProperty, skos:definition "The material the stationary phase is comprised of used in chromatography." ; skos:inScheme nmdc:nmdc . -nmdc:status a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "status" ; - rdfs:domain nmdc:QualityControlReport ; - rdfs:range nmdc:StatusEnum ; - skos:inScheme nmdc:nmdc . - nmdc:stoichiometry a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "stoichiometry" ; @@ -14293,6 +14538,13 @@ nmdc:unbinned_contig_num a owl:ObjectProperty, rdfs:range linkml:Integer ; skos:inScheme nmdc:workflow_execution_activity . +nmdc:unit a owl:Class, + linkml:TypeDefinition ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onDataRange nmdc:unit ; + owl:onProperty linkml:topValue ; + owl:qualifiedCardinality 1 ] . + nmdc:was_informed_by a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "was_informed_by" ; @@ -14301,6 +14553,19 @@ nmdc:was_informed_by a owl:ObjectProperty, skos:inScheme nmdc:prov ; skos:mappingRelation prov:wasInformedBy . +nmdc:zinc a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "zinc" ; + dcterms:title "zinc" ; + rdfs:range nmdc:QuantityValue ; + rdfs:seeAlso ; + skos:altLabel "zinc" ; + skos:definition "Concentration of zinc in the sample" ; + skos:inScheme nmdc:nmdc ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "mg/kg (ppm)" . + a owl:Class, nmdc:DoiProviderEnum, nmdc:ProcessingInstitutionEnum ; @@ -14320,31 +14585,16 @@ nmdc:was_informed_by a owl:ObjectProperty, linkml:topValue a owl:DatatypeProperty ; rdfs:label "value" . - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "air_temp_regm" ; - dcterms:title "air temperature regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "air temperature regimen" ; - skos:definition "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" ; - skos:inScheme ; - nmdc:expected_value "temperature value;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "meter" . - - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "humidity_regm" ; - dcterms:title "humidity regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "humidity regimen" ; - skos:definition "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" ; + rdfs:label "samp_name" ; + dcterms:title "sample name" ; + rdfs:range linkml:String ; + rdfs:subPropertyOf ; + skos:altLabel "sample name" ; + skos:definition "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." ; skos:inScheme ; - nmdc:expected_value "humidity value;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram per cubic meter" . + nmdc:expected_value "text" . nmdc:BiosampleProcessing a owl:Class, linkml:ClassDefinition ; @@ -14359,10 +14609,10 @@ nmdc:BiosampleProcessing a owl:Class, owl:maxCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], nmdc:PlannedProcess ; skos:altLabel "material processing" ; @@ -14377,36 +14627,36 @@ nmdc:ChemicalEntity a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:inchi ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:chemical_formula ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:smiles ], + owl:onProperty nmdc:inchi ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:inchi_key ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:inchi ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:smiles ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:inchi_key ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:inchi ], + owl:minCardinality 0 ; + owl:onProperty nmdc:chemical_formula ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:inchi_key ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:chemical_formula ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:chemical_formula ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:inchi ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:smiles ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:inchi_key ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:chemical_formula ], + owl:onProperty nmdc:smiles ], nmdc:OntologyClass ; skos:altLabel "chemical", "chemical compound", @@ -14423,31 +14673,31 @@ nmdc:ChromatographicSeparationProcess a owl:Class, dcterms:contributor ORCID:0000-0002-1368-8217, ORCID:0009-0001-1555-1601 ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:temperature ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ordered_mobile_phases ], + owl:allValuesFrom nmdc:StationaryPhaseEnum ; + owl:onProperty nmdc:stationary_phase ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:stationary_phase ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:has_input ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:StationaryPhaseEnum ; owl:onProperty nmdc:stationary_phase ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:ordered_mobile_phases ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:temperature ], [ a owl:Restriction ; owl:allValuesFrom [ owl:unionOf ( nmdc:Biosample nmdc:ProcessedSample ) ] ; owl:onProperty nmdc:has_input ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:stationary_phase ], + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty nmdc:temperature ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; + owl:maxCardinality 1 ; owl:onProperty nmdc:temperature ], [ a owl:Restriction ; owl:allValuesFrom nmdc:Solution ; @@ -14461,26 +14711,26 @@ nmdc:CollectingBiosamplesFromSite a owl:Class, rdfs:label "CollectingBiosamplesFromSite" ; dcterms:title "Collecting Biosamples From Site" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:Site ; - owl:onProperty nmdc:has_input ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:has_input ], - [ a owl:Restriction ; owl:allValuesFrom nmdc:Biosample ; owl:onProperty nmdc:has_output ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:Site ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:has_input ], nmdc:PlannedProcess ; skos:closeMatch OBI:0000744 ; skos:inScheme nmdc:nmdc ; @@ -14491,29 +14741,29 @@ nmdc:CreditAssociation a owl:Class, rdfs:label "CreditAssociation" ; rdfs:seeAlso ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:PersonValue ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty nmdc:applies_to_person ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:PersonValue ; owl:onProperty nmdc:applies_to_person ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:applied_roles ], + owl:minCardinality 0 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:applies_to_person ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:CreditEnum ; + owl:minCardinality 1 ; owl:onProperty nmdc:applied_roles ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ] ; + owl:allValuesFrom nmdc:CreditEnum ; + owl:onProperty nmdc:applied_roles ] ; skos:altLabel "associated researchers", "credit table", "study role" ; @@ -14527,82 +14777,82 @@ nmdc:FieldResearchSite a owl:Class, dcterms:title "Field Research Site" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:habitat ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:NamedThing ; owl:onProperty nmdc:part_of ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:GeolocationValue ; owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:part_of ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:habitat ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; + owl:maxCardinality 1 ; owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:habitat ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:habitat ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], nmdc:Site ; skos:altLabel "research plot" ; skos:definition "A site, outside of a laboratory, from which biosamples may be collected." ; @@ -14621,73 +14871,73 @@ nmdc:FiltrationProcess a owl:Class, ORCID:0009-0008-4013-7737 ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:conditionings ], + owl:onProperty nmdc:is_pressurized ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:container_size ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:volume ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:filter_material ], + owl:onProperty nmdc:separation_method ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:is_pressurized ], + owl:onProperty nmdc:separation_method ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:filter_pore_size ], + owl:onProperty nmdc:container_size ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:filtration_category ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:separation_method ], + owl:onProperty nmdc:is_pressurized ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:filtration_category ], + owl:onProperty nmdc:conditionings ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:volume ], + owl:onProperty nmdc:container_size ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:volume ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:filter_material ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:filter_pore_size ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:SeparationMethodEnum ; + owl:onProperty nmdc:separation_method ], [ a owl:Restriction ; owl:allValuesFrom linkml:Boolean ; owl:onProperty nmdc:is_pressurized ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:volume ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:filter_material ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty nmdc:filter_pore_size ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:filter_material ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:is_pressurized ], + owl:minCardinality 0 ; + owl:onProperty nmdc:container_size ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:container_size ], + owl:onProperty nmdc:filtration_category ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:container_size ], + owl:minCardinality 0 ; + owl:onProperty nmdc:volume ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:conditionings ], + owl:onProperty nmdc:filter_material ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:filter_pore_size ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:SeparationMethodEnum ; - owl:onProperty nmdc:separation_method ], + owl:onProperty nmdc:conditionings ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:separation_method ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:filtration_category ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:filtration_category ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:filter_pore_size ], nmdc:PlannedProcess ; skos:definition "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." ; skos:inScheme nmdc:nmdc ; @@ -14699,265 +14949,232 @@ nmdc:FunctionalAnnotation a owl:Class, rdfs:seeAlso , ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:has_function ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:subject ], + owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:has_function ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:GeneProduct ; owl:onProperty nmdc:subject ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetagenomeAnnotationActivity ; - owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:subject ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:OntologyClass ; owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:has_function ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:was_generated_by ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:type ] ; - skos:definition "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" ; - skos:editorialNote "move id slot usage patterns to has_function slot usage?" ; - skos:inScheme nmdc:annotation ; - skos:narrowMatch . - -nmdc:GeolocationValue a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeolocationValue" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:longitude ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:latitude ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:has_raw_value ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:latitude ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd: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})?)$" ] ) ] ) ] ; + owl:onProperty nmdc:has_function ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:longitude ], + owl:onProperty nmdc:has_function ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:has_raw_value ], + owl:minCardinality 0 ; + owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:latitude ], + owl:allValuesFrom nmdc:GeneProduct ; + owl:onProperty nmdc:subject ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:longitude ], + owl:allValuesFrom nmdc:OntologyClass ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:has_raw_value ], - nmdc:AttributeValue ; - skos:definition "A normalized value for a location on the earth's surface" ; - skos:editorialNote "what did 'to_str: {latitude} {longitude}' mean?" ; - skos:inScheme nmdc:core ; - skos:mappingRelation . + owl:onProperty nmdc:subject ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:MetagenomeAnnotationActivity ; + owl:onProperty nmdc:was_generated_by ] ; + skos:definition "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" ; + skos:editorialNote "move id slot usage patterns to has_function slot usage?" ; + skos:inScheme nmdc:annotation ; + skos:narrowMatch . nmdc:MagBin a owl:Class, linkml:ClassDefinition ; rdfs:label "MagBin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:completeness ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:bin_quality ], + owl:onProperty nmdc:gtdbtk_domain ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:bin_name ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:type ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:gtdbtk_class ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:members_id ], + owl:onProperty nmdc:num_23s ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:contamination ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:num_t_rna ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:num_16s ], + owl:onProperty nmdc:members_id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gtdbtk_species ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:bin_name ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:total_bases ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:num_5s ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:gtdbtk_class ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:num_16s ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:num_5s ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:bin_name ], + owl:onProperty nmdc:gtdbtk_class ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:num_23s ], + owl:onProperty nmdc:gtdbtk_phylum ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:gtdbtk_order ], + owl:onProperty nmdc:gtdbtk_family ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:gtdbtk_domain ], + owl:onProperty nmdc:gtdbtk_family ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:gtdbtk_genus ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:number_of_contig ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:bin_name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:num_23s ], + owl:onProperty nmdc:num_t_rna ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gene_count ], + owl:onProperty nmdc:num_16s ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:gtdbtk_domain ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:gene_count ], + owl:onProperty nmdc:members_id ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:gtdbtk_domain ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gtdbtk_genus ], + owl:onProperty nmdc:contamination ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:members_id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:number_of_contig ], + owl:onProperty nmdc:completeness ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:bin_name ], + owl:onProperty nmdc:gtdbtk_genus ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gtdbtk_order ], + owl:onProperty nmdc:total_bases ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gtdbtk_species ], + owl:onProperty nmdc:num_5s ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:num_t_rna ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:gtdbtk_order ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:num_16s ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gtdbtk_phylum ], + owl:onProperty nmdc:gtdbtk_order ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:bin_name ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gtdbtk_family ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:gtdbtk_phylum ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:members_id ], + owl:onProperty nmdc:num_23s ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:gtdbtk_family ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:gtdbtk_phylum ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:num_t_rna ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:members_id ], + owl:onProperty nmdc:bin_quality ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:num_5s ], + owl:onProperty nmdc:gtdbtk_class ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:bin_quality ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:contamination ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:num_23s ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:num_5s ], + owl:onProperty nmdc:completeness ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:number_of_contig ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:gtdbtk_species ], + owl:onProperty nmdc:gtdbtk_domain ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:total_bases ], + owl:onProperty nmdc:gene_count ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:num_5s ], + owl:minCardinality 0 ; + owl:onProperty nmdc:gene_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:contamination ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gtdbtk_class ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:gtdbtk_species ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:gtdbtk_order ], + owl:onProperty nmdc:gene_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:gtdbtk_species ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:total_bases ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:gtdbtk_class ], + owl:onProperty nmdc:gtdbtk_order ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:completeness ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:num_16s ], + owl:onProperty nmdc:contamination ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:gtdbtk_phylum ], + owl:minCardinality 0 ; + owl:onProperty nmdc:gtdbtk_species ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:completeness ], + owl:onProperty nmdc:total_bases ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:gtdbtk_genus ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:num_t_rna ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:bin_quality ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:gtdbtk_family ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:total_bases ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:num_t_rna ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gene_count ], + owl:onProperty nmdc:bin_quality ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:number_of_contig ], + owl:onProperty nmdc:num_23s ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:gtdbtk_family ] ; + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:number_of_contig ] ; skos:inScheme nmdc:core . nmdc:MaterialEntity a owl:Class, @@ -14977,8 +15194,8 @@ nmdc:SolutionComponent a owl:Class, linkml:ClassDefinition ; rdfs:label "SolutionComponent" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:concentration ], + owl:allValuesFrom nmdc:CompoundEnum ; + owl:onProperty nmdc:compound ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:compound ], @@ -14989,8 +15206,8 @@ nmdc:SolutionComponent a owl:Class, owl:minCardinality 0 ; owl:onProperty nmdc:concentration ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:CompoundEnum ; - owl:onProperty nmdc:compound ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:concentration ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:concentration ] ; @@ -15027,6 +15244,12 @@ nmdc:gold_identifiers a owl:ObjectProperty, rdfs:seeAlso ; skos:inScheme nmdc:external_identifiers . +nmdc:has_failure_categorization a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "has_failure_categorization" ; + rdfs:range nmdc:FailureCategorization ; + skos:inScheme nmdc:nmdc . + nmdc:read_qc_analysis_statistic a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "read_qc_analysis_statistic" ; @@ -15047,17 +15270,32 @@ nmdc:DataObject a owl:Class, linkml:ClassDefinition ; rdfs:label "DataObject" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom nmdc:bytes ; + owl:onProperty nmdc:file_size_bytes ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:url ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:data_object_type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:file_size_bytes ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:compression_type ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:was_generated_by ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FileTypeEnum ; - owl:onProperty nmdc:data_object_type ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:url ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:Activity ; + owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:description ], @@ -15066,103 +15304,147 @@ nmdc:DataObject a owl:Class, owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:compression_type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:compression_type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:md5_checksum ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:description ], + owl:minCardinality 0 ; + owl:onProperty nmdc:compression_type ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:bytes ; - owl:onProperty nmdc:file_size_bytes ], + owl:minCardinality 0 ; + owl:onProperty nmdc:url ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:was_generated_by ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:md5_checksum ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:name ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:description ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:description ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:description ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:data_object_type ], + owl:onProperty nmdc:name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:compression_type ], + owl:minCardinality 1 ; + owl:onProperty nmdc:name ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:name ], + owl:onProperty nmdc:md5_checksum ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:FileTypeEnum ; + owl:onProperty nmdc:data_object_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:compression_type ], + owl:onProperty nmdc:data_object_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:file_size_bytes ], + nmdc:NamedThing ; + skos:definition "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects." ; + skos:inScheme nmdc:nmdc . + +nmdc:FailureCategorization a owl:Class, + linkml:ClassDefinition ; + rdfs:label "FailureCategorization" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom nmdc:FailureWhereEnum ; + owl:onProperty nmdc:qc_failure_where ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:md5_checksum ], + owl:onProperty nmdc:qc_failure_where ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:md5_checksum ], + owl:onProperty nmdc:qc_failure_where ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:data_object_type ], + owl:allValuesFrom nmdc:FailureWhatEnum ; + owl:onProperty nmdc:qc_failure_what ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:file_size_bytes ], + owl:onProperty nmdc:qc_failure_what ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:url ], + owl:onProperty nmdc:qc_failure_what ] ; + skos:inScheme nmdc:nmdc . + +nmdc:GeolocationValue a owl:Class, + linkml:ClassDefinition ; + rdfs:label "GeolocationValue" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom nmdc:decimal_degree ; + owl:onProperty nmdc:latitude ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty nmdc:name ], + owl:onProperty nmdc:latitude ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Activity ; - owl:onProperty nmdc:was_generated_by ], + owl:minCardinality 0 ; + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:minCardinality 1 ; + owl:onProperty nmdc:longitude ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:allValuesFrom nmdc:decimal_degree ; + owl:onProperty nmdc:longitude ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:url ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:longitude ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:name ], + owl:onProperty nmdc:latitude ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:url ], - nmdc:NamedThing ; - skos:definition "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects." ; - skos:inScheme nmdc:nmdc . + owl:maxCardinality 1 ; + owl:onProperty nmdc:has_raw_value ], + nmdc:AttributeValue ; + skos:definition "A normalized value for a location on the earth's surface" ; + skos:editorialNote "what did 'to_str: {latitude} {longitude}' mean?" ; + skos:inScheme nmdc:core ; + skos:mappingRelation . nmdc:Pooling a owl:Class, linkml:ClassDefinition ; rdfs:label "Pooling" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:has_input ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:has_output ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:has_output ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:allValuesFrom owl:Thing ; + owl:onProperty nmdc:has_output ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom owl:Thing ; owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], nmdc:BiosampleProcessing ; skos:definition "physical combination of several instances of like material." ; @@ -15174,80 +15456,80 @@ nmdc:Reaction a owl:Class, linkml:ClassDefinition ; rdfs:label "Reaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Boolean ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:direction ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:is_stereo ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:is_transport ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:direction ], + owl:minCardinality 0 ; + owl:onProperty nmdc:is_balanced ], [ a owl:Restriction ; owl:allValuesFrom linkml:Boolean ; - owl:onProperty nmdc:is_balanced ], + owl:onProperty nmdc:is_stereo ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ReactionParticipant ; - owl:onProperty nmdc:left_participants ], + owl:minCardinality 0 ; + owl:onProperty nmdc:smarts_string ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Boolean ; + owl:onProperty nmdc:is_transport ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:left_participants ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ReactionParticipant ; - owl:onProperty nmdc:right_participants ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:is_balanced ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:is_stereo ], + owl:onProperty nmdc:smarts_string ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:right_participants ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:is_transport ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:direction ], + owl:onProperty nmdc:is_diastereoselective ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:is_fully_characterized ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:is_transport ], + owl:minCardinality 0 ; + owl:onProperty nmdc:right_participants ], [ a owl:Restriction ; owl:allValuesFrom linkml:Boolean ; owl:onProperty nmdc:is_diastereoselective ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Boolean ; - owl:onProperty nmdc:is_fully_characterized ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:smarts_string ], + owl:allValuesFrom nmdc:ReactionParticipant ; + owl:onProperty nmdc:left_participants ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:is_fully_characterized ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:direction ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ReactionParticipant ; + owl:onProperty nmdc:right_participants ], [ a owl:Restriction ; owl:allValuesFrom linkml:Boolean ; - owl:onProperty nmdc:is_stereo ], + owl:onProperty nmdc:is_balanced ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:smarts_string ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:is_stereo ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:is_balanced ], + owl:allValuesFrom linkml:Boolean ; + owl:onProperty nmdc:is_fully_characterized ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:is_balanced ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:is_diastereoselective ], + owl:onProperty nmdc:is_stereo ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:is_diastereoselective ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:is_transport ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:smarts_string ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:direction ], nmdc:FunctionalAnnotationTerm ; skos:definition "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" ; skos:exactMatch ; @@ -15258,19 +15540,19 @@ nmdc:ReactionParticipant a owl:Class, rdfs:label "ReactionParticipant" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:stoichiometry ], + owl:onProperty nmdc:chemical ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:chemical ], [ a owl:Restriction ; owl:allValuesFrom nmdc:ChemicalEntity ; owl:onProperty nmdc:chemical ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:chemical ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; owl:onProperty nmdc:stoichiometry ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:stoichiometry ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:stoichiometry ] ; @@ -15281,19 +15563,19 @@ nmdc:Solution a owl:Class, linkml:ClassDefinition ; rdfs:label "Solution" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:SolutionComponent ; - owl:onProperty nmdc:has_solution_components ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty nmdc:volume ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:volume ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:has_solution_components ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; + owl:allValuesFrom nmdc:SolutionComponent ; + owl:onProperty nmdc:has_solution_components ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:volume ] ; skos:altLabel "mixture", "solvent" ; @@ -15304,6 +15586,13 @@ nmdc:Solution a owl:Class, skos:note "The solution class may be used to instantiate a single component in the has_solution_components slot", "We acknowledge that users of the nmdc-schema may instantiate Solution with only a single component which goes against the letter of the description." . +nmdc:decimal_degree a owl:Class, + linkml:TypeDefinition ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onDataRange nmdc:decimal_degree ; + owl:onProperty linkml:topValue ; + owl:qualifiedCardinality 1 ] . + nmdc:dna_cont_type a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "dna_cont_type" ; @@ -15313,6 +15602,20 @@ nmdc:dna_cont_type a owl:ObjectProperty, skos:inScheme ; sh:order 10 . +nmdc:dna_cont_well a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "dna_cont_well" ; + dcterms:title "DNA plate position" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" ] ) ] ; + skos:inScheme ; + skos:note "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).", + "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", + "Leave blank if the sample will be shipped in a tube.", + "Required when 'plate' is selected for container type." ; + sh:order 11 . + nmdc:gold_path_field a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "gold_path_field" ; @@ -15343,29 +15646,6 @@ nmdc:rna_cont_well a owl:ObjectProperty, "Required when 'plate' is selected for container type." ; sh:order 11 . - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "biotic_regm" ; - dcterms:title "biotic regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "biotic regimen" ; - skos:definition "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi." ; - skos:inScheme ; - nmdc:expected_value "free text" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "biotic_relationship" ; - dcterms:title "observed biotic relationship" ; - rdfs:range nmdc:BioticRelationshipEnum ; - rdfs:subPropertyOf ; - skos:altLabel "observed biotic relationship" ; - skos:definition "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" ; - skos:inScheme ; - nmdc:expected_value "enumeration" . - a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "chimera_check" ; @@ -15377,16 +15657,28 @@ nmdc:rna_cont_well a owl:ObjectProperty, skos:inScheme ; nmdc:expected_value "name and version of software, parameters used" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "experimental_factor" ; - dcterms:title "experimental factor" ; - rdfs:range nmdc:ControlledTermValue ; - rdfs:subPropertyOf ; - skos:altLabel "experimental factor" ; - skos:definition "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" ; + rdfs:label "cur_vegetation" ; + dcterms:title "current vegetation" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "current vegetation" ; + skos:definition "Vegetation classification from one or more standard classification systems, or agricultural crop" ; + skos:inScheme ; + nmdc:expected_value "current vegetation type" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "elev" ; + dcterms:title "elevation" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "elevation" ; + skos:definition "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." ; skos:inScheme ; - nmdc:expected_value "text or EFO and/or OBI" . + nmdc:expected_value "measurement value" . a owl:ObjectProperty, linkml:SlotDefinition ; @@ -15399,49 +15691,22 @@ nmdc:rna_cont_well a owl:ObjectProperty, skos:inScheme ; nmdc:expected_value "country or sea name (INSDC or GAZ): region(GAZ), specific location name" . - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "growth_facil" ; - dcterms:title "growth facility" ; - rdfs:range nmdc:ControlledTermValue ; - rdfs:subPropertyOf ; - skos:altLabel "growth facility" ; - skos:definition "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" ; - skos:inScheme ; - nmdc:expected_value "free text or CO" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "host_taxid" ; - dcterms:title "host taxid" ; - rdfs:range nmdc:ControlledIdentifiedTermValue ; - rdfs:subPropertyOf ; - skos:altLabel "host taxid" ; - skos:definition "NCBI taxon id of the host, e.g. 9606" ; - skos:inScheme ; - skos:note "Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value" ; - nmdc:expected_value "NCBI taxon identifier" ; - nmdc:occurrence "1" . - a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "investigation field" ; skos:definition "field describing aspect of the investigation/study to which the sample belongs" ; skos:inScheme . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "light_regm" ; - dcterms:title "light regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "light regimen" ; - skos:definition "Information about treatment(s) involving exposure to light, including both light intensity and quality." ; + rdfs:label "lat_lon" ; + dcterms:title "geographic location (latitude and longitude)" ; + rdfs:range nmdc:GeolocationValue ; + rdfs:subPropertyOf ; + skos:altLabel "geographic location (latitude and longitude)" ; + skos:definition "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system" ; skos:inScheme ; - nmdc:expected_value "exposure type;light intensity;light quality" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "lux; micrometer, nanometer, angstrom" . + nmdc:expected_value "decimal degrees, limit to 8 decimal points" . a owl:ObjectProperty, linkml:SlotDefinition ; @@ -15499,42 +15764,6 @@ nmdc:rna_cont_well a owl:ObjectProperty, skos:inScheme ; nmdc:expected_value "FWD: forward primer sequence;REV:reverse primer sequence" . - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "phosphate" ; - dcterms:title "phosphate" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "phosphate" ; - skos:definition "Concentration of phosphate" ; - skos:inScheme ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "samp_collec_method" ; - dcterms:title "sample collection method" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf ; - skos:altLabel "sample collection method" ; - skos:definition "The method employed for collecting the sample." ; - skos:inScheme ; - nmdc:expected_value "PMID,DOI,url , or text" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "samp_size" ; - dcterms:title "amount or size of sample collected" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "amount or size of sample collected" ; - skos:definition "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected." ; - skos:inScheme ; - nmdc:expected_value "measurement value" ; - nmdc:preferred_unit "millliter, gram, milligram, liter" . - a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "samp_vol_we_dna_ext" ; @@ -15613,35 +15842,35 @@ nmdc:Doi a owl:Class, linkml:ClassDefinition ; rdfs:label "Doi" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom nmdc:DoiProviderEnum ; owl:onProperty nmdc:doi_provider ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:doi_category ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^doi:10.\\d{2,9}/.*$" ] ) ] ) ] ; owl:onProperty nmdc:doi_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:doi_category ], [ a owl:Restriction ; owl:allValuesFrom nmdc:DoiCategoryEnum ; owl:onProperty nmdc:doi_category ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:doi_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:doi_provider ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty nmdc:doi_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:doi_category ], + owl:minCardinality 0 ; + owl:onProperty nmdc:doi_provider ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:DoiProviderEnum ; - owl:onProperty nmdc:doi_provider ] ; + owl:minCardinality 1 ; + owl:onProperty nmdc:doi_category ] ; skos:altLabel "DOIs", "digital object identifiers" ; skos:definition "A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation. The DOI system is particularly used for electronic documents." ; @@ -15652,53 +15881,53 @@ nmdc:LibraryPreparation a owl:Class, linkml:ClassDefinition ; rdfs:label "LibraryPreparation" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:library_preparation_kit ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:onProperty nmdc:library_preparation_kit ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:has_input ], + owl:allValuesFrom nmdc:LibraryTypeEnum ; + owl:onProperty nmdc:library_type ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:has_input ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:library_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:library_preparation_kit ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:LibraryTypeEnum ; owl:onProperty nmdc:library_type ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:pcr_cycles ], + owl:onProperty nmdc:library_preparation_kit ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; owl:onProperty nmdc:pcr_cycles ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:library_preparation_kit ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:pcr_cycles ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:library_type ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty nmdc:has_output ], + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:library_type ], + owl:onProperty nmdc:pcr_cycles ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:library_preparation_kit ], + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty nmdc:has_output ], nmdc:BiosampleProcessing ; skos:altLabel "LibraryConstruction" ; skos:closeMatch OBI:0000711 ; @@ -15725,12 +15954,6 @@ nmdc:SampleTypeEnum a owl:Class, linkml:permissible_values , . -nmdc:StatusEnum a owl:Class, - linkml:EnumDefinition ; - owl:unionOf ( ) ; - linkml:permissible_values , - . - nmdc:StudyCategoryEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -15744,20 +15967,6 @@ nmdc:add_date a owl:ObjectProperty, skos:definition "The date on which the information was added to the database." ; skos:inScheme nmdc:nmdc . -nmdc:ammonium_nitrogen a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ammonium_nitrogen" ; - dcterms:title "ammonium nitrogen" ; - rdfs:range nmdc:QuantityValue ; - rdfs:seeAlso ; - skos:altLabel "NH4-N", - "ammonium_nitrogen" ; - skos:definition "Concentration of ammonium nitrogen in the sample" ; - skos:inScheme nmdc:nmdc ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "mg/kg" . - nmdc:asm_score a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "asm_score" ; @@ -15886,6 +16095,42 @@ nmdc:dna_concentration a owl:ObjectProperty, skos:note "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." ; sh:order 