diff --git a/RELEASE_NOTES_v7.7.2_to_v7.8.0.md b/CHANGELOG.md similarity index 52% rename from RELEASE_NOTES_v7.7.2_to_v7.8.0.md rename to CHANGELOG.md index 13290165a4..3ef73fe4e7 100644 --- a/RELEASE_NOTES_v7.7.2_to_v7.8.0.md +++ b/CHANGELOG.md @@ -1,3 +1,59 @@ +# Changelog + +All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/) beginning with the 8.1.0 version. Previous content was copied over without reformatting. + +Versioning for this project is based on [Semantic Versioning](https://semver.org/spec/v2.0.0.html) with the following guidelines: + +* Patch versions: changes that have no effect on the data format described by the schema. For example: updates to slot descriptions, adding examples. +* Minor versions: changes that have backwards-compatible effects on the data format. For example: adding a new, non-required slot to a class, broadening the range of a slot. +* Major version: changes that have backwards-incompatible effects of the data format. These changes will require existing data to be migrated in order to be compatible with the new version. For example: adding a required slot to a class, changing a slot from multivalued to single-valued. + +## Unreleased + +## 8.1.0 - 2023-10-03 + +### Fixed + +- Remove incorrect description of `lat_lon` slot +- Remove non-monotonic range override on `used` slot of `MetaproteomicsAnalysisActivity` class. + +## 8.0.0 - 2023-09-21 + +### Overhaul of the definition and usage of CURIe prefixes. +- Most notably, the `default_curi_maps` assertions have been +removed from all schema source file, like `src/schema/nmdc.yaml`. All prefixes that will be used in the schema +(`slot_uri`s, `mappings`, `id_prefixes`, etc.) must be defined in either `nmdc.yaml` or another source field that it +`imports`. There is now a single file that contains all prefix definitions across the merged schema: +`project/jsonld/nmdc.context.jsonld`. Note that it uses two pattern for expanding prefixes, Both are accessed from the +`@context` outer key. + - direct: `"EFO": "http://www.ebi.ac.uk/efo/"` + - via an `@id` inner key: `"ENVO": { "@id": "http://purl.obolibrary.org/obo/ENVO_"}`. +Other keys in these dictionaries can usually be ignored. +- The `GOLD` prefix is no longer allowed in the schema or any schema compliant data. Only `gold` is allowed now. +- A discussion of prefixes, CURIes, identifiers and mappings has been added: `src/docs/prefixes_curies_ids_mappings_etc.md` +- https://bioregistry.io is now consistently preferred over http://identifiers.org as a CURIe resolving service. +The version is this release is a draft, and community members are welcome to ask questions or make suggestions. + +### New data migration code: +- `Extraction`s must replace usages of the `sample_mass` slot with `input_mass` +- replacement of `GOLD` prefixes with `gold` prefixes in three classes +- updates to `src/data` files: `/valid` shows the post migration state. + +### Other +- SPARQL queries have beena dded or updated in `assets/sparql` + - see also `nmdc_schema/class_sparql.py` +- example python QC code, using LinkML SchemaView, has been added + - `nmdc_schema/list_id_prefixes_and_patterns.py` + - `nmdc_schema/list_slot_usages.py` + - `nmdc_schema/list_structured_patterns.py` +- many definitional attributes of slots have been moved out of per-class `slot_usage` blocks. +Especially in `src/schema/workflow_execution_activity.yaml`. Likewise, all class should not assert their slots with a +`slots` list, not implicitly via the `slot_usage` blocks. `required: true`, customized `range`s and customized `description`s +can still be found in `slot_usage` blocks. Not that some of these are non-monotonic and need further attention. +An exampl would be when the global definition of a slot uses an enumeration `range` but a slot_usage uses a `string` `range`. + +## 7.8.0 - 2023-08-30 + - More aggressive .gitigore for cleaner merges - for releases: git add -f examples nmdc_schema project src - Refactored Makefile and project.Makefile diff --git a/RELEASE_NOTES_v7.8.0_to_v8.0.0.md b/RELEASE_NOTES_v7.8.0_to_v8.0.0.md deleted file mode 100644 index 88c8a1536e..0000000000 --- a/RELEASE_NOTES_v7.8.0_to_v8.0.0.md +++ /dev/null @@ -1,32 +0,0 @@ -## Overhaul of the definition and usage of CURIe prefixes. -- Most notably, the `default_curi_maps` assertions have been -removed from all schema source file, like `src/schema/nmdc.yaml`. All prefixes that will be used in the schema -(`slot_uri`s, `mappings`, `id_prefixes`, etc.) must be defined in either `nmdc.yaml` or another source field that it -`imports`. There is now a single file that contains all prefix definitions across the merged schema: -`project/jsonld/nmdc.context.jsonld`. Note that it uses two pattern for expanding prefixes, Both are accessed from the -`@context` outer key. - - direct: `"EFO": "http://www.ebi.ac.uk/efo/"` - - via an `@id` inner key: `"ENVO": { "@id": "http://purl.obolibrary.org/obo/ENVO_"}`. -Other keys in these dictionaries can usually be ignored. -- The `GOLD` prefix is no longer allowed in the schema or any schema compliant data. Only `gold` is allowed now. -- A discussion of prefixes, CURIes, identifiers and mappings has been added: `src/docs/prefixes_curies_ids_mappings_etc.md` -- https://bioregistry.io is now consistently preferred over http://identifiers.org as a CURIe resolving service. -The version is this release is a draft, and community members are welcome to ask questions or make suggestions. - -## New data migration code: -- `Extraction`s must replace usages of the `sample_mass` slot with `input_mass` -- replacement of `GOLD` prefixes with `gold` prefixes in three classes -- updates to `src/data` files: `/valid` shows the post migration state. - -## Other -- SPARQL queries have beena dded or updated in `assets/sparql` - - see also `nmdc_schema/class_sparql.py` -- example python QC code, using LinkML SchemaView, has been added - - `nmdc_schema/list_id_prefixes_and_patterns.py` - - `nmdc_schema/list_slot_usages.py` - - `nmdc_schema/list_structured_patterns.py` -- many definitional attributes of slots have been moved out of per-class `slot_usage` blocks. -Especially in `src/schema/workflow_execution_activity.yaml`. Likewise, all class should not assert their slots with a -`slots` list, not implicitly via the `slot_usage` blocks. `required: true`, customized `range`s and customized `description`s -can still be found in `slot_usage` blocks. Not that some of these are non-monotonic and need further attention. -An exampl would be when the global definition of a slot uses an enumeration `range` but a slot_usage uses a `string` `range`. diff --git a/examples/output/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.ttl b/examples/output/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.ttl index 45e32c2743..0d5b09759b 100644 --- a/examples/output/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.ttl +++ b/examples/output/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.ttl @@ -217,9 +217,9 @@ nmdc:bsm-99-dtTMNb a nmdc:Biosample ; MIXS:0000647 [ a nmdc:QuantityValue ; nmdc:has_raw_value "MIxS does not provide an example" ] ; MIXS:0000652 [ a nmdc:TextValue ; - nmdc:has_raw_value "arsenic;0.09 micrograms per gram" ], + nmdc:has_raw_value "mercury;0.09 micrograms per gram" ], [ a nmdc:TextValue ; - nmdc:has_raw_value "mercury;0.09 micrograms per gram" ] ; + nmdc:has_raw_value "arsenic;0.09 micrograms per gram" ] ; MIXS:0000735 [ a nmdc:QuantityValue ; nmdc:has_raw_value "0.2 micrometer" ] ; MIXS:0000736 [ a nmdc:QuantityValue ; diff --git a/examples/output/Database-functional-annotations.ttl b/examples/output/Database-functional-annotations.ttl index 2972ec0c72..0450730895 100644 --- a/examples/output/Database-functional-annotations.ttl +++ b/examples/output/Database-functional-annotations.ttl @@ -2,33 +2,33 @@ [] a nmdc:Database ; nmdc:functional_annotation_set [ a nmdc:FunctionalAnnotation ; - nmdc:has_function "CATH:1.10.10.200" ], - [ a nmdc:FunctionalAnnotation ; - nmdc:has_function "MetaNetX:MNXR101574" ], + nmdc:has_function "EC:1.1.1.1" ], [ a nmdc:FunctionalAnnotation ; - nmdc:has_function "KEGG_PATHWAY:rsk00410" ], + nmdc:has_function "EGGNOG:veNOG12876" ], [ a nmdc:FunctionalAnnotation ; nmdc:has_function "KEGG.ORTHOLOGY:K00001" ], [ a nmdc:FunctionalAnnotation ; - nmdc:has_function "EGGNOG:veNOG12876" ], + nmdc:has_function "RHEA:12345" ], [ a nmdc:FunctionalAnnotation ; nmdc:has_function "PANTHER.FAMILY:PTHR12345" ], [ a nmdc:FunctionalAnnotation ; - nmdc:has_function "MetaCyc:RXN-14904" ], + nmdc:has_function "CATH:1.10.10.200" ], [ a nmdc:FunctionalAnnotation ; - nmdc:has_function "PFAM:PF11779" ], + nmdc:has_function "SUPFAM:SSF57615" ], [ a nmdc:FunctionalAnnotation ; - nmdc:has_function "TIGRFAM:TIGR00010" ], + nmdc:has_function "SEED:Biotin_biosynthesis" ], [ a nmdc:FunctionalAnnotation ; - nmdc:has_function "RHEA:12345" ], + nmdc:has_function "KEGG.REACTION:R00100" ], [ a nmdc:FunctionalAnnotation ; - nmdc:has_function "SEED:Biotin_biosynthesis" ], + nmdc:has_function "MetaCyc:RXN-14904" ], [ a nmdc:FunctionalAnnotation ; - nmdc:has_function "SUPFAM:SSF57615" ], + nmdc:has_function "PFAM:PF11779" ], [ a nmdc:FunctionalAnnotation ; nmdc:has_function "GO:0032571" ], [ a nmdc:FunctionalAnnotation ; - nmdc:has_function "EC:1.1.1.1" ], + nmdc:has_function "TIGRFAM:TIGR00010" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "KEGG_PATHWAY:rsk00410" ], [ a nmdc:FunctionalAnnotation ; - nmdc:has_function "KEGG.REACTION:R00100" ] . + nmdc:has_function "MetaNetX:MNXR101574" ] . diff --git a/examples/output/Database-mags-activities.ttl b/examples/output/Database-mags-activities.ttl index f60d97aeb3..247b203dc5 100644 --- a/examples/output/Database-mags-activities.ttl +++ b/examples/output/Database-mags-activities.ttl @@ -17,17 +17,6 @@ nmdc:wfmag-99-5MiDJM a nmdc:MagsAnalysisActivity ; nmdc:input_contig_num 169782 ; nmdc:low_depth_contig_num 0 ; nmdc:mags_list [ a nmdc:MagBin ; - nmdc:bin_name "bins.3" ; - nmdc:bin_quality "LQ" ; - nmdc:completeness "2.0"^^xsd:float ; - nmdc:contamination "0.0"^^xsd:float ; - nmdc:gene_count 294 ; - nmdc:num_16s 0 ; - nmdc:num_23s 0 ; - nmdc:num_5s 0 ; - nmdc:num_t_rna 1 ; - nmdc:number_of_contig 11 ], - [ a nmdc:MagBin ; nmdc:bin_name "bins.2" ; nmdc:bin_quality "LQ" ; nmdc:completeness "51.25"^^xsd:float ; @@ -38,6 +27,17 @@ nmdc:wfmag-99-5MiDJM a nmdc:MagsAnalysisActivity ; nmdc:num_5s 1 ; nmdc:num_t_rna 26 ; nmdc:number_of_contig 426 ], + [ a nmdc:MagBin ; + nmdc:bin_name "bins.3" ; + nmdc:bin_quality "LQ" ; + nmdc:completeness "2.0"^^xsd:float ; + nmdc:contamination "0.0"^^xsd:float ; + nmdc:gene_count 294 ; + nmdc:num_16s 0 ; + nmdc:num_23s 0 ; + nmdc:num_5s 0 ; + nmdc:num_t_rna 1 ; + nmdc:number_of_contig 11 ], [ a nmdc:MagBin ; nmdc:bin_name "bins.1" ; nmdc:bin_quality "LQ" ; @@ -71,16 +71,16 @@ nmdc:wfmag-99-VOgM5i a nmdc:MagsAnalysisActivity ; nmdc:input_contig_num 78376 ; nmdc:low_depth_contig_num 0 ; nmdc:mags_list [ a nmdc:MagBin ; - nmdc:bin_name "bins.3" ; + nmdc:bin_name "bins.2" ; nmdc:bin_quality "LQ" ; - nmdc:completeness "17.61"^^xsd:float ; + nmdc:completeness "0.0"^^xsd:float ; nmdc:contamination "0.0"^^xsd:float ; - nmdc:gene_count 313 ; + nmdc:gene_count 383 ; nmdc:num_16s 0 ; nmdc:num_23s 0 ; nmdc:num_5s 0 ; - nmdc:num_t_rna 7 ; - nmdc:number_of_contig 58 ], + nmdc:num_t_rna 5 ; + nmdc:number_of_contig 74 ], [ a nmdc:MagBin ; nmdc:bin_name "bins.1" ; nmdc:bin_quality "LQ" ; @@ -93,16 +93,16 @@ nmdc:wfmag-99-VOgM5i a nmdc:MagsAnalysisActivity ; nmdc:num_t_rna 4 ; nmdc:number_of_contig 74 ], [ a nmdc:MagBin ; - nmdc:bin_name "bins.2" ; + nmdc:bin_name "bins.3" ; nmdc:bin_quality "LQ" ; - nmdc:completeness "0.0"^^xsd:float ; + nmdc:completeness "17.61"^^xsd:float ; nmdc:contamination "0.0"^^xsd:float ; - nmdc:gene_count 383 ; + nmdc:gene_count 313 ; nmdc:num_16s 0 ; nmdc:num_23s 0 ; nmdc:num_5s 0 ; - nmdc:num_t_rna 5 ; - nmdc:number_of_contig 74 ] ; + nmdc:num_t_rna 7 ; + nmdc:number_of_contig 58 ] ; nmdc:name "MAGs activiity 1781_86089" ; nmdc:started_at_time "2021-01-10T00:00:00+00:00" ; nmdc:too_short_contig_num 75364 ; diff --git a/examples/output/README.md b/examples/output/README.md index e19d70e553..26a9657f1c 100644 --- a/examples/output/README.md +++ b/examples/output/README.md @@ -1,14 +1,8 @@ -## Database-biosamples-1 +## Database-biosamples-dna-in-tube ### Input ```yaml biosample_set: -- add_date: 28-JUL-14 12.00.00.000000000 AM - community: microbial communities - description: Bulk Aqueous phase filtered water - ecosystem: Environmental - ecosystem_category: Aquatic - ecosystem_subtype: Groundwater - ecosystem_type: Freshwater +- dna_cont_type: tube env_broad_scale: has_raw_value: ENVO:00002030 term: @@ -21,432 +15,76 @@ biosample_set: has_raw_value: ENVO:00005792 term: id: ENVO:00005792 - geo_loc_name: - has_raw_value: Lithgow - gold_biosample_identifiers: - - gold:Gb0101224 - habitat: Coalbed water id: nmdc:bsm-99-dtTMNb - lat_lon: - has_raw_value: -33.460524 150.168149 - latitude: -33.460524 - longitude: 150.168149 - location: from the Lithgow State Coal Mine, New South Wales, Australia - mod_date: 26-AUG-16 01.50.27.000000000 PM - name: Lithgow State Coal Mine Calcium nutrients (early) - ncbi_taxonomy_name: coal metagenome - part_of: - - gold:Gs0110115 - samp_taxon_id: - has_raw_value: coal metagenome [NCBITaxon:1260732] - term: - id: NCBITaxon:1260732 - name: coal metagenome - sample_collection_site: Lithgow State Coal Mine - specific_ecosystem: Coalbed water - type: nmdc:Biosample -- add_date: 28-JUL-14 12.00.00.000000000 AM - biosample_categories: - - LTER - - SIP - community: microbial communities - description: Bulk Aqueous phase filtered water - ecosystem: Environmental - ecosystem_category: Aquatic - ecosystem_subtype: Groundwater - ecosystem_type: Freshwater - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - geo_loc_name: - has_raw_value: Lithgow - gold_biosample_identifiers: - - gold:Gb0101224 - habitat: Coalbed water - id: nmdc:bsm-99-AtTUOs - lat_lon: - has_raw_value: -33.460524 150.168149 - latitude: -33.460524 - longitude: 150.168149 - location: from the Lithgow State Coal Mine, New South Wales, Australia - mod_date: 26-AUG-16 01.50.27.000000000 PM - name: Lithgow State Coal Mine Calcium nutrients (early) - ncbi_taxonomy_name: coal metagenome - part_of: - - gold:Gs0110115 - samp_taxon_id: - has_raw_value: coal metagenome [NCBITaxon:1260732] - term: - id: NCBITaxon:1260732 - name: coal metagenome - sample_collection_site: Lithgow State Coal Mine - specific_ecosystem: Coalbed water - type: nmdc:Biosample -- add_date: 28-JUL-14 12.00.00.000000000 AM - community: microbial communities - description: Bulk Aqueous phase filtered water - ecosystem: Environmental - ecosystem_category: Aquatic - ecosystem_subtype: Groundwater - ecosystem_type: Freshwater - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - geo_loc_name: - has_raw_value: Lithgow - gold_biosample_identifiers: - - gold:Gb0101225 - habitat: Coalbed water - id: nmdc:bsm-99-eBVHjN - lat_lon: - has_raw_value: -33.460524 150.168149 - latitude: -33.460524 - longitude: 150.168149 - location: from the Lithgow State Coal Mine, New South Wales, Australia - mod_date: 26-AUG-16 01.50.27.000000000 PM - name: Lithgow State Coal Mine Calcium nutrients Extra - ncbi_taxonomy_name: coal metagenome - part_of: - - gold:Gs0110115 - samp_taxon_id: - has_raw_value: coal metagenome [NCBITaxon:1260732] - term: - id: NCBITaxon:1260732 - name: coal metagenome - sample_collection_site: Lithgow State Coal Mine - specific_ecosystem: Coalbed water - type: nmdc:Biosample -- add_date: 28-JUL-14 12.00.00.000000000 AM - community: microbial communities - description: Bulk Aqueous phase filtered water - ecosystem: Environmental - ecosystem_category: Aquatic - ecosystem_subtype: Groundwater - ecosystem_type: Freshwater - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - geo_loc_name: - has_raw_value: Lithgow - gold_biosample_identifiers: - - gold:Gb0101226 - habitat: Coalbed water - id: nmdc:bsm-99-TDPHTh - lat_lon: - has_raw_value: -33.460524 150.168149 - latitude: -33.460524 - longitude: 150.168149 - location: from the Lithgow State Coal Mine, New South Wales, Australia - mod_date: 26-AUG-16 01.50.27.000000000 PM - name: Lithgow State Coal Mine Calcium nutrients - ncbi_taxonomy_name: coal metagenome part_of: - gold:Gs0110115 - samp_taxon_id: - has_raw_value: coal metagenome [NCBITaxon:1260732] - term: - id: NCBITaxon:1260732 - name: coal metagenome - sample_collection_site: Lithgow State Coal Mine - specific_ecosystem: Coalbed water - type: nmdc:Biosample ``` -## Database-nucleic-extraction +## Database-mags-activities ### Input ```yaml -extraction_set: -- description: DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7 - end_date: '2019-11-08' - extraction_method: phenol/chloroform extraction - extraction_target: DNA +mags_activity_set: +- binned_contig_num: 489 + ended_at_time: '2021-01-10T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov has_input: - - generic:xxx + - nmdc:0a3d00715d01ad7b8f3aee59b674dfe9 + - nmdc:668d207be5ea844f988fbfb2813564cc + - nmdc:b7e9c8d0bffdd13ace6f862a61fa87d2 has_output: - - generic:xxx - id: nmdc:extrp-99-abcdef - input_mass: - has_numeric_value: 0.25 - has_unit: gram - name: DNA extraction of NEON sample WREF_072-O-20190618-COMP - processing_institution: Battelle - start_date: '2019-11-08' - -``` -## FunctionalAnnotationAggMember-minimal -### Input -```yaml -count: 120 -gene_function_id: KEGG.ORTHOLOGY:K00627 -metagenome_annotation_id: nmdc:8253bcdcd0387177ff895c38a047c719 - -``` -## Database-extraction_set-minimal -### Input -```yaml -extraction_set: -- has_input: - - generic:xxx - has_output: - - generic:yyy - id: nmdc:extrp-99-abcdef - name: DNA extraction of NEON sample WREF_072-O-20190618-COMP - -``` -## Database-biosamples-sites -### Input -```yaml -biosample_set: -- collected_from: nmdc:frsite-99-SPreao - description: Root microbial communities from poplar common garden site in Clatskanie, - Oregon, USA - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - gold_biosample_identifiers: - - gold:Gb0305833 - id: nmdc:bsm-99-J9FcnC - name: Root microbial communities from poplar common garden site in Clatskanie, Oregon, - USA - BESC-13-CL1_35_33 endosphere - part_of: - - nmdc:sty-99-U21mUX -- collected_from: nmdc:frsite-99-SPreao - description: Rhizosphere soil microbial communities from poplar common garden site - in Clatskanie, Oregon, USA - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - gold_biosample_identifiers: - - gold:Gb0291692 - id: nmdc:bsm-99-BdlWdQ - name: Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, - Oregon, USA - BESC-13-CL1_35_33 - part_of: - - nmdc:sty-99-U21mUX -- collected_from: nmdc:frsite-99-SPreao - description: Bulk soil microbial communities from poplar common garden site in Clatskanie, - Oregon, USA - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - gold_biosample_identifiers: - - gold:Gb0291582 - id: nmdc:bsm-99-vn74Wq - name: Bulk soil microbial communities from poplar common garden site in Clatskanie, - Oregon, USA - BESC-13-CL1_35_33 - part_of: - - nmdc:sty-99-U21mUX -- collected_from: nmdc:frsite-99-h2mYFG - description: Root microbial communities from poplar common garden site in Clatskanie, - Oregon, USA - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - gold_biosample_identifiers: - - gold:Gb0305834 - id: nmdc:bsm-99-P8FdpS - name: Root microbial communities from poplar common garden site in Clatskanie, Oregon, - USA - BESC-13-CL2_39_29 endosphere - part_of: - - nmdc:sty-99-U21mUX -- collected_from: nmdc:frsite-99-h2mYFG - description: Rhizosphere soil microbial communities from poplar common garden site - in Clatskanie, Oregon, USA - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - gold_biosample_identifiers: - - gold:Gb0291693 - id: nmdc:bsm-99-ugBwz3 - name: Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, - Oregon, USA - BESC-13-CL2_39_29 - part_of: - - nmdc:sty-99-U21mUX -- collected_from: nmdc:frsite-99-h2mYFG - description: Bulk soil microbial communities from poplar common garden site in Clatskanie, - Oregon, USA - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - gold_biosample_identifiers: - - gold:Gb0291583 - id: nmdc:bsm-99-tN5lxM - name: Bulk soil microbial communities from poplar common garden site in Clatskanie, - Oregon, USA - BESC-13-CL2_39_29 - part_of: - - nmdc:sty-99-U21mUX -collecting_biosamples_from_site_set: -- has_input: - - nmdc:frsite-99-SPreao - has_output: - - nmdc:bsm-99-J9FcnC - - nmdc:bsm-99-BdlWdQ - - nmdc:bsm-99-vn74Wq - id: nmdc:clsite-99-Cq00d1 - name: Collection of biosamples from BESC-13-CL1_35_33 -- has_input: - - nmdc:frsite-99-h2mYFG - has_output: - - nmdc:bsm-99-P8FdpS - - nmdc:bsm-99-ugBwz3 - - nmdc:bsm-99-tN5lxM - id: nmdc:clsite-99-yzmLBN - name: Collection of biosamples from BESC-13-CL2_39_29 -field_research_site_set: -- description: Bioscales tree BESC-13-CL1_35_33 - id: nmdc:frsite-99-SPreao - name: BESC-13-CL1_35_33 -- description: Bioscales tree BESC-13-CL2_39_29 - id: nmdc:frsite-99-h2mYFG - name: BESC-13-CL2_39_29 - -``` -## Database-mags-activities -### Input -```yaml -mags_activity_set: -- binned_contig_num: 489 - ended_at_time: '2021-01-10T00:00:00+00:00' - execution_resource: NERSC - Cori - git_url: https://img.jgi.doe.gov - has_input: - - nmdc:0a3d00715d01ad7b8f3aee59b674dfe9 - - nmdc:668d207be5ea844f988fbfb2813564cc - - nmdc:b7e9c8d0bffdd13ace6f862a61fa87d2 - has_output: - - nmdc:818f5a47d1371295f9313909ea12eb50 - - nmdc:e0b7421514f976cb7ad8c343cf3077a9 - - nmdc:a755bb87aded36aefbd8022506a793c7 - - nmdc:1346fe25b6ff22180eb3a51204e0b1fc - id: nmdc:wfmag-99-5MiDJM - input_contig_num: 169782 - low_depth_contig_num: 0 - mags_list: - - bin_name: bins.1 - bin_quality: LQ - completeness: 11.42 - contamination: 0.21 - gene_count: 250 - num_16s: 0 - num_23s: 0 - num_5s: 1 - num_t_rna: 1 - number_of_contig: 52 - - bin_name: bins.2 - bin_quality: LQ - completeness: 51.25 - contamination: 10.34 - gene_count: 2548 - num_16s: 0 - num_23s: 0 - num_5s: 1 - num_t_rna: 26 - number_of_contig: 426 - - bin_name: bins.3 - bin_quality: LQ - completeness: 2 - contamination: 0 - gene_count: 294 - num_16s: 0 - num_23s: 0 - num_5s: 0 - num_t_rna: 1 - number_of_contig: 11 - name: MAGs activiity 1781_86101 - started_at_time: '2021-01-10T00:00:00+00:00' - too_short_contig_num: 159810 - type: nmdc:MAGsAnalysisActivity - unbinned_contig_num: 9483 - was_informed_by: gold:Gp0115663 -- binned_contig_num: 206 - ended_at_time: '2021-01-10T00:00:00+00:00' - execution_resource: NERSC - Cori - git_url: https://img.jgi.doe.gov - has_input: - - nmdc:b78f599c21fb31b00d3f8a3c56daeb88 - - nmdc:662dc676b0b5a486248357f5b887c18b - - nmdc:bc034c7024043ea88b44d0897bb5bece + - nmdc:818f5a47d1371295f9313909ea12eb50 + - nmdc:e0b7421514f976cb7ad8c343cf3077a9 + - nmdc:a755bb87aded36aefbd8022506a793c7 + - nmdc:1346fe25b6ff22180eb3a51204e0b1fc + id: nmdc:wfmag-99-5MiDJM + input_contig_num: 169782 + low_depth_contig_num: 0 + mags_list: + - bin_name: bins.1 + bin_quality: LQ + completeness: 11.42 + contamination: 0.21 + gene_count: 250 + num_16s: 0 + num_23s: 0 + num_5s: 1 + num_t_rna: 1 + number_of_contig: 52 + - bin_name: bins.2 + bin_quality: LQ + completeness: 51.25 + contamination: 10.34 + gene_count: 2548 + num_16s: 0 + num_23s: 0 + num_5s: 1 + num_t_rna: 26 + number_of_contig: 426 + - bin_name: bins.3 + bin_quality: LQ + completeness: 2 + contamination: 0 + gene_count: 294 + num_16s: 0 + num_23s: 0 + num_5s: 0 + num_t_rna: 1 + number_of_contig: 11 + name: MAGs activiity 1781_86101 + started_at_time: '2021-01-10T00:00:00+00:00' + too_short_contig_num: 159810 + type: nmdc:MAGsAnalysisActivity + unbinned_contig_num: 9483 + was_informed_by: gold:Gp0115663 +- binned_contig_num: 206 + ended_at_time: '2021-01-10T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:b78f599c21fb31b00d3f8a3c56daeb88 + - nmdc:662dc676b0b5a486248357f5b887c18b + - nmdc:bc034c7024043ea88b44d0897bb5bece has_output: - nmdc:c24915651cfdfc91f3e6b5bac679c3af - nmdc:e8ec230bfe68a272b34540e7f5ab5b2b @@ -494,205 +132,19 @@ mags_activity_set: was_informed_by: gold:Gp0115664 ``` -## DataObject-exhaustive +## Database-extraction_set-minimal ### Input ```yaml -alternative_identifiers: -- prefix:value1 -- prefix:value2 -compression_type: any string -data_object_type: Crispr Terms -description: Crispr Terms for nmdc:ann0vx38 -file_size_bytes: 1234 -id: nmdc:dobj-11-dtTMNb -md5_checksum: 22afa3d49b73eaec2e9787a6b88fbdc3 -name: Crispr Terms -type: nmdc:DataObject -url: http://example.com -was_generated_by: nmdc:invalid_id +extraction_set: +- has_input: + - generic:xxx + has_output: + - generic:yyy + id: nmdc:extrp-99-abcdef + name: DNA extraction of NEON sample WREF_072-O-20190618-COMP ``` -## Study-exhaustive -### Input -```yaml -alternative_descriptions: -- any string 1 -- any