5 . +nmdc:ecosystem a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "ecosystem" ; + rdfs:seeAlso ; + rdfs:subPropertyOf nmdc:gold_path_field ; + skos:definition "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." ; + skos:inScheme nmdc:nmdc ; + skos:note "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." . + +nmdc:ecosystem_category a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "ecosystem_category" ; + rdfs:seeAlso ; + rdfs:subPropertyOf nmdc:gold_path_field ; + skos:definition "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." ; + skos:inScheme nmdc:nmdc ; + skos:note "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." . + +nmdc:ecosystem_subtype a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "ecosystem_subtype" ; + rdfs:seeAlso ; + rdfs:subPropertyOf nmdc:gold_path_field ; + skos:definition "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path." ; + skos:inScheme nmdc:nmdc ; + skos:note "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." . + +nmdc:ecosystem_type a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "ecosystem_type" ; + rdfs:seeAlso ; + rdfs:subPropertyOf nmdc:gold_path_field ; + skos:definition "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." ; + skos:inScheme nmdc:nmdc ; + skos:note "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." . + nmdc:ended_at_time a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "ended_at_time" ; @@ -15974,54 +16219,9 @@ nmdc:insdc_bioproject_identifiers a owl:ObjectProperty, nmdc:instrument_name a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "instrument_name" ; - rdfs:domain nmdc:PlannedProcess ; - skos:definition "The name of the instrument that was used for processing the sample." ; - skos:inScheme nmdc:basic_slots . - -nmdc:lbc_thirty a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "lbc_thirty" ; - dcterms:title "lime buffer capacity (at 30 minutes)" ; - rdfs:range nmdc:QuantityValue ; - rdfs:seeAlso , - ; - skos:altLabel "lbc30", - "lbc_thirty", - "lime buffer capacity (at 30 minutes)" ; - skos:definition "lime buffer capacity, determined after 30 minute incubation" ; - skos:inScheme nmdc:nmdc ; - skos:note "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "ppm CaCO3/pH" . - -nmdc:lbceq a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "lbceq" ; - dcterms:title "lime buffer capacity (after 5 day incubation)" ; - rdfs:range nmdc:QuantityValue ; - rdfs:seeAlso ; - skos:altLabel "lbceq", - "lime buffer capacity (at 5-day equilibrium)" ; - skos:definition "lime buffer capacity, determined at equilibrium after 5 day incubation" ; - skos:inScheme nmdc:nmdc ; - skos:note "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "ppm CaCO3/pH" . - -nmdc:manganese a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "manganese" ; - dcterms:title "manganese" ; - rdfs:range nmdc:QuantityValue ; - rdfs:seeAlso ; - skos:altLabel "manganese" ; - skos:definition "Concentration of manganese in the sample" ; - skos:inScheme nmdc:nmdc ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "mg/kg (ppm)" . + rdfs:domain nmdc:PlannedProcess ; + skos:definition "The name of the instrument that was used for processing the sample." ; + skos:inScheme nmdc:basic_slots . nmdc:mod_date a owl:ObjectProperty, linkml:SlotDefinition ; @@ -16030,35 +16230,6 @@ nmdc:mod_date a owl:ObjectProperty, skos:definition "The last date on which the database information was modified." ; skos:inScheme nmdc:nmdc . -nmdc:nitrate_nitrogen a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "nitrate_nitrogen" ; - dcterms:title "nitrate_nitrogen" ; - rdfs:range nmdc:QuantityValue ; - rdfs:seeAlso ; - skos:altLabel "NO3-N", - "nitrate_nitrogen" ; - skos:definition "Concentration of nitrate nitrogen in the sample" ; - skos:inScheme nmdc:nmdc ; - skos:note "often below some specified limit of detection" ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "mg/kg" . - -nmdc:nitrite_nitrogen a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "nitrite_nitrogen" ; - dcterms:title "nitrite_nitrogen" ; - rdfs:range nmdc:QuantityValue ; - rdfs:seeAlso ; - skos:altLabel "NO2-N", - "nitrite_nitrogen" ; - skos:definition "Concentration of nitrite nitrogen in the sample" ; - skos:inScheme nmdc:nmdc ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "mg/kg" . - nmdc:num_aligned_reads a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "num_aligned_reads" ; @@ -16091,6 +16262,13 @@ nmdc:processing_institution a owl:ObjectProperty, skos:definition "The organization that processed the sample." ; skos:inScheme nmdc:basic_slots . +nmdc:qc_comment a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "qc_comment" ; + rdfs:range linkml:String ; + skos:definition "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file)." ; + skos:inScheme nmdc:basic_slots . + nmdc:scaf_bp a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "scaf_bp" ; @@ -16187,6 +16365,15 @@ nmdc:scaffolds a owl:ObjectProperty, skos:definition "Total sequence count of all scaffolds." ; skos:inScheme nmdc:workflow_execution_activity . +nmdc:specific_ecosystem a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "specific_ecosystem" ; + rdfs:seeAlso ; + rdfs:subPropertyOf nmdc:gold_path_field ; + skos:definition "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." ; + skos:inScheme nmdc:nmdc ; + skos:note "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." . + nmdc:started_at_time a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "started_at_time" ; @@ -16225,108 +16412,75 @@ nmdc:version a owl:ObjectProperty, rdfs:range linkml:String ; skos:inScheme nmdc:workflow_execution_activity . -nmdc:zinc a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "zinc" ; - dcterms:title "zinc" ; - rdfs:range nmdc:QuantityValue ; - rdfs:seeAlso ; - skos:altLabel "zinc" ; - skos:definition "Concentration of zinc in the sample" ; - skos:inScheme nmdc:nmdc ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "mg/kg (ppm)" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "samp_name" ; - dcterms:title "sample name" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf ; - skos:altLabel "sample name" ; - skos:definition "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." ; - skos:inScheme ; - nmdc:expected_value "text" . - nmdc:Extraction a owl:Class, linkml:ClassDefinition ; rdfs:label "Extraction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:extractant ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:volume ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExtractionTargetEnum ; - owl:onProperty nmdc:extraction_method ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:input_mass ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:quality_control_report ], + owl:onProperty nmdc:input_mass ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:has_output ], + owl:minCardinality 0 ; + owl:onProperty nmdc:extractant ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:volume ], + owl:allValuesFrom nmdc:ExtractionTargetEnum ; + owl:onProperty nmdc:extraction_target ], [ a owl:Restriction ; - owl:allValuesFrom [ owl:unionOf ( nmdc:Biosample nmdc:ProcessedSample ) ] ; - owl:onProperty nmdc:has_input ], + owl:minCardinality 0 ; + owl:onProperty nmdc:extraction_target ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:allValuesFrom nmdc:ExtractionTargetEnum ; + owl:onProperty nmdc:extraction_method ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:quality_control_report ], + owl:onProperty nmdc:extraction_method ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:extraction_target ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:has_input ], + owl:onProperty nmdc:input_mass ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom nmdc:Solution ; owl:onProperty nmdc:extractant ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:extraction_method ], + owl:minCardinality 1 ; + owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:volume ], + owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:input_mass ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExtractionTargetEnum ; - owl:onProperty nmdc:extraction_target ], + owl:onProperty nmdc:volume ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Solution ; - owl:onProperty nmdc:extractant ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:input_mass ], + owl:allValuesFrom [ owl:unionOf ( nmdc:Biosample nmdc:ProcessedSample ) ] ; + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:volume ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:input_mass ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:extraction_method ], + owl:onProperty nmdc:extractant ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:extraction_target ], + owl:minCardinality 1 ; + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QualityControlReport ; - owl:onProperty nmdc:quality_control_report ], + owl:minCardinality 0 ; + owl:onProperty nmdc:extraction_method ], nmdc:PlannedProcess ; skos:definition "A material separation in which a desired component of an input material is separated from the remainder." ; skos:exactMatch OBI:0302884, @@ -16344,233 +16498,233 @@ nmdc:OmicsProcessing a owl:Class, linkml:ClassDefinition ; rdfs:label "OmicsProcessing" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:add_date ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:instrument_name ], + owl:onProperty nmdc:insdc_bioproject_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:instrument_name ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^bioproject:PRJ[DEN][A-Z][0-9]+$" ] ) ] ; owl:onProperty nmdc:insdc_bioproject_identifiers ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:mod_date ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:omics_type ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ProcessingInstitutionEnum ; - owl:onProperty nmdc:processing_institution ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:add_date ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:PersonValue ; + owl:onProperty nmdc:principal_investigator ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^gold:Gp[0-9]+$" ] ) ] ; + owl:onProperty nmdc:gold_sequencing_project_identifiers ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:insdc_experiment_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:ncbi_project_name ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gold_sequencing_project_identifiers ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:part_of ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledTermValue ; - owl:onProperty nmdc:omics_type ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:processing_institution ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:mod_date ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:principal_investigator ], + owl:minCardinality 0 ; + owl:onProperty nmdc:add_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom [ owl:intersectionOf ( nmdc:Study [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^nmdc:sty-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$" ] ) ] ) ] ; owl:onProperty nmdc:part_of ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:processing_institution ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:insdc_bioproject_identifiers ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:gold_sequencing_project_identifiers ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:principal_investigator ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:add_date ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:omics_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:gold_sequencing_project_identifiers ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:add_date ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:gold_sequencing_project_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom [ owl:intersectionOf ( nmdc:DataObject [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd: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_\\.-]+)?$" ] ) ] ) ] ; + owl:onProperty nmdc:has_output ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:mod_date ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:omics_type ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:mod_date ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:principal_investigator ], + owl:onProperty nmdc:insdc_bioproject_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:ncbi_project_name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:insdc_bioproject_identifiers ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:principal_investigator ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:processing_institution ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:part_of ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^insdc.sra:(E|D|S)RX[0-9]{6,}$" ] ) ] ; - owl:onProperty nmdc:insdc_experiment_identifiers ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:instrument_name ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^nmdc:(bsm|procsm)-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$" ] ) ] ; - owl:onProperty nmdc:has_input ], + owl:withRestrictions ( [ xsd:pattern "^insdc.sra:(E|D|S)RX[0-9]{6,}$" ] ) ] ; + owl:onProperty nmdc:insdc_experiment_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom [ owl:intersectionOf ( nmdc:DataObject [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd: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_\\.-]+)?$" ] ) ] ) ] ; - owl:onProperty nmdc:has_output ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:has_input ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:mod_date ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:add_date ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:minCardinality 0 ; + owl:onProperty nmdc:mod_date ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:ProcessingInstitutionEnum ; + owl:onProperty nmdc:processing_institution ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:insdc_experiment_identifiers ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:instrument_name ], + owl:allValuesFrom [ owl:intersectionOf ( nmdc:NamedThing [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^nmdc:(bsm|procsm)-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$" ] ) ] ) ] ; + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:PersonValue ; - owl:onProperty nmdc:principal_investigator ], + owl:allValuesFrom nmdc:ControlledTermValue ; + owl:onProperty nmdc:omics_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:insdc_experiment_identifiers ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^gold:Gp[0-9]+$" ] ) ] ; - owl:onProperty nmdc:gold_sequencing_project_identifiers ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:instrument_name ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:has_output ], + owl:onProperty nmdc:ncbi_project_name ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ncbi_project_name ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:instrument_name ], nmdc:PlannedProcess ; skos:altLabel "experiment", "omics assay", @@ -16584,13 +16738,13 @@ nmdc:OntologyClass a owl:Class, linkml:ClassDefinition ; rdfs:label "OntologyClass" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ; owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], @@ -16607,58 +16761,64 @@ nmdc:PersonValue a owl:Class, [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:name ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:email ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:orcid ], + owl:onProperty nmdc:email ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:websites ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty nmdc:profile_image_url ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:name ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$" ] ) ] ) ] ; + owl:onProperty nmdc:websites ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:has_raw_value ], + owl:onProperty nmdc:websites ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:profile_image_url ], + owl:onProperty nmdc:orcid ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:profile_image_url ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:orcid ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:email ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:email ], - [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$" ] ) ] ) ] ; - owl:onProperty nmdc:websites ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty nmdc:orcid ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:email ], + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:profile_image_url ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:has_raw_value ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:email ], nmdc:AttributeValue ; skos:definition "An attribute value representing a person" ; skos:inScheme nmdc:core . +nmdc:StatusEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + . + nmdc:biomaterial_purity a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "biomaterial_purity" ; @@ -16686,23 +16846,6 @@ nmdc:ArchStrucEnum a owl:Class, , . -nmdc:ControlledIdentifiedTermValue a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ControlledIdentifiedTermValue" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:term ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:term ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:term ], - nmdc:ControlledTermValue ; - skos:definition "A controlled term or class from an ontology, requiring the presence of term with an id" ; - skos:editorialNote "To be used for slots like env_broad_scale" ; - skos:inScheme nmdc:core . - nmdc:DoorDirectEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -16724,96 +16867,87 @@ nmdc:FurnitureEnum a owl:Class, , . -nmdc:GeneProduct a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneProduct" ; - rdfs:subClassOf nmdc:NamedThing ; - skos:definition "A molecule encoded by a gene that has an evolved function" ; - skos:editorialNote "we may include a more general gene product class in future to allow for ncRNA annotation" ; - skos:exactMatch ; - skos:inScheme nmdc:core . - nmdc:GenomeFeature a owl:Class, linkml:ClassDefinition ; rdfs:label "GenomeFeature" ; rdfs:seeAlso ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:strand ], - [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:feature_type ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:Integer [ a rdfs:Datatype ; - owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; - owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:maxInclusive 2 ] ) ] ) ] ; - owl:onProperty nmdc:phase ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:GeneProduct ; - owl:onProperty nmdc:encodes ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 1 ; owl:onProperty nmdc:start ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:OntologyClass ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty nmdc:seqid ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:feature_type ], + owl:minCardinality 0 ; + owl:onProperty nmdc:phase ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty nmdc:end ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:strand ], + owl:onProperty nmdc:encodes ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:start ], + owl:onProperty nmdc:encodes ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:end ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:seqid ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Integer [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:maxInclusive 2 ] ) ] ) ] ; + owl:onProperty nmdc:phase ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:end ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:start ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:strand ], + owl:onProperty nmdc:feature_type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:feature_type ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:seqid ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:end ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:strand ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:phase ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:end ], + owl:onProperty nmdc:strand ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:seqid ], + owl:onProperty nmdc:start ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:feature_type ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom nmdc:GeneProduct ; owl:onProperty nmdc:encodes ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:OntologyClass ; - owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:phase ], + owl:onProperty nmdc:seqid ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:strand ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:encodes ] ; + owl:onProperty nmdc:phase ] ; skos:definition "A feature localized to an interval along a genome" ; skos:inScheme nmdc:annotation ; skos:note "corresponds to an entry in GFF3" . @@ -16893,20 +17027,6 @@ nmdc:YesNoEnum a owl:Class, linkml:permissible_values , . -nmdc:dna_cont_well a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "dna_cont_well" ; - dcterms:title "DNA plate position" ; - rdfs:range [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" ] ) ] ; - skos:inScheme ; - skos:note "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).", - "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", - "Leave blank if the sample will be shipped in a tube.", - "Required when 'plate' is selected for container type." ; - sh:order 11 . - nmdc:external_database_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "external_database_identifiers" ; @@ -16931,6 +17051,13 @@ nmdc:has_numeric_value a owl:ObjectProperty, skos:mappingRelation , . +nmdc:qc_status a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "qc_status" ; + rdfs:range nmdc:StatusEnum ; + skos:definition "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" ; + skos:inScheme nmdc:nmdc . + nmdc:study_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "study_identifiers" ; @@ -16942,23 +17069,23 @@ nmdc:ProcessedSample a owl:Class, rdfs:label "ProcessedSample" ; dcterms:title "Processed Sample" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:dna_concentration ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:biomaterial_purity ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty nmdc:dna_absorb1 ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:biomaterial_purity ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:external_database_identifiers ], + owl:onProperty nmdc:dna_concentration ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:minCardinality 0 ; + owl:onProperty nmdc:dna_absorb1 ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:intersectionOf ( linkml:Float [ a rdfs:Datatype ; @@ -16968,29 +17095,29 @@ nmdc:ProcessedSample a owl:Class, owl:withRestrictions ( [ xsd:maxInclusive 2000 ] ) ] ) ] ; owl:onProperty nmdc:dna_concentration ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:dna_absorb1 ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:dna_absorb1 ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:biomaterial_purity ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_concentration ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( nmdc:external_identifier [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; + owl:minCardinality 0 ; owl:onProperty nmdc:external_database_identifiers ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty nmdc:biomaterial_purity ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:dna_absorb1 ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:biomaterial_purity ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( nmdc:external_identifier [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; + owl:onProperty nmdc:external_database_identifiers ], nmdc:MaterialEntity ; skos:inScheme nmdc:core . @@ -17004,51 +17131,6 @@ nmdc:alternative_identifiers a owl:ObjectProperty, skos:definition "A list of alternative identifiers for the entity." ; skos:inScheme nmdc:basic_slots . -nmdc:ecosystem a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ecosystem" ; - rdfs:seeAlso ; - rdfs:subPropertyOf nmdc:gold_path_field ; - skos:definition "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." ; - skos:inScheme nmdc:nmdc ; - skos:note "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." . - -nmdc:ecosystem_category a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ecosystem_category" ; - rdfs:seeAlso ; - rdfs:subPropertyOf nmdc:gold_path_field ; - skos:definition "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." ; - skos:inScheme nmdc:nmdc ; - skos:note "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." . - -nmdc:ecosystem_subtype a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ecosystem_subtype" ; - rdfs:seeAlso ; - rdfs:subPropertyOf nmdc:gold_path_field ; - skos:definition "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path." ; - skos:inScheme nmdc:nmdc ; - skos:note "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." . - -nmdc:ecosystem_type a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ecosystem_type" ; - rdfs:seeAlso ; - rdfs:subPropertyOf nmdc:gold_path_field ; - skos:definition "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." ; - skos:inScheme nmdc:nmdc ; - skos:note "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." . - -nmdc:specific_ecosystem a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "specific_ecosystem" ; - rdfs:seeAlso ; - rdfs:subPropertyOf nmdc:gold_path_field ; - skos:definition "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." ; - skos:inScheme nmdc:nmdc ; - skos:note "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." . - nmdc:url a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "url" ; @@ -17070,6 +17152,14 @@ nmdc:was_generated_by a owl:ObjectProperty, skos:inScheme nmdc:prov ; skos:mappingRelation prov:wasGeneratedBy . +nmdc:BioticRelationshipEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . + nmdc:BuildingSettingEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -17078,6 +17168,23 @@ nmdc:BuildingSettingEnum a owl:Class, , . +nmdc:ControlledIdentifiedTermValue a owl:Class, + linkml:ClassDefinition ; + rdfs:label "ControlledIdentifiedTermValue" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty nmdc:term ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:term ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:term ], + nmdc:ControlledTermValue ; + skos:definition "A controlled term or class from an ontology, requiring the presence of term with an id" ; + skos:editorialNote "To be used for slots like env_broad_scale" ; + skos:inScheme nmdc:core . + nmdc:DoiCategoryEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -17102,6 +17209,15 @@ nmdc:DoorLocEnum a owl:Class, , . +nmdc:GeneProduct a owl:Class, + linkml:ClassDefinition ; + rdfs:label "GeneProduct" ; + rdfs:subClassOf nmdc:NamedThing ; + skos:definition "A molecule encoded by a gene that has an evolved function" ; + skos:editorialNote "we may include a more general gene product class in future to allow for ncRNA annotation" ; + skos:exactMatch ; + skos:inScheme nmdc:core . + nmdc:GrowthHabitEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -17221,42 +17337,34 @@ nmdc:AttributeValue a owl:Class, rdfs:label "AttributeValue" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:has_raw_value ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:has_raw_value ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Activity ; - owl:onProperty nmdc:was_generated_by ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:was_generated_by ], + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_raw_value ] ; + owl:allValuesFrom nmdc:Activity ; + owl:onProperty nmdc:was_generated_by ] ; skos:definition "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" ; skos:inScheme nmdc:core . -nmdc:BioticRelationshipEnum a owl:Class, - linkml:EnumDefinition ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - nmdc:InstrumentVendorEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -17280,61 +17388,64 @@ nmdc:Activity a owl:Class, linkml:ClassDefinition ; rdfs:label "Activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:Activity ; - owl:onProperty nmdc:was_informed_by ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:name ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:started_at_time ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:was_informed_by ], + owl:onProperty nmdc:ended_at_time ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd: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)?)?)?)?$" ] ) ] ) ] ; owl:onProperty nmdc:started_at_time ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:used ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:started_at_time ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:onProperty nmdc:used ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:name ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:was_informed_by ], + owl:onProperty nmdc:used ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" ] ) ] ; owl:onProperty nmdc:ended_at_time ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ended_at_time ], + owl:onProperty nmdc:was_informed_by ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:used ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:started_at_time ], + owl:onProperty nmdc:was_informed_by ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:ended_at_time ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:Activity ; + owl:onProperty nmdc:was_informed_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:name ], - [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd: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)?)?)?)?$" ] ) ] ) ] ; - owl:onProperty nmdc:started_at_time ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:used ] ; @@ -17399,6 +17510,15 @@ nmdc:DoorTypeMetalEnum a owl:Class, , . +nmdc:FailureWhatEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + nmdc:FloorCondEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -17588,5227 +17708,5033 @@ nmdc:Biosample a owl:Class, linkml:ClassDefinition ; rdfs:label "Biosample" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:neon_biosample_identifiers ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem_subtype ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:gaseous_environment ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:igsn_biosample_identifiers ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:microbial_biomass_c ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:dna_isolate_meth ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:specific_ecosystem ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_samp_id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem_subtype ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ecosystem_category ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:CurLandUseEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:rna_container_id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ecosystem_category ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:JgiContTypeEnum ; - owl:onProperty nmdc:rna_cont_type ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:flooding ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:DoorTypeMetalEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:DeposEnvEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:location ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem_subtype ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:microbial_biomass_c ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TrainStopLocEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:alternative_identifiers ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:proposal_rna ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:env_broad_scale ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem_category ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:env_medium ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:IndoorSurfEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^(cat|dog|rodent|snake|other);\\d+$" ] ) ] ) ] ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:sieving ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:mod_date ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:rna_isolate_meth ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem_category ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:DnaSampleFormatEnum ; - owl:onProperty nmdc:dna_sample_format ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:SoilHorizonEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:non_microb_biomass_method ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:HcProducedEnum ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:dna_container_id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:tot_org_c_meth ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:elev ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem_category ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:micro_biomass_c_meth ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:SampCollectPointEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:dna_container_id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:experimental_factor_other ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:filter_method ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:zinc ], + owl:onProperty nmdc:isotope_exposure ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:dna_dnase ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:emsl_biosample_identifiers ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:WallTextureEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:FloorWaterMoldEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ammonium_nitrogen ], + owl:onProperty nmdc:dna_samp_id ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Float [ a rdfs:Datatype ; owl:onDatatype xsd:integer ; owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:maxInclusive 2000 ] ) ] ) ] ; - owl:onProperty nmdc:rna_sample_name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:GenderRestroomEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:slope_aspect ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem_type ], + owl:withRestrictions ( [ xsd:maxInclusive 1000 ] ) ] ) ] ; + owl:onProperty nmdc:rna_concentration ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledTermValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:PlantSexEnum ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:dna_container_id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:BuildingSettingEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:rna_samp_id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:SrDepEnvEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:env_broad_scale ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:collection_time_inc ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:onProperty nmdc:mod_date ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:GeolocationValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:rna_collect_site ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_cont_well ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:DoorMatEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:HcrEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:extreme_event ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:rna_cont_well ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:lbc_thirty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty nmdc:ammonium_nitrogen ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:annual_precpt ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:dna_sample_name ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:dna_collect_site ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:lbc_thirty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:rna_seq_project_pi ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:project_id ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ControlledTermValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:WindowCoverEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:slope_gradient ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:add_date ], + owl:onProperty nmdc:host_name ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:WindowCondEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:sample_collection_site ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WindowLocEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:YesNoEnum ; + owl:onProperty nmdc:dna_dnase ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:gold_biosample_identifiers ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:dna_seq_project_pi ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:source_mat_id ], + owl:onProperty nmdc:habitat ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:AnalysisTypeEnum ; + owl:onProperty nmdc:analysis_type ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:micro_biomass_n_meth ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:Boolean ; + owl:onProperty nmdc:embargoed ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:collection_time ], + owl:onProperty nmdc:soluble_iron_micromol ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:season_precpt ], + owl:onProperty nmdc:dna_isolate_meth ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:non_microb_biomass_method ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:nitrite_nitrogen ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:location ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledIdentifiedTermValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:SampSubtypeEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:proport_woa_temperature ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:lbceq ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:dna_project_contact ], + owl:onProperty nmdc:ecosystem_type ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:dna_absorb2 ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:ecosystem ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty nmdc:manganese ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:ecosystem_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:soluble_iron_micromol ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:CeilTextureEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:WindowMatEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gold_biosample_identifiers ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:dna_absorb1 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:WindowVertPosEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:WaterFeatTypeEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:dna_seq_project_pi ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:experimental_factor_other ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:sample_collection_site ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:cur_vegetation ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem_type ], + owl:onProperty nmdc:rna_seq_project_name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:onProperty nmdc:other_treatment ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$" ] ) ] ; - owl:onProperty nmdc:img_identifiers ], + owl:allValuesFrom nmdc:TillageEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:dna_absorb1 ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:WeekdayEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:emsl_biosample_identifiers ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:dna_absorb2 ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TrainStopLocEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:other_treatment ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_concentration ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:subsurface_depth ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:ammonium_nitrogen ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:subsurface_depth ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:zinc ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:slope_aspect ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:habitat ], + owl:allValuesFrom nmdc:TrainStatLocEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:tot_org_carb ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:soluble_iron_micromol ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:env_local_scale ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:Float [ a rdfs:Datatype ; - owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; - owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:maxInclusive 1000 ] ) ] ) ] ; - owl:onProperty nmdc:dna_volume ], + owl:allValuesFrom nmdc:DrainageClassEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:isotope_exposure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ArchStrucEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:SurfMaterialEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:FloorStrucEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:HcrGeolAgeEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:non_microb_biomass_method ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:YesNoEnum ; - owl:onProperty nmdc:dna_dnase ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:rna_cont_well ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:alternative_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_absorb2 ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:host_name ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:rna_isolate_meth ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_seq_project_name ], + owl:allValuesFrom nmdc:ControlledTermValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:SeasonUseEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_container_id ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:analysis_type ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:onProperty nmdc:micro_biomass_c_meth ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuadPosEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:env_medium ], + owl:minCardinality 0 ; + owl:onProperty nmdc:dna_volume ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" ] ) ] ; - owl:onProperty nmdc:dna_cont_well ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ecosystem_subtype ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:soluble_iron_micromol ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:watering_regm ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:tot_org_carb ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:DoorTypeWoodEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:WallTextureEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty nmdc:rna_project_contact ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:type ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:RnaSampleFormatEnum ; + owl:onProperty nmdc:rna_sample_format ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:emsl_biosample_identifiers ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:WallFinishMatEnum ; 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owl:maxCardinality 1 ; - owl:onProperty nmdc:nitrite_nitrogen ], + owl:onProperty nmdc:dna_container_id ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:oxy_stat_samp ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:collection_date_inc ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; 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owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:neon_biosample_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:habitat ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:part_of ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_seq_project_pi ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:RoomTypeEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:nitrate_nitrogen ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:ph_meth ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledTermValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:FloorCondEnum ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Double ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WindowTypeEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:non_microb_biomass ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:salinity_category ], + owl:allValuesFrom nmdc:RoomCondtEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:rna_collect_site ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:rna_seq_project_pi ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:rna_cont_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:collection_time ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:cur_vegetation_meth ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TimestampValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:rna_concentration ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:org_nitro_method ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:dna_samp_id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:dna_seq_project ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:replicate_number ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledIdentifiedTermValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:SampWeatherEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:tot_org_carb ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:dna_samp_id ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:emsl_biosample_identifiers ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:rna_seq_project_pi ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], + owl:onProperty nmdc:rna_sample_format ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$" ] ) ] ; + owl:onProperty nmdc:img_identifiers ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:BiolStatEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:microbial_biomass_c ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^(cat|dog|rodent|snake|other);\\d+$" ] ) ] ) ] ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:dna_cont_well ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:alternative_identifiers ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TrainStatLocEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:DrawingsEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:collection_date_inc ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:minCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" ] ) ] ; + owl:onProperty nmdc:rna_cont_well ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledTermValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:onProperty nmdc:rna_seq_project ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_container_id ], + owl:minCardinality 0 ; + owl:onProperty nmdc:micro_biomass_n_meth ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:proposal_dna ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:proposal_dna ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FloorFinishMatEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:non_microb_biomass_method ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_sample_format ], + owl:allValuesFrom nmdc:TimestampValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:collected_from ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:gaseous_environment ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:HandidnessEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:CeilFinishMatEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:annual_precpt ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:dna_cont_well ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:lbc_thirty ], + owl:allValuesFrom nmdc:ShadingDeviceTypeEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:project_id ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:collected_from ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:dna_cont_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:nitrite_nitrogen ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:water_cont_soil_meth ], + owl:allValuesFrom nmdc:SpecificEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:add_date ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:nitrate_nitrogen ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:maxInclusive 2000 ] ) ] ) ] ; + owl:onProperty nmdc:rna_sample_name ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledTermValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:add_date ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FilterTypeEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; 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- owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:al_sat ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_absorb2 ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TimestampValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:biosample_categories ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:micro_biomass_c_meth ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; 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+ owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:specific_ecosystem ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WaterFeatTypeEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:DnaSampleFormatEnum ; + owl:onProperty nmdc:dna_sample_format ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:ControlledTermValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:rna_sample_format ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:microbial_biomass_c ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WallSurfTreatmentEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_collect_site ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:rna_organisms ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty nmdc:env_package ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:insdc_biosample_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:ControlledIdentifiedTermValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:other_treatment ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:sample_shipped ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:project_id ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:rna_project_contact ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:SrKerogTypeEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$" ] ) ] ) ] ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:RoomLocEnum ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:infiltrations ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:SubstructureTypeEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ControlledIdentifiedTermValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:igsn_biosample_identifiers ], + owl:onProperty nmdc:location ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:proposal_dna ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:IntWallCondEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:salinity_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:dnase_rna ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:RoomTypeEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_collect_site ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:salinity_category ], + owl:onProperty nmdc:technical_reps ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:non_microb_biomass ], + owl:allValuesFrom linkml:Float ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:bulk_elect_conductivity ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ owl:intersectionOf ( nmdc:Study [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd: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_\\.-]+)?$" ] ) ] ) ] ; - owl:onProperty nmdc:part_of ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:DoorMoveEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:lbc_thirty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:HostSexEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:community ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledTermValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:ControlledIdentifiedTermValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:env_package ], + owl:onProperty nmdc:insdc_biosample_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:tot_nitro_cont_meth ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:tot_org_c_meth ], + owl:onProperty nmdc:collected_from ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:tot_carb ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledIdentifiedTermValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ecosystem ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:rna_project_contact ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:SampSubtypeEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:specific_ecosystem ], + owl:onProperty nmdc:collection_time ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:JgiContTypeEnum ; - owl:onProperty nmdc:dna_cont_type ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:rna_volume ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:Float [ a rdfs:Datatype ; - owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; - owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:maxInclusive 1000 ] ) ] ) ] ; - owl:onProperty nmdc:rna_volume ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:specific_ecosystem ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:Float [ a rdfs:Datatype ; - owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; - owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:maxInclusive 2000 ] ) ] ) ] ; - owl:onProperty nmdc:dna_concentration ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:collection_time_inc ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:ControlledTermValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:WindowVertPosEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:replicate_number ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:HeatCoolTypeEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:micro_biomass_n_meth ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:RoomSampPosEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:micro_biomass_n_meth ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:rna_absorb2 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:dna_seq_project_pi ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:dna_sample_name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:salinity_meth ], + owl:onProperty nmdc:other_treatment ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledTermValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:rna_isolate_meth ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:GrowthHabitEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:lat_lon ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:ecosystem_subtype ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" ] ) ] ; - owl:onProperty nmdc:dna_cont_well ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:rna_sample_name ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TimestampValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:start_date_inc ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:microbial_biomass_n ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:WallConstTypeEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:bulk_elect_conductivity ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:dna_sample_format ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^biosample:SAM[NED]([A-Z])?[0-9]+$" ] ) ] ; - owl:onProperty nmdc:insdc_biosample_identifiers ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:WindowLocEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty nmdc:gold_biosample_identifiers ], + owl:allValuesFrom nmdc:GenderRestroomEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:RoomLocEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:SrLithologyEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:SurfMaterialEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:host_name ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; 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owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:proposal_dna ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FloorStrucEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:SurfAirContEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_volume ], + owl:allValuesFrom nmdc:BuildDocsEnum ; + owl:onProperty ], + [ a owl:Restriction ; 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owl:minCardinality 0 ; owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:SedimentTypeEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty nmdc:env_package ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:neon_biosample_identifiers ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:env_package ], [ a owl:Restriction ; 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- owl:onProperty ], + owl:allValuesFrom nmdc:SrGeolAgeEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ecosystem ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:sample_type ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:host_name ], + owl:minCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ShadingDeviceCondEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:cur_vegetation ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:zinc ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:sample_collection_site ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TimestampValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:dna_cont_type ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:tot_nitro_cont_meth ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:SampCollectPointEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:rna_isolate_meth ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:HcrGeolAgeEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:filter_method ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:proposal_rna ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:start_time_inc ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:dna_collect_site ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:igsn_biosample_identifiers ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:microbial_biomass_c ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:DrawingsEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:rna_seq_project ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:DoorMoveEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:OxyStatSampEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:insdc_biosample_identifiers ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:dna_seq_project ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ncbi_taxonomy_name ], + owl:allValuesFrom nmdc:DoorDirectEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:dna_project_contact ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:rna_seq_project_name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:nitrite_nitrogen ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:elev ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:VisMediaEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:sample_link ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:gold_biosample_identifiers ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:WallSurfTreatmentEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:allValuesFrom nmdc:SoilHorizonEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:IndoorSpaceEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:SubstructureTypeEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:isotope_exposure ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:rna_collect_site ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:rna_seq_project_name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:technical_reps ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:rna_absorb1 ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:rna_volume ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:community ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; 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+ owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:rna_absorb2 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:ControlledTermValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:al_sat_meth ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:tot_nitro_cont_meth ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:lbceq ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:GrowthHabitEnum ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:rna_project_contact ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:lbceq ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:dna_concentration ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:img_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:bulk_elect_conductivity ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:ammonium_nitrogen ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:BioticRelationshipEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ControlledIdentifiedTermValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:YesNoEnum ; + owl:onProperty nmdc:dnase_rna ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:HandidnessEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:dna_samp_id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:DoorTypeWoodEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:rna_absorb2 ], + owl:minCardinality 0 ; + owl:onProperty nmdc:non_microb_biomass ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Boolean ; - owl:onProperty nmdc:embargoed ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:rna_project_contact ], + owl:onProperty nmdc:dna_seq_project_name ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:ecosystem_category ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:sample_collection_site ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:bulk_elect_conductivity ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:nitrate_nitrogen ], + owl:allValuesFrom nmdc:IndoorSurfEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:host_name ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledTermValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:start_date_inc ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:manganese ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ExtWallOrientEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:dna_volume ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:RelSampLocEnum ; - owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:RoomConnectedEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:dnase_rna ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:ecosystem_category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:FaoClassEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ncbi_taxonomy_name ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:start_time_inc ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:dna_absorb1 ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ExtWindowOrientEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:dna_seq_project ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:lbceq ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:cur_vegetation ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:IntWallCondEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:neon_biosample_identifiers ], + owl:allValuesFrom nmdc:SampleTypeEnum ; + owl:onProperty nmdc:sample_type ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:microbial_biomass_n ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_samp_id ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:nitrate_nitrogen ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:tot_org_c_meth ], + owl:onProperty nmdc:ecosystem_subtype ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom [ owl:intersectionOf ( nmdc:Study [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd: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_\\.-]+)?$" ] ) ] ) ] ; + owl:onProperty nmdc:part_of ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:ammonium_nitrogen ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:org_nitro_method ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:mod_date ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:SampleTypeEnum ; - owl:onProperty nmdc:sample_type ], + owl:minCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:CeilFinishMatEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:WindowHorizPosEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:dna_isolate_meth ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:nitrate_nitrogen ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:collection_time ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem_category ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:CeilTypeEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:ControlledTermValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:start_time_inc ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; + owl:allValuesFrom nmdc:ControlledTermValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:start_date_inc ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:rna_absorb1 ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:FloorWaterMoldEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:tot_carb ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TimestampValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ArchStrucEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:collected_from ], + owl:onProperty nmdc:collection_date_inc ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:zinc ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:oxy_stat_samp ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:add_date ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:ecosystem_category ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WeekdayEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:lat_lon ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:lat_lon ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:elev ], + owl:onProperty nmdc:collection_time_inc ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:annual_precpt ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_isolate_meth ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:microbial_biomass_c ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:dna_container_id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:salinity_meth ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:SampDisStageEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:sample_shipped ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_dnase ], + owl:onProperty nmdc:start_time_inc ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:habitat ], + owl:onProperty nmdc:rna_samp_id ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:manganese ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem ], + owl:onProperty nmdc:rna_absorb2 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:dna_concentration ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:proport_woa_temperature ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:cur_vegetation_meth ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$" ] ) ] ) ] ; + owl:onProperty nmdc:infiltrations ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:proposal_rna ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; + owl:onProperty nmdc:alternative_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:BuildOccupTypeEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:dna_volume ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:community ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:non_microb_biomass ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:non_microb_biomass ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:collection_time_inc ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:CeilTypeEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:fire ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:mod_date ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:DoorDirectEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:salinity_category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:dna_absorb2 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:non_microb_biomass ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:rna_isolate_meth ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:proposal_dna ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ncbi_taxonomy_name ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:MechStrucEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:neon_biosample_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:rna_samp_id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ammonium_nitrogen ], + owl:allValuesFrom nmdc:SampFloorEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Float [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:maxInclusive 2000 ] ) ] ) ] ; + owl:onProperty nmdc:dna_concentration ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:SrGeolAgeEnum ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:tot_nitro_content ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:habitat ], + owl:onProperty nmdc:dna_organisms ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:extreme_event ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:bulk_elect_conductivity ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:JgiContTypeEnum ; + owl:onProperty nmdc:dna_cont_type ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExtWallOrientEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:filter_method ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:SedimentTypeEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:BuildDocsEnum ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:start_date_inc ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:igsn_biosample_identifiers ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_seq_project ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:manganese ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:mod_date ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ControlledTermValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:type ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:dna_concentration ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:Double ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WindowCondEnum ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:specific_ecosystem ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" ] ) ] ; + owl:onProperty nmdc:dna_cont_well ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:habitat ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:dna_dnase ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:collection_date_inc ], + owl:onProperty nmdc:dna_organisms ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:flooding ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:dna_absorb2 ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:lbceq ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:emsl_biosample_identifiers ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TimestampValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:rna_volume ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:water_content ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:env_local_scale ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:start_time_inc ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:BioticRelationshipEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:DoorCondEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem_subtype ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:project_id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:img_identifiers ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:isotope_exposure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^biosample:SAM[NED]([A-Z])?[0-9]+$" ] ) ] ; + owl:onProperty nmdc:insdc_biosample_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:micro_biomass_n_meth ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:tot_nitro_content ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:neon_biosample_identifiers ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:start_date_inc ], + owl:onProperty nmdc:dna_seq_project_name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:rna_absorb1 ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:collection_date_inc ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:zinc ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:micro_biomass_c_meth ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:sample_shipped ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^gold:Gb[0-9]+$" ] ) ] ) ] ; + owl:onProperty nmdc:gold_biosample_identifiers ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:micro_biomass_c_meth ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:other_treatment ], + owl:onProperty nmdc:non_microb_biomass_method ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_organisms ], + owl:allValuesFrom nmdc:CeilTextureEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" ] ) ] ; - owl:onProperty nmdc:rna_cont_well ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:AnalysisTypeEnum ; - owl:onProperty nmdc:analysis_type ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_sample_name ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:nitrate_nitrogen ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:dna_seq_project_pi ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:RoomSampPosEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:subsurface_depth ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:WindowTypeEnum ; 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owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:env_medium ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:SrDepEnvEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:tot_nitro_content ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:microbial_biomass_n ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:manganese ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:sample_link ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:env_package ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:SampFloorEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:dna_project_contact ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:DoorLocEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:technical_reps ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:start_time_inc ], + owl:allValuesFrom nmdc:TidalStageEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:manganese ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:climate_environment ], + owl:onProperty nmdc:rna_container_id ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WallFinishMatEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:rna_sample_name ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ammonium_nitrogen ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty nmdc:sample_shipped ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:lbc_thirty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:microbial_biomass_n ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:dna_seq_project_pi ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:salinity_meth ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:SeasonUseEnum ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_isolate_meth ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty nmdc:micro_biomass_c_meth ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:sample_collection_site ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:water_cont_soil_meth ], + owl:allValuesFrom nmdc:FloorFinishMatEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:slope_gradient ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:OccupDocumentEnum ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:ammonium_nitrogen ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:BiosampleCategoryEnum ; + owl:onProperty nmdc:biosample_categories ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FurnitureEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:rna_cont_well ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$" ] ) ] ) ] ; - owl:onProperty nmdc:fire ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:other_treatment ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:img_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:rna_organisms ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:intersectionOf ( linkml:Float [ a rdfs:Datatype ; @@ -22816,223 +22742,205 @@ nmdc:Biosample a owl:Class, owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; owl:onDatatype xsd:integer ; owl:withRestrictions ( [ xsd:maxInclusive 1000 ] ) ] ) ] ; - owl:onProperty nmdc:rna_concentration ], + owl:onProperty nmdc:rna_volume ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:nitrite_nitrogen ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:nitrate_nitrogen ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:SampCaptStatusEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:ncbi_taxonomy_name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:FaoClassEnum ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:rna_absorb1 ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_cont_well ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:org_nitro_method ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:CeilCondEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:specific_ecosystem ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:lbc_thirty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WallLocEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:collection_time_inc ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ecosystem_type ], + owl:onProperty nmdc:manganese ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_cont_type ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:watering_regm ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:al_sat ], + owl:allValuesFrom nmdc:VisMediaEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:gold_biosample_identifiers ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:lbceq ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TimestampValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:env_local_scale ], + owl:allValuesFrom nmdc:HcrEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:season_precpt ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:YesNoEnum ; - owl:onProperty nmdc:dnase_rna ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ph_meth ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:RoomCondtEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:FloorCondEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:SampDisStageEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:SrLithologyEnum ; + owl:onProperty ], nmdc:MaterialEntity ; owl:hasKey ( ) ; skos:altLabel "biospecimen", @@ -23215,51 +23123,6 @@ nmdc:FloorStrucEnum a owl:Class, , . -nmdc:NamedThing a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedThing" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:description ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:description ], - [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; - owl:onProperty nmdc:alternative_identifiers ], - [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:alternative_identifiers ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:description ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ] ; - skos:definition "a databased entity or concept/class" ; - skos:inScheme nmdc:core . - nmdc:SampCollectPointEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -23275,279 +23138,290 @@ nmdc:Study a owl:Class, linkml:ClassDefinition ; rdfs:label "Study" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:principal_investigator ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:jgi_portal_study_identifiers ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:associated_dois ], + [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^jgi.proposal:\\d+$" ] ) ] ; owl:onProperty nmdc:jgi_portal_study_identifiers ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:type ], + owl:allValuesFrom nmdc:Study ; + owl:onProperty nmdc:part_of ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem_type ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:StudyCategoryEnum ; - owl:onProperty nmdc:study_category ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:objective ], + owl:onProperty nmdc:ecosystem_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:alternative_identifiers ], + owl:minCardinality 0 ; + owl:onProperty nmdc:gold_study_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:specific_ecosystem ], + owl:minCardinality 0 ; + owl:onProperty nmdc:gnps_task_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^gold:Gs[0-9]+$" ] ) ] ; - owl:onProperty nmdc:gold_study_identifiers ], + owl:allValuesFrom nmdc:StudyCategoryEnum ; + owl:onProperty nmdc:study_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:jgi_portal_study_identifiers ], + owl:onProperty nmdc:neon_study_identifiers ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:insdc_bioproject_identifiers ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:alternative_titles ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:Study ; - owl:onProperty nmdc:part_of ], + owl:onProperty nmdc:specific_ecosystem ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:gold_study_identifiers ], + owl:onProperty nmdc:notes ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:related_identifiers ], + owl:minCardinality 0 ; + owl:onProperty nmdc:relevant_protocols ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:funding_sources ], + owl:onProperty nmdc:ecosystem_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:relevant_protocols ], + owl:onProperty nmdc:alternative_titles ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem ], + owl:onProperty nmdc:relevant_protocols ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:description ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:objective ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:mgnify_project_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ecosystem_category ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:jgi_portal_study_identifiers ], + owl:onProperty nmdc:objective ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:alternative_identifiers ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:alternative_names ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ecosystem_type ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^mgnify.proj:[A-Z]+[0-9]+$" ] ) ] ; + owl:onProperty nmdc:mgnify_project_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:part_of ], + owl:onProperty nmdc:alternative_descriptions ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ecosystem ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$" ] ) ] ) ] ; + owl:onProperty nmdc:websites ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:PersonValue ; - owl:onProperty nmdc:principal_investigator ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^gold:Gs[0-9]+$" ] ) ] ; + owl:onProperty nmdc:gold_study_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gnps_task_identifiers ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:emsl_project_identifiers ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty nmdc:title ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:associated_dois ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:relevant_protocols ], + owl:onProperty nmdc:title ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:study_image ], + owl:onProperty nmdc:notes ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:onProperty nmdc:ecosystem_type ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:description ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:ecosystem_subtype ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:ecosystem_category ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:emsl_project_identifiers ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^gnps\\.task:[a-f0-9]+$" ] ) ] ; - owl:onProperty nmdc:gnps_task_identifiers ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:neon_study_identifiers ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem_subtype ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:funding_sources ], + owl:withRestrictions ( [ xsd:pattern "^bioproject:PRJ[DEN][A-Z][0-9]+$" ] ) ] ; + owl:onProperty nmdc:insdc_bioproject_identifiers ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom nmdc:CreditAssociation ; owl:onProperty nmdc:has_credit_associations ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:title ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:name ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:study_category ], + owl:onProperty nmdc:description ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem_category ], + owl:allValuesFrom nmdc:ImageValue ; + owl:onProperty nmdc:study_image ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:alternative_descriptions ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:study_category ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:funding_sources ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ecosystem_subtype ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:insdc_bioproject_identifiers ], + owl:onProperty nmdc:funding_sources ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^emsl\\.project:[0-9]{5}$" ] ) ] ; owl:onProperty nmdc:emsl_project_identifiers ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem_subtype ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:related_identifiers ], + owl:onProperty nmdc:name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:related_identifiers ], + owl:onProperty nmdc:specific_ecosystem ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:alternative_names ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ImageValue ; owl:onProperty nmdc:study_image ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:principal_investigator ], + owl:onProperty nmdc:study_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:specific_ecosystem ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gold_study_identifiers ], + owl:onProperty nmdc:description ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:notes ], + owl:onProperty nmdc:ecosystem_category ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:title ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:name ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:alternative_titles ], + owl:minCardinality 0 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:description ], + owl:onProperty nmdc:insdc_bioproject_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:websites ], + owl:minCardinality 0 ; + owl:onProperty nmdc:emsl_project_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:mgnify_project_identifiers ], + owl:onProperty nmdc:ecosystem ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:emsl_project_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:specific_ecosystem ], + owl:onProperty nmdc:jgi_portal_study_identifiers ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:gnps_task_identifiers ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; + owl:onProperty nmdc:alternative_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:insdc_bioproject_identifiers ], + owl:onProperty nmdc:ecosystem_type ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:related_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:objective ], + owl:onProperty nmdc:part_of ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:principal_investigator ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:neon_study_identifiers ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:notes ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:gold_study_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:name ], + owl:onProperty nmdc:related_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:websites ], + owl:onProperty nmdc:ecosystem_subtype ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:alternative_descriptions ], + owl:onProperty nmdc:has_credit_associations ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:Doi ; + owl:onProperty nmdc:associated_dois ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:PersonValue ; + owl:onProperty nmdc:principal_investigator ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:websites ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^mgnify.proj:[A-Z]+[0-9]+$" ] ) ] ; - owl:onProperty nmdc:mgnify_project_identifiers ], + owl:withRestrictions ( [ xsd:pattern "^gnps\\.task:[a-f0-9]+$" ] ) ] ; + owl:onProperty nmdc:gnps_task_identifiers ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:study_category ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:notes ], + owl:onProperty nmdc:neon_study_identifiers ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:principal_investigator ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:ecosystem_subtype ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:notes ], + owl:onProperty nmdc:ecosystem ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:gnps_task_identifiers ], + owl:onProperty nmdc:objective ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:title ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:alternative_names ], + owl:onProperty nmdc:ecosystem ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Doi ; - owl:onProperty nmdc:associated_dois ], + owl:minCardinality 0 ; + owl:onProperty nmdc:alternative_names ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:neon_study_identifiers ], + owl:minCardinality 0 ; + owl:onProperty nmdc:name ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:CreditAssociation ; - owl:onProperty nmdc:has_credit_associations ], + owl:minCardinality 0 ; + owl:onProperty nmdc:mgnify_project_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem_type ], + owl:onProperty nmdc:mgnify_project_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem ], + owl:onProperty nmdc:insdc_bioproject_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:description ], + owl:onProperty nmdc:related_identifiers ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:alternative_titles ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:alternative_identifiers ], nmdc:NamedThing ; skos:altLabel "investigation", "project", @@ -23573,113 +23447,23 @@ nmdc:VisMediaEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; linkml:permissible_values , - , - , - , - , - , - . - -nmdc:WeekdayEnum a owl:Class, - linkml:EnumDefinition ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - . - -nmdc:WorkflowExecutionActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "WorkflowExecutionActivity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:execution_resource ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:has_output ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:execution_resource ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:version ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:ended_at_time ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:execution_resource ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:has_input ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ended_at_time ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:started_at_time ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:git_url ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:has_output ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:git_url ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ended_at_time ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:part_of ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:started_at_time ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:part_of ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:started_at_time ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:version ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:has_input ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:git_url ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:version ], - nmdc:Activity ; - skos:altLabel "analysis" ; - skos:definition "Represents an instance of an execution of a particular workflow" ; - skos:inScheme nmdc:workflow_execution_activity ; - skos:note "Each instance of this (and all other) activities is a distinct run with start and stop times, potentially with different inputs and outputs" . + , + , + , + , + , + . + +nmdc:WeekdayEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + . nmdc:BiolStatEnum a owl:Class, linkml:EnumDefinition ; @@ -23802,13 +23586,268 @@ nmdc:SurfAirContEnum a owl:Class, , . -nmdc:has_output a owl:ObjectProperty, +nmdc:WorkflowExecutionActivity a owl:Class, + linkml:ClassDefinition ; + rdfs:label "WorkflowExecutionActivity" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:ended_at_time ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:started_at_time ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:ended_at_time ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:git_url ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:started_at_time ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:FailureCategorization ; + owl:onProperty nmdc:has_failure_categorization ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:NamedThing ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:execution_resource ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:qc_comment ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:qc_status ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:ended_at_time ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:execution_resource ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:part_of ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:NamedThing ; + owl:onProperty nmdc:part_of ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:StatusEnum ; + owl:onProperty nmdc:qc_status ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:started_at_time ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:qc_comment ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:qc_comment ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:qc_status ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:version ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:git_url ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:execution_resource ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:git_url ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:NamedThing ; + owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:version ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_failure_categorization ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:version ], + nmdc:Activity ; + skos:altLabel "analysis" ; + skos:definition "Represents an instance of an execution of a particular workflow" ; + skos:inScheme nmdc:workflow_execution_activity ; + skos:note "Each instance of this (and all other) activities is a distinct run with start and stop times, potentially with different inputs and outputs" . + +nmdc:name a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "has_output" ; - rdfs:domain nmdc:NamedThing ; - rdfs:range nmdc:NamedThing ; - skos:altLabel "output" ; - skos:definition "An output biosample to a processing step" ; + rdfs:label "name" ; + rdfs:range linkml:String ; + skos:definition "A human readable label for an entity" ; + skos:inScheme nmdc:basic_slots . + +nmdc:NamedThing a owl:Class, + linkml:ClassDefinition ; + rdfs:label "NamedThing" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:alternative_identifiers ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:description ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:name ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:name ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:description ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; + owl:onProperty nmdc:alternative_identifiers ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:description ] ; + skos:definition "a databased entity or concept/class" ; + skos:inScheme nmdc:core . + +nmdc:PlannedProcess a owl:Class, + linkml:ClassDefinition ; + rdfs:label "PlannedProcess" ; + dcterms:title "Planned Process" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty nmdc:designated_class ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:instrument_name ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:instrument_name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:qc_status ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:StatusEnum ; + owl:onProperty nmdc:qc_status ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:end_date ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:start_date ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ProcessingInstitutionEnum ; + owl:onProperty nmdc:processing_institution ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:NamedThing ; + owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:qc_comment ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:end_date ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:qc_status ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:processing_institution ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:start_date ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:designated_class ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_failure_categorization ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:processing_institution ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:start_date ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:designated_class ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:instrument_name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:protocol_link ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:NamedThing ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:FailureCategorization ; + owl:onProperty nmdc:has_failure_categorization ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:end_date ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:protocol_link ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:qc_comment ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:qc_comment ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:Protocol ; + owl:onProperty nmdc:protocol_link ], + nmdc:NamedThing ; + skos:exactMatch OBI:0000011 ; skos:inScheme nmdc:core . nmdc:DoiProviderEnum a owl:Class, @@ -23850,80 +23889,6 @@ nmdc:MechStrucEnum a owl:Class, , . -nmdc:PlannedProcess a owl:Class, - linkml:ClassDefinition ; - rdfs:label "PlannedProcess" ; - dcterms:title "Planned Process" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:designated_class ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:processing_institution ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:end_date ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:start_date ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:end_date ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:start_date ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_output ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:Protocol ; - owl:onProperty nmdc:protocol_link ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ProcessingInstitutionEnum ; - owl:onProperty nmdc:processing_institution ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:instrument_name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:start_date ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:designated_class ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_input ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:instrument_name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:end_date ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:protocol_link ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:has_input ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:processing_institution ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:instrument_name ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:has_output ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:protocol_link ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:designated_class ], - nmdc:NamedThing ; - skos:exactMatch OBI:0000011 ; - skos:inScheme nmdc:core . - nmdc:RoomSampPosEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -23963,12 +23928,14 @@ nmdc:TillageEnum a owl:Class, , . -nmdc:name a owl:ObjectProperty, +nmdc:has_output a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "name" ; - rdfs:range linkml:String ; - skos:definition "A human readable label for an entity" ; - skos:inScheme nmdc:basic_slots . + rdfs:label "has_output" ; + rdfs:domain nmdc:NamedThing ; + rdfs:range nmdc:NamedThing ; + skos:altLabel "output" ; + skos:definition "An output biosample to a processing step" ; + skos:inScheme nmdc:core . nmdc:CeilFinishMatEnum a owl:Class, linkml:EnumDefinition ; @@ -23984,6 +23951,22 @@ nmdc:CeilFinishMatEnum a owl:Class, , . +nmdc:ControlledTermValue a owl:Class, + linkml:ClassDefinition ; + rdfs:label "ControlledTermValue" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:term ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:OntologyClass ; + owl:onProperty nmdc:term ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:term ], + nmdc:AttributeValue ; + skos:definition "A controlled term or class from an ontology" ; + skos:inScheme nmdc:core . + nmdc:DoorMatEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -24012,6 +23995,20 @@ nmdc:DoorTypeWoodEnum a owl:Class, , . +nmdc:FailureWhereEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + . + nmdc:has_input a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "has_input" ; @@ -24021,22 +24018,6 @@ nmdc:has_input a owl:ObjectProperty, skos:definition "An input to a process." ; skos:inScheme nmdc:core . -nmdc:ControlledTermValue a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ControlledTermValue" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:term ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:OntologyClass ; - owl:onProperty nmdc:term ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:term ], - nmdc:AttributeValue ; - skos:definition "A controlled term or class from an ontology" ; - skos:inScheme nmdc:core . - nmdc:RoomConnectedEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -24078,227 +24059,227 @@ nmdc:Database a owl:Class, linkml:ClassDefinition ; rdfs:label "Database" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:read_qc_analysis_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetagenomeAnnotationActivity ; - owl:onProperty nmdc:metagenome_annotation_activity_set ], + owl:allValuesFrom nmdc:OmicsProcessing ; + owl:onProperty nmdc:omics_processing_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:MagsAnalysisActivity ; - owl:onProperty nmdc:mags_activity_set ], + owl:allValuesFrom nmdc:Study ; + owl:onProperty nmdc:study_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:library_preparation_set ], + owl:allValuesFrom nmdc:FunctionalAnnotation ; + owl:onProperty nmdc:functional_annotation_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:mags_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:DataObject ; - owl:onProperty nmdc:data_object_set ], + owl:onProperty nmdc:metagenome_assembly_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:functional_annotation_set ], + owl:minCardinality 0 ; + owl:onProperty nmdc:read_based_taxonomy_analysis_activity_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FieldResearchSite ; - owl:onProperty nmdc:field_research_site_set ], + owl:minCardinality 0 ; + owl:onProperty nmdc:metagenome_annotation_activity_set ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:metatranscriptome_activity_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:collecting_biosamples_from_site_set ], + owl:allValuesFrom nmdc:Pooling ; + owl:onProperty nmdc:pooling_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FunctionalAnnotation ; - owl:onProperty nmdc:functional_annotation_set ], + owl:minCardinality 0 ; + owl:onProperty nmdc:library_preparation_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:metagenome_sequencing_activity_set ], + owl:onProperty nmdc:activity_set ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:planned_process_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:metabolomics_analysis_activity_set ], + owl:onProperty nmdc:read_qc_analysis_activity_set ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:metagenome_annotation_activity_set ], [ a owl:Restriction ; owl:allValuesFrom nmdc:PlannedProcess ; owl:onProperty nmdc:planned_process_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:functional_annotation_set ], + owl:onProperty nmdc:field_research_site_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:activity_set ], + owl:onProperty nmdc:functional_annotation_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:LibraryPreparation ; - owl:onProperty nmdc:library_preparation_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:read_based_taxonomy_analysis_activity_set ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:library_preparation_set ], + owl:allValuesFrom nmdc:FieldResearchSite ; + owl:onProperty nmdc:field_research_site_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:metaproteomics_analysis_activity_set ], + owl:allValuesFrom nmdc:CollectingBiosamplesFromSite ; + owl:onProperty nmdc:collecting_biosamples_from_site_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:genome_feature_set ], + owl:onProperty nmdc:omics_processing_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:metagenome_sequencing_activity_set ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:read_based_taxonomy_analysis_activity_set ], + owl:onProperty nmdc:metabolomics_analysis_activity_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Biosample ; - owl:onProperty nmdc:biosample_set ], + owl:allValuesFrom nmdc:WorkflowExecutionActivity ; + owl:onProperty nmdc:activity_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:OmicsProcessing ; - owl:onProperty nmdc:omics_processing_set ], + owl:minCardinality 0 ; + owl:onProperty nmdc:processed_sample_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:planned_process_set ], + owl:onProperty nmdc:metagenome_sequencing_activity_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:read_qc_analysis_activity_set ], + owl:onProperty nmdc:biosample_set ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:MetagenomeAnnotationActivity ; + owl:onProperty nmdc:metagenome_annotation_activity_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:data_object_set ], + owl:onProperty nmdc:omics_processing_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ProcessedSample ; - owl:onProperty nmdc:processed_sample_set ], + owl:allValuesFrom nmdc:ReadBasedTaxonomyAnalysisActivity ; + owl:onProperty nmdc:read_based_taxonomy_analysis_activity_set ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:nom_analysis_activity_set ], + owl:allValuesFrom nmdc:MagsAnalysisActivity ; + owl:onProperty nmdc:mags_activity_set ], [ a owl:Restriction ; owl:allValuesFrom nmdc:MetaproteomicsAnalysisActivity ; owl:onProperty nmdc:metaproteomics_analysis_activity_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:mags_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:Pooling ; - owl:onProperty nmdc:pooling_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:CollectingBiosamplesFromSite ; - owl:onProperty nmdc:collecting_biosamples_from_site_set ], + owl:onProperty nmdc:study_set ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:metagenome_assembly_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:data_object_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:biosample_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:WorkflowExecutionActivity ; - owl:onProperty nmdc:activity_set ], + owl:onProperty nmdc:genome_feature_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:NomAnalysisActivity ; - owl:onProperty nmdc:nom_analysis_activity_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:collecting_biosamples_from_site_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ReadQcAnalysisActivity ; - owl:onProperty nmdc:read_qc_analysis_activity_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:metatranscriptome_activity_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetagenomeSequencingActivity ; - owl:onProperty nmdc:metagenome_sequencing_activity_set ], + owl:allValuesFrom nmdc:Biosample ; + owl:onProperty nmdc:biosample_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:omics_processing_set ], + owl:onProperty nmdc:mags_activity_set ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:pooling_set ], + owl:allValuesFrom nmdc:NomAnalysisActivity ; + owl:onProperty nmdc:nom_analysis_activity_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:biosample_set ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:metaproteomics_analysis_activity_set ], + owl:onProperty nmdc:genome_feature_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:pooling_set ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:DataObject ; + owl:onProperty nmdc:data_object_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:metagenome_annotation_activity_set ], + owl:onProperty nmdc:read_qc_analysis_activity_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:omics_processing_set ], + owl:onProperty nmdc:metabolomics_analysis_activity_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:study_set ], + owl:onProperty nmdc:metaproteomics_analysis_activity_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:field_research_site_set ], + owl:allValuesFrom nmdc:ProcessedSample ; + owl:onProperty nmdc:processed_sample_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:metatranscriptome_activity_set ], + owl:minCardinality 0 ; + owl:onProperty nmdc:metagenome_sequencing_activity_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:extraction_set ], + owl:allValuesFrom nmdc:GenomeFeature ; + owl:onProperty nmdc:genome_feature_set ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ReadQcAnalysisActivity ; + owl:onProperty nmdc:read_qc_analysis_activity_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:metabolomics_analysis_activity_set ], + owl:onProperty nmdc:functional_annotation_agg ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:nom_analysis_activity_set ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:planned_process_set ], + owl:onProperty nmdc:library_preparation_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetagenomeAssembly ; - owl:onProperty nmdc:metagenome_assembly_set ], + owl:allValuesFrom nmdc:MetatranscriptomeActivity ; + owl:onProperty nmdc:metatranscriptome_activity_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:data_object_set ], + owl:onProperty nmdc:functional_annotation_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:genome_feature_set ], + owl:onProperty nmdc:data_object_set ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty nmdc:pooling_set ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:field_research_site_set ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:collecting_biosamples_from_site_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:processed_sample_set ], + owl:allValuesFrom nmdc:MetagenomeAssembly ; + owl:onProperty nmdc:metagenome_assembly_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetatranscriptomeActivity ; - owl:onProperty nmdc:metatranscriptome_activity_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:activity_set ], [ a owl:Restriction ; owl:allValuesFrom nmdc:Extraction ; owl:onProperty nmdc:extraction_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetabolomicsAnalysisActivity ; - owl:onProperty nmdc:metabolomics_analysis_activity_set ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:activity_set ], [ a owl:Restriction ; owl:allValuesFrom nmdc:FunctionalAnnotationAggMember ; owl:onProperty nmdc:functional_annotation_agg ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:metagenome_annotation_activity_set ], + owl:onProperty nmdc:planned_process_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:functional_annotation_agg ], + owl:onProperty nmdc:study_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:read_based_taxonomy_analysis_activity_set ], + owl:allValuesFrom nmdc:MetabolomicsAnalysisActivity ; + owl:onProperty nmdc:metabolomics_analysis_activity_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:processed_sample_set ], + owl:onProperty nmdc:nom_analysis_activity_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:GenomeFeature ; - owl:onProperty nmdc:genome_feature_set ], + owl:minCardinality 0 ; + owl:onProperty nmdc:mags_activity_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ReadBasedTaxonomyAnalysisActivity ; - owl:onProperty nmdc:read_based_taxonomy_analysis_activity_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:processed_sample_set ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:study_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:nom_analysis_activity_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Study ; - owl:onProperty nmdc:study_set ], + owl:minCardinality 0 ; + owl:onProperty nmdc:extraction_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:metagenome_assembly_set ], + owl:onProperty nmdc:extraction_set ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:metaproteomics_analysis_activity_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:extraction_set ] ; + owl:onProperty nmdc:biosample_set ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:LibraryPreparation ; + owl:onProperty nmdc:library_preparation_set ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:MetagenomeSequencingActivity ; + owl:onProperty nmdc:metagenome_sequencing_activity_set ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:metagenome_assembly_set ] ; skos:altLabel "NMDC metadata object" ; skos:definition "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. For MongoDB, the lists of objects that Database slots point to correspond to **collections**." ; skos:inScheme nmdc:nmdc . @@ -24593,6 +24574,14 @@ nmdc:StationaryPhaseEnum a owl:Class, , . +nmdc:type a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "type" ; + rdfs:range linkml:String ; + rdfs:seeAlso ; + skos:definition "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects." ; + skos:inScheme nmdc:basic_slots . + nmdc:RoomTypeEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -24652,14 +24641,6 @@ nmdc:FaoClassEnum a owl:Class, , . -nmdc:type a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "type" ; - rdfs:range linkml:String ; - rdfs:seeAlso ; - skos:definition "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects." ; - skos:inScheme nmdc:basic_slots . - nmdc:PlantSexEnum a owl:Class, linkml:EnumDefinition ; owl:unionOf ( ) ; @@ -24840,10 +24821,10 @@ nmdc:TextValue a owl:Class, owl:minCardinality 0 ; owl:onProperty nmdc:language ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:language_code ; + owl:maxCardinality 1 ; owl:onProperty nmdc:language ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:language_code ; owl:onProperty nmdc:language ], nmdc:AttributeValue ; skos:definition "A basic string value" ; @@ -24853,50 +24834,50 @@ nmdc:QuantityValue a owl:Class, linkml:ClassDefinition ; rdfs:label "QuantityValue" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_numeric_value ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:has_unit ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_minimum_numeric_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:has_minimum_numeric_value ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:has_maximum_numeric_value ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Double ; + owl:minCardinality 0 ; owl:onProperty nmdc:has_numeric_value ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:has_maximum_numeric_value ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:has_numeric_value ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:has_unit ], + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:has_raw_value ], + owl:onProperty nmdc:has_maximum_numeric_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:has_raw_value ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; owl:onProperty nmdc:has_minimum_numeric_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:has_numeric_value ], + owl:minCardinality 0 ; + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:has_maximum_numeric_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:unit ; owl:onProperty nmdc:has_unit ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_minimum_numeric_value ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_unit ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_minimum_numeric_value ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Double ; + owl:onProperty nmdc:has_numeric_value ], nmdc:AttributeValue ; skos:definition "A simple quantity, e.g. 2cm" ; skos:inScheme nmdc:core ; @@ -24909,32 +24890,15 @@ nmdc:QuantityValue a owl:Class, skos:inScheme . [] a owl:Restriction ; - rdfs:subClassOf nmdc:Extraction ; - owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:Extraction . - -[] a owl:Restriction ; - rdfs:subClassOf nmdc:SubSamplingProcess ; + rdfs:subClassOf nmdc:CollectingBiosamplesFromSite ; owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:SubSamplingProcess . - -[] rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty nmdc:doi_provider ; - owl:someValuesFrom linkml:String ] ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:onProperty nmdc:doi_category ; - owl:someValuesFrom linkml:String ] nmdc:Doi ) . + owl:someValuesFrom nmdc:CollectingBiosamplesFromSite . [] a owl:Restriction ; rdfs:subClassOf nmdc:OmicsProcessing ; owl:onProperty nmdc:designated_class ; owl:someValuesFrom nmdc:OmicsProcessing . -[] a owl:Restriction ; - rdfs:subClassOf nmdc:BiosampleProcessing ; - owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:BiosampleProcessing . - [] a owl:Restriction ; rdfs:subClassOf nmdc:FiltrationProcess ; owl:onProperty nmdc:designated_class ; @@ -24946,9 +24910,18 @@ nmdc:QuantityValue a owl:Class, owl:someValuesFrom nmdc:MixingProcess . [] a owl:Restriction ; - rdfs:subClassOf nmdc:PlannedProcess ; + rdfs:subClassOf nmdc:SubSamplingProcess ; owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:PlannedProcess . + owl:someValuesFrom nmdc:SubSamplingProcess . + +[] rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty nmdc:dna_cont_type ; + owl:someValuesFrom linkml:String ] ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:onProperty nmdc:dna_cont_well ; + owl:someValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern ".+" ] ) ] ] nmdc:Biosample ) . [] rdfs:subClassOf [ a owl:Restriction ; owl:onProperty nmdc:dna_cont_well ; @@ -24960,42 +24933,49 @@ nmdc:QuantityValue a owl:Class, owl:someValuesFrom linkml:String ] nmdc:Biosample ) . [] a owl:Restriction ; - rdfs:subClassOf nmdc:CollectingBiosamplesFromSite ; - owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:CollectingBiosamplesFromSite . - -[] a owl:Restriction ; - rdfs:subClassOf nmdc:ChromatographicSeparationProcess ; - owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:ChromatographicSeparationProcess . - -[] a owl:Restriction ; - rdfs:subClassOf nmdc:Pooling ; + rdfs:subClassOf nmdc:LibraryPreparation ; owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:Pooling . + owl:someValuesFrom nmdc:LibraryPreparation . [] rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty nmdc:dna_cont_type ; + owl:onProperty nmdc:rna_cont_type ; owl:someValuesFrom linkml:String ] ; owl:intersectionOf ( [ a owl:Restriction ; - owl:onProperty nmdc:dna_cont_well ; + owl:onProperty nmdc:rna_cont_well ; owl:someValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern ".+" ] ) ] ] nmdc:Biosample ) . +[] a owl:Restriction ; + rdfs:subClassOf nmdc:BiosampleProcessing ; + owl:onProperty nmdc:designated_class ; + owl:someValuesFrom nmdc:BiosampleProcessing . + [] rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty nmdc:rna_cont_type ; - owl:someValuesFrom linkml:String ] ; + owl:onProperty nmdc:has_output ; + owl:someValuesFrom owl:Thing ] ; owl:intersectionOf ( [ a owl:Restriction ; - owl:onProperty nmdc:rna_cont_well ; - owl:someValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern ".+" ] ) ] ] nmdc:Biosample ) . + owl:onProperty nmdc:qc_status ; + owl:someValuesFrom linkml:String ] nmdc:WorkflowExecutionActivity ) . + +[] rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty nmdc:has_output ; + owl:someValuesFrom owl:Thing ] ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:onProperty nmdc:qc_status ; + owl:someValuesFrom linkml:String ] nmdc:WorkflowExecutionActivity ) . [] a owl:Restriction ; - rdfs:subClassOf nmdc:LibraryPreparation ; + rdfs:subClassOf nmdc:Pooling ; owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:LibraryPreparation . + owl:someValuesFrom nmdc:Pooling . + +[] rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty nmdc:doi_provider ; + owl:someValuesFrom linkml:String ] ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:onProperty nmdc:doi_category ; + owl:someValuesFrom linkml:String ] nmdc:Doi ) . [] rdfs:subClassOf [ a owl:Restriction ; owl:onProperty nmdc:rna_cont_well ; @@ -25006,3 +24986,18 @@ nmdc:QuantityValue a owl:Class, owl:onProperty nmdc:rna_cont_type ; owl:someValuesFrom linkml:String ] nmdc:Biosample ) . +[] a owl:Restriction ; + rdfs:subClassOf nmdc:ChromatographicSeparationProcess ; + owl:onProperty nmdc:designated_class ; + owl:someValuesFrom nmdc:ChromatographicSeparationProcess . + +[] a owl:Restriction ; + rdfs:subClassOf nmdc:PlannedProcess ; + owl:onProperty nmdc:designated_class ; + owl:someValuesFrom nmdc:PlannedProcess . + +[] a owl:Restriction ; + rdfs:subClassOf nmdc:Extraction ; + owl:onProperty nmdc:designated_class ; + owl:someValuesFrom nmdc:Extraction . +