string 2 -alternative_identifiers: -- generic:abc1 -alternative_names: -- any string 1 -- any string 2 -alternative_titles: -- any string 1 -- any string 2 -description: see also name, title, objective, various alternatives -ecosystem: unconstrained text. should be validated against the controlled vocabulary, - by the sample's environmental package. would also be nice to align the CV with MIxS - environmental triads -ecosystem_category: unconstrained text -ecosystem_subtype: unconstrained text -ecosystem_type: unconstrained text -ess_dive_datasets: -- any string 1 -- any string 2 -funding_sources: -- any string 1 -- any string 2 -gold_study_identifiers: -- gold:Gs12345 -- gold:Gs90909 -has_credit_associations: -- applied_role: Funding acquisition - applied_roles: - - Supervision - - Conceptualization - applies_to_person: - email: jcventer@jcvi.org - has_raw_value: Craig Venter - name: J. Craig Venter - orcid: ORCID:0000-0002-7086-765X - profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg - was_generated_by: nmdc:any_string_1 - websites: - - https://www.jcvi.org/ - - https://www.jcvi.org/about/j-craig-venter - type: any string -- applied_roles: - - Investigation - - Supervision - applies_to_person: - name: Tanja Davidsen -id: nmdc:sty-11-ab -mgnify_project_identifiers: -- mgnify.proj:ABC123 -name: see also description, title, objective, various alternatives -objective: This record, an instance of class Study from the nmdc-schema was had authored, - so that the NMDC team would have at least one instance, using all slots, with a - mixture of reasonable values and minimally compliant values. -part_of: -- nmdc:sty-11-34xj1157 -principal_investigator: - email: jcventer@jcvi.org - has_raw_value: Craig Venter - name: J. Craig Venter - orcid: ORCID:0000-0002-7086-765X - profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg - was_generated_by: nmdc:any_string_1 - websites: - - https://www.jcvi.org/ - - https://www.jcvi.org/about/j-craig-venter -publication_dois: -- doi:10.1126/science.1058040 -publications: -- any string 1 -- any string 2 -related_identifiers: any string R1 -relevant_protocols: -- any string 1 -- any string 2 -specific_ecosystem: unconstrained text -study_category: research_study -study_image: -- description: Photo of Craig Venter Institute, Rockville, Maryland - display_order: '1' - has_raw_value: https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg - url: https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg - was_generated_by: nmdc:any_string_1 -- description: Photo of Craig Venter Institute, La Jolla, California - display_order: '2' - has_raw_value: https://today.ucsd.edu/news_uploads/140213ventor2.jpg - url: https://today.ucsd.edu/news_uploads/140213ventor2.jpg - was_generated_by: nmdc:any_string_1 -title: Sample Exhaustive Biosample instance. Although all of these values should pass - validation, that does not mean that any Biosample of any type would necessarily - have this particular combination of values. -type: any string -websites: -- https://w3id.org/nmdc -- https://w3id.org/linkml - -``` -## Database-biosamples-rna-in-tube -### Input -```yaml -biosample_set: -- env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - id: nmdc:bsm-99-dtTMNb - part_of: - - gold:Gs0110115 - rna_cont_type: tube - -``` -## Database-multiple-paths -### Input -```yaml -biosample_set: -- env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - id: nmdc:bsm-99-dtTMNb - name: real biosample from the field - part_of: - - gold:Gs0110115 -- env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - id: nmdc:bsm-99-XYZ - name: one DNA library, like an analytical sample - part_of: - - gold:Gs0110115 -omics_processing_set: -- add_date: 30-OCT-14 12.00.00.000000000 AM - alternative_identifiers: - - gold:Gp0108335 - has_input: - - gold:Gb0108335 - has_output: - - jgi:551a20d30d878525404e90d5 - id: nmdc:omprc-99-zUCd5N - mod_date: 22-MAY-20 06.13.12.927000000 PM - name: a process in which a biosample was sequenced? - ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying - carbon transformations - Permafrost 712P3D - omics_type: - has_raw_value: Metagenome - part_of: - - gold:Gs0112340 - processing_institution: JGI - type: nmdc:OmicsProcessing - -``` -## Database-metagenome-assembly +## Database-metagenome-assembly ### Input ```yaml metagenome_assembly_set: @@ -827,1306 +279,840 @@ metagenome_assembly_set: was_informed_by: gold:Gp0061275 ``` -## Database-study-set-with-dois +## Database-nom_analysis_activity_set ### Input ```yaml -study_set: -- award_dois: - - doi:10.25585/1487763 - - doi:10.25585/1487765 - dataset_dois: - - doi:10.1333/s00897980202a - - doi:10.1093/acprof:oso/9780195159561.001.1 - description: Thawing permafrost is one of the largest soil carbon pools on the planet. - The goal of this project is to study microbial communities that participate in - the soil carbon cycle. +nom_analysis_activity_set: +- ended_at_time: '2018-11-13T20:20:39+00:00' + execution_resource: xxx + git_url: xxx + has_input: + - nmdc:1 + - nmdc:2 + has_output: + - nmdc:3 + - nmdc:4 + id: nmdc:wfnom-99-abcdefg + started_at_time: '2018-11-13T20:20:39+00:00' + type: xxx + was_informed_by: nmdc:act-99-abcdefg + +``` +## Database-nmdc-example +### Input +```yaml +biosample_set: +- add_date: 17-MAR-17 04.55.54.717000000 PM + community: microbial communities + description: Permafrost microbial communities from Stordalen Mire, Sweden ecosystem: Environmental ecosystem_category: Terrestrial ecosystem_subtype: Wetlands ecosystem_type: Soil - gnps_task_identifiers: - - gnps.task:4b848c342a4f4abc871bdf8a09a60807 - gold_study_identifiers: + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: 'Sweden: Stordalen' + gold_biosample_identifiers: + - gold:Gb0150408 + habitat: Fen + id: nmdc:bsm-99-isqhuW + lat_lon: + has_raw_value: 68.35 19.05 + latitude: 68.35 + longitude: 19.05 + location: Stordalen Mire, Sweden + mod_date: 08-JAN-20 02.49.23.000000000 PM + name: Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG + ncbi_taxonomy_name: permafrost metagenome + part_of: - gold:Gs0128849 - id: nmdc:sty-99-FkQIsc - name: Permafrost microbial communities from Stordalen Mire, Sweden - principal_investigator: - has_raw_value: Virginia Rich - publication_dois: - - doi:10.21/FQSQT4T3 - - doi:10.1016/j.foodchem.2008.11.065 + samp_name: 11E1M metaG + sample_collection_site: Mire fen specific_ecosystem: Permafrost - study_category: research_study - type: nmdc:Study + type: nmdc:Biosample +- add_date: 17-AUG-17 05.38.34.719000000 PM + community: microbial communities + description: Forest soil from Barre Woods Harvard Forest LTER site was incubated + at 10C with heavy water. Sample is from a control plot at ambient soil temperature, + organic horizon - top 4cm of soil + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Unclassified + ecosystem_type: Soil + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: 'USA: Massachusetts' + gold_biosample_identifiers: + - gold:Gb0157174 + habitat: soil + id: nmdc:bsm-99-dge3H9 + lat_lon: + has_raw_value: 42.481016 -72.178343 + latitude: 42.481016 + longitude: -72.178343 + location: Barre Woods Harvard Forest LTER site, Petersham, Massachusetts, United + States + mod_date: 08-JAN-20 02.49.23.000000000 PM + name: Forest soil microbial communities from Barre Woods Harvard Forest LTER site, + Petersham, Massachusetts, United States - Inc-BW-C-14-O + ncbi_taxonomy_name: soil metagenome + part_of: + - gold:Gs0128849 + samp_name: Inc-BW-C-14-O + sample_collection_site: forest soil + specific_ecosystem: Forest Soil + type: nmdc:Biosample +- add_date: 29-MAR-18 01.27.40.709000000 PM + community: microbial communities + description: Rhizosphere microbial communities from Carex aquatilis grown in submerged + peat from a thermokarst bog, University of Washington, Seatle, WA, United States + ecosystem: Host-associated + ecosystem_category: Plants + ecosystem_subtype: Soil + ecosystem_type: Rhizosphere + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: 'USA: Seattle, Washington' + gold_biosample_identifiers: + - gold:Gb0188037 + habitat: rhizosphere + host_name: Carex aquatilis + id: nmdc:bsm-99-dc6tg6 + lat_lon: + has_raw_value: 47.6516 -122.3045 + latitude: 47.6516 + longitude: -122.3045 + location: University of Washington, Seatle, WA, United States + mod_date: 08-JAN-20 02.49.25.000000000 PM + name: Rhizosphere microbial communities from Carex aquatilis grown in University + of Washington, Seatle, WA, United States - 4-1-23 metaG + ncbi_taxonomy_name: rhizosphere metagenome + part_of: + - gold:Gs0128849 + samp_name: 4-1-23 metaG + sample_collection_site: Peat Soil + specific_ecosystem: Unclassified + type: nmdc:Biosample +data_object_set: +- description: Raw sequencer read data + file_size_bytes: 9208349052 + id: nmdc:dobj-99-dkJ8xX + name: 11340.8.202049.GTCTCCT-AAGGAGA.fastq.gz + type: nmdc:DataObject +- description: Raw sequencer read data + file_size_bytes: 34243309819 + id: nmdc:dobj-99-7zrm55 + name: 11839.4.222578.GAGCTCA-TTGAGCT.fastq.gz + type: nmdc:DataObject +- description: Raw sequencer read data + file_size_bytes: 7580035314 + id: nmdc:dobj-99-sQQw0I + name: 12660.4.274923.GATCGTAC-GTACGATC.fastq.gz + type: nmdc:DataObject +omics_processing_set: +- add_date: 17-AUG-17 05.08.38.451000000 PM + alternative_identifiers: + - gold:Gp0225767 + description: Forest soil from Barre Woods Harvard Forest LTER site was incubated + at 10C with heavy water. Sample is from a control plot at ambient soil temperature, + organic horizon - top 4cm of soil + has_input: + - gold:Gb0157174 + has_output: + - jgi:599c3a117ded5e41edd7da77 + id: nmdc:omprc-99-9XUVVF + mod_date: 16-OCT-20 02.04.01.374000000 AM + name: Forest soil microbial communities from Barre Woods Harvard Forest LTER site, + Petersham, Massachusetts, United States - Inc-BW-C-14-O + ncbi_project_name: Forest soil microbial communities from Barre Woods Harvard Forest + LTER site, Petersham, Massachusetts, United States - Inc-BW-C-14-O + omics_type: + has_raw_value: Metagenome + part_of: + - gold:Gs0130354 + processing_institution: JGI + type: nmdc:OmicsProcessing +- add_date: 17-MAR-17 04.55.44.822000000 PM + alternative_identifiers: + - gold:Gp0208560 + description: Permafrost microbial communities from Stordalen Mire, Sweden + has_input: + - gold:Gb0150408 + has_output: + - jgi:58b653757ded5e7a2af951c4 + id: nmdc:omprc-99-dk9vgI + mod_date: 22-MAY-20 06.38.19.576000000 PM + name: Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG + ncbi_project_name: Permafrost microbial communities from Stordalen Mire, Sweden + - 611E1M metaG + omics_type: + has_raw_value: Metagenome + part_of: + - gold:Gs0128849 + processing_institution: JGI + type: nmdc:OmicsProcessing +- add_date: 29-MAR-18 01.27.30.036000000 PM + alternative_identifiers: + - gold:Gp0306221 + description: Rhizosphere microbial communities from Carex aquatilis grown in submerged + peat from a thermokarst bog, University of Washington, Seatle, WA, United States + has_input: + - gold:Gb0188037 + has_output: + - jgi:5baa816646d1e63f764deb37 + id: nmdc:omprc-99-MVW1FV + mod_date: 04-APR-20 08.26.35.067000000 AM + name: Rhizosphere microbial communities from Carex aquatilis grown in University + of Washington, Seatle, WA, United States - 4-1-23 metaG + ncbi_project_name: Rhizosphere microbial communities from Carex aquatilis grown + in University of Washington, Seatle, WA, United States - 4-1-23 metaG + omics_type: + has_raw_value: Metagenome + part_of: + - gold:Gs0134277 + processing_institution: JGI + type: nmdc:OmicsProcessing +study_set: +- award_dois: + - doi:10.25585/1488217 + description: Thawing permafrost is one of the largest soil carbon pools on the planet. + The goal of this project is to study microbial communities that participate in + the soil carbon cycle. + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Wetlands + ecosystem_type: Soil + gold_study_identifiers: + - gold:Gs0128849 + id: nmdc:sty-99-FkQIsc + name: Permafrost microbial communities from Stordalen Mire, Sweden + principal_investigator: + has_raw_value: Virginia Rich + specific_ecosystem: Permafrost + study_category: research_study + type: nmdc:Study +- award_dois: + - doi:10.25585/1488215 + description: The goal of this study is to learn the molecular mechanisms underlying + changes in the temperature sensitive respiration response of forest soils to long-term + experimental warming + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Unclassified + ecosystem_type: Soil + gold_study_identifiers: + - gold:Gs0130354 + id: nmdc:sty-99-oJmAOs + name: Forest soil microbial communities from Barre Woods Harvard Forest LTER site, + Petersham, Massachusetts, United States + principal_investigator: + has_raw_value: Jeffrey Blanchard + specific_ecosystem: Forest Soil + study_category: consortium + type: nmdc:Study +- award_dois: + - doi:10.25585/1488209 + description: The goal of this study is to advance understanding of the response + of methane production and methane oxidation to changes in plant productivity so + that modeled representations of these processes and interactions can be improved. + ecosystem: Host-associated + ecosystem_category: Plants + ecosystem_subtype: Rhizosphere + ecosystem_type: Roots + gold_study_identifiers: + - gold:Gs0134277 + id: nmdc:sty-99-3bQQ4j + name: Rhizosphere microbial communities from Carex aquatilis grown in University + of Washington, Seatle, WA, United States + principal_investigator: + has_raw_value: Rebecca Neumann + specific_ecosystem: Soil + study_category: research_study + type: nmdc:Study ``` -## Database-biosample-exhasutive +## Database-study-set-with-consortia-and-parents ### Input ```yaml -biosample_set: -- abs_air_humidity: - has_raw_value: xxx - add_date: '2021-03-31' - add_recov_method: - has_raw_value: xxx - additional_info: - has_raw_value: xxx - address: - has_raw_value: xxx - adj_room: - has_raw_value: xxx - aero_struc: - has_raw_value: xxx - agrochem_addition: - - has_raw_value: lime;1 kg/acre;2022-11-16T16:05:42+0000 - air_PM_concen: - - has_raw_value: xxx - air_temp: - has_raw_value: xxx - air_temp_regm: - - has_raw_value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - al_sat: - has_raw_value: 0.1 mg/kg - al_sat_meth: - has_raw_value: https://journaljeai.com/index.php/JEAI/article/view/583 - alkalinity: - has_raw_value: 50 milligram per liter - alkalinity_method: - has_raw_value: https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity - alkyl_diethers: - has_raw_value: 0.005 mole per liter - alt: - has_raw_value: 100 meter - alternative_identifiers: - - generic:abc123 - aminopept_act: - has_raw_value: 0.269 mole per liter per hour - ammonium: - has_raw_value: 1.5 milligram per liter - ammonium_nitrogen: - has_raw_value: 0.5 milligram per liter - amount_light: - has_raw_value: xxx - analysis_type: - - metabolomics - - metagenomics - ances_data: - has_raw_value: xxx - annual_precpt: - has_raw_value: 0.5 milligram per liter - annual_temp: - has_raw_value: 12.5 degree Celsius - antibiotic_regm: - - has_raw_value: xxx - api: - has_raw_value: xxx - arch_struc: building - aromatics_pc: - has_raw_value: xxx - asphaltenes_pc: - has_raw_value: xxx - atmospheric_data: - - has_raw_value: xxx - avg_dew_point: - has_raw_value: xxx - avg_occup: - has_raw_value: xxx - avg_temp: - has_raw_value: xxx - bac_prod: - has_raw_value: xxx - bac_resp: - has_raw_value: xxx - bacteria_carb_prod: - has_raw_value: 2.53 microgram per liter per hour - barometric_press: - has_raw_value: xxx - basin: - has_raw_value: xxx - bathroom_count: - has_raw_value: xxx - bedroom_count: - has_raw_value: xxx - benzene: - has_raw_value: xxx - biochem_oxygen_dem: - has_raw_value: xxx - biocide: - has_raw_value: xxx - biocide_admin_method: - has_raw_value: xxx - biol_stat: wild - biomass: - - has_raw_value: xxx - biosample_categories: - - LTER - - FICUS - biotic_regm: - has_raw_value: sample inoculated with Rhizobium spp. Culture - biotic_relationship: parasite - bishomohopanol: - has_raw_value: 14 microgram per liter - blood_press_diast: - has_raw_value: xxx - blood_press_syst: - has_raw_value: xxx - bromide: - has_raw_value: 0.05 parts per million - build_docs: building information model - build_occup_type: - - office - building_setting: urban - built_struc_age: - has_raw_value: xxx - built_struc_set: - has_raw_value: xxx - built_struc_type: - has_raw_value: xxx - calcium: - has_raw_value: 0.2 micromole per liter - carb_dioxide: - has_raw_value: xxx - carb_monoxide: - has_raw_value: xxx - carb_nitro_ratio: - has_raw_value: '0.417361111' - ceil_area: - has_raw_value: xxx - ceil_cond: new - ceil_finish_mat: drywall - ceil_struc: - has_raw_value: xxx - ceil_texture: crows feet - ceil_thermal_mass: - has_raw_value: xxx - ceil_type: cathedral - ceil_water_mold: - has_raw_value: xxx - chem_administration: - - has_raw_value: agar [CHEBI:2509];2018-05-11T20:00Z - chem_mutagen: - - has_raw_value: xxx - chem_oxygen_dem: - has_raw_value: xxx - chem_treat_method: xxx - chem_treatment: - has_raw_value: xxx - chimera_check: - has_raw_value: xxx - chloride: - has_raw_value: 5000 milligram per liter - chlorophyll: - has_raw_value: 5 milligram per cubic meter - climate_environment: - - has_raw_value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - collected_from: nmdc:unconstrained_site_identifier_string - collection_date: - has_raw_value: xxx - collection_date_inc: '2023-01-29' - collection_time: 05:42+0000 - collection_time_inc: 13:42+0000 - community: no_example_from_mixs - conduc: - has_raw_value: xxx - cool_syst_id: - has_raw_value: xxx - crop_rotation: - has_raw_value: yes;R2/2017-01-01/2018-12-31/P6M - cult_root_med: - has_raw_value: xxx - cur_land_use: farmstead - cur_vegetation: - has_raw_value: MIxS doesn't provide any guidance more specific than "text" - cur_vegetation_meth: - has_raw_value: https://link.springer.com/article/10.1023/A:1011975321668 - date_last_rain: - has_raw_value: xxx - density: - has_raw_value: 1000 kilogram per cubic meter - depos_env: other - depth: - has_maximum_numeric_value: 2.5 - has_minimum_numeric_value: 1.5 - has_numeric_value: 2.0 - has_raw_value: 1.5 to 2.5 meters (that may not be the pattern the submission schema - expects). Extractions below require external migration logic. - has_unit: meter - description: unconstrained text - dew_point: - has_raw_value: xxx - diether_lipids: - - has_raw_value: xxx - diss_carb_dioxide: - has_raw_value: 5 milligram per liter - diss_hydrogen: - has_raw_value: 0.3 micromole per liter - diss_inorg_carb: - has_raw_value: 2059 micromole per kilogram - diss_inorg_nitro: - has_raw_value: xxx - diss_inorg_phosp: - has_raw_value: 56.5 micromole per liter - diss_iron: - has_raw_value: xxx - diss_org_carb: - has_raw_value: 197 micromole per liter - diss_org_nitro: - has_raw_value: 0.05 micromole per liter - diss_oxygen: - has_raw_value: 175 micromole per kilogram - diss_oxygen_fluid: - has_raw_value: xxx - dna_absorb1: 2.02 - dna_absorb2: 2.02 - dna_collect_site: untreated pond water - dna_concentration: 100 - dna_container_id: Pond_MT_041618 - dna_dnase: 'yes' - dna_isolate_meth: phenol/chloroform extraction - dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles - (1%) - dna_project_contact: John Jones - dna_samp_id: '187654' - dna_sample_format: 10 mM Tris-HCl - dna_sample_name: JGI_pond_041618 - dna_seq_project: '1191234' - dna_seq_project_name: JGI Pond metagenomics - dna_seq_project_pi: Jane Johnson - dna_volume: 25 - dnase_rna: 'yes' - door_comp_type: revolving - door_cond: damaged - door_direct: inward - door_loc: north - door_mat: aluminum - door_move: collapsible - door_size: - has_raw_value: xxx - door_type: composite - door_type_metal: collapsible - door_type_wood: battened - door_water_mold: - has_raw_value: xxx - down_par: - has_raw_value: xxx - drainage_class: well - drawings: operation - ecosystem: unconstrained text. should be validated against the controlled vocabulary, - by the sample's environmental package. would also be nice to align the CV with - MIxS environmental triads - ecosystem_category: unconstrained text - ecosystem_subtype: unconstrained text - ecosystem_type: unconstrained text - efficiency_percent: - has_raw_value: xxx - elev: 100 - elevator: - has_raw_value: xxx - embargoed: true - emsl_biosample_identifiers: - - generic:abc123 - emulsions: - - has_raw_value: xxx - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - env_package: - has_raw_value: unconstrained text. should require the name of a MIxS EnvironmentalPackage - class. have asked MIxS to return this term to their model. UPDATE VALIDATION - RULES/PATTERN/ENUM! - escalator: - has_raw_value: xxx - ethylbenzene: - has_raw_value: xxx - exp_duct: - has_raw_value: xxx - exp_pipe: - has_raw_value: xxx - experimental_factor: - has_raw_value: unconstrained text, unlike the MIxS environmental triad - experimental_factor_other: unconstrained text, but presumably expects 'term label - [term id]' - ext_door: - has_raw_value: xxx - ext_wall_orient: north - ext_window_orient: north - extreme_event: '2023-01-15' - fao_class: Fluvisols - fertilizer_regm: - - has_raw_value: xxx - field: - has_raw_value: xxx - filter_method: Basix PES, 13-100-106 FisherSci is an example value, but unconstrained - text is accepted at this point - filter_type: - - HEPA - fire: 2000-11 to 2000-12 - fireplace_type: - has_raw_value: xxx - flooding: '2000-01-15' - floor_age: - has_raw_value: xxx - floor_area: - has_raw_value: xxx - floor_cond: new - floor_count: - has_raw_value: xxx - floor_finish_mat: tile - floor_struc: balcony - floor_thermal_mass: - has_raw_value: xxx - floor_water_mold: condensation - fluor: - has_raw_value: xxx - freq_clean: - has_raw_value: xxx - freq_cook: - has_raw_value: xxx - fungicide_regm: - - has_raw_value: xxx - furniture: cabinet - gaseous_environment: - - has_raw_value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - gaseous_substances: - - has_raw_value: xxx - gender_restroom: female - genetic_mod: - has_raw_value: xxx - geo_loc_name: - has_raw_value: 'USA: Maryland, Bethesda' - glucosidase_act: - has_raw_value: 5 mol per liter per hour - gold_biosample_identifiers: - - gold:Gb123456789 - - gold:Gb90909090 - gravidity: - has_raw_value: xxx - gravity: - - has_raw_value: xxx - growth_facil: - has_raw_value: Growth chamber [CO_715:0000189] - growth_habit: erect - growth_hormone_regm: - - has_raw_value: xxx - habitat: unconstrained text - hall_count: - has_raw_value: xxx - handidness: ambidexterity - hc_produced: Oil - hcr: Shale - hcr_fw_salinity: - has_raw_value: xxx - hcr_geol_age: Archean - hcr_pressure: - has_raw_value: xxx - hcr_temp: - has_raw_value: xxx - heat_cool_type: - - radiant system - heat_deliv_loc: north - heat_sys_deliv_meth: xxx - heat_system_id: - has_raw_value: xxx - heavy_metals: - - has_raw_value: mercury;0.09 micrograms per gram - - has_raw_value: arsenic;0.09 micrograms per gram - heavy_metals_meth: - - has_raw_value: https://link.springer.com/article/10.1007/s42452-019-1578-x - height_carper_fiber: - has_raw_value: xxx - herbicide_regm: - - has_raw_value: xxx - horizon_meth: - has_raw_value: xxx - host_age: - has_raw_value: xxx - host_body_habitat: - has_raw_value: xxx - host_body_product: - has_raw_value: xxx - host_body_site: - has_raw_value: xxx - host_body_temp: - has_raw_value: xxx - host_color: - has_raw_value: xxx - host_common_name: - has_raw_value: xxx - host_diet: - - has_raw_value: xxx - host_dry_mass: - has_raw_value: xxx - host_family_relation: - - xxx - host_genotype: - has_raw_value: xxx - host_growth_cond: - has_raw_value: xxx - host_height: - has_raw_value: xxx - host_last_meal: - - has_raw_value: xxx - host_length: - has_raw_value: xxx - host_life_stage: - has_raw_value: xxx - host_name: snail is an example value, but unconstrained text is accepted at this - point - host_phenotype: - has_raw_value: xxx - host_sex: female - host_shape: - has_raw_value: xxx - host_subject_id: - has_raw_value: xxx - host_subspecf_genlin: - - xxx - host_substrate: - has_raw_value: xxx - host_symbiont: - - xxx - host_taxid: - has_raw_value: NCBITaxon:9606 - term: - id: NCBITaxon:9606 - host_tot_mass: - has_raw_value: xxx - host_wet_mass: - has_raw_value: xxx - humidity: - has_raw_value: xxx - humidity_regm: - - has_raw_value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - id: nmdc:bsm-99-dtTMNb - igsn_biosample_identifiers: - - any:curie_1 - - any:curie_2 - img_identifiers: - - img.taxon:abc123 - indoor_space: bedroom - indoor_surf: cabinet - indust_eff_percent: - has_raw_value: xxx - inorg_particles: - - has_raw_value: xxx - insdc_biosample_identifiers: - - biosample:SAMN123456789 - - biosample:SAMN000 - inside_lux: - has_raw_value: xxx - int_wall_cond: new - isotope_exposure: 13C glucose - iw_bt_date_well: - has_raw_value: xxx - iwf: - has_raw_value: xxx - last_clean: - has_raw_value: xxx - lat_lon: - has_raw_value: 50.586825 6.408977 - latitude: 50.586825 - longitude: 6.408977 - lbc_thirty: - has_raw_value: 543 mg/kg - lbceq: - has_raw_value: 1575 mg/kg - light_intensity: - has_raw_value: xxx - light_regm: - has_raw_value: incandescent light;10 lux;450 nanometer - light_type: - - none - link_addit_analys: - has_raw_value: https://pubmed.ncbi.nlm.nih.gov/2315679/ - link_class_info: - has_raw_value: https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf - link_climate_info: - has_raw_value: https://www.int-res.com/abstracts/cr/v14/n3/p161-173/ - lithology: Basement - local_class: - has_raw_value: jicama soil - local_class_meth: - has_raw_value: https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083 - location: unconstrained text. should we even keep this slot? check if it has been - used in MongoDB. - magnesium: - has_raw_value: 52.8 micromole per kilogram - manganese: - has_raw_value: 24.7 mg/kg - max_occup: - has_raw_value: xxx - mean_frict_vel: - has_raw_value: 0.5 meter per second - mean_peak_frict_vel: - has_raw_value: 1 meter per second - mech_struc: subway - mechanical_damage: - - has_raw_value: xxx - methane: - has_raw_value: xxx - micro_biomass_c_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 - micro_biomass_meth: xxx - micro_biomass_n_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 - microbial_biomass: - has_raw_value: xxx - microbial_biomass_c: 0.05 ug C/g dry soil - microbial_biomass_n: 0.05 ug N/g dry soil - mineral_nutr_regm: - - has_raw_value: xxx - misc_param: - - has_raw_value: Bicarbonate ion concentration;2075 micromole per kilogram - mod_date: '2023-01-25' - n_alkanes: - - has_raw_value: n-hexadecane;100 milligram per liter - name: Sample Exhaustive Biosample instance. Although all of these values should - pass validation, that does not mean that any Biosample of any type would necessarily - have this particular combination of values. - ncbi_taxonomy_name: soil metagenome - nitrate: - has_raw_value: 65 micromole per liter - nitrite: - has_raw_value: 0.5 micromole per liter - nitrite_nitrogen: - has_raw_value: 1.2 mg/kg - nitro: - has_raw_value: xxx - non_microb_biomass: insect 0.23 ug; plant 1g - non_microb_biomass_method: https://doi.org/10.1038/s41467-021-26181-3 - non_min_nutr_regm: - - xxx - nucl_acid_amp: - has_raw_value: xxx - nucl_acid_ext: - has_raw_value: xxx - number_pets: - has_raw_value: xxx - number_plants: - has_raw_value: xxx - number_resident: - has_raw_value: xxx - occup_density_samp: - has_raw_value: xxx - occup_document: estimate - occup_samp: - has_raw_value: xxx - org_carb: - has_raw_value: xxx - org_count_qpcr_info: xxx - org_matter: - has_raw_value: 1.75 milligram per cubic meter - org_nitro: - has_raw_value: 4 micromole per liter - org_nitro_method: https://doi.org/10.1016/0038-0717(85)90144-0 - org_particles: - - has_raw_value: xxx - organism_count: - - has_raw_value: ATP - other_treatment: unconstrained text - owc_tvdss: - has_raw_value: xxx - oxy_stat_samp: aerobic - oxygen: - has_raw_value: xxx - part_of: - - nmdc:unconstrained_study_identifier_string1_needs_pattern_materialization_what_about_referential_integrity - - nmdc:unconstrained_study_identifier_string2 - part_org_carb: - has_raw_value: 1.92 micromole per liter - part_org_nitro: - has_raw_value: xxx - particle_class: - - has_raw_value: xxx - pcr_cond: - has_raw_value: xxx - pcr_primers: - has_raw_value: xxx - permeability: - has_raw_value: xxx - perturbation: - - has_raw_value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M - pesticide_regm: - - has_raw_value: xxx - petroleum_hydrocarb: - has_raw_value: 0.05 micromole per liter - ph: 99.99 - ph_meth: - has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf - ph_regm: - - has_raw_value: xxx - phaeopigments: - - has_raw_value: 2.5 milligram per cubic meter - phosphate: - has_raw_value: 0.7 micromole per liter - phosplipid_fatt_acid: - - has_raw_value: 2.98 milligram per liter - photon_flux: - has_raw_value: xxx - plant_growth_med: - has_raw_value: xxx - plant_product: - has_raw_value: xxx - plant_sex: Androdioecious - plant_struc: - has_raw_value: xxx - pollutants: - - has_raw_value: xxx - pool_dna_extracts: - has_raw_value: yes, 5 - porosity: - has_raw_value: xxx - potassium: - has_raw_value: 463 milligram per liter - pour_point: - has_raw_value: xxx - pre_treatment: - has_raw_value: xxx - pres_animal_insect: cat;3 - pressure: - has_raw_value: 50 atmosphere - prev_land_use_meth: xxx - previous_land_use: - has_raw_value: xxx - primary_prod: - has_raw_value: xxx - primary_treatment: - has_raw_value: xxx - prod_rate: - has_raw_value: xxx - prod_start_date: - has_raw_value: xxx - profile_position: summit - project_id: no example from MIxS - proport_woa_temperature: no example from MIxS - proposal_dna: '504000' - proposal_rna: '504000' - quad_pos: North side - radiation_regm: - - has_raw_value: xxx - rainfall_regm: - - has_raw_value: xxx - reactor_type: - has_raw_value: xxx - redox_potential: - has_raw_value: 300 millivolt - rel_air_humidity: - has_raw_value: xxx - rel_humidity_out: - has_raw_value: xxx - rel_samp_loc: edge of car - replicate_number: '1' - reservoir: - has_raw_value: xxx - resins_pc: - has_raw_value: xxx - rna_absorb1: 2.02 - rna_absorb2: 2.02 - rna_collect_site: untreated pond water - rna_concentration: 100 - rna_container_id: Pond_MT_041618 - rna_isolate_meth: phenol/chloroform extraction - rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles - (1%) - rna_project_contact: John Jones - rna_samp_id: '187654' - rna_sample_format: 10 mM Tris-HCl - rna_sample_name: JGI_pond_041618 - rna_seq_project: '1191234' - rna_seq_project_name: JGI Pond metagenomics - rna_seq_project_pi: Jane Johnson - rna_volume: 25 - room_air_exch_rate: - has_raw_value: xxx - room_architec_elem: xxx - room_condt: new - room_connected: attic - room_count: - has_raw_value: xxx - room_dim: - has_raw_value: xxx - room_door_dist: - has_raw_value: xxx - room_door_share: - has_raw_value: xxx - room_hallway: - has_raw_value: xxx - room_loc: corner room - room_moist_dam_hist: 123 - room_net_area: - has_raw_value: xxx - room_occup: - has_raw_value: xxx - room_samp_pos: north corner - room_type: attic - room_vol: - has_raw_value: xxx - room_wall_share: - has_raw_value: xxx - room_window_count: 123 - root_cond: - has_raw_value: xxx - root_med_carbon: - has_raw_value: xxx - root_med_macronutr: - has_raw_value: xxx - root_med_micronutr: - has_raw_value: xxx - root_med_ph: - has_raw_value: xxx - root_med_regl: - has_raw_value: xxx - root_med_solid: - has_raw_value: xxx - root_med_suppl: - has_raw_value: xxx - salinity: - has_raw_value: 25 practical salinity unit - salinity_category: halotolerant is an example from the schema, but MIxS doesn't - provide this slot any more - salinity_meth: - has_raw_value: PMID:22895776 - salt_regm: - - has_raw_value: xxx - samp_capt_status: other - samp_collec_device: xxx - samp_collec_method: swabbing - samp_collect_point: well - samp_dis_stage: dissemination - samp_floor: basement - samp_loc_corr_rate: - has_raw_value: xxx - samp_mat_process: - has_raw_value: filtering of seawater - samp_md: - has_raw_value: xxx - samp_name: see also name - samp_preserv: - has_raw_value: xxx - samp_room_id: - has_raw_value: xxx - samp_size: - has_raw_value: 5 liters - samp_sort_meth: - - has_raw_value: xxx - samp_store_dur: - has_raw_value: P1Y6M - samp_store_loc: - has_raw_value: Freezer no:5 - samp_store_temp: - has_raw_value: -80 degree Celsius - samp_subtype: biofilm - samp_taxon_id: - has_raw_value: soil metagenome [NCBItaxon:410658] - term: - id: NCBItaxon:410658 - name: soil metagenome - samp_time_out: - has_raw_value: xxx - samp_transport_cond: - has_raw_value: xxx - samp_tvdss: - has_raw_value: xxx - samp_type: - has_raw_value: xxx - samp_vol_we_dna_ext: - has_raw_value: 1500 milliliter - samp_weather: cloudy - samp_well_name: - has_raw_value: xxx - sample_collection_site: unconstrained text - sample_link: - - IGSN:DSJ0284 - - any:curie - sample_shipped: 15 g - sample_type: water_extract_soil - saturates_pc: - has_raw_value: xxx - season: - has_raw_value: xxx - season_environment: - - has_raw_value: xxx - season_precpt: - has_raw_value: 75 millimeters - season_temp: - has_raw_value: 18 degree Celsius - season_use: Spring - secondary_treatment: - has_raw_value: xxx - sediment_type: biogenous - seq_meth: - has_raw_value: xxx - seq_quality_check: - has_raw_value: xxx - sewage_type: - has_raw_value: xxx - shad_dev_water_mold: xxx - shading_device_cond: damaged - shading_device_loc: - has_raw_value: xxx - shading_device_mat: - has_raw_value: xxx - shading_device_type: tree - sieving: - has_raw_value: MIxS does not provide an example - silicate: - has_raw_value: xxx - size_frac: - has_raw_value: xxx - size_frac_low: - has_raw_value: 0.2 micrometer - size_frac_up: - has_raw_value: 20 micrometer - slope_aspect: - has_raw_value: MIxS does not provide an example - slope_gradient: - has_raw_value: MIxS does not provide an example - sludge_retent_time: - has_raw_value: xxx - sodium: - has_raw_value: 10.5 milligram per liter - soil_horizon: O horizon - soil_text_measure: - has_raw_value: xxx - soil_texture_meth: xxx - soil_type: - has_raw_value: plinthosol [ENVO:00002250] - soil_type_meth: - has_raw_value: Frederick series - solar_irradiance: - has_raw_value: xxx - soluble_inorg_mat: - - has_raw_value: xxx - soluble_iron_micromol: MIxS doesn't provide an example - soluble_org_mat: - - has_raw_value: xxx - soluble_react_phosp: - has_raw_value: xxx - source_mat_id: - has_raw_value: MPI012345 - space_typ_state: - has_raw_value: xxx - specific: operation - specific_ecosystem: unconstrained text - specific_humidity: - has_raw_value: xxx - sr_dep_env: Lacustine - sr_geol_age: Archean - sr_kerog_type: other - sr_lithology: Clastic - standing_water_regm: - - has_raw_value: xxx - start_date_inc: '2023-01-27' - start_time_inc: 13:42+0000 - store_cond: - has_raw_value: -20 degree Celsius freezer;P2Y10D - substructure_type: - - basement - subsurface_depth: - has_raw_value: MIxS does not provide an example - sulfate: - has_raw_value: 5 micromole per liter - sulfate_fw: - has_raw_value: xxx - sulfide: - has_raw_value: 2 micromole per liter - surf_air_cont: - - dust - surf_humidity: - has_raw_value: xxx - surf_material: adobe - surf_moisture: - has_raw_value: xxx - surf_moisture_ph: 123 - surf_temp: - has_raw_value: xxx - suspend_part_matter: - has_raw_value: xxx - suspend_solids: - - has_raw_value: xxx - tan: - has_raw_value: xxx - target_gene: - has_raw_value: xxx - target_subfragment: - has_raw_value: xxx - technical_reps: '2' - temp: - has_raw_value: 25 degree Celsius - temp_out: - has_raw_value: xxx - tertiary_treatment: - has_raw_value: xxx - tidal_stage: high tide - tillage: - - chisel - tiss_cult_growth_med: - has_raw_value: xxx - toluene: - has_raw_value: xxx - tot_carb: - has_raw_value: MIxS does not provide an example - tot_depth_water_col: - has_raw_value: 500 meter - tot_diss_nitro: - has_raw_value: 40 microgram per liter - tot_inorg_nitro: - has_raw_value: xxx - tot_iron: - has_raw_value: xxx - tot_nitro: - has_raw_value: xxx - tot_nitro_cont_meth: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 - tot_nitro_content: - has_raw_value: 35 milligrams Nitrogen per kilogram of soil - tot_org_c_meth: - has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf - tot_org_carb: - has_raw_value: 2% - tot_part_carb: - has_raw_value: xxx - tot_phosp: - has_raw_value: 0.03 milligram per liter - tot_phosphate: - has_raw_value: xxx - tot_sulfur: - has_raw_value: xxx - train_line: red - train_stat_loc: south station above ground - train_stop_loc: end - turbidity: - has_raw_value: xxx - tvdss_of_hcr_press: - has_raw_value: xxx - tvdss_of_hcr_temp: - has_raw_value: xxx - typ_occup_density: 123 - type: nmdc:Biosample. change this to require a class name or an enumeration - ventilation_rate: - has_raw_value: xxx - ventilation_type: - has_raw_value: xxx - vfa: - has_raw_value: xxx - vfa_fw: - has_raw_value: xxx - vis_media: photos - viscosity: - has_raw_value: xxx - volatile_org_comp: - - has_raw_value: xxx - wall_area: - has_raw_value: xxx - wall_const_type: frame construction - wall_finish_mat: plaster - wall_height: - has_raw_value: xxx - wall_loc: north - wall_surf_treatment: painted - wall_texture: knockdown - wall_thermal_mass: - has_raw_value: xxx - wall_water_mold: - has_raw_value: xxx - wastewater_type: - has_raw_value: xxx - water_cont_soil_meth: MIxS doesn't provide an example - water_content: - - MIxS doesn't provide an example 1 - - MIxS doesn't provide an example 2 - water_current: - has_raw_value: xxx - water_cut: - has_raw_value: xxx - water_feat_size: - has_raw_value: xxx - water_feat_type: fountain - water_prod_rate: - has_raw_value: xxx - water_temp_regm: - - has_raw_value: xxx - watering_regm: - - has_raw_value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - weekday: Monday - win: - has_raw_value: xxx - wind_direction: - has_raw_value: xxx - wind_speed: - has_raw_value: xxx - window_cond: damaged - window_cover: blinds - window_horiz_pos: left - window_loc: north - window_mat: fiberglass - window_open_freq: - has_raw_value: xxx - window_size: - has_raw_value: xxx - window_status: - has_raw_value: xxx - window_type: single-hung sash window - window_vert_pos: bottom - window_water_mold: - has_raw_value: xxx - xylene: - has_raw_value: xxx - zinc: - has_raw_value: 2.5 mg/kg - -``` -## Database-omics-processings -### Input -```yaml -omics_processing_set: -- add_date: 30-OCT-14 12.00.00.000000000 AM - alternative_identifiers: - - gold:Gp0108335 - has_input: - - gold:Gb0108335 - has_output: - - jgi:551a20d30d878525404e90d5 - id: nmdc:omprc-99-zUCd5N - mod_date: 22-MAY-20 06.13.12.927000000 PM - name: Thawing permafrost microbial communities from the Arctic, studying carbon - transformations - Permafrost 712P3D - ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying - carbon transformations - Permafrost 712P3D - omics_type: - has_raw_value: Metagenome +study_set: +- description: The parent consortium of all the NEON consortia + id: nmdc:sty-11-34xj1152 + name: NEON Parent Consortium + study_category: consortium +- description: The National Science Foundation's National Ecological Observatory Network + (NEON) is a continental-scale observation facility operated by Battelle and designed + to collect long-term open access ecological data to better understand how U.S. + ecosystems are changing. + funding_sources: + - 'NSF#1724433 National Ecological Observatory Network: Operations Activities' + gold_study_identifiers: + - gold:Gs0144570 + - gold:Gs0161344 + id: nmdc:sty-11-34xj1150 + name: 'National Ecological Observatory Network: soil metagenomes (DP1.10107.001)' part_of: - - gold:Gs0112340 - processing_institution: JGI - type: nmdc:OmicsProcessing -- add_date: 30-OCT-14 12.00.00.000000000 AM - alternative_identifiers: - - gold:Gp0108340 - has_input: - - gold:Gb0108340 - has_output: - - jgi:551a20d50d878525404e90d7 - id: nmdc:omprc-99-gKlQlF - mod_date: 22-MAY-20 06.10.59.590000000 PM - name: Thawing permafrost microbial communities from the Arctic, studying carbon - transformations - Permafrost 612S3M - ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying - carbon transformations - Permafrost 612S3M - omics_type: - has_raw_value: Metagenome + - nmdc:sty-11-34xj1152 + principal_investigator: + email: kthibault@battelleecology.org + has_raw_value: Kate Thibault + name: Kate Thibault + orcid: orcid:0000-0003-3477-6424 + profile_image_url: https://portal.nersc.gov/project/m3408/profile_images/thibault_katy.jpg + study_category: consortium + study_image: + - url: https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg + title: 'National Ecological Observatory Network: soil metagenomes (DP1.10107.001)' + type: nmdc:Study + websites: + - https://www.neonscience.org/ + - https://data.neonscience.org/data-products/DP1.10107.001 + - https://data.neonscience.org/api/v0/documents/NEON.DOC.014048vO + - https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf +- description: The National Science Foundation's National Ecological Observatory Network + (NEON) is a continental-scale observation facility operated by Battelle and designed + to collect long-term open access ecological data to better understand how U.S. + ecosystems are changing. + funding_sources: + - 'NSF#1724433 National Ecological Observatory Network: Operations Activities' + id: nmdc:sty-11-hht5sb92 + name: 'National Ecological Observatory Network: surface water metagenomes (DP1.20281.001)' part_of: - - gold:Gs0112340 - processing_institution: JGI - type: nmdc:OmicsProcessing -- add_date: 30-OCT-14 12.00.00.000000000 AM - alternative_identifiers: - - gold:Gp0108341 - has_input: - - gold:Gb0108341 - has_output: - - jgi:551a20d90d878525404e90e1 - id: nmdc:omprc-99-5kgIJR - mod_date: 22-MAY-20 06.09.46.171000000 PM - name: Thawing permafrost microbial communities from the Arctic, studying carbon - transformations - Permafrost 712S3S - ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying - carbon transformations - Permafrost 712S3S - omics_type: - has_raw_value: Metagenome + - nmdc:sty-11-34xj1152 + principal_investigator: + email: kthibault@battelleecology.org + has_raw_value: Kate Thibault + name: Kate Thibault + orcid: orcid:0000-0003-3477-6424 + study_category: consortium + study_image: + - url: https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg + title: 'National Ecological Observatory Network: surface water metagenomes (DP1.20281.001)' + type: nmdc:Study + websites: + - https://www.neonscience.org/ + - https://data.neonscience.org/data-products/DP1.20281.001 + - https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf +- description: The National Science Foundation's National Ecological Observatory Network + (NEON) is a continental-scale observation facility operated by Battelle and designed + to collect long-term open access ecological data to better understand how U.S. + ecosystems are changing. + funding_sources: + - 'NSF#1724433 National Ecological Observatory Network: Operations Activities' + id: nmdc:sty-11-pzmd0x14 + name: 'National Ecological Observatory Network: benthic metagenomes (DP1.20279.001)' part_of: - - gold:Gs0112340 - processing_institution: JGI - type: nmdc:OmicsProcessing + - nmdc:sty-11-34xj1152 + principal_investigator: + email: kthibault@battelleecology.org + name: Kate Thibault + orcid: orcid:0000-0003-3477-6424 + study_category: consortium + study_image: + - url: https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg + title: 'National Ecological Observatory Network: benthic metagenomes (DP1.20279.001)' + type: nmdc:Study + websites: + - https://www.neonscience.org/ + - https://data.neonscience.org/data-products/DP1.20279.001 + - https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf ``` -## Database-biosamples-rna-in-plate-valid-well-val +## Biosample-embargoed ### Input ```yaml -biosample_set: -- env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - id: nmdc:bsm-99-dtTMNb - part_of: - - gold:Gs0110115 - rna_cont_type: plate - rna_cont_well: B2 +embargoed: true +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +id: nmdc:bsm-99-dtTMNb +part_of: +- gold:Gs0110115 ``` -## Database-neon_Biosample_to_DataObject_NEON +## OmicsProcessing-1 ### Input ```yaml -biosample_set: -- env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - id: nmdc:bsm-99-abcdef1 - part_of: - - nmdc:sty-11-34xj1150 -- env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - id: nmdc:bsm-99-abcdef2 - part_of: - - nmdc:sty-11-34xj1150 -- env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - id: nmdc:bsm-99-abcdef3 - part_of: - - nmdc:sty-11-34xj1150 -data_object_set: -- data_object_type: Metagenome Raw Read 1 - description: Test R1 data - id: nmdc:dobj-12-jdhk9537 - name: BMI_HY7W2BGXG_Plate19S_13WellG10_R1.fastq.gz - type: nmdc:DataObject - url: https://storage.neonscience.org/neon-microbial-raw-seq-files/2020/BMI_HY7W2BGXG_mms_R1/BMI_HY7W2BGXG_Plate19S_13WellG10_R1.fastq.gz -- data_object_type: Metagenome Raw Read 2 - description: Test R2 data - id: nmdc:dobj-12-yx0tfp52 - name: W2BGXG_Plate19S_13WellG10_R2.fastq.gz - type: nmdc:DataObject - url: https://storage.neonscience.org/neon-microbial-raw-seq-files/2020/BMI_HY7W2BGXG_mms_R2/BMI_HY7W2BGXG_Plate19S_13WellG10_R2.fastq.gz -- data_object_type: Filtered Sequencing Reads - description: Test filtered data for NEON - id: nmdc:dobj-12-71q7wv80 - name: 1472_51293.filtered.fastq.gz - type: nmdc:DataObject - url: https://data.microbiomedata.org/data/1472_51293/qa/1472_51293.filtered.fastq.gz -extraction_set: -- end_date: '2021-01-15' - extraction_target: DNA - has_input: - - nmdc:procsm-99-xyz1 - has_output: - - nmdc:procsm-99-xyz2 - id: nmdc:extrp-99-abcdef - name: first dna extraction set - start_date: '2021-01-15' -library_preparation_set: -- end_date: '2021-01-15' - has_input: - - nmdc:procsm-99-xyz2 - has_output: - - nmdc:procsm-99-xyz3 - id: nmdc:libprp-99-abcdef - library_type: DNA - name: DNA library preparation of NEON sample TREE_001-O-20170707-COMP-DNA1 - start_date: '2021-01-15' -omics_processing_set: -- has_input: - - nmdc:procsm-99-xyz3 - has_output: - - nmdc:dobj-12-jdhk9537 - - nmdc:dobj-12-yx0tfp52 - id: nmdc:omprc-11-s9xj2r24 - instrument_name: Illumina NovaSeq S4 - name: Test NEON data - omics_type: - has_raw_value: Metagenome - part_of: - - nmdc:sty-11-34xj1150 - processing_institution: Battelle - type: nmdc:OmicsProcessing -pooling_set: -- description: This is the first pooling process that has ever occurred on earth - end_date: '2021-01-14' - has_input: - - nmdc:bsm-99-abcdef1 - - nmdc:bsm-99-abcdef2 - - nmdc:bsm-99-abcdef3 - has_output: - - nmdc:procsm-99-xyz1 - id: nmdc:poolp-99-abcdef - name: first pooling process - start_date: '2021-01-14' -processed_sample_set: -- id: nmdc:procsm-99-xyz1 - name: first processed sample set -- id: nmdc:procsm-99-xyz2 - name: first DNA extract -- id: nmdc:procsm-99-xyz3 - name: first library -read_qc_analysis_activity_set: -- ended_at_time: '2023-03-23T17:17:05.111725+00:00' - execution_resource: NERSC-Cori - git_url: https://github.com/microbiomedata/ReadsQC - has_input: - - nmdc:dobj-12-jdhk9537 - - nmdc:dobj-12-yx0tfp52 - has_output: - - nmdc:dobj-12-71q7wv80 - - nmdc:dobj-12-y236qp68 - id: nmdc:wfrqc-12-63da5n74 - name: 'TEST Read QC Activity for nmdc:wfrqc-12-63da5n74 ' - part_of: - - nmdc:wfrqc-11-hcr2by04.1 - started_at_time: '2023-03-23T17:17:05.111689+00:00' - type: nmdc:ReadQCAnalysisActivity - version: b1.0.7 - was_informed_by: nmdc:omprc-11-s9xj2r24 +add_date: 30-OCT-14 12.00.00.000000000 AM +alternative_identifiers: +- gold:Gp0108335 +has_input: +- gold:Gb0108335 +has_output: +- jgi:551a20d30d878525404e90d5 +id: nmdc:omprc-99-zUCd5N +mod_date: 22-MAY-20 06.13.12.927000000 PM +name: Thawing permafrost microbial communities from the Arctic, studying carbon transformations + - Permafrost 712P3D +ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D +omics_type: + has_raw_value: Metagenome +part_of: +- gold:Gs0112340 +processing_institution: JGI +type: nmdc:OmicsProcessing + +``` +## Biosample-exhaustive-issue-796-bye-yq-for-7-4-10 +### Input +```yaml +add_date: '2021-03-31' +agrochem_addition: +- has_raw_value: lime;1 kg/acre;2022-11-16T16:05:42+0000 +air_temp_regm: +- has_raw_value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +al_sat: + has_raw_value: 0.1 mg/kg +al_sat_meth: + has_raw_value: https://journaljeai.com/index.php/JEAI/article/view/583 +alkalinity: + has_raw_value: 50 milligram per liter +alkalinity_method: + has_raw_value: https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity +alkyl_diethers: + has_raw_value: 0.005 mole per liter +alt: + has_raw_value: 100 meter +alternative_identifiers: +- generic:abc123 +aminopept_act: + has_raw_value: 0.269 mole per liter per hour +ammonium: + has_raw_value: 1.5 milligram per liter +ammonium_nitrogen: + has_raw_value: 0.5 milligram per liter +analysis_type: +- metabolomics +- metagenomics +annual_precpt: + has_raw_value: 0.5 milligram per liter +annual_temp: + has_raw_value: 12.5 degree Celsius +bacteria_carb_prod: + has_raw_value: 2.53 microgram per liter per hour +biosample_categories: +- LTER +- FICUS +biotic_regm: + has_raw_value: sample inoculated with Rhizobium spp. Culture +biotic_relationship: parasite +bishomohopanol: + has_raw_value: 14 microgram per liter +bromide: + has_raw_value: 0.05 parts per million +calcium: + has_raw_value: 0.2 micromole per liter +carb_nitro_ratio: + has_raw_value: '0.417361111' +chem_administration: +- has_raw_value: agar [CHEBI:2509];2018-05-11T20:00Z +chloride: + has_raw_value: 5000 milligram per liter +chlorophyll: + has_raw_value: 5 milligram per cubic meter +climate_environment: +- has_raw_value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +collected_from: nmdc:unconstrained_site_identifier_string +collection_date: + has_raw_value: '2018-05-11' +collection_date_inc: '2023-01-29' +collection_time: 05:42+0000 +collection_time_inc: 13:42+0000 +community: no_example_from_mixs +crop_rotation: + has_raw_value: yes;R2/2017-01-01/2018-12-31/P6M +cur_land_use: farmstead +cur_vegetation: + has_raw_value: MIxS doesn't provide any guidance more specific than "text" +cur_vegetation_meth: + has_raw_value: https://link.springer.com/article/10.1023/A:1011975321668 +density: + has_raw_value: 1000 kilogram per cubic meter +depth: + has_maximum_numeric_value: 2.5 + has_minimum_numeric_value: 1.5 + has_numeric_value: 2.0 + has_raw_value: 1.5 to 2.5 meters (that may not be the pattern the submission schema + expects). Extractions below require external migration logic. + has_unit: meter +description: unconstrained text +diss_carb_dioxide: + has_raw_value: 5 milligram per liter +diss_hydrogen: + has_raw_value: 0.3 micromole per liter +diss_inorg_carb: + has_raw_value: 2059 micromole per kilogram +diss_inorg_phosp: + has_raw_value: 56.5 micromole per liter +diss_org_carb: + has_raw_value: 197 micromole per liter +diss_org_nitro: + has_raw_value: 0.05 micromole per liter +diss_oxygen: + has_raw_value: 175 micromole per kilogram +dna_absorb1: 2.02 +dna_absorb2: 2.02 +dna_collect_site: untreated pond water +dna_concentration: 100 +dna_container_id: Pond_MT_041618 +dna_dnase: 'yes' +dna_isolate_meth: phenol/chloroform extraction +dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) +dna_project_contact: John Jones +dna_samp_id: '187654' +dna_sample_format: 10 mM Tris-HCl +dna_sample_name: JGI_pond_041618 +dna_seq_project: '1191234' +dna_seq_project_name: JGI Pond metagenomics +dna_seq_project_pi: Jane Johnson +dna_volume: 25 +dnase_rna: 'yes' +drainage_class: well +ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with MIxS + environmental triads +ecosystem_category: unconstrained text +ecosystem_subtype: unconstrained text +ecosystem_type: unconstrained text +elev: 100 +embargoed: true +emsl_biosample_identifiers: +- generic:abc123 +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +env_package: + has_raw_value: unconstrained text. should require the name of a MIxS EnvironmentalPackage + class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM! +experimental_factor: + has_raw_value: unconstrained text, unlike the MIxS environmental triad +experimental_factor_other: unconstrained text, but presumably expects 'term label + [term id]' +extreme_event: '2023-01-15' +fao_class: Fluvisols +filter_method: Basix PES, 13-100-106 FisherSci is an example value, but unconstrained + text is accepted at this point +fire: 2000-11 to 2000-12 +flooding: '2000-01-15' +gaseous_environment: +- has_raw_value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +geo_loc_name: + has_raw_value: 'USA: Maryland, Bethesda' +glucosidase_act: + has_raw_value: 5 mol per liter per hour +gold_biosample_identifiers: +- gold:Gb123456789 +- gold:Gb90909090 +growth_facil: + has_raw_value: Growth chamber [CO_715:0000189] +habitat: unconstrained text +heavy_metals: +- has_raw_value: mercury;0.09 micrograms per gram +- has_raw_value: arsenic;0.09 micrograms per gram +heavy_metals_meth: +- has_raw_value: https://link.springer.com/article/10.1007/s42452-019-1578-x +host_name: snail is an example value, but unconstrained text is accepted at this point +host_taxid: + has_raw_value: NCBITaxon:9606 + term: + id: NCBITaxon:9606 +humidity_regm: +- has_raw_value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +id: nmdc:bsm-99-dtTMNb +igsn_biosample_identifiers: +- any:curie_1 +- any:curie_2 +img_identifiers: +- img.taxon:abc123 +insdc_biosample_identifiers: +- biosample:SAMN123456789 +- biosample:SAMN000 +isotope_exposure: 13C glucose +lat_lon: + has_raw_value: 50.586825 6.408977 + latitude: 50.586825 + longitude: 6.408977 +lbc_thirty: + has_raw_value: 543 mg/kg +lbceq: + has_raw_value: 1575 mg/kg +light_regm: + has_raw_value: incandescent light;10 lux;450 nanometer +link_addit_analys: + has_raw_value: https://pubmed.ncbi.nlm.nih.gov/2315679/ +link_class_info: + has_raw_value: https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf +link_climate_info: + has_raw_value: https://www.int-res.com/abstracts/cr/v14/n3/p161-173/ +local_class: + has_raw_value: jicama soil +local_class_meth: + has_raw_value: https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083 +location: unconstrained text. should we even keep this slot? check if it ahs been + used in MongoDB. +magnesium: + has_raw_value: 52.8 micromole per kilogram +manganese: + has_raw_value: 24.7 mg/kg +mean_frict_vel: + has_raw_value: 0.5 meter per second +mean_peak_frict_vel: + has_raw_value: 1 meter per second +micro_biomass_c_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 +micro_biomass_n_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 +microbial_biomass_c: 0.05 ug C/g dry soil +microbial_biomass_n: 0.05 ug N/g dry soil +misc_param: +- has_raw_value: Bicarbonate ion concentration;2075 micromole per kilogram +mod_date: '2023-01-25' +n_alkanes: +- has_raw_value: n-hexadecane;100 milligram per liter +name: Sample Exhaustive Biosample instance. Although all of these values should pass + validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. +ncbi_taxonomy_name: soil metagenome +nitrate: + has_raw_value: 65 micromole per liter +nitrate_nitrogen: + has_raw_value: 0.29 mg/kg +nitrite: + has_raw_value: 0.5 micromole per liter +nitrite_nitrogen: + has_raw_value: 1.2 mg/kg +non_microb_biomass: insect 0.23 ug; plant 1g +non_microb_biomass_method: https://doi.org/10.1038/s41467-021-26181-3 +org_matter: + has_raw_value: 1.75 milligram per cubic meter +org_nitro: + has_raw_value: 4 micromole per liter +org_nitro_method: https://doi.org/10.1016/0038-0717(85)90144-0 +organism_count: +- has_raw_value: ATP +other_treatment: unconstrained text +oxy_stat_samp: aerobic +part_of: +- nmdc:unconstrained_study_identifier_string1_needs_pattern_materialization_what_about_referential_integrity +- nmdc:unconstrained_study_identifier_string2 +part_org_carb: + has_raw_value: 1.92 micromole per liter +perturbation: +- has_raw_value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M +petroleum_hydrocarb: + has_raw_value: 0.05 micromole per liter +ph: 11.22 +ph_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf +phaeopigments: +- has_raw_value: 2.5 milligram per cubic meter +phosphate: + has_raw_value: 0.7 micromole per liter +phosplipid_fatt_acid: +- has_raw_value: 2.98 milligram per liter +pool_dna_extracts: + has_raw_value: yes, 5 +potassium: + has_raw_value: 463 milligram per liter +pressure: + has_raw_value: 50 atmosphere +profile_position: summit +project_id: no example from MIxS +proport_woa_temperature: no example from MIxS +proposal_dna: '504000' +proposal_rna: '504000' +redox_potential: + has_raw_value: 300 millivolt +replicate_number: '1' +rna_absorb1: 2.02 +rna_absorb2: 2.02 +rna_collect_site: untreated pond water +rna_concentration: 100 +rna_cont_type: plate +rna_cont_well: C2 +rna_container_id: Pond_MT_041618 +rna_isolate_meth: phenol/chloroform extraction +rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) +rna_project_contact: John Jones +rna_samp_id: '187654' +rna_sample_format: 10 mM Tris-HCl +rna_sample_name: JGI_pond_041618 +rna_seq_project: '1191234' +rna_seq_project_name: JGI Pond metagenomics +rna_seq_project_pi: Jane Johnson +rna_volume: 25 +salinity: + has_raw_value: 25 practical salinity unit +salinity_category: halotolerant is an example from the schema, but MIxS doesn't provide + this slot any more +salinity_meth: + has_raw_value: PMID:22895776 +samp_collec_method: swabbing +samp_mat_process: + has_raw_value: filtering of seawater +samp_name: see also name +samp_size: + has_raw_value: 5 liters +samp_store_dur: + has_raw_value: P1Y6M +samp_store_loc: + has_raw_value: Freezer no:5 +samp_store_temp: + has_raw_value: -80 degree Celsius +samp_taxon_id: + has_raw_value: soil metagenome [NCBItaxon:410658] + term: + id: NCBItaxon:410658 + name: soil metagenome +samp_vol_we_dna_ext: + has_raw_value: 1500 milliliter +sample_collection_site: unconstrained text +sample_link: +- IGSN:DSJ0284 +- any:curie +sample_shipped: 15 g +sample_type: water_extract_soil +season_precpt: + has_raw_value: 75 millimeters +season_temp: + has_raw_value: 18 degree Celsius +sieving: + has_raw_value: MIxS does not provide an example +size_frac_low: + has_raw_value: 0.2 micrometer +size_frac_up: + has_raw_value: 20 micrometer +slope_aspect: + has_raw_value: MIxS does not provide an example +slope_gradient: + has_raw_value: MIxS does not provide an example +sodium: + has_raw_value: 10.5 milligram per liter +soil_type: + has_raw_value: plinthosol [ENVO:00002250] +soil_type_meth: + has_raw_value: Frederick series +soluble_iron_micromol: MIxS doesn't provide an example +source_mat_id: + has_raw_value: MPI012345 +specific_ecosystem: unconstrained text +start_date_inc: '2023-01-27' +start_time_inc: 13:42+0000 +store_cond: + has_raw_value: -20 degree Celsius freezer;P2Y10D +subsurface_depth: + has_raw_value: MIxS does not provide an example +sulfate: + has_raw_value: 5 micromole per liter +sulfide: + has_raw_value: 2 micromole per liter +technical_reps: '2' +temp: + has_raw_value: 25 degree Celsius +tidal_stage: high tide +tillage: +- chisel +tot_carb: + has_raw_value: MIxS does not provide an example +tot_depth_water_col: + has_raw_value: 500 meter +tot_diss_nitro: + has_raw_value: 40 microgram per liter +tot_nitro_cont_meth: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 +tot_nitro_content: + has_raw_value: 35 milligrams Nitrogen per kilogram of soil +tot_org_c_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf +tot_org_carb: + has_raw_value: 2% +tot_phosp: + has_raw_value: 0.03 milligram per liter +type: nmdc:Biosample. change this to require a class name or an enumeration +water_cont_soil_meth: MIxS doesn't provide an example +water_content: +- MIxS doesn't provide an example 1 +- MIxS doesn't provide an example 2 +watering_regm: +- has_raw_value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +zinc: + has_raw_value: 2.5 mg/kg ``` -## DataObject-1 +## Database-processed_sample-extract-exhaustive ### Input ```yaml -description: Metagenome Contig Coverage Stats for gold:Gp0061273 -file_size_bytes: 32787380 -id: nmdc:dobj-99-izwYW6 -name: mapping_stats.txt -type: nmdc:DataObject +processed_sample_set: +- biomaterial_purity: + has_numeric_value: 2 + description: Extracted DNA from WOOD_024-M-20190715-COMP + external_database_identifiers: + - neon.identifier:19S_31_2826 + id: nmdc:procsm-99-dtTMNb + name: WOOD_024-M-20190715-COMP-DNA1 + nucleic_acid_concentration: + has_numeric_value: 47.0 + instrument_name: Promega Quantus Fluorometer ``` -## Database-functional_annotation_agg +## Database-study_set-emsl_project_doi ### Input ```yaml -functional_annotation_agg: -- count: 120 - gene_function_id: KEGG.ORTHOLOGY:K00627 - metagenome_annotation_id: nmdc:8253bcdcd0387177ff895c38a047c719 +study_set: +- emsl_project_dois: + - doi:10.46936/intm.proj.2021.60141/60000423 + id: nmdc:sty-11-ab + study_category: research_study ``` ## Biosample-soil_horizon @@ -2150,135 +1136,28 @@ part_of: soil_horizon: M horizon ``` -## Database-study-set-with-consortia-and-parents -### Input -```yaml -study_set: -- description: The parent consortium of all the NEON consortia - id: nmdc:sty-11-34xj1152 - name: NEON Parent Consortium - study_category: consortium -- description: The National Science Foundation's National Ecological Observatory Network - (NEON) is a continental-scale observation facility operated by Battelle and designed - to collect long-term open access ecological data to better understand how U.S. - ecosystems are changing. - funding_sources: - - 'NSF#1724433 National Ecological Observatory Network: Operations Activities' - gold_study_identifiers: - - gold:Gs0144570 - - gold:Gs0161344 - id: nmdc:sty-11-34xj1150 - name: 'National Ecological Observatory Network: soil metagenomes (DP1.10107.001)' - part_of: - - nmdc:sty-11-34xj1152 - principal_investigator: - email: kthibault@battelleecology.org - has_raw_value: Kate Thibault - name: Kate Thibault - orcid: orcid:0000-0003-3477-6424 - profile_image_url: https://portal.nersc.gov/project/m3408/profile_images/thibault_katy.jpg - study_category: consortium - study_image: - - url: https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg - title: 'National Ecological Observatory Network: soil metagenomes (DP1.10107.001)' - type: nmdc:Study - websites: - - https://www.neonscience.org/ - - https://data.neonscience.org/data-products/DP1.10107.001 - - https://data.neonscience.org/api/v0/documents/NEON.DOC.014048vO - - https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf -- description: The National Science Foundation's National Ecological Observatory Network - (NEON) is a continental-scale observation facility operated by Battelle and designed - to collect long-term open access ecological data to better understand how U.S. - ecosystems are changing. - funding_sources: - - 'NSF#1724433 National Ecological Observatory Network: Operations Activities' - id: nmdc:sty-11-hht5sb92 - name: 'National Ecological Observatory Network: surface water metagenomes (DP1.20281.001)' - part_of: - - nmdc:sty-11-34xj1152 - principal_investigator: - email: kthibault@battelleecology.org - has_raw_value: Kate Thibault - name: Kate Thibault - orcid: orcid:0000-0003-3477-6424 - study_category: consortium - study_image: - - url: https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg - title: 'National Ecological Observatory Network: surface water metagenomes (DP1.20281.001)' - type: nmdc:Study - websites: - - https://www.neonscience.org/ - - https://data.neonscience.org/data-products/DP1.20281.001 - - https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf -- description: The National Science Foundation's National Ecological Observatory Network - (NEON) is a continental-scale observation facility operated by Battelle and designed - to collect long-term open access ecological data to better understand how U.S. - ecosystems are changing. - funding_sources: - - 'NSF#1724433 National Ecological Observatory Network: Operations Activities' - id: nmdc:sty-11-pzmd0x14 - name: 'National Ecological Observatory Network: benthic metagenomes (DP1.20279.001)' - part_of: - - nmdc:sty-11-34xj1152 - principal_investigator: - email: kthibault@battelleecology.org - name: Kate Thibault - orcid: orcid:0000-0003-3477-6424 - study_category: consortium - study_image: - - url: https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg - title: 'National Ecological Observatory Network: benthic metagenomes (DP1.20279.001)' - type: nmdc:Study - websites: - - https://www.neonscience.org/ - - https://data.neonscience.org/data-products/DP1.20279.001 - - https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf - -``` -## Database-processed_sample-extract-exhaustive -### Input -```yaml -processed_sample_set: -- biomaterial_purity: - has_numeric_value: 2 - description: Extracted DNA from WOOD_024-M-20190715-COMP - external_database_identifiers: - - neon.identifier:19S_31_2826 - id: nmdc:procsm-99-dtTMNb - name: WOOD_024-M-20190715-COMP-DNA1 - nucleic_acid_concentration: - has_numeric_value: 47.0 - instrument_name: Promega Quantus Fluorometer - -``` -## Study-minimal -### Input -```yaml -id: nmdc:sty-11-ab - -``` -## Database-processed_sample-minimal -### Input -```yaml -processed_sample_set: -- id: nmdc:procsm-99-dtTMNb - -``` -## Database-pooling_set-minimal -### Input -```yaml -pooling_set: -- id: nmdc:poolp-9x9-1x - name: first pooling process - -``` -## DataObject-minimal +## ReadQcAnalysisActivity-1 ### Input ```yaml -description: Crispr Terms for nmdc:ann0vx38 -id: nmdc:dobj-11-dtTMNb -name: Crispr Terms +ended_at_time: '2021-09-15T10:13:20+00:00' +execution_resource: execution_resource1 +git_url: git_url1 +has_input: +- jgi:534819030d87850d7aea2a16 +has_output: +- nmdc:ae40d7ae535c92b6d347915d8b1ac125 +- nmdc:bd723452a107e973fcc6734ff7894bb9 +id: nmdc:wfrqc-99-ABCDEF +input_base_count: 300.0 +input_read_bases: 300.0 +input_read_count: 10.0 +name: name1 +output_base_count: 100.0 +output_read_bases: 100.0 +output_read_count: 3.0 +started_at_time: '2021-08-05T14:48:51+00:00' +type: type1 +was_informed_by: gold:Gp0061273 ``` ## Database-neon-story @@ -2372,66 +1251,6 @@ processed_sample_set: - id: nmdc:procsm-99-xyz3 name: first library -``` -## Pooling-exhaustive -### Input -```yaml -alternative_identifiers: -- generic:xxx -description: xxx -has_input: -- generic:xxx -- generic:yyy -has_output: -- generic:xxx -id: nmdc:poolp-9x9-1x -name: first pooling process - -``` -## ReadQcAnalysisActivity-1 -### Input -```yaml -ended_at_time: '2021-09-15T10:13:20+00:00' -execution_resource: execution_resource1 -git_url: git_url1 -has_input: -- jgi:534819030d87850d7aea2a16 -has_output: -- nmdc:ae40d7ae535c92b6d347915d8b1ac125 -- nmdc:bd723452a107e973fcc6734ff7894bb9 -id: nmdc:wfrqc-99-ABCDEF -input_base_count: 300.0 -input_read_bases: 300.0 -input_read_count: 10.0 -name: name1 -output_base_count: 100.0 -output_read_bases: 100.0 -output_read_count: 3.0 -started_at_time: '2021-08-05T14:48:51+00:00' -type: type1 -was_informed_by: gold:Gp0061273 - -``` -## Database-biosamples-minimal -### Input -```yaml -biosample_set: -- env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - id: nmdc:bsm-99-dtTMNb - part_of: - - gold:Gs0110115 - ``` ## Biosample-exhasutive ### Input @@ -3452,607 +2271,1857 @@ zinc: has_raw_value: 2.5 mg/kg ``` -## DataObject-2 -### Input -```yaml -description: Assembled scaffold fasta for gold:Gp0061273 -file_size_bytes: 205297945 -id: nmdc:dobj-99-PqBJvW -name: assembly_scaffolds.fna -type: nmdc:DataObject - -``` -## Biosample-embargoed -### Input -```yaml -embargoed: true -env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 -env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 -env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 -id: nmdc:bsm-99-dtTMNb -part_of: -- gold:Gs0110115 - -``` -## Database-MetabolomicsAnalysisActivity-1 -### Input -```yaml -metabolomics_analysis_activity_set: -- ended_at_time: '2021-09-15T10:13:20+00:00' - execution_resource: NERSC cori - git_url: https://example.org/WorkflowExecutionActivity - has_calibration: calibration with 0.01% phosphoric acid - has_input: - - nmdc:i1 - - nmdc:i2 - has_output: - - nmdc:o1 - - nmdc:o2 - id: nmdc:wfmb-99-ABCDEF - name: Metabolomics Analysis Activity for nmdc:wfmb-99-ABCDEF - started_at_time: '2021-08-05T14:48:51+00:00' - type: WorkflowExecutionActivity - was_informed_by: nmdc:a1 - -``` -## Database-library-prep-exhausive -### Input -```yaml -library_preparation_set: -- description: DNA extraction of NEON sample TREE_001-O-20170707-COMP-DNA1 using SOP - BMI_metagenomicsSequencingSOP_v2 - end_date: '2018-09-26' - has_input: - - generic:xxx - has_output: - - generic:xxx - id: nmdc:libprp-99-xxx2 - library_preparation_kit: KAPA HyperPrep Kit - library_type: DNA - name: DNA library creation of NEON sample TREE_001-O-20170707-COMP-DNA1 - pcr_cycles: 0 - processing_institution: Battelle - start_date: '2018-09-26' -- description: RNA extraction of NEON sample TREE_001-O-20170707-COMP-DNA1 using SOP - XX - end_date: '2018-09-26' - has_input: - - generic:xxy - has_output: - - generic:xxz - id: nmdc:libprp-99-xxx1 - library_preparation_kit: TruSeq RNA Library Prep Kit v2 - library_type: RNA - name: RNA library creation of NEON sample TREE_001-O-20170707-COMP-DNA1 - pcr_cycles: 12 - processing_institution: Battelle - start_date: '2018-09-26' - -``` -## Database-extraction_set-exhaustive -### Input -```yaml -extraction_set: -- description: DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7 - end_date: '2019-11-08' - extraction_method: phenol/chloroform extraction - extraction_target: DNA - has_input: - - generic:xxx - has_output: - - generic:xxx - id: nmdc:extrp-99-abcdef - input_mass: - has_numeric_value: 0.25 - has_unit: gram - name: DNA extraction of NEON sample WREF_072-O-20190618-COMP - processing_institution: Battelle - protocol_link: - name: BMI_dnaExtractionSOP_v7 - url: https://data.neonscience.org/documents/10179/2431540/BMI_dnaExtractionSOP_v7/61204962-bb01-a0b9-3354-ccdaab5132c3 - quality_control_report: - status: pass - start_date: '2019-11-08' - -``` -## Database-with-MetagenomeSequencingActivity -### Input -```yaml -metagenome_sequencing_activity_set: -- ended_at_time: '2021-09-15T10:13:20+00:00' - execution_resource: JGI - git_url: '' - has_input: - - nmdc:unvalidated_placeholder - has_output: - - nmdc:22afa3d49b73eaec2e9787a6b88fbdc3 - id: nmdc:wfmsa-99-qwertyuiop - name: Sequencing Activity for nmdc:mga0vx38 - part_of: - - nmdc:mga0vx38 - started_at_time: '2021-08-05T14:48:51+00:00' - type: nmdc:MetagenomeSequencing - version: v1.0.0 - was_informed_by: gold:Gp0213371 - -``` -## Biosample-minimal-2 -### Input -```yaml -env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 -env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 -env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 -id: nmdc:bsm-99-dtTMNb -part_of: -- gold:Gs0110115 - -``` -## Database-nom_analysis_activity_set +## Study-minimal ### Input ```yaml -nom_analysis_activity_set: -- ended_at_time: '2018-11-13T20:20:39+00:00' - execution_resource: xxx - git_url: xxx - has_input: - - nmdc:1 - - nmdc:2 - has_output: - - nmdc:3 - - nmdc:4 - id: nmdc:wfnom-99-abcdefg - started_at_time: '2018-11-13T20:20:39+00:00' - type: xxx - was_informed_by: nmdc:act-99-abcdefg +id: nmdc:sty-11-ab ``` -## DataObject-MB-unknown-enum-pv +## Database-biosamples-dna-in-plate-valid-well-val ### Input ```yaml -data_object_type: Crispr Terms -description: Crispr Terms for nmdc:ann0vx38 -file_size_bytes: 1234 -id: nmdc:dobj-11-dtTMNb -md5_checksum: 22afa3d49b73eaec2e9787a6b88fbdc3 -name: Crispr Terms -type: nmdc:DataObject -url: http://example.com +biosample_set: +- dna_cont_type: plate + dna_cont_well: B2 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - gold:Gs0110115 ``` -## Biosample-exhaustive-issue-796-bye-yq-for-7-4-10 +## Study-exhaustive ### Input ```yaml -add_date: '2021-03-31' -agrochem_addition: -- has_raw_value: lime;1 kg/acre;2022-11-16T16:05:42+0000 -air_temp_regm: -- has_raw_value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -al_sat: - has_raw_value: 0.1 mg/kg -al_sat_meth: - has_raw_value: https://journaljeai.com/index.php/JEAI/article/view/583 -alkalinity: - has_raw_value: 50 milligram per liter -alkalinity_method: - has_raw_value: https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity -alkyl_diethers: - has_raw_value: 0.005 mole per liter -alt: - has_raw_value: 100 meter +alternative_descriptions: +- any string 1 +- any string 2 alternative_identifiers: -- generic:abc123 -aminopept_act: - has_raw_value: 0.269 mole per liter per hour -ammonium: - has_raw_value: 1.5 milligram per liter -ammonium_nitrogen: - has_raw_value: 0.5 milligram per liter -analysis_type: -- metabolomics -- metagenomics -annual_precpt: - has_raw_value: 0.5 milligram per liter -annual_temp: - has_raw_value: 12.5 degree Celsius -bacteria_carb_prod: - has_raw_value: 2.53 microgram per liter per hour -biosample_categories: -- LTER -- FICUS -biotic_regm: - has_raw_value: sample inoculated with Rhizobium spp. Culture -biotic_relationship: parasite -bishomohopanol: - has_raw_value: 14 microgram per liter -bromide: - has_raw_value: 0.05 parts per million -calcium: - has_raw_value: 0.2 micromole per liter -carb_nitro_ratio: - has_raw_value: '0.417361111' -chem_administration: -- has_raw_value: agar [CHEBI:2509];2018-05-11T20:00Z -chloride: - has_raw_value: 5000 milligram per liter -chlorophyll: - has_raw_value: 5 milligram per cubic meter -climate_environment: -- has_raw_value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -collected_from: nmdc:unconstrained_site_identifier_string -collection_date: - has_raw_value: '2018-05-11' -collection_date_inc: '2023-01-29' -collection_time: 05:42+0000 -collection_time_inc: 13:42+0000 -community: no_example_from_mixs -crop_rotation: - has_raw_value: yes;R2/2017-01-01/2018-12-31/P6M -cur_land_use: farmstead -cur_vegetation: - has_raw_value: MIxS doesn't provide any guidance more specific than "text" -cur_vegetation_meth: - has_raw_value: https://link.springer.com/article/10.1023/A:1011975321668 -density: - has_raw_value: 1000 kilogram per cubic meter -depth: - has_maximum_numeric_value: 2.5 - has_minimum_numeric_value: 1.5 - has_numeric_value: 2.0 - has_raw_value: 1.5 to 2.5 meters (that may not be the pattern the submission schema - expects). Extractions below require external migration logic. - has_unit: meter -description: unconstrained text -diss_carb_dioxide: - has_raw_value: 5 milligram per liter -diss_hydrogen: - has_raw_value: 0.3 micromole per liter -diss_inorg_carb: - has_raw_value: 2059 micromole per kilogram -diss_inorg_phosp: - has_raw_value: 56.5 micromole per liter -diss_org_carb: - has_raw_value: 197 micromole per liter -diss_org_nitro: - has_raw_value: 0.05 micromole per liter -diss_oxygen: - has_raw_value: 175 micromole per kilogram -dna_absorb1: 2.02 -dna_absorb2: 2.02 -dna_collect_site: untreated pond water -dna_concentration: 100 -dna_container_id: Pond_MT_041618 -dna_dnase: 'yes' -dna_isolate_meth: phenol/chloroform extraction -dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles - (1%) -dna_project_contact: John Jones -dna_samp_id: '187654' -dna_sample_format: 10 mM Tris-HCl -dna_sample_name: JGI_pond_041618 -dna_seq_project: '1191234' -dna_seq_project_name: JGI Pond metagenomics -dna_seq_project_pi: Jane Johnson -dna_volume: 25 -dnase_rna: 'yes' -drainage_class: well +- generic:abc1 +alternative_names: +- any string 1 +- any string 2 +alternative_titles: +- any string 1 +- any string 2 +description: see also name, title, objective, various alternatives ecosystem: unconstrained text. should be validated against the controlled vocabulary, by the sample's environmental package. would also be nice to align the CV with MIxS environmental triads ecosystem_category: unconstrained text ecosystem_subtype: unconstrained text ecosystem_type: unconstrained text -elev: 100 -embargoed: true -emsl_biosample_identifiers: -- generic:abc123 -env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 -env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 -env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 -env_package: - has_raw_value: unconstrained text. should require the name of a MIxS EnvironmentalPackage - class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM! -experimental_factor: - has_raw_value: unconstrained text, unlike the MIxS environmental triad -experimental_factor_other: unconstrained text, but presumably expects 'term label - [term id]' -extreme_event: '2023-01-15' -fao_class: Fluvisols -filter_method: Basix PES, 13-100-106 FisherSci is an example value, but unconstrained - text is accepted at this point -fire: 2000-11 to 2000-12 -flooding: '2000-01-15' -gaseous_environment: -- has_raw_value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -geo_loc_name: - has_raw_value: 'USA: Maryland, Bethesda' -glucosidase_act: - has_raw_value: 5 mol per liter per hour -gold_biosample_identifiers: -- gold:Gb123456789 -- gold:Gb90909090 -growth_facil: - has_raw_value: Growth chamber [CO_715:0000189] -habitat: unconstrained text -heavy_metals: -- has_raw_value: mercury;0.09 micrograms per gram -- has_raw_value: arsenic;0.09 micrograms per gram -heavy_metals_meth: -- has_raw_value: https://link.springer.com/article/10.1007/s42452-019-1578-x -host_name: snail is an example value, but unconstrained text is accepted at this point -host_taxid: - has_raw_value: NCBITaxon:9606 - term: - id: NCBITaxon:9606 -humidity_regm: -- has_raw_value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -id: nmdc:bsm-99-dtTMNb -igsn_biosample_identifiers: -- any:curie_1 -- any:curie_2 -img_identifiers: -- img.taxon:abc123 -insdc_biosample_identifiers: -- biosample:SAMN123456789 -- biosample:SAMN000 -isotope_exposure: 13C glucose -lat_lon: - has_raw_value: 50.586825 6.408977 - latitude: 50.586825 - longitude: 6.408977 -lbc_thirty: - has_raw_value: 543 mg/kg -lbceq: - has_raw_value: 1575 mg/kg -light_regm: - has_raw_value: incandescent light;10 lux;450 nanometer -link_addit_analys: - has_raw_value: https://pubmed.ncbi.nlm.nih.gov/2315679/ -link_class_info: - has_raw_value: https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf -link_climate_info: - has_raw_value: https://www.int-res.com/abstracts/cr/v14/n3/p161-173/ -local_class: - has_raw_value: jicama soil -local_class_meth: - has_raw_value: https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083 -location: unconstrained text. should we even keep this slot? check if it ahs been - used in MongoDB. -magnesium: - has_raw_value: 52.8 micromole per kilogram -manganese: - has_raw_value: 24.7 mg/kg -mean_frict_vel: - has_raw_value: 0.5 meter per second -mean_peak_frict_vel: - has_raw_value: 1 meter per second -micro_biomass_c_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 -micro_biomass_n_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 -microbial_biomass_c: 0.05 ug C/g dry soil -microbial_biomass_n: 0.05 ug N/g dry soil -misc_param: -- has_raw_value: Bicarbonate ion concentration;2075 micromole per kilogram -mod_date: '2023-01-25' -n_alkanes: -- has_raw_value: n-hexadecane;100 milligram per liter -name: Sample Exhaustive Biosample instance. Although all of these values should pass +ess_dive_datasets: +- any string 1 +- any string 2 +funding_sources: +- any string 1 +- any string 2 +gold_study_identifiers: +- gold:Gs12345 +- gold:Gs90909 +has_credit_associations: +- applied_role: Funding acquisition + applied_roles: + - Supervision + - Conceptualization + applies_to_person: + email: jcventer@jcvi.org + has_raw_value: Craig Venter + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + was_generated_by: nmdc:any_string_1 + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter + type: any string +- applied_roles: + - Investigation + - Supervision + applies_to_person: + name: Tanja Davidsen +id: nmdc:sty-11-ab +mgnify_project_identifiers: +- mgnify.proj:ABC123 +name: see also description, title, objective, various alternatives +objective: This record, an instance of class Study from the nmdc-schema was had authored, + so that the NMDC team would have at least one instance, using all slots, with a + mixture of reasonable values and minimally compliant values. +part_of: +- nmdc:sty-11-34xj1157 +principal_investigator: + email: jcventer@jcvi.org + has_raw_value: Craig Venter + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + was_generated_by: nmdc:any_string_1 + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter +publication_dois: +- doi:10.1126/science.1058040 +publications: +- any string 1 +- any string 2 +related_identifiers: any string R1 +relevant_protocols: +- any string 1 +- any string 2 +specific_ecosystem: unconstrained text +study_category: research_study +study_image: +- description: Photo of Craig Venter Institute, Rockville, Maryland + display_order: '1' + has_raw_value: https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg + url: https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg + was_generated_by: nmdc:any_string_1 +- description: Photo of Craig Venter Institute, La Jolla, California + display_order: '2' + has_raw_value: https://today.ucsd.edu/news_uploads/140213ventor2.jpg + url: https://today.ucsd.edu/news_uploads/140213ventor2.jpg + was_generated_by: nmdc:any_string_1 +title: Sample Exhaustive Biosample instance. Although all of these values should pass validation, that does not mean that any Biosample of any type would necessarily have this particular combination of values. -ncbi_taxonomy_name: soil metagenome -nitrate: - has_raw_value: 65 micromole per liter -nitrate_nitrogen: - has_raw_value: 0.29 mg/kg -nitrite: - has_raw_value: 0.5 micromole per liter -nitrite_nitrogen: - has_raw_value: 1.2 mg/kg -non_microb_biomass: insect 0.23 ug; plant 1g -non_microb_biomass_method: https://doi.org/10.1038/s41467-021-26181-3 -org_matter: - has_raw_value: 1.75 milligram per cubic meter -org_nitro: - has_raw_value: 4 micromole per liter -org_nitro_method: https://doi.org/10.1016/0038-0717(85)90144-0 -organism_count: -- has_raw_value: ATP -other_treatment: unconstrained text -oxy_stat_samp: aerobic +type: any string +websites: +- https://w3id.org/nmdc +- https://w3id.org/linkml + +``` +## DataObject-1 +### Input +```yaml +description: Metagenome Contig Coverage Stats for gold:Gp0061273 +file_size_bytes: 32787380 +id: nmdc:dobj-99-izwYW6 +name: mapping_stats.txt +type: nmdc:DataObject + +``` +## Database-with-MetagenomeSequencingActivity +### Input +```yaml +metagenome_sequencing_activity_set: +- ended_at_time: '2021-09-15T10:13:20+00:00' + execution_resource: JGI + git_url: '' + has_input: + - nmdc:unvalidated_placeholder + has_output: + - nmdc:22afa3d49b73eaec2e9787a6b88fbdc3 + id: nmdc:wfmsa-99-qwertyuiop + name: Sequencing Activity for nmdc:mga0vx38 + part_of: + - nmdc:mga0vx38 + started_at_time: '2021-08-05T14:48:51+00:00' + type: nmdc:MetagenomeSequencing + version: v1.0.0 + was_informed_by: gold:Gp0213371 + +``` +## Database-biosamples-rna-in-plate-valid-well-val +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - gold:Gs0110115 + rna_cont_type: plate + rna_cont_well: B2 + +``` +## Database-biosamples-sites +### Input +```yaml +biosample_set: +- collected_from: nmdc:frsite-99-SPreao + description: Root microbial communities from poplar common garden site in Clatskanie, + Oregon, USA + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + gold_biosample_identifiers: + - gold:Gb0305833 + id: nmdc:bsm-99-J9FcnC + name: Root microbial communities from poplar common garden site in Clatskanie, Oregon, + USA - BESC-13-CL1_35_33 endosphere + part_of: + - nmdc:sty-99-U21mUX +- collected_from: nmdc:frsite-99-SPreao + description: Rhizosphere soil microbial communities from poplar common garden site + in Clatskanie, Oregon, USA + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + gold_biosample_identifiers: + - gold:Gb0291692 + id: nmdc:bsm-99-BdlWdQ + name: Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA - BESC-13-CL1_35_33 + part_of: + - nmdc:sty-99-U21mUX +- collected_from: nmdc:frsite-99-SPreao + description: Bulk soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + gold_biosample_identifiers: + - gold:Gb0291582 + id: nmdc:bsm-99-vn74Wq + name: Bulk soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA - BESC-13-CL1_35_33 + part_of: + - nmdc:sty-99-U21mUX +- collected_from: nmdc:frsite-99-h2mYFG + description: Root microbial communities from poplar common garden site in Clatskanie, + Oregon, USA + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + gold_biosample_identifiers: + - gold:Gb0305834 + id: nmdc:bsm-99-P8FdpS + name: Root microbial communities from poplar common garden site in Clatskanie, Oregon, + USA - BESC-13-CL2_39_29 endosphere + part_of: + - nmdc:sty-99-U21mUX +- collected_from: nmdc:frsite-99-h2mYFG + description: Rhizosphere soil microbial communities from poplar common garden site + in Clatskanie, Oregon, USA + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + gold_biosample_identifiers: + - gold:Gb0291693 + id: nmdc:bsm-99-ugBwz3 + name: Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA - BESC-13-CL2_39_29 + part_of: + - nmdc:sty-99-U21mUX +- collected_from: nmdc:frsite-99-h2mYFG + description: Bulk soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + gold_biosample_identifiers: + - gold:Gb0291583 + id: nmdc:bsm-99-tN5lxM + name: Bulk soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA - BESC-13-CL2_39_29 + part_of: + - nmdc:sty-99-U21mUX +collecting_biosamples_from_site_set: +- has_input: + - nmdc:frsite-99-SPreao + has_output: + - nmdc:bsm-99-J9FcnC + - nmdc:bsm-99-BdlWdQ + - nmdc:bsm-99-vn74Wq + id: nmdc:clsite-99-Cq00d1 + name: Collection of biosamples from BESC-13-CL1_35_33 +- has_input: + - nmdc:frsite-99-h2mYFG + has_output: + - nmdc:bsm-99-P8FdpS + - nmdc:bsm-99-ugBwz3 + - nmdc:bsm-99-tN5lxM + id: nmdc:clsite-99-yzmLBN + name: Collection of biosamples from BESC-13-CL2_39_29 +field_research_site_set: +- description: Bioscales tree BESC-13-CL1_35_33 + id: nmdc:frsite-99-SPreao + name: BESC-13-CL1_35_33 +- description: Bioscales tree BESC-13-CL2_39_29 + id: nmdc:frsite-99-h2mYFG + name: BESC-13-CL2_39_29 + +``` +## MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json +### Input +```yaml +ended_at_time: '2021-09-15T10:13:20+00:00' +execution_resource: JGI +git_url: '' +has_input: +- nmdc:unvalidated_placeholder +has_output: +- nmdc:22afa3d49b73eaec2e9787a6b88fbdc3 +id: nmdc:wfmsa-99-qwertyuiop +name: Sequencing Activity for nmdc:mga0vx38 part_of: -- nmdc:unconstrained_study_identifier_string1_needs_pattern_materialization_what_about_referential_integrity -- nmdc:unconstrained_study_identifier_string2 -part_org_carb: - has_raw_value: 1.92 micromole per liter -perturbation: -- has_raw_value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M -petroleum_hydrocarb: - has_raw_value: 0.05 micromole per liter -ph: 11.22 -ph_meth: - has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf -phaeopigments: -- has_raw_value: 2.5 milligram per cubic meter -phosphate: - has_raw_value: 0.7 micromole per liter -phosplipid_fatt_acid: -- has_raw_value: 2.98 milligram per liter -pool_dna_extracts: - has_raw_value: yes, 5 -potassium: - has_raw_value: 463 milligram per liter -pressure: - has_raw_value: 50 atmosphere -profile_position: summit -project_id: no example from MIxS -proport_woa_temperature: no example from MIxS -proposal_dna: '504000' -proposal_rna: '504000' -redox_potential: - has_raw_value: 300 millivolt -replicate_number: '1' -rna_absorb1: 2.02 -rna_absorb2: 2.02 -rna_collect_site: untreated pond water -rna_concentration: 100 -rna_cont_type: plate -rna_cont_well: C2 -rna_container_id: Pond_MT_041618 -rna_isolate_meth: phenol/chloroform extraction -rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles - (1%) -rna_project_contact: John Jones -rna_samp_id: '187654' -rna_sample_format: 10 mM Tris-HCl -rna_sample_name: JGI_pond_041618 -rna_seq_project: '1191234' -rna_seq_project_name: JGI Pond metagenomics -rna_seq_project_pi: Jane Johnson -rna_volume: 25 -salinity: - has_raw_value: 25 practical salinity unit -salinity_category: halotolerant is an example from the schema, but MIxS doesn't provide - this slot any more -salinity_meth: - has_raw_value: PMID:22895776 -samp_collec_method: swabbing -samp_mat_process: - has_raw_value: filtering of seawater -samp_name: see also name -samp_size: - has_raw_value: 5 liters -samp_store_dur: - has_raw_value: P1Y6M -samp_store_loc: - has_raw_value: Freezer no:5 -samp_store_temp: - has_raw_value: -80 degree Celsius -samp_taxon_id: - has_raw_value: soil metagenome [NCBItaxon:410658] +- nmdc:mga0vx38 +started_at_time: '2021-08-05T14:48:51+00:00' +type: nmdc:MetagenomeSequencing +version: v1.0.0 +was_informed_by: gold:Gp0213371 + +``` +## FunctionalAnnotation-minimal +### Input +```yaml +has_function: KEGG_PATHWAY:abc12345 + +``` +## Database-MetabolomicsAnalysisActivity-1 +### Input +```yaml +metabolomics_analysis_activity_set: +- ended_at_time: '2021-09-15T10:13:20+00:00' + execution_resource: NERSC cori + git_url: https://example.org/WorkflowExecutionActivity + has_calibration: calibration with 0.01% phosphoric acid + has_input: + - nmdc:i1 + - nmdc:i2 + has_output: + - nmdc:o1 + - nmdc:o2 + id: nmdc:wfmb-99-ABCDEF + name: Metabolomics Analysis Activity for nmdc:wfmb-99-ABCDEF + started_at_time: '2021-08-05T14:48:51+00:00' + type: WorkflowExecutionActivity + was_informed_by: nmdc:a1 + +``` +## DataObject-exhaustive +### Input +```yaml +alternative_identifiers: +- prefix:value1 +- prefix:value2 +compression_type: any string +data_object_type: Crispr Terms +description: Crispr Terms for nmdc:ann0vx38 +file_size_bytes: 1234 +id: nmdc:dobj-11-dtTMNb +md5_checksum: 22afa3d49b73eaec2e9787a6b88fbdc3 +name: Crispr Terms +type: nmdc:DataObject +url: http://example.com +was_generated_by: nmdc:invalid_id + +``` +## Biosample-minimal +### Input +```yaml +env_broad_scale: + has_raw_value: ENVO:00002030 term: - id: NCBItaxon:410658 - name: soil metagenome -samp_vol_we_dna_ext: - has_raw_value: 1500 milliliter -sample_collection_site: unconstrained text -sample_link: -- IGSN:DSJ0284 -- any:curie -sample_shipped: 15 g -sample_type: water_extract_soil -season_precpt: - has_raw_value: 75 millimeters -season_temp: - has_raw_value: 18 degree Celsius -sieving: - has_raw_value: MIxS does not provide an example -size_frac_low: - has_raw_value: 0.2 micrometer -size_frac_up: - has_raw_value: 20 micrometer -slope_aspect: - has_raw_value: MIxS does not provide an example -slope_gradient: - has_raw_value: MIxS does not provide an example -sodium: - has_raw_value: 10.5 milligram per liter -soil_type: - has_raw_value: plinthosol [ENVO:00002250] -soil_type_meth: - has_raw_value: Frederick series -soluble_iron_micromol: MIxS doesn't provide an example -source_mat_id: - has_raw_value: MPI012345 -specific_ecosystem: unconstrained text -start_date_inc: '2023-01-27' -start_time_inc: 13:42+0000 -store_cond: - has_raw_value: -20 degree Celsius freezer;P2Y10D -subsurface_depth: - has_raw_value: MIxS does not provide an example -sulfate: - has_raw_value: 5 micromole per liter -sulfide: - has_raw_value: 2 micromole per liter -technical_reps: '2' -temp: - has_raw_value: 25 degree Celsius -tidal_stage: high tide -tillage: -- chisel -tot_carb: - has_raw_value: MIxS does not provide an example -tot_depth_water_col: - has_raw_value: 500 meter -tot_diss_nitro: - has_raw_value: 40 microgram per liter -tot_nitro_cont_meth: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 -tot_nitro_content: - has_raw_value: 35 milligrams Nitrogen per kilogram of soil -tot_org_c_meth: - has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf -tot_org_carb: - has_raw_value: 2% -tot_phosp: - has_raw_value: 0.03 milligram per liter -type: nmdc:Biosample. change this to require a class name or an enumeration -water_cont_soil_meth: MIxS doesn't provide an example -water_content: -- MIxS doesn't provide an example 1 -- MIxS doesn't provide an example 2 -watering_regm: -- has_raw_value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -zinc: - has_raw_value: 2.5 mg/kg + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +id: nmdc:bsm-99-dtTMNb +part_of: +- gold:Gs0110115 + +``` +## Database-biosample-exhasutive +### Input +```yaml +biosample_set: +- abs_air_humidity: + has_raw_value: xxx + add_date: '2021-03-31' + add_recov_method: + has_raw_value: xxx + additional_info: + has_raw_value: xxx + address: + has_raw_value: xxx + adj_room: + has_raw_value: xxx + aero_struc: + has_raw_value: xxx + agrochem_addition: + - has_raw_value: lime;1 kg/acre;2022-11-16T16:05:42+0000 + air_PM_concen: + - has_raw_value: xxx + air_temp: + has_raw_value: xxx + air_temp_regm: + - has_raw_value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + al_sat: + has_raw_value: 0.1 mg/kg + al_sat_meth: + has_raw_value: https://journaljeai.com/index.php/JEAI/article/view/583 + alkalinity: + has_raw_value: 50 milligram per liter + alkalinity_method: + has_raw_value: https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity + alkyl_diethers: + has_raw_value: 0.005 mole per liter + alt: + has_raw_value: 100 meter + alternative_identifiers: + - generic:abc123 + aminopept_act: + has_raw_value: 0.269 mole per liter per hour + ammonium: + has_raw_value: 1.5 milligram per liter + ammonium_nitrogen: + has_raw_value: 0.5 milligram per liter + amount_light: + has_raw_value: xxx + analysis_type: + - metabolomics + - metagenomics + ances_data: + has_raw_value: xxx + annual_precpt: + has_raw_value: 0.5 milligram per liter + annual_temp: + has_raw_value: 12.5 degree Celsius + antibiotic_regm: + - has_raw_value: xxx + api: + has_raw_value: xxx + arch_struc: building + aromatics_pc: + has_raw_value: xxx + asphaltenes_pc: + has_raw_value: xxx + atmospheric_data: + - has_raw_value: xxx + avg_dew_point: + has_raw_value: xxx + avg_occup: + has_raw_value: xxx + avg_temp: + has_raw_value: xxx + bac_prod: + has_raw_value: xxx + bac_resp: + has_raw_value: xxx + bacteria_carb_prod: + has_raw_value: 2.53 microgram per liter per hour + barometric_press: + has_raw_value: xxx + basin: + has_raw_value: xxx + bathroom_count: + has_raw_value: xxx + bedroom_count: + has_raw_value: xxx + benzene: + has_raw_value: xxx + biochem_oxygen_dem: + has_raw_value: xxx + biocide: + has_raw_value: xxx + biocide_admin_method: + has_raw_value: xxx + biol_stat: wild + biomass: + - has_raw_value: xxx + biosample_categories: + - LTER + - FICUS + biotic_regm: + has_raw_value: sample inoculated with Rhizobium spp. Culture + biotic_relationship: parasite + bishomohopanol: + has_raw_value: 14 microgram per liter + blood_press_diast: + has_raw_value: xxx + blood_press_syst: + has_raw_value: xxx + bromide: + has_raw_value: 0.05 parts per million + build_docs: building information model + build_occup_type: + - office + building_setting: urban + built_struc_age: + has_raw_value: xxx + built_struc_set: + has_raw_value: xxx + built_struc_type: + has_raw_value: xxx + calcium: + has_raw_value: 0.2 micromole per liter + carb_dioxide: + has_raw_value: xxx + carb_monoxide: + has_raw_value: xxx + carb_nitro_ratio: + has_raw_value: '0.417361111' + ceil_area: + has_raw_value: xxx + ceil_cond: new + ceil_finish_mat: drywall + ceil_struc: + has_raw_value: xxx + ceil_texture: crows feet + ceil_thermal_mass: + has_raw_value: xxx + ceil_type: cathedral + ceil_water_mold: + has_raw_value: xxx + chem_administration: + - has_raw_value: agar [CHEBI:2509];2018-05-11T20:00Z + chem_mutagen: + - has_raw_value: xxx + chem_oxygen_dem: + has_raw_value: xxx + chem_treat_method: xxx + chem_treatment: + has_raw_value: xxx + chimera_check: + has_raw_value: xxx + chloride: + has_raw_value: 5000 milligram per liter + chlorophyll: + has_raw_value: 5 milligram per cubic meter + climate_environment: + - has_raw_value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + collected_from: nmdc:unconstrained_site_identifier_string + collection_date: + has_raw_value: xxx + collection_date_inc: '2023-01-29' + collection_time: 05:42+0000 + collection_time_inc: 13:42+0000 + community: no_example_from_mixs + conduc: + has_raw_value: xxx + cool_syst_id: + has_raw_value: xxx + crop_rotation: + has_raw_value: yes;R2/2017-01-01/2018-12-31/P6M + cult_root_med: + has_raw_value: xxx + cur_land_use: farmstead + cur_vegetation: + has_raw_value: MIxS doesn't provide any guidance more specific than "text" + cur_vegetation_meth: + has_raw_value: https://link.springer.com/article/10.1023/A:1011975321668 + date_last_rain: + has_raw_value: xxx + density: + has_raw_value: 1000 kilogram per cubic meter + depos_env: other + depth: + has_maximum_numeric_value: 2.5 + has_minimum_numeric_value: 1.5 + has_numeric_value: 2.0 + has_raw_value: 1.5 to 2.5 meters (that may not be the pattern the submission schema + expects). Extractions below require external migration logic. + has_unit: meter + description: unconstrained text + dew_point: + has_raw_value: xxx + diether_lipids: + - has_raw_value: xxx + diss_carb_dioxide: + has_raw_value: 5 milligram per liter + diss_hydrogen: + has_raw_value: 0.3 micromole per liter + diss_inorg_carb: + has_raw_value: 2059 micromole per kilogram + diss_inorg_nitro: + has_raw_value: xxx + diss_inorg_phosp: + has_raw_value: 56.5 micromole per liter + diss_iron: + has_raw_value: xxx + diss_org_carb: + has_raw_value: 197 micromole per liter + diss_org_nitro: + has_raw_value: 0.05 micromole per liter + diss_oxygen: + has_raw_value: 175 micromole per kilogram + diss_oxygen_fluid: + has_raw_value: xxx + dna_absorb1: 2.02 + dna_absorb2: 2.02 + dna_collect_site: untreated pond water + dna_concentration: 100 + dna_container_id: Pond_MT_041618 + dna_dnase: 'yes' + dna_isolate_meth: phenol/chloroform extraction + dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) + dna_project_contact: John Jones + dna_samp_id: '187654' + dna_sample_format: 10 mM Tris-HCl + dna_sample_name: JGI_pond_041618 + dna_seq_project: '1191234' + dna_seq_project_name: JGI Pond metagenomics + dna_seq_project_pi: Jane Johnson + dna_volume: 25 + dnase_rna: 'yes' + door_comp_type: revolving + door_cond: damaged + door_direct: inward + door_loc: north + door_mat: aluminum + door_move: collapsible + door_size: + has_raw_value: xxx + door_type: composite + door_type_metal: collapsible + door_type_wood: battened + door_water_mold: + has_raw_value: xxx + down_par: + has_raw_value: xxx + drainage_class: well + drawings: operation + ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with + MIxS environmental triads + ecosystem_category: unconstrained text + ecosystem_subtype: unconstrained text + ecosystem_type: unconstrained text + efficiency_percent: + has_raw_value: xxx + elev: 100 + elevator: + has_raw_value: xxx + embargoed: true + emsl_biosample_identifiers: + - generic:abc123 + emulsions: + - has_raw_value: xxx + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + env_package: + has_raw_value: unconstrained text. should require the name of a MIxS EnvironmentalPackage + class. have asked MIxS to return this term to their model. UPDATE VALIDATION + RULES/PATTERN/ENUM! + escalator: + has_raw_value: xxx + ethylbenzene: + has_raw_value: xxx + exp_duct: + has_raw_value: xxx + exp_pipe: + has_raw_value: xxx + experimental_factor: + has_raw_value: unconstrained text, unlike the MIxS environmental triad + experimental_factor_other: unconstrained text, but presumably expects 'term label + [term id]' + ext_door: + has_raw_value: xxx + ext_wall_orient: north + ext_window_orient: north + extreme_event: '2023-01-15' + fao_class: Fluvisols + fertilizer_regm: + - has_raw_value: xxx + field: + has_raw_value: xxx + filter_method: Basix PES, 13-100-106 FisherSci is an example value, but unconstrained + text is accepted at this point + filter_type: + - HEPA + fire: 2000-11 to 2000-12 + fireplace_type: + has_raw_value: xxx + flooding: '2000-01-15' + floor_age: + has_raw_value: xxx + floor_area: + has_raw_value: xxx + floor_cond: new + floor_count: + has_raw_value: xxx + floor_finish_mat: tile + floor_struc: balcony + floor_thermal_mass: + has_raw_value: xxx + floor_water_mold: condensation + fluor: + has_raw_value: xxx + freq_clean: + has_raw_value: xxx + freq_cook: + has_raw_value: xxx + fungicide_regm: + - has_raw_value: xxx + furniture: cabinet + gaseous_environment: + - has_raw_value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + gaseous_substances: + - has_raw_value: xxx + gender_restroom: female + genetic_mod: + has_raw_value: xxx + geo_loc_name: + has_raw_value: 'USA: Maryland, Bethesda' + glucosidase_act: + has_raw_value: 5 mol per liter per hour + gold_biosample_identifiers: + - gold:Gb123456789 + - gold:Gb90909090 + gravidity: + has_raw_value: xxx + gravity: + - has_raw_value: xxx + growth_facil: + has_raw_value: Growth chamber [CO_715:0000189] + growth_habit: erect + growth_hormone_regm: + - has_raw_value: xxx + habitat: unconstrained text + hall_count: + has_raw_value: xxx + handidness: ambidexterity + hc_produced: Oil + hcr: Shale + hcr_fw_salinity: + has_raw_value: xxx + hcr_geol_age: Archean + hcr_pressure: + has_raw_value: xxx + hcr_temp: + has_raw_value: xxx + heat_cool_type: + - radiant system + heat_deliv_loc: north + heat_sys_deliv_meth: xxx + heat_system_id: + has_raw_value: xxx + heavy_metals: + - has_raw_value: mercury;0.09 micrograms per gram + - has_raw_value: arsenic;0.09 micrograms per gram + heavy_metals_meth: + - has_raw_value: https://link.springer.com/article/10.1007/s42452-019-1578-x + height_carper_fiber: + has_raw_value: xxx + herbicide_regm: + - has_raw_value: xxx + horizon_meth: + has_raw_value: xxx + host_age: + has_raw_value: xxx + host_body_habitat: + has_raw_value: xxx + host_body_product: + has_raw_value: xxx + host_body_site: + has_raw_value: xxx + host_body_temp: + has_raw_value: xxx + host_color: + has_raw_value: xxx + host_common_name: + has_raw_value: xxx + host_diet: + - has_raw_value: xxx + host_dry_mass: + has_raw_value: xxx + host_family_relation: + - xxx + host_genotype: + has_raw_value: xxx + host_growth_cond: + has_raw_value: xxx + host_height: + has_raw_value: xxx + host_last_meal: + - has_raw_value: xxx + host_length: + has_raw_value: xxx + host_life_stage: + has_raw_value: xxx + host_name: snail is an example value, but unconstrained text is accepted at this + point + host_phenotype: + has_raw_value: xxx + host_sex: female + host_shape: + has_raw_value: xxx + host_subject_id: + has_raw_value: xxx + host_subspecf_genlin: + - xxx + host_substrate: + has_raw_value: xxx + host_symbiont: + - xxx + host_taxid: + has_raw_value: NCBITaxon:9606 + term: + id: NCBITaxon:9606 + host_tot_mass: + has_raw_value: xxx + host_wet_mass: + has_raw_value: xxx + humidity: + has_raw_value: xxx + humidity_regm: + - has_raw_value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + id: nmdc:bsm-99-dtTMNb + igsn_biosample_identifiers: + - any:curie_1 + - any:curie_2 + img_identifiers: + - img.taxon:abc123 + indoor_space: bedroom + indoor_surf: cabinet + indust_eff_percent: + has_raw_value: xxx + inorg_particles: + - has_raw_value: xxx + insdc_biosample_identifiers: + - biosample:SAMN123456789 + - biosample:SAMN000 + inside_lux: + has_raw_value: xxx + int_wall_cond: new + isotope_exposure: 13C glucose + iw_bt_date_well: + has_raw_value: xxx + iwf: + has_raw_value: xxx + last_clean: + has_raw_value: xxx + lat_lon: + has_raw_value: 50.586825 6.408977 + latitude: 50.586825 + longitude: 6.408977 + lbc_thirty: + has_raw_value: 543 mg/kg + lbceq: + has_raw_value: 1575 mg/kg + light_intensity: + has_raw_value: xxx + light_regm: + has_raw_value: incandescent light;10 lux;450 nanometer + light_type: + - none + link_addit_analys: + has_raw_value: https://pubmed.ncbi.nlm.nih.gov/2315679/ + link_class_info: + has_raw_value: https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf + link_climate_info: + has_raw_value: https://www.int-res.com/abstracts/cr/v14/n3/p161-173/ + lithology: Basement + local_class: + has_raw_value: jicama soil + local_class_meth: + has_raw_value: https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083 + location: unconstrained text. should we even keep this slot? check if it has been + used in MongoDB. + magnesium: + has_raw_value: 52.8 micromole per kilogram + manganese: + has_raw_value: 24.7 mg/kg + max_occup: + has_raw_value: xxx + mean_frict_vel: + has_raw_value: 0.5 meter per second + mean_peak_frict_vel: + has_raw_value: 1 meter per second + mech_struc: subway + mechanical_damage: + - has_raw_value: xxx + methane: + has_raw_value: xxx + micro_biomass_c_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 + micro_biomass_meth: xxx + micro_biomass_n_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 + microbial_biomass: + has_raw_value: xxx + microbial_biomass_c: 0.05 ug C/g dry soil + microbial_biomass_n: 0.05 ug N/g dry soil + mineral_nutr_regm: + - has_raw_value: xxx + misc_param: + - has_raw_value: Bicarbonate ion concentration;2075 micromole per kilogram + mod_date: '2023-01-25' + n_alkanes: + - has_raw_value: n-hexadecane;100 milligram per liter + name: Sample Exhaustive Biosample instance. Although all of these values should + pass validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. + ncbi_taxonomy_name: soil metagenome + nitrate: + has_raw_value: 65 micromole per liter + nitrite: + has_raw_value: 0.5 micromole per liter + nitrite_nitrogen: + has_raw_value: 1.2 mg/kg + nitro: + has_raw_value: xxx + non_microb_biomass: insect 0.23 ug; plant 1g + non_microb_biomass_method: https://doi.org/10.1038/s41467-021-26181-3 + non_min_nutr_regm: + - xxx + nucl_acid_amp: + has_raw_value: xxx + nucl_acid_ext: + has_raw_value: xxx + number_pets: + has_raw_value: xxx + number_plants: + has_raw_value: xxx + number_resident: + has_raw_value: xxx + occup_density_samp: + has_raw_value: xxx + occup_document: estimate + occup_samp: + has_raw_value: xxx + org_carb: + has_raw_value: xxx + org_count_qpcr_info: xxx + org_matter: + has_raw_value: 1.75 milligram per cubic meter + org_nitro: + has_raw_value: 4 micromole per liter + org_nitro_method: https://doi.org/10.1016/0038-0717(85)90144-0 + org_particles: + - has_raw_value: xxx + organism_count: + - has_raw_value: ATP + other_treatment: unconstrained text + owc_tvdss: + has_raw_value: xxx + oxy_stat_samp: aerobic + oxygen: + has_raw_value: xxx + part_of: + - nmdc:unconstrained_study_identifier_string1_needs_pattern_materialization_what_about_referential_integrity + - nmdc:unconstrained_study_identifier_string2 + part_org_carb: + has_raw_value: 1.92 micromole per liter + part_org_nitro: + has_raw_value: xxx + particle_class: + - has_raw_value: xxx + pcr_cond: + has_raw_value: xxx + pcr_primers: + has_raw_value: xxx + permeability: + has_raw_value: xxx + perturbation: + - has_raw_value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M + pesticide_regm: + - has_raw_value: xxx + petroleum_hydrocarb: + has_raw_value: 0.05 micromole per liter + ph: 99.99 + ph_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf + ph_regm: + - has_raw_value: xxx + phaeopigments: + - has_raw_value: 2.5 milligram per cubic meter + phosphate: + has_raw_value: 0.7 micromole per liter + phosplipid_fatt_acid: + - has_raw_value: 2.98 milligram per liter + photon_flux: + has_raw_value: xxx + plant_growth_med: + has_raw_value: xxx + plant_product: + has_raw_value: xxx + plant_sex: Androdioecious + plant_struc: + has_raw_value: xxx + pollutants: + - has_raw_value: xxx + pool_dna_extracts: + has_raw_value: yes, 5 + porosity: + has_raw_value: xxx + potassium: + has_raw_value: 463 milligram per liter + pour_point: + has_raw_value: xxx + pre_treatment: + has_raw_value: xxx + pres_animal_insect: cat;3 + pressure: + has_raw_value: 50 atmosphere + prev_land_use_meth: xxx + previous_land_use: + has_raw_value: xxx + primary_prod: + has_raw_value: xxx + primary_treatment: + has_raw_value: xxx + prod_rate: + has_raw_value: xxx + prod_start_date: + has_raw_value: xxx + profile_position: summit + project_id: no example from MIxS + proport_woa_temperature: no example from MIxS + proposal_dna: '504000' + proposal_rna: '504000' + quad_pos: North side + radiation_regm: + - has_raw_value: xxx + rainfall_regm: + - has_raw_value: xxx + reactor_type: + has_raw_value: xxx + redox_potential: + has_raw_value: 300 millivolt + rel_air_humidity: + has_raw_value: xxx + rel_humidity_out: + has_raw_value: xxx + rel_samp_loc: edge of car + replicate_number: '1' + reservoir: + has_raw_value: xxx + resins_pc: + has_raw_value: xxx + rna_absorb1: 2.02 + rna_absorb2: 2.02 + rna_collect_site: untreated pond water + rna_concentration: 100 + rna_container_id: Pond_MT_041618 + rna_isolate_meth: phenol/chloroform extraction + rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) + rna_project_contact: John Jones + rna_samp_id: '187654' + rna_sample_format: 10 mM Tris-HCl + rna_sample_name: JGI_pond_041618 + rna_seq_project: '1191234' + rna_seq_project_name: JGI Pond metagenomics + rna_seq_project_pi: Jane Johnson + rna_volume: 25 + room_air_exch_rate: + has_raw_value: xxx + room_architec_elem: xxx + room_condt: new + room_connected: attic + room_count: + has_raw_value: xxx + room_dim: + has_raw_value: xxx + room_door_dist: + has_raw_value: xxx + room_door_share: + has_raw_value: xxx + room_hallway: + has_raw_value: xxx + room_loc: corner room + room_moist_dam_hist: 123 + room_net_area: + has_raw_value: xxx + room_occup: + has_raw_value: xxx + room_samp_pos: north corner + room_type: attic + room_vol: + has_raw_value: xxx + room_wall_share: + has_raw_value: xxx + room_window_count: 123 + root_cond: + has_raw_value: xxx + root_med_carbon: + has_raw_value: xxx + root_med_macronutr: + has_raw_value: xxx + root_med_micronutr: + has_raw_value: xxx + root_med_ph: + has_raw_value: xxx + root_med_regl: + has_raw_value: xxx + root_med_solid: + has_raw_value: xxx + root_med_suppl: + has_raw_value: xxx + salinity: + has_raw_value: 25 practical salinity unit + salinity_category: halotolerant is an example from the schema, but MIxS doesn't + provide this slot any more + salinity_meth: + has_raw_value: PMID:22895776 + salt_regm: + - has_raw_value: xxx + samp_capt_status: other + samp_collec_device: xxx + samp_collec_method: swabbing + samp_collect_point: well + samp_dis_stage: dissemination + samp_floor: basement + samp_loc_corr_rate: + has_raw_value: xxx + samp_mat_process: + has_raw_value: filtering of seawater + samp_md: + has_raw_value: xxx + samp_name: see also name + samp_preserv: + has_raw_value: xxx + samp_room_id: + has_raw_value: xxx + samp_size: + has_raw_value: 5 liters + samp_sort_meth: + - has_raw_value: xxx + samp_store_dur: + has_raw_value: P1Y6M + samp_store_loc: + has_raw_value: Freezer no:5 + samp_store_temp: + has_raw_value: -80 degree Celsius + samp_subtype: biofilm + samp_taxon_id: + has_raw_value: soil metagenome [NCBItaxon:410658] + term: + id: NCBItaxon:410658 + name: soil metagenome + samp_time_out: + has_raw_value: xxx + samp_transport_cond: + has_raw_value: xxx + samp_tvdss: + has_raw_value: xxx + samp_type: + has_raw_value: xxx + samp_vol_we_dna_ext: + has_raw_value: 1500 milliliter + samp_weather: cloudy + samp_well_name: + has_raw_value: xxx + sample_collection_site: unconstrained text + sample_link: + - IGSN:DSJ0284 + - any:curie + sample_shipped: 15 g + sample_type: water_extract_soil + saturates_pc: + has_raw_value: xxx + season: + has_raw_value: xxx + season_environment: + - has_raw_value: xxx + season_precpt: + has_raw_value: 75 millimeters + season_temp: + has_raw_value: 18 degree Celsius + season_use: Spring + secondary_treatment: + has_raw_value: xxx + sediment_type: biogenous + seq_meth: + has_raw_value: xxx + seq_quality_check: + has_raw_value: xxx + sewage_type: + has_raw_value: xxx + shad_dev_water_mold: xxx + shading_device_cond: damaged + shading_device_loc: + has_raw_value: xxx + shading_device_mat: + has_raw_value: xxx + shading_device_type: tree + sieving: + has_raw_value: MIxS does not provide an example + silicate: + has_raw_value: xxx + size_frac: + has_raw_value: xxx + size_frac_low: + has_raw_value: 0.2 micrometer + size_frac_up: + has_raw_value: 20 micrometer + slope_aspect: + has_raw_value: MIxS does not provide an example + slope_gradient: + has_raw_value: MIxS does not provide an example + sludge_retent_time: + has_raw_value: xxx + sodium: + has_raw_value: 10.5 milligram per liter + soil_horizon: O horizon + soil_text_measure: + has_raw_value: xxx + soil_texture_meth: xxx + soil_type: + has_raw_value: plinthosol [ENVO:00002250] + soil_type_meth: + has_raw_value: Frederick series + solar_irradiance: + has_raw_value: xxx + soluble_inorg_mat: + - has_raw_value: xxx + soluble_iron_micromol: MIxS doesn't provide an example + soluble_org_mat: + - has_raw_value: xxx + soluble_react_phosp: + has_raw_value: xxx + source_mat_id: + has_raw_value: MPI012345 + space_typ_state: + has_raw_value: xxx + specific: operation + specific_ecosystem: unconstrained text + specific_humidity: + has_raw_value: xxx + sr_dep_env: Lacustine + sr_geol_age: Archean + sr_kerog_type: other + sr_lithology: Clastic + standing_water_regm: + - has_raw_value: xxx + start_date_inc: '2023-01-27' + start_time_inc: 13:42+0000 + store_cond: + has_raw_value: -20 degree Celsius freezer;P2Y10D + substructure_type: + - basement + subsurface_depth: + has_raw_value: MIxS does not provide an example + sulfate: + has_raw_value: 5 micromole per liter + sulfate_fw: + has_raw_value: xxx + sulfide: + has_raw_value: 2 micromole per liter + surf_air_cont: + - dust + surf_humidity: + has_raw_value: xxx + surf_material: adobe + surf_moisture: + has_raw_value: xxx + surf_moisture_ph: 123 + surf_temp: + has_raw_value: xxx + suspend_part_matter: + has_raw_value: xxx + suspend_solids: + - has_raw_value: xxx + tan: + has_raw_value: xxx + target_gene: + has_raw_value: xxx + target_subfragment: + has_raw_value: xxx + technical_reps: '2' + temp: + has_raw_value: 25 degree Celsius + temp_out: + has_raw_value: xxx + tertiary_treatment: + has_raw_value: xxx + tidal_stage: high tide + tillage: + - chisel + tiss_cult_growth_med: + has_raw_value: xxx + toluene: + has_raw_value: xxx + tot_carb: + has_raw_value: MIxS does not provide an example + tot_depth_water_col: + has_raw_value: 500 meter + tot_diss_nitro: + has_raw_value: 40 microgram per liter + tot_inorg_nitro: + has_raw_value: xxx + tot_iron: + has_raw_value: xxx + tot_nitro: + has_raw_value: xxx + tot_nitro_cont_meth: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 + tot_nitro_content: + has_raw_value: 35 milligrams Nitrogen per kilogram of soil + tot_org_c_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf + tot_org_carb: + has_raw_value: 2% + tot_part_carb: + has_raw_value: xxx + tot_phosp: + has_raw_value: 0.03 milligram per liter + tot_phosphate: + has_raw_value: xxx + tot_sulfur: + has_raw_value: xxx + train_line: red + train_stat_loc: south station above ground + train_stop_loc: end + turbidity: + has_raw_value: xxx + tvdss_of_hcr_press: + has_raw_value: xxx + tvdss_of_hcr_temp: + has_raw_value: xxx + typ_occup_density: 123 + type: nmdc:Biosample. change this to require a class name or an enumeration + ventilation_rate: + has_raw_value: xxx + ventilation_type: + has_raw_value: xxx + vfa: + has_raw_value: xxx + vfa_fw: + has_raw_value: xxx + vis_media: photos + viscosity: + has_raw_value: xxx + volatile_org_comp: + - has_raw_value: xxx + wall_area: + has_raw_value: xxx + wall_const_type: frame construction + wall_finish_mat: plaster + wall_height: + has_raw_value: xxx + wall_loc: north + wall_surf_treatment: painted + wall_texture: knockdown + wall_thermal_mass: + has_raw_value: xxx + wall_water_mold: + has_raw_value: xxx + wastewater_type: + has_raw_value: xxx + water_cont_soil_meth: MIxS doesn't provide an example + water_content: + - MIxS doesn't provide an example 1 + - MIxS doesn't provide an example 2 + water_current: + has_raw_value: xxx + water_cut: + has_raw_value: xxx + water_feat_size: + has_raw_value: xxx + water_feat_type: fountain + water_prod_rate: + has_raw_value: xxx + water_temp_regm: + - has_raw_value: xxx + watering_regm: + - has_raw_value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + weekday: Monday + win: + has_raw_value: xxx + wind_direction: + has_raw_value: xxx + wind_speed: + has_raw_value: xxx + window_cond: damaged + window_cover: blinds + window_horiz_pos: left + window_loc: north + window_mat: fiberglass + window_open_freq: + has_raw_value: xxx + window_size: + has_raw_value: xxx + window_status: + has_raw_value: xxx + window_type: single-hung sash window + window_vert_pos: bottom + window_water_mold: + has_raw_value: xxx + xylene: + has_raw_value: xxx + zinc: + has_raw_value: 2.5 mg/kg + +``` +## Database-biosamples-rna-in-tube +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - gold:Gs0110115 + rna_cont_type: tube + +``` +## MetabolomicsAnalysisActivity-1 +### Input +```yaml +ended_at_time: '2021-09-15T10:13:20+00:00' +execution_resource: NERSC cori +git_url: https://example.org/WorkflowExecutionActivity +has_calibration: calibration with 0.01% phosphoric acid +has_input: +- nmdc:i1 +- nmdc:i2 +has_output: +- nmdc:o1 +- nmdc:o2 +id: nmdc:wfmb-99-ABCDEF +started_at_time: '2021-08-05T14:48:51+00:00' +type: WorkflowExecutionActivity +was_informed_by: nmdc:a1 + +``` +## Database-pooling_set-minimal +### Input +```yaml +pooling_set: +- id: nmdc:poolp-9x9-1x + name: first pooling process + +``` +## Database-biosamples-1 +### Input +```yaml +biosample_set: +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101224 + habitat: Coalbed water + id: nmdc:bsm-99-dtTMNb + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients (early) + ncbi_taxonomy_name: coal metagenome + part_of: + - gold:Gs0110115 + samp_taxon_id: + has_raw_value: coal metagenome [NCBITaxon:1260732] + term: + id: NCBITaxon:1260732 + name: coal metagenome + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + biosample_categories: + - LTER + - SIP + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101224 + habitat: Coalbed water + id: nmdc:bsm-99-AtTUOs + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients (early) + ncbi_taxonomy_name: coal metagenome + part_of: + - gold:Gs0110115 + samp_taxon_id: + has_raw_value: coal metagenome [NCBITaxon:1260732] + term: + id: NCBITaxon:1260732 + name: coal metagenome + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101225 + habitat: Coalbed water + id: nmdc:bsm-99-eBVHjN + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients Extra + ncbi_taxonomy_name: coal metagenome + part_of: + - gold:Gs0110115 + samp_taxon_id: + has_raw_value: coal metagenome [NCBITaxon:1260732] + term: + id: NCBITaxon:1260732 + name: coal metagenome + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101226 + habitat: Coalbed water + id: nmdc:bsm-99-TDPHTh + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients + ncbi_taxonomy_name: coal metagenome + part_of: + - gold:Gs0110115 + samp_taxon_id: + has_raw_value: coal metagenome [NCBITaxon:1260732] + term: + id: NCBITaxon:1260732 + name: coal metagenome + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample + +``` +## DataObject-minimal +### Input +```yaml +description: Crispr Terms for nmdc:ann0vx38 +id: nmdc:dobj-11-dtTMNb +name: Crispr Terms + +``` +## Database-library-prep-exhausive +### Input +```yaml +library_preparation_set: +- description: DNA extraction of NEON sample TREE_001-O-20170707-COMP-DNA1 using SOP + BMI_metagenomicsSequencingSOP_v2 + end_date: '2018-09-26' + has_input: + - generic:xxx + has_output: + - generic:xxx + id: nmdc:libprp-99-xxx2 + library_preparation_kit: KAPA HyperPrep Kit + library_type: DNA + name: DNA library creation of NEON sample TREE_001-O-20170707-COMP-DNA1 + pcr_cycles: 0 + processing_institution: Battelle + start_date: '2018-09-26' +- description: RNA extraction of NEON sample TREE_001-O-20170707-COMP-DNA1 using SOP + XX + end_date: '2018-09-26' + has_input: + - generic:xxy + has_output: + - generic:xxz + id: nmdc:libprp-99-xxx1 + library_preparation_kit: TruSeq RNA Library Prep Kit v2 + library_type: RNA + name: RNA library creation of NEON sample TREE_001-O-20170707-COMP-DNA1 + pcr_cycles: 12 + processing_institution: Battelle + start_date: '2018-09-26' ``` -## OmicsProcessing-1 +## Database-multiple-paths ### Input ```yaml -add_date: 30-OCT-14 12.00.00.000000000 AM -alternative_identifiers: -- gold:Gp0108335 -has_input: -- gold:Gb0108335 -has_output: -- jgi:551a20d30d878525404e90d5 -id: nmdc:omprc-99-zUCd5N -mod_date: 22-MAY-20 06.13.12.927000000 PM -name: Thawing permafrost microbial communities from the Arctic, studying carbon transformations - - Permafrost 712P3D -ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying - carbon transformations - Permafrost 712P3D -omics_type: - has_raw_value: Metagenome +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + name: real biosample from the field + part_of: + - gold:Gs0110115 +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-XYZ + name: one DNA library, like an analytical sample + part_of: + - gold:Gs0110115 +omics_processing_set: +- add_date: 30-OCT-14 12.00.00.000000000 AM + alternative_identifiers: + - gold:Gp0108335 + has_input: + - gold:Gb0108335 + has_output: + - jgi:551a20d30d878525404e90d5 + id: nmdc:omprc-99-zUCd5N + mod_date: 22-MAY-20 06.13.12.927000000 PM + name: a process in which a biosample was sequenced? + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D + omics_type: + has_raw_value: Metagenome + part_of: + - gold:Gs0112340 + processing_institution: JGI + type: nmdc:OmicsProcessing + +``` +## DataObject-3 +### Input +```yaml +description: Metagenome Contig Coverage Stats for gold:Gp0061273 +file_size_bytes: 32787380 +id: nmdc:dobj-99-izwYW6 +name: mapping_stats.txt +type: nmdc:DataObject + +``` +## Database-multi-id-study +### Input +```yaml +study_set: +- gnps_task_identifiers: + - gnps.task:4b848c342a4f4abc871bdf8a09a60807 + - gnps.task:51cc733a80ed41139ecdd1bedf3c01af + - gnps.task:8062948726c543dba53ec58c0f1ebb25 + - gnps.task:f8efbde4cc154db6a4cf269072d42d40 + id: nmdc:sty-11-r2h77870 + jgi_portal_study_identifiers: + - jgi.proposal:507130 + study_category: research_study + +``` +## DataObject-2 +### Input +```yaml +description: Assembled scaffold fasta for gold:Gp0061273 +file_size_bytes: 205297945 +id: nmdc:dobj-99-PqBJvW +name: assembly_scaffolds.fna +type: nmdc:DataObject + +``` +## Biosample-minimal-2 +### Input +```yaml +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +id: nmdc:bsm-99-dtTMNb part_of: -- gold:Gs0112340 -processing_institution: JGI -type: nmdc:OmicsProcessing +- gold:Gs0110115 + +``` +## Study-credit-1 +### Input +```yaml +has_credit_associations: +- applied_roles: + - Data curation + applies_to_person: + orcid: orcid:0000-0002-1825-00 +- applied_roles: + - Software + applies_to_person: + orcid: orcid:0000-0001-9076-6066 +id: nmdc:sty-99-WoeqAi +study_category: research_study ``` ## Database-pooling_set-exhaustive @@ -4071,69 +4140,40 @@ pooling_set: name: first pooling process ``` -## Database-study-set-with-gnps-id +## Pooling-minimal ### Input ```yaml -study_set: -- award_dois: - - doi:10.25585/1488217 - description: Thawing permafrost is one of the largest soil carbon pools on the planet. - The goal of this project is to study microbial communities that participate in - the soil carbon cycle. - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Wetlands - ecosystem_type: Soil - gnps_task_identifiers: - - gnps.task:4b848c342a4f4abc871bdf8a09a60807 - gold_study_identifiers: - - gold:Gs0128849 - id: nmdc:sty-99-FkQIsc - name: Permafrost microbial communities from Stordalen Mire, Sweden - principal_investigator: - has_raw_value: Virginia Rich - specific_ecosystem: Permafrost - study_category: research_study - type: nmdc:Study +id: nmdc:poolp-9x9-1x +name: first pooling process ``` -## Database-multi-id-study +## Database-processed_sample-minimal ### Input ```yaml -study_set: -- gnps_task_identifiers: - - gnps.task:4b848c342a4f4abc871bdf8a09a60807 - - gnps.task:51cc733a80ed41139ecdd1bedf3c01af - - gnps.task:8062948726c543dba53ec58c0f1ebb25 - - gnps.task:f8efbde4cc154db6a4cf269072d42d40 - id: nmdc:sty-11-r2h77870 - jgi_portal_study_identifiers: - - jgi.proposal:507130 - study_category: research_study +processed_sample_set: +- id: nmdc:procsm-99-dtTMNb ``` -## DataObject-3 +## Pooling-exhaustive ### Input ```yaml -description: Metagenome Contig Coverage Stats for gold:Gp0061273 -file_size_bytes: 32787380 -id: nmdc:dobj-99-izwYW6 -name: mapping_stats.txt -type: nmdc:DataObject +alternative_identifiers: +- generic:xxx +description: xxx +has_input: +- generic:xxx +- generic:yyy +has_output: +- generic:xxx +id: nmdc:poolp-9x9-1x +name: first pooling process ``` -## Database-nmdc-example +## Database-biosamples-minimal ### Input ```yaml biosample_set: -- add_date: 17-MAR-17 04.55.54.717000000 PM - community: microbial communities - description: Permafrost microbial communities from Stordalen Mire, Sweden - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Wetlands - ecosystem_type: Soil - env_broad_scale: +- env_broad_scale: has_raw_value: ENVO:00002030 term: id: ENVO:00002030 @@ -4145,36 +4185,31 @@ biosample_set: has_raw_value: ENVO:00005792 term: id: ENVO:00005792 - geo_loc_name: - has_raw_value: 'Sweden: Stordalen' - gold_biosample_identifiers: - - gold:Gb0150408 - habitat: Fen - id: nmdc:bsm-99-isqhuW - lat_lon: - has_raw_value: 68.35 19.05 - latitude: 68.35 - longitude: 19.05 - location: Stordalen Mire, Sweden - mod_date: 08-JAN-20 02.49.23.000000000 PM - name: Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG - ncbi_taxonomy_name: permafrost metagenome + id: nmdc:bsm-99-dtTMNb + part_of: + - gold:Gs0110115 + +``` +## Database-neon_Biosample_to_DataObject_NEON +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-abcdef1 part_of: - - gold:Gs0128849 - samp_name: 11E1M metaG - sample_collection_site: Mire fen - specific_ecosystem: Permafrost - type: nmdc:Biosample -- add_date: 17-AUG-17 05.38.34.719000000 PM - community: microbial communities - description: Forest soil from Barre Woods Harvard Forest LTER site was incubated - at 10C with heavy water. Sample is from a control plot at ambient soil temperature, - organic horizon - top 4cm of soil - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: + - nmdc:sty-11-34xj1150 +- env_broad_scale: has_raw_value: ENVO:00002030 term: id: ENVO:00002030 @@ -4186,37 +4221,10 @@ biosample_set: has_raw_value: ENVO:00005792 term: id: ENVO:00005792 - geo_loc_name: - has_raw_value: 'USA: Massachusetts' - gold_biosample_identifiers: - - gold:Gb0157174 - habitat: soil - id: nmdc:bsm-99-dge3H9 - lat_lon: - has_raw_value: 42.481016 -72.178343 - latitude: 42.481016 - longitude: -72.178343 - location: Barre Woods Harvard Forest LTER site, Petersham, Massachusetts, United - States - mod_date: 08-JAN-20 02.49.23.000000000 PM - name: Forest soil microbial communities from Barre Woods Harvard Forest LTER site, - Petersham, Massachusetts, United States - Inc-BW-C-14-O - ncbi_taxonomy_name: soil metagenome + id: nmdc:bsm-99-abcdef2 part_of: - - gold:Gs0128849 - samp_name: Inc-BW-C-14-O - sample_collection_site: forest soil - specific_ecosystem: Forest Soil - type: nmdc:Biosample -- add_date: 29-MAR-18 01.27.40.709000000 PM - community: microbial communities - description: Rhizosphere microbial communities from Carex aquatilis grown in submerged - peat from a thermokarst bog, University of Washington, Seatle, WA, United States - ecosystem: Host-associated - ecosystem_category: Plants - ecosystem_subtype: Soil - ecosystem_type: Rhizosphere - env_broad_scale: + - nmdc:sty-11-34xj1150 +- env_broad_scale: has_raw_value: ENVO:00002030 term: id: ENVO:00002030 @@ -4228,200 +4236,113 @@ biosample_set: has_raw_value: ENVO:00005792 term: id: ENVO:00005792 - geo_loc_name: - has_raw_value: 'USA: Seattle, Washington' - gold_biosample_identifiers: - - gold:Gb0188037 - habitat: rhizosphere - host_name: Carex aquatilis - id: nmdc:bsm-99-dc6tg6 - lat_lon: - has_raw_value: 47.6516 -122.3045 - latitude: 47.6516 - longitude: -122.3045 - location: University of Washington, Seatle, WA, United States - mod_date: 08-JAN-20 02.49.25.000000000 PM - name: Rhizosphere microbial communities from Carex aquatilis grown in University - of Washington, Seatle, WA, United States - 4-1-23 metaG - ncbi_taxonomy_name: rhizosphere metagenome + id: nmdc:bsm-99-abcdef3 part_of: - - gold:Gs0128849 - samp_name: 4-1-23 metaG - sample_collection_site: Peat Soil - specific_ecosystem: Unclassified - type: nmdc:Biosample + - nmdc:sty-11-34xj1150 data_object_set: -- description: Raw sequencer read data - file_size_bytes: 9208349052 - id: nmdc:dobj-99-dkJ8xX - name: 11340.8.202049.GTCTCCT-AAGGAGA.fastq.gz +- data_object_type: Metagenome Raw Read 1 + description: Test R1 data + id: nmdc:dobj-12-jdhk9537 + name: BMI_HY7W2BGXG_Plate19S_13WellG10_R1.fastq.gz type: nmdc:DataObject -- description: Raw sequencer read data - file_size_bytes: 34243309819 - id: nmdc:dobj-99-7zrm55 - name: 11839.4.222578.GAGCTCA-TTGAGCT.fastq.gz + url: https://storage.neonscience.org/neon-microbial-raw-seq-files/2020/BMI_HY7W2BGXG_mms_R1/BMI_HY7W2BGXG_Plate19S_13WellG10_R1.fastq.gz +- data_object_type: Metagenome Raw Read 2 + description: Test R2 data + id: nmdc:dobj-12-yx0tfp52 + name: W2BGXG_Plate19S_13WellG10_R2.fastq.gz type: nmdc:DataObject -- description: Raw sequencer read data - file_size_bytes: 7580035314 - id: nmdc:dobj-99-sQQw0I - name: 12660.4.274923.GATCGTAC-GTACGATC.fastq.gz + url: https://storage.neonscience.org/neon-microbial-raw-seq-files/2020/BMI_HY7W2BGXG_mms_R2/BMI_HY7W2BGXG_Plate19S_13WellG10_R2.fastq.gz +- data_object_type: Filtered Sequencing Reads + description: Test filtered data for NEON + id: nmdc:dobj-12-71q7wv80 + name: 1472_51293.filtered.fastq.gz type: nmdc:DataObject -omics_processing_set: -- add_date: 17-AUG-17 05.08.38.451000000 PM - alternative_identifiers: - - gold:Gp0225767 - description: Forest soil from Barre Woods Harvard Forest LTER site was incubated - at 10C with heavy water. Sample is from a control plot at ambient soil temperature, - organic horizon - top 4cm of soil - has_input: - - gold:Gb0157174 - has_output: - - jgi:599c3a117ded5e41edd7da77 - id: nmdc:omprc-99-9XUVVF - mod_date: 16-OCT-20 02.04.01.374000000 AM - name: Forest soil microbial communities from Barre Woods Harvard Forest LTER site, - Petersham, Massachusetts, United States - Inc-BW-C-14-O - ncbi_project_name: Forest soil microbial communities from Barre Woods Harvard Forest - LTER site, Petersham, Massachusetts, United States - Inc-BW-C-14-O - omics_type: - has_raw_value: Metagenome - part_of: - - gold:Gs0130354 - processing_institution: JGI - type: nmdc:OmicsProcessing -- add_date: 17-MAR-17 04.55.44.822000000 PM - alternative_identifiers: - - gold:Gp0208560 - description: Permafrost microbial communities from Stordalen Mire, Sweden + url: https://data.microbiomedata.org/data/1472_51293/qa/1472_51293.filtered.fastq.gz +extraction_set: +- end_date: '2021-01-15' + extraction_target: DNA has_input: - - gold:Gb0150408 + - nmdc:procsm-99-xyz1 has_output: - - jgi:58b653757ded5e7a2af951c4 - id: nmdc:omprc-99-dk9vgI - mod_date: 22-MAY-20 06.38.19.576000000 PM - name: Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG - ncbi_project_name: Permafrost microbial communities from Stordalen Mire, Sweden - - 611E1M metaG - omics_type: - has_raw_value: Metagenome - part_of: - - gold:Gs0128849 - processing_institution: JGI - type: nmdc:OmicsProcessing -- add_date: 29-MAR-18 01.27.30.036000000 PM - alternative_identifiers: - - gold:Gp0306221 - description: Rhizosphere microbial communities from Carex aquatilis grown in submerged - peat from a thermokarst bog, University of Washington, Seatle, WA, United States + - nmdc:procsm-99-xyz2 + id: nmdc:extrp-99-abcdef + name: first dna extraction set + start_date: '2021-01-15' +library_preparation_set: +- end_date: '2021-01-15' has_input: - - gold:Gb0188037 + - nmdc:procsm-99-xyz2 has_output: - - jgi:5baa816646d1e63f764deb37 - id: nmdc:omprc-99-MVW1FV - mod_date: 04-APR-20 08.26.35.067000000 AM - name: Rhizosphere microbial communities from Carex aquatilis grown in University - of Washington, Seatle, WA, United States - 4-1-23 metaG - ncbi_project_name: Rhizosphere microbial communities from Carex aquatilis grown - in University of Washington, Seatle, WA, United States - 4-1-23 metaG - omics_type: - has_raw_value: Metagenome - part_of: - - gold:Gs0134277 - processing_institution: JGI - type: nmdc:OmicsProcessing -study_set: -- award_dois: - - doi:10.25585/1488217 - description: Thawing permafrost is one of the largest soil carbon pools on the planet. - The goal of this project is to study microbial communities that participate in - the soil carbon cycle. - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Wetlands - ecosystem_type: Soil - gold_study_identifiers: - - gold:Gs0128849 - id: nmdc:sty-99-FkQIsc - name: Permafrost microbial communities from Stordalen Mire, Sweden - principal_investigator: - has_raw_value: Virginia Rich - specific_ecosystem: Permafrost - study_category: research_study - type: nmdc:Study -- award_dois: - - doi:10.25585/1488215 - description: The goal of this study is to learn the molecular mechanisms underlying - changes in the temperature sensitive respiration response of forest soils to long-term - experimental warming - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - gold_study_identifiers: - - gold:Gs0130354 - id: nmdc:sty-99-oJmAOs - name: Forest soil microbial communities from Barre Woods Harvard Forest LTER site, - Petersham, Massachusetts, United States - principal_investigator: - has_raw_value: Jeffrey Blanchard - specific_ecosystem: Forest Soil - study_category: consortium - type: nmdc:Study -- award_dois: - - doi:10.25585/1488209 - description: The goal of this study is to advance understanding of the response - of methane production and methane oxidation to changes in plant productivity so - that modeled representations of these processes and interactions can be improved. - ecosystem: Host-associated - ecosystem_category: Plants - ecosystem_subtype: Rhizosphere - ecosystem_type: Roots - gold_study_identifiers: - - gold:Gs0134277 - id: nmdc:sty-99-3bQQ4j - name: Rhizosphere microbial communities from Carex aquatilis grown in University - of Washington, Seatle, WA, United States - principal_investigator: - has_raw_value: Rebecca Neumann - specific_ecosystem: Soil - study_category: research_study - type: nmdc:Study - -``` -## Pooling-minimal -### Input -```yaml -id: nmdc:poolp-9x9-1x -name: first pooling process - -``` -## Database-study_set-emsl_project_doi -### Input -```yaml -study_set: -- emsl_project_dois: - - doi:10.46936/intm.proj.2021.60141/60000423 - id: nmdc:sty-11-ab - study_category: research_study + - nmdc:procsm-99-xyz3 + id: nmdc:libprp-99-abcdef + library_type: DNA + name: DNA library preparation of NEON sample TREE_001-O-20170707-COMP-DNA1 + start_date: '2021-01-15' +omics_processing_set: +- has_input: + - nmdc:procsm-99-xyz3 + has_output: + - nmdc:dobj-12-jdhk9537 + - nmdc:dobj-12-yx0tfp52 + id: nmdc:omprc-11-s9xj2r24 + instrument_name: Illumina NovaSeq S4 + name: Test NEON data + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-11-34xj1150 + processing_institution: Battelle + type: nmdc:OmicsProcessing +pooling_set: +- description: This is the first pooling process that has ever occurred on earth + end_date: '2021-01-14' + has_input: + - nmdc:bsm-99-abcdef1 + - nmdc:bsm-99-abcdef2 + - nmdc:bsm-99-abcdef3 + has_output: + - nmdc:procsm-99-xyz1 + id: nmdc:poolp-99-abcdef + name: first pooling process + start_date: '2021-01-14' +processed_sample_set: +- id: nmdc:procsm-99-xyz1 + name: first processed sample set +- id: nmdc:procsm-99-xyz2 + name: first DNA extract +- id: nmdc:procsm-99-xyz3 + name: first library +read_qc_analysis_activity_set: +- ended_at_time: '2023-03-23T17:17:05.111725+00:00' + execution_resource: NERSC-Cori + git_url: https://github.com/microbiomedata/ReadsQC + has_input: + - nmdc:dobj-12-jdhk9537 + - nmdc:dobj-12-yx0tfp52 + has_output: + - nmdc:dobj-12-71q7wv80 + - nmdc:dobj-12-y236qp68 + id: nmdc:wfrqc-12-63da5n74 + name: 'TEST Read QC Activity for nmdc:wfrqc-12-63da5n74 ' + part_of: + - nmdc:wfrqc-11-hcr2by04.1 + started_at_time: '2023-03-23T17:17:05.111689+00:00' + type: nmdc:ReadQCAnalysisActivity + version: b1.0.7 + was_informed_by: nmdc:omprc-11-s9xj2r24 ``` -## MetabolomicsAnalysisActivity-1 +## DataObject-MB-unknown-enum-pv ### Input ```yaml -ended_at_time: '2021-09-15T10:13:20+00:00' -execution_resource: NERSC cori -git_url: https://example.org/WorkflowExecutionActivity -has_calibration: calibration with 0.01% phosphoric acid -has_input: -- nmdc:i1 -- nmdc:i2 -has_output: -- nmdc:o1 -- nmdc:o2 -id: nmdc:wfmb-99-ABCDEF -started_at_time: '2021-08-05T14:48:51+00:00' -type: WorkflowExecutionActivity -was_informed_by: nmdc:a1 +data_object_type: Crispr Terms +description: Crispr Terms for nmdc:ann0vx38 +file_size_bytes: 1234 +id: nmdc:dobj-11-dtTMNb +md5_checksum: 22afa3d49b73eaec2e9787a6b88fbdc3 +name: Crispr Terms +type: nmdc:DataObject +url: http://example.com ``` ## Biosample-with-fire @@ -4445,172 +4366,226 @@ part_of: - gold:Gs0110115 ``` -## Biosample-minimal +## Database-functional-annotations ### Input ```yaml -env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 -env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 -env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 -id: nmdc:bsm-99-dtTMNb -part_of: -- gold:Gs0110115 +functional_annotation_set: +- has_function: KEGG_PATHWAY:rsk00410 +- has_function: KEGG.REACTION:R00100 +- has_function: RHEA:12345 +- has_function: MetaCyc:RXN-14904 +- has_function: EC:1.1.1.1 +- has_function: GO:0032571 +- has_function: MetaNetX:MNXR101574 +- has_function: SEED:Biotin_biosynthesis +- has_function: KEGG.ORTHOLOGY:K00001 +- has_function: EGGNOG:veNOG12876 +- has_function: PFAM:PF11779 +- has_function: TIGRFAM:TIGR00010 +- has_function: SUPFAM:SSF57615 +- has_function: CATH:1.10.10.200 +- has_function: PANTHER.FAMILY:PTHR12345 ``` -## MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json +## Database-nucleic-extraction ### Input ```yaml -ended_at_time: '2021-09-15T10:13:20+00:00' -execution_resource: JGI -git_url: '' -has_input: -- nmdc:unvalidated_placeholder -has_output: -- nmdc:22afa3d49b73eaec2e9787a6b88fbdc3 -id: nmdc:wfmsa-99-qwertyuiop -name: Sequencing Activity for nmdc:mga0vx38 -part_of: -- nmdc:mga0vx38 -started_at_time: '2021-08-05T14:48:51+00:00' -type: nmdc:MetagenomeSequencing -version: v1.0.0 -was_informed_by: gold:Gp0213371 +extraction_set: +- description: DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7 + end_date: '2019-11-08' + extraction_method: phenol/chloroform extraction + extraction_target: DNA + has_input: + - generic:xxx + has_output: + - generic:xxx + id: nmdc:extrp-99-abcdef + input_mass: + has_numeric_value: 0.25 + has_unit: gram + name: DNA extraction of NEON sample WREF_072-O-20190618-COMP + processing_institution: Battelle + start_date: '2019-11-08' ``` -## Study-credit-1 +## FunctionalAnnotationAggMember-minimal ### Input ```yaml -has_credit_associations: -- applied_roles: - - Data curation - applies_to_person: - orcid: orcid:0000-0002-1825-00 -- applied_roles: - - Software - applies_to_person: - orcid: orcid:0000-0001-9076-6066 -id: nmdc:sty-99-WoeqAi -study_category: research_study +count: 120 +gene_function_id: KEGG.ORTHOLOGY:K00627 +metagenome_annotation_id: nmdc:8253bcdcd0387177ff895c38a047c719 ``` -## FunctionalAnnotation-exhaustive +## Database-functional_annotation_agg ### Input ```yaml -has_function: KEGG_PATHWAY:abc12345 -subject: nmdc:gene_product_1 -was_generated_by: nmdc:activity_1 +functional_annotation_agg: +- count: 120 + gene_function_id: KEGG.ORTHOLOGY:K00627 + metagenome_annotation_id: nmdc:8253bcdcd0387177ff895c38a047c719 ``` -## FunctionalAnnotation-minimal +## Database-extraction_set-exhaustive ### Input ```yaml -has_function: KEGG_PATHWAY:abc12345 +extraction_set: +- description: DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7 + end_date: '2019-11-08' + extraction_method: phenol/chloroform extraction + extraction_target: DNA + has_input: + - generic:xxx + has_output: + - generic:xxx + id: nmdc:extrp-99-abcdef + input_mass: + has_numeric_value: 0.25 + has_unit: gram + name: DNA extraction of NEON sample WREF_072-O-20190618-COMP + processing_institution: Battelle + protocol_link: + name: BMI_dnaExtractionSOP_v7 + url: https://data.neonscience.org/documents/10179/2431540/BMI_dnaExtractionSOP_v7/61204962-bb01-a0b9-3354-ccdaab5132c3 + quality_control_report: + status: pass + start_date: '2019-11-08' ``` -## Database-biosamples-dna-in-tube +## Database-study-set-with-gnps-id ### Input ```yaml -biosample_set: -- dna_cont_type: tube - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - id: nmdc:bsm-99-dtTMNb - part_of: - - gold:Gs0110115 +study_set: +- award_dois: + - doi:10.25585/1488217 + description: Thawing permafrost is one of the largest soil carbon pools on the planet. + The goal of this project is to study microbial communities that participate in + the soil carbon cycle. + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Wetlands + ecosystem_type: Soil + gnps_task_identifiers: + - gnps.task:4b848c342a4f4abc871bdf8a09a60807 + gold_study_identifiers: + - gold:Gs0128849 + id: nmdc:sty-99-FkQIsc + name: Permafrost microbial communities from Stordalen Mire, Sweden + principal_investigator: + has_raw_value: Virginia Rich + specific_ecosystem: Permafrost + study_category: research_study + type: nmdc:Study ``` -## Database-biosamples-dna-in-plate-valid-well-val +## FunctionalAnnotation-exhaustive ### Input ```yaml -biosample_set: -- dna_cont_type: plate - dna_cont_well: B2 - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - id: nmdc:bsm-99-dtTMNb - part_of: - - gold:Gs0110115 +has_function: KEGG_PATHWAY:abc12345 +subject: nmdc:gene_product_1 +was_generated_by: nmdc:activity_1 ``` -## Database-functional-annotations +## Database-study-set-with-dois ### Input ```yaml -functional_annotation_set: -- has_function: KEGG_PATHWAY:rsk00410 -- has_function: KEGG.REACTION:R00100 -- has_function: RHEA:12345 -- has_function: MetaCyc:RXN-14904 -- has_function: EC:1.1.1.1 -- has_function: GO:0032571 -- has_function: MetaNetX:MNXR101574 -- has_function: SEED:Biotin_biosynthesis -- has_function: KEGG.ORTHOLOGY:K00001 -- has_function: EGGNOG:veNOG12876 -- has_function: PFAM:PF11779 -- has_function: TIGRFAM:TIGR00010 -- has_function: SUPFAM:SSF57615 -- has_function: CATH:1.10.10.200 -- has_function: PANTHER.FAMILY:PTHR12345 +study_set: +- award_dois: + - doi:10.25585/1487763 + - doi:10.25585/1487765 + dataset_dois: + - doi:10.1333/s00897980202a + - doi:10.1093/acprof:oso/9780195159561.001.1 + description: Thawing permafrost is one of the largest soil carbon pools on the planet. + The goal of this project is to study microbial communities that participate in + the soil carbon cycle. + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Wetlands + ecosystem_type: Soil + gnps_task_identifiers: + - gnps.task:4b848c342a4f4abc871bdf8a09a60807 + gold_study_identifiers: + - gold:Gs0128849 + id: nmdc:sty-99-FkQIsc + name: Permafrost microbial communities from Stordalen Mire, Sweden + principal_investigator: + has_raw_value: Virginia Rich + publication_dois: + - doi:10.21/FQSQT4T3 + - doi:10.1016/j.foodchem.2008.11.065 + specific_ecosystem: Permafrost + study_category: research_study + type: nmdc:Study ``` -## Database-Biosample-invalid_id +## Database-omics-processings ### Input ```yaml -biosample_set: -- env_broad_scale: - term: - id: ENVO:00002030 - env_local_scale: - term: - id: ENVO:00002169 - env_medium: - term: - id: ENVO:00005792 - id: local +omics_processing_set: +- add_date: 30-OCT-14 12.00.00.000000000 AM + alternative_identifiers: + - gold:Gp0108335 + has_input: + - gold:Gb0108335 + has_output: + - jgi:551a20d30d878525404e90d5 + id: nmdc:omprc-99-zUCd5N + mod_date: 22-MAY-20 06.13.12.927000000 PM + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 712P3D + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D + omics_type: + has_raw_value: Metagenome part_of: - - gold:Gs0128849 + - gold:Gs0112340 + processing_institution: JGI + type: nmdc:OmicsProcessing +- add_date: 30-OCT-14 12.00.00.000000000 AM + alternative_identifiers: + - gold:Gp0108340 + has_input: + - gold:Gb0108340 + has_output: + - jgi:551a20d50d878525404e90d7 + id: nmdc:omprc-99-gKlQlF + mod_date: 22-MAY-20 06.10.59.590000000 PM + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 612S3M + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 612S3M + omics_type: + has_raw_value: Metagenome + part_of: + - gold:Gs0112340 + processing_institution: JGI + type: nmdc:OmicsProcessing +- add_date: 30-OCT-14 12.00.00.000000000 AM + alternative_identifiers: + - gold:Gp0108341 + has_input: + - gold:Gb0108341 + has_output: + - jgi:551a20d90d878525404e90e1 + id: nmdc:omprc-99-5kgIJR + mod_date: 22-MAY-20 06.09.46.171000000 PM + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 712S3S + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712S3S + omics_type: + has_raw_value: Metagenome + part_of: + - gold:Gs0112340 + processing_institution: JGI + type: nmdc:OmicsProcessing ``` -## Database-Biosample-invalid_range +## Database-biosamples-high-rna_volume ### Input ```yaml biosample_set: -- add_date: 28-JUL-14 12.00.00.000000000 AM - community: microbial communities - description: Bulk Aqueous phase filtered water - ecosystem: Environmental - ecosystem_category: Aquatic - ecosystem_subtype: Groundwater - ecosystem_type: Freshwater - env_broad_scale: +- env_broad_scale: has_raw_value: ENVO:00002030 term: id: ENVO:00002030 @@ -4622,101 +4597,73 @@ biosample_set: has_raw_value: ENVO:00005792 term: id: ENVO:00005792 - geo_loc_name: - has_raw_value: Lithgow - gold_biosample_identifiers: - - gold:Gb0101224 - habitat: Coalbed water - id: nmdc:bsm-6057d02c-664c-41c9-8486-3624ca845747 - lat_lon: - has_raw_value: 100 - latitude: '-33.460524' - longitude: '150.168149' - location: from the Lithgow State Coal Mine, New South Wales, Australia - mod_date: 26-AUG-16 01.50.27.000000000 PM - name: Lithgow State Coal Mine Calcium nutrients (early) - ncbi_taxonomy_name: coal metagenome + id: nmdc:bsm-99-dtTMNb part_of: - - gold:Gs0128849 - sample_collection_site: Lithgow State Coal Mine - specific_ecosystem: Coalbed water - type: nmdc:Biosample -- add_date: 28-JUL-14 12.00.00.000000000 AM - community: microbial communities - description: Bulk Aqueous phase filtered water - ecosystem: Environmental - ecosystem_category: Aquatic - ecosystem_subtype: Groundwater - ecosystem_type: Freshwater - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - geo_loc_name: - has_raw_value: Lithgow - gold_biosample_identifiers: - - gold:Gb0101225 - habitat: Coalbed water - id: nmdc:bsm-e924072f-98b5-4f88-a796-a7ba1d8ddd92 - lat_lon: - has_raw_value: -33.460524 150.168149 - latitude: -33.460524 - longitude: 150.168149 - location: from the Lithgow State Coal Mine, New South Wales, Australia - mod_date: 26-AUG-16 01.50.27.000000000 PM - name: Lithgow State Coal Mine Calcium nutrients Extra - ncbi_taxonomy_name: coal metagenome + - gold:Gs0110115 + rna_volume: 1200 + +``` +## Database-invalid-omics-processing +### Input +```yaml +omics_processing_set: +- add_date: 30-OCT-14 12.00.00.000000000 AM + alternative_identifiers: + - gold:Gp0108335 + has_input: + - gold:Gb0108335 + has_output: + - jgi:551a20d30d878525404e90d5 + id: nmdc:omprc-99-zUCd5N + mod_date: 22-MAY-20 06.13.12.927000000 PM + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 712P3D + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D + omics_type: + has_awesome_value: Metagenome part_of: - - gold:Gs0128849 - sample_collection_site: Lithgow State Coal Mine - specific_ecosystem: Coalbed water - type: nmdc:Biosample -- add_date: 28-JUL-14 12.00.00.000000000 AM - community: microbial communities - description: Bulk Aqueous phase filtered water - ecosystem: Environmental - ecosystem_category: Aquatic - ecosystem_subtype: Groundwater - ecosystem_type: Freshwater - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - geo_loc_name: - has_raw_value: Lithgow - gold_biosample_identifiers: - - gold:Gb0101226 - habitat: Coalbed water - id: nmdc:bsm-61c3332d-f654-4db8-8d2f-59475894daa5 - lat_lon: - has_raw_value: -33.460524 150.168149 - latitude: -33.460524 - longitude: 150.168149 - location: from the Lithgow State Coal Mine, New South Wales, Australia - mod_date: 26-AUG-16 01.50.27.000000000 PM - name: Lithgow State Coal Mine Calcium nutrients - ncbi_taxonomy_name: coal metagenome + - gold:Gs0112340 + processing_institution: JGI + type: nmdc:OmicsProcessing +- add_date: 30-OCT-14 12.00.00.000000000 AM + alternative_identifiers: + - gold:Gp0108340 + has_input: + - gold:Gb0108340 + has_output: + - jgi:551a20d50d878525404e90d7 + id: nmdc:omprc-99-gKlQlF + mod_date: 22-MAY-20 06.10.59.590000000 PM + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 612S3M + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 612S3M + omics_type: + has_raw_value: Metagenome part_of: - - gold:Gs0128849 - sample_collection_site: Lithgow State Coal Mine - specific_ecosystem: Coalbed water - type: nmdc:Biosample + - gold:Gs0112340 + processing_institution: JGI + type: nmdc:OmicsProcessing +- add_date: 30-OCT-14 12.00.00.000000000 AM + alternative_identifiers: + - gold:Gp0108341 + has_input: + - gold:Gb0108341 + has_output: + - jgi:551a20d90d878525404e90e1 + id: nmdc:omprc-99-5kgIJR + mod_date: 22-MAY-20 06.09.46.171000000 PM + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 712S3S + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712S3S + omics_type: + has_raw_value: Metagenome + part_of: + - gold:Gs0112340 + processing_institution: JGI + type: nmdc:OmicsProcessing ``` ## Biosample-invalid_fire @@ -4739,45 +4686,6 @@ id: nmdc:bsm-99-dtTMNb part_of: - gold:Gs0110115 -``` -## Study-invalid-1 -### Input -```yaml -has_credit_associations: -- applied_role: Value Not In Enum 1 - applies_to_person: - orcid: orcid:0000-0002-1825-00 - type: credit association -- applied_role: ValueNotInEnum2 - applies_to_person: - orcid: orcid:0000-0001-9076-6066 - type: credit association -id: example:123 - -``` -## Database-biosamples-lat_lon-with-GLV-missing-longitude -### Input -```yaml -biosample_set: -- env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - id: nmdc:bsm-99-dtTMNb - lat_lon: - has_raw_value: -33.460524 150.168149 - latitude: -33.460524 - part_of: - - gold:Gs0110115 - ``` ## Database-invalid-studies ### Input @@ -4830,6 +4738,43 @@ study_set: specific_ecosystem: Permafrost type: nmdc:Study +``` +## Study-invalid-1 +### Input +```yaml +has_credit_associations: +- applied_role: Value Not In Enum 1 + applies_to_person: + orcid: orcid:0000-0002-1825-00 + type: credit association +- applied_role: ValueNotInEnum2 + applies_to_person: + orcid: orcid:0000-0001-9076-6066 + type: credit association +id: example:123 + +``` +## Database-biosamples-rna-in-bucket +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - gold:Gs0110115 + rna_cont_type: bucket + ``` ## Database-biosample_mismatch_regex ### Input @@ -4952,32 +4897,96 @@ biosample_set: type: nmdc:Biosample ``` -## Database-plannedprocess-incorrect _date_slot +## Biosample-non_boolean_embargo ### Input ```yaml -extraction_set: -- extraction_date: 2021-01-15 - extraction_target: DNA - has_inputs: - - bare:pool_out_1 - has_outputs: - - bare:dna_extract_1 - id: bare:des1 - name: first dna extraction set -library_preparation_set: -- has_inputs: - - bare:dna_extract_1 - has_outputs: - - bare:library_1 - id: bare:lcs1 - library_type: DNA - name: DNA library preparation of NEON sample TREE_001-O-20170707-COMP-DNA1 - processed_date: 2021-01-15 +embargoed: 999 +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +id: nmdc:bsm-99-dtTMNb +part_of: +- gold:Gs0110115 ``` -## Biosample-missing-id +## Study-illegal-funding_sources +### Input +```yaml +abstract: Nothing was studied. +alternative_descriptions: +- any string 1 +- any string 2 +alternative_names: +- any string 1 +- any string 2 +alternative_titles: +- any string 1 +- any string 2 +description: see also name, title, objective, various alternatives +ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with MIxS + environmental triads +ecosystem_category: unconstrained text +ecosystem_subtype: unconstrained text +ecosystem_type: unconstrained text +ess_dive_datasets: +- any string 1 +- any string 2 +funding_sources: +- This is an example of a funding source with too long of a description. Funding sources + should be no more than 150 characters. Any longer is unnecessary and excessive. + Its very very very very very very very very very long. +- any string 2 +gold_study_identifiers: +- gold:Gs12345 +- gold:Gs90909 +id: nmdc:sty-11-ab +mgnify_project_identifiers: +- mgnify.proj:ABC123 +name: see also description, title, objective, various alternatives +objective: This record, an instance of class Study from the nmdc-schema was had authored, + so that the NMDC team would have at least one instance, using all slots, with a + mixture of reasonable values and minimally compliant values. +principal_investigator: + email: jcventer@jcvi.org + has_raw_value: Craig Venter + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + was_generated_by: nmdc:any_string_1 + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter +publications: +- any string 1 +- any string 2 +related_identifiers: any string R1 +relevant_protocols: +- any string 1 +- any string 2 +specific_ecosystem: unconstrained text +title: Sample Exhaustive Biosample instance. Although all of these values should pass + validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. +type: any string +websites: +- https://w3id.org/nmdc +- https://w3id.org/linkml + +``` +## Biosample-invalid-embargoed ### Input ```yaml +embargoed: 999 env_broad_scale: has_raw_value: ENVO:00002030 term: @@ -4990,8 +4999,64 @@ env_medium: has_raw_value: ENVO:00005792 term: id: ENVO:00005792 +id: nmdc:bsm-99-dtTMNb +part_of: +- gold:Gs0110115 + +``` +## FunctionalAnnotation-invalid-function +### Input +```yaml +has_function: KEGG_PATHWAY:XOXOXOXO + +``` +## Database-Extraction-invalid-sample_mass +### Input +```yaml +extraction_set: +- description: DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7 + end_date: '2019-11-08' + extraction_method: phenol/chloroform extraction + extraction_target: DNA + has_input: + - generic:xxx + has_output: + - generic:xxx + id: nmdc:extrp-99-abcdef + name: DNA extraction of NEON sample WREF_072-O-20190618-COMP + processing_institution: Battelle + protocol_link: + name: BMI_dnaExtractionSOP_v7 + url: https://data.neonscience.org/documents/10179/2431540/BMI_dnaExtractionSOP_v7/61204962-bb01-a0b9-3354-ccdaab5132c3 + quality_control_report: + status: pass + sample_mass: + has_numeric_value: 0.25 + has_unit: gram + start_date: '2019-11-08' + +``` +## OmicsProcessing-no-id +### Input +```yaml +add_date: 30-OCT-14 12.00.00.000000000 AM +alternative_identifiers: +- gold:Gp0108335 +has_input: +- gold:Gb0108335 +has_output: +- jgi:551a20d30d878525404e90d5 +mod_date: 22-MAY-20 06.13.12.927000000 PM +name: Thawing permafrost microbial communities from the Arctic, studying carbon transformations + - Permafrost 712P3D +ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D +omics_type: + has_raw_value: Metagenome part_of: -- gold:Gs0110115 +- gold:Gs0112340 +processing_institution: JGI +type: nmdc:OmicsProcessing ``` ## OmicsProcessing-invalid-omics-type @@ -5018,140 +5083,32 @@ processing_institution: JGI type: nmdc:OmicsProcessing ``` -## Database-biosamples-high-rna_volume -### Input -```yaml -biosample_set: -- env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - id: nmdc:bsm-99-dtTMNb - part_of: - - gold:Gs0110115 - rna_volume: 1200 - -``` -## Database-biosamples-lat_lon-with-GLV-missing-latitude +## DataObject-no-id-or-name ### Input ```yaml -biosample_set: -- env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - id: nmdc:bsm-99-dtTMNb - lat_lon: - has_raw_value: -33.460524 150.168149 - longitude: 150.168149 - part_of: - - gold:Gs0110115 +description: Crispr Terms for nmdc:ann0vx38 ``` -## Study-include-abstract +## MetagenomeSequencingActivity-no_parthood ### Input ```yaml -study_set: -- abstract: This study is about a thing. - alternative_descriptions: - - any string 1 - - any string 2 - alternative_identifiers: - - generic:abc1 - alternative_names: - - any string 1 - - any string 2 - alternative_titles: - - any string 1 - - any string 2 - description: see also name, title, objective, various alternatives - ecosystem: unconstrained text. should be validated against the controlled vocabulary, - by the sample's environmental package. would also be nice to align the CV with - MIxS environmental triads - ecosystem_category: unconstrained text - ecosystem_subtype: unconstrained text - ecosystem_type: unconstrained text - ess_dive_datasets: - - any string 1 - - any string 2 - funding_sources: - - any string 1 - - any string 2 - gold_study_identifiers: - - gold:Gs12345 - - gold:Gs90909 - has_credit_associations: - - applied_role: Funding acquisition - applied_roles: - - Supervision - - Conceptualization - applies_to_person: - email: jcventer@jcvi.org - has_raw_value: Craig Venter - name: J. Craig Venter - orcid: ORCID:0000-0002-7086-765X - profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg - was_generated_by: nmdc:any_string_1 - websites: - - https://www.jcvi.org/ - - https://www.jcvi.org/about/j-craig-venter - type: any string - - applied_roles: - - Investigation - - Supervision - applies_to_person: - name: Tanja Davidsen - id: nmdc:sty-11-ab - mgnify_project_identifiers: - - mgnify.proj:ABC123 - name: see also description, title, objective, various alternatives - objective: This record, an instance of class Study from the nmdc-schema was had - authored, so that the NMDC team would have at least one instance, using all slots, - with a mixture of reasonable values and minimally compliant values. - principal_investigator: - email: jcventer@jcvi.org - has_raw_value: Craig Venter - name: J. Craig Venter - orcid: ORCID:0000-0002-7086-765X - profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg - was_generated_by: nmdc:any_string_1 - websites: - - https://www.jcvi.org/ - - https://www.jcvi.org/about/j-craig-venter - publications: - - any string 1 - - any string 2 - related_identifiers: any string R1 - relevant_protocols: - - any string 1 - - any string 2 - specific_ecosystem: unconstrained text - title: Sample Exhaustive Biosample instance. Although all of these values should - pass validation, that does not mean that any Biosample of any type would necessarily - have this particular combination of values. - type: any string - websites: - - https://w3id.org/nmdc - - https://w3id.org/linkml +ended_at_time: '2021-09-15T10:13:20+00:00' +execution_resource: JGI +git_url: '' +has_input: +- nmdc:unvalidated_placeholder +has_output: +- nmdc:22afa3d49b73eaec2e9787a6b88fbdc3 +id: nmdc:wfmsa-99-qwertyuiop +name: Sequencing Activity for nmdc:mga0vx38 +part_of: null +started_at_time: '2021-08-05T14:48:51+00:00' +type: nmdc:MetagenomeSequencing +version: v1.0.0 +was_informed_by: gold:Gp0213371 ``` -## Database-biosample_single_multi_value_mixup +## Database-Biosample-invalid_range ### Input ```yaml biosample_set: @@ -5176,14 +5133,14 @@ biosample_set: id: ENVO:00005792 geo_loc_name: has_raw_value: Lithgow - habitat: Coalbed water - id: + gold_biosample_identifiers: - gold:Gb0101224 - - gold:Gb0101225 + habitat: Coalbed water + id: nmdc:bsm-6057d02c-664c-41c9-8486-3624ca845747 lat_lon: - has_raw_value: -33.460524 150.168149 - latitude: -33.460524 - longitude: 150.168149 + has_raw_value: 100 + latitude: '-33.460524' + longitude: '150.168149' location: from the Lithgow State Coal Mine, New South Wales, Australia mod_date: 26-AUG-16 01.50.27.000000000 PM name: Lithgow State Coal Mine Calcium nutrients (early) @@ -5192,9 +5149,7 @@ biosample_set: - gold:Gs0128849 sample_collection_site: Lithgow State Coal Mine specific_ecosystem: Coalbed water - type: - - nmdc:Biosample - - nmdc:FunctionalAnnotation + type: nmdc:Biosample - add_date: 28-JUL-14 12.00.00.000000000 AM community: microbial communities description: Bulk Aqueous phase filtered water @@ -5219,7 +5174,7 @@ biosample_set: gold_biosample_identifiers: - gold:Gb0101225 habitat: Coalbed water - id: nmdc:e924072f-98b5-4f88-a796-a7ba1d8ddd92 + id: nmdc:bsm-e924072f-98b5-4f88-a796-a7ba1d8ddd92 lat_lon: has_raw_value: -33.460524 150.168149 latitude: -33.460524 @@ -5257,7 +5212,7 @@ biosample_set: gold_biosample_identifiers: - gold:Gb0101226 habitat: Coalbed water - id: nmdc:61c3332d-f654-4db8-8d2f-59475894daa5 + id: nmdc:bsm-61c3332d-f654-4db8-8d2f-59475894daa5 lat_lon: has_raw_value: -33.460524 150.168149 latitude: -33.460524 @@ -5273,69 +5228,30 @@ biosample_set: type: nmdc:Biosample ``` -## Database-invalid-functional-annotations -### Input -```yaml -functional_annotation_set: -- has_function: KEGG_PATHWAY:XOXOXOXO -- has_function: KEGG_PATHWAY:iIiIiIiI - -``` -## FunctionalAnnotation-invalid-function -### Input -```yaml -has_function: KEGG_PATHWAY:XOXOXOXO - -``` -## Database-biosamples-dna-in-bucket -### Input -```yaml -biosample_set: -- dna_cont_type: bucket - env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 - env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 - env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 - id: nmdc:bsm-99-dtTMNb - part_of: - - gold:Gs0110115 - -``` -## Database-Extraction-invalid-sample_mass +## Database-plannedprocess-incorrect _date_slot ### Input ```yaml extraction_set: -- description: DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7 - end_date: '2019-11-08' - extraction_method: phenol/chloroform extraction +- extraction_date: 2021-01-15 extraction_target: DNA - has_input: - - generic:xxx - has_output: - - generic:xxx - id: nmdc:extrp-99-abcdef - name: DNA extraction of NEON sample WREF_072-O-20190618-COMP - processing_institution: Battelle - protocol_link: - name: BMI_dnaExtractionSOP_v7 - url: https://data.neonscience.org/documents/10179/2431540/BMI_dnaExtractionSOP_v7/61204962-bb01-a0b9-3354-ccdaab5132c3 - quality_control_report: - status: pass - sample_mass: - has_numeric_value: 0.25 - has_unit: gram - start_date: '2019-11-08' + has_inputs: + - bare:pool_out_1 + has_outputs: + - bare:dna_extract_1 + id: bare:des1 + name: first dna extraction set +library_preparation_set: +- has_inputs: + - bare:dna_extract_1 + has_outputs: + - bare:library_1 + id: bare:lcs1 + library_type: DNA + name: DNA library preparation of NEON sample TREE_001-O-20170707-COMP-DNA1 + processed_date: 2021-01-15 ``` -## Database-biosample_undeclared_slot +## Database-biosample_single_multi_value_mixup ### Input ```yaml biosample_set: @@ -5358,13 +5274,12 @@ biosample_set: has_raw_value: ENVO:00005792 term: id: ENVO:00005792 - foo: bar geo_loc_name: has_raw_value: Lithgow - gold_biosample_identifiers: - - gold:Gb0101224 habitat: Coalbed water - id: nmdc:bsm-6057d02c-664c-41c9-8486-3624ca845747 + id: + - gold:Gb0101224 + - gold:Gb0101225 lat_lon: has_raw_value: -33.460524 150.168149 latitude: -33.460524 @@ -5377,7 +5292,9 @@ biosample_set: - gold:Gs0128849 sample_collection_site: Lithgow State Coal Mine specific_ecosystem: Coalbed water - type: nmdc:Biosample + type: + - nmdc:Biosample + - nmdc:FunctionalAnnotation - add_date: 28-JUL-14 12.00.00.000000000 AM community: microbial communities description: Bulk Aqueous phase filtered water @@ -5402,7 +5319,7 @@ biosample_set: gold_biosample_identifiers: - gold:Gb0101225 habitat: Coalbed water - id: nmdc:bsm-e924072f-98b5-4f88-a796-a7ba1d8ddd92 + id: nmdc:e924072f-98b5-4f88-a796-a7ba1d8ddd92 lat_lon: has_raw_value: -33.460524 150.168149 latitude: -33.460524 @@ -5440,7 +5357,7 @@ biosample_set: gold_biosample_identifiers: - gold:Gb0101226 habitat: Coalbed water - id: nmdc:bsm-61c3332d-f654-4db8-8d2f-59475894daa5 + id: nmdc:61c3332d-f654-4db8-8d2f-59475894daa5 lat_lon: has_raw_value: -33.460524 150.168149 latitude: -33.460524 @@ -5455,6 +5372,30 @@ biosample_set: specific_ecosystem: Coalbed water type: nmdc:Biosample +``` +## Database-biosamples-lat_lon-with-GLV-missing-latitude +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + lat_lon: + has_raw_value: -33.460524 150.168149 + longitude: 150.168149 + part_of: + - gold:Gs0110115 + ``` ## Biosample-incomplete_napa_id ### Input @@ -5499,66 +5440,41 @@ specific_ecosystem: Coalbed water type: nmdc:Biosample ``` -## MetagenomeSequencingActivity-no_parthood +## Biosample-missing-id ### Input ```yaml -ended_at_time: '2021-09-15T10:13:20+00:00' -execution_resource: JGI -git_url: '' -has_input: -- nmdc:unvalidated_placeholder -has_output: -- nmdc:22afa3d49b73eaec2e9787a6b88fbdc3 -id: nmdc:wfmsa-99-qwertyuiop -name: Sequencing Activity for nmdc:mga0vx38 -part_of: null -started_at_time: '2021-08-05T14:48:51+00:00' -type: nmdc:MetagenomeSequencing -version: v1.0.0 -was_informed_by: gold:Gp0213371 +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +part_of: +- gold:Gs0110115 ``` -## Database-biosamples-rna-in-bucket +## Database-Biosample-invalid_id ### Input ```yaml biosample_set: - env_broad_scale: - has_raw_value: ENVO:00002030 term: id: ENVO:00002030 env_local_scale: - has_raw_value: ENVO:00002169 term: id: ENVO:00002169 env_medium: - has_raw_value: ENVO:00005792 term: id: ENVO:00005792 - id: nmdc:bsm-99-dtTMNb + id: local part_of: - - gold:Gs0110115 - rna_cont_type: bucket - -``` -## Biosample-non_boolean_embargo -### Input -```yaml -embargoed: 999 -env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 -env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 -env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 -id: nmdc:bsm-99-dtTMNb -part_of: -- gold:Gs0110115 + - gold:Gs0128849 ``` ## Database-biosample_missing_required_field @@ -5666,176 +5582,275 @@ biosample_set: type: nmdc:Biosample ``` -## Database-invalid-omics-processing +## Database-biosample_undeclared_slot ### Input ```yaml -omics_processing_set: -- add_date: 30-OCT-14 12.00.00.000000000 AM - alternative_identifiers: - - gold:Gp0108335 - has_input: - - gold:Gb0108335 - has_output: - - jgi:551a20d30d878525404e90d5 - id: nmdc:omprc-99-zUCd5N - mod_date: 22-MAY-20 06.13.12.927000000 PM - name: Thawing permafrost microbial communities from the Arctic, studying carbon - transformations - Permafrost 712P3D - ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying - carbon transformations - Permafrost 712P3D - omics_type: - has_awesome_value: Metagenome +biosample_set: +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + foo: bar + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101224 + habitat: Coalbed water + id: nmdc:bsm-6057d02c-664c-41c9-8486-3624ca845747 + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients (early) + ncbi_taxonomy_name: coal metagenome part_of: - - gold:Gs0112340 - processing_institution: JGI - type: nmdc:OmicsProcessing -- add_date: 30-OCT-14 12.00.00.000000000 AM - alternative_identifiers: - - gold:Gp0108340 - has_input: - - gold:Gb0108340 - has_output: - - jgi:551a20d50d878525404e90d7 - id: nmdc:omprc-99-gKlQlF - mod_date: 22-MAY-20 06.10.59.590000000 PM - name: Thawing permafrost microbial communities from the Arctic, studying carbon - transformations - Permafrost 612S3M - ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying - carbon transformations - Permafrost 612S3M - omics_type: - has_raw_value: Metagenome + - gold:Gs0128849 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101225 + habitat: Coalbed water + id: nmdc:bsm-e924072f-98b5-4f88-a796-a7ba1d8ddd92 + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients Extra + ncbi_taxonomy_name: coal metagenome part_of: - - gold:Gs0112340 - processing_institution: JGI - type: nmdc:OmicsProcessing -- add_date: 30-OCT-14 12.00.00.000000000 AM - alternative_identifiers: - - gold:Gp0108341 - has_input: - - gold:Gb0108341 - has_output: - - jgi:551a20d90d878525404e90e1 - id: nmdc:omprc-99-5kgIJR - mod_date: 22-MAY-20 06.09.46.171000000 PM - name: Thawing permafrost microbial communities from the Arctic, studying carbon - transformations - Permafrost 712S3S - ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying - carbon transformations - Permafrost 712S3S - omics_type: - has_raw_value: Metagenome + - gold:Gs0128849 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101226 + habitat: Coalbed water + id: nmdc:bsm-61c3332d-f654-4db8-8d2f-59475894daa5 + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients + ncbi_taxonomy_name: coal metagenome part_of: - - gold:Gs0112340 - processing_institution: JGI - type: nmdc:OmicsProcessing + - gold:Gs0128849 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample ``` -## OmicsProcessing-no-id +## Database-study_set-bad-emsl-doi-slot-name ### Input ```yaml -add_date: 30-OCT-14 12.00.00.000000000 AM -alternative_identifiers: -- gold:Gp0108335 -has_input: -- gold:Gb0108335 -has_output: -- jgi:551a20d30d878525404e90d5 -mod_date: 22-MAY-20 06.13.12.927000000 PM -name: Thawing permafrost microbial communities from the Arctic, studying carbon transformations - - Permafrost 712P3D -ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying - carbon transformations - Permafrost 712P3D -omics_type: - has_raw_value: Metagenome -part_of: -- gold:Gs0112340 -processing_institution: JGI -type: nmdc:OmicsProcessing +study_set: +- emsl_proposal_dois: + - doi:10.46936/intm.proj.2021.60141/60000423 + id: nmdc:sty-11-ab ``` -## Study-illegal-funding_sources +## Database-biosamples-lat_lon-with-GLV-missing-longitude ### Input ```yaml -abstract: Nothing was studied. -alternative_descriptions: -- any string 1 -- any string 2 -alternative_names: -- any string 1 -- any string 2 -alternative_titles: -- any string 1 -- any string 2 -description: see also name, title, objective, various alternatives -ecosystem: unconstrained text. should be validated against the controlled vocabulary, - by the sample's environmental package. would also be nice to align the CV with MIxS - environmental triads -ecosystem_category: unconstrained text -ecosystem_subtype: unconstrained text -ecosystem_type: unconstrained text -ess_dive_datasets: -- any string 1 -- any string 2 -funding_sources: -- This is an example of a funding source with too long of a description. Funding sources - should be no more than 150 characters. Any longer is unnecessary and excessive. - Its very very very very very very very very very long. -- any string 2 -gold_study_identifiers: -- gold:Gs12345 -- gold:Gs90909 -id: nmdc:sty-11-ab -mgnify_project_identifiers: -- mgnify.proj:ABC123 -name: see also description, title, objective, various alternatives -objective: This record, an instance of class Study from the nmdc-schema was had authored, - so that the NMDC team would have at least one instance, using all slots, with a - mixture of reasonable values and minimally compliant values. -principal_investigator: - email: jcventer@jcvi.org - has_raw_value: Craig Venter - name: J. Craig Venter - orcid: ORCID:0000-0002-7086-765X - profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg - was_generated_by: nmdc:any_string_1 +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + part_of: + - gold:Gs0110115 + +``` +## Database-biosamples-dna-in-bucket +### Input +```yaml +biosample_set: +- dna_cont_type: bucket + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - gold:Gs0110115 + +``` +## Study-include-abstract +### Input +```yaml +study_set: +- abstract: This study is about a thing. + alternative_descriptions: + - any string 1 + - any string 2 + alternative_identifiers: + - generic:abc1 + alternative_names: + - any string 1 + - any string 2 + alternative_titles: + - any string 1 + - any string 2 + description: see also name, title, objective, various alternatives + ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with + MIxS environmental triads + ecosystem_category: unconstrained text + ecosystem_subtype: unconstrained text + ecosystem_type: unconstrained text + ess_dive_datasets: + - any string 1 + - any string 2 + funding_sources: + - any string 1 + - any string 2 + gold_study_identifiers: + - gold:Gs12345 + - gold:Gs90909 + has_credit_associations: + - applied_role: Funding acquisition + applied_roles: + - Supervision + - Conceptualization + applies_to_person: + email: jcventer@jcvi.org + has_raw_value: Craig Venter + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + was_generated_by: nmdc:any_string_1 + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter + type: any string + - applied_roles: + - Investigation + - Supervision + applies_to_person: + name: Tanja Davidsen + id: nmdc:sty-11-ab + mgnify_project_identifiers: + - mgnify.proj:ABC123 + name: see also description, title, objective, various alternatives + objective: This record, an instance of class Study from the nmdc-schema was had + authored, so that the NMDC team would have at least one instance, using all slots, + with a mixture of reasonable values and minimally compliant values. + principal_investigator: + email: jcventer@jcvi.org + has_raw_value: Craig Venter + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + was_generated_by: nmdc:any_string_1 + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter + publications: + - any string 1 + - any string 2 + related_identifiers: any string R1 + relevant_protocols: + - any string 1 + - any string 2 + specific_ecosystem: unconstrained text + title: Sample Exhaustive Biosample instance. Although all of these values should + pass validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. + type: any string websites: - - https://www.jcvi.org/ - - https://www.jcvi.org/about/j-craig-venter -publications: -- any string 1 -- any string 2 -related_identifiers: any string R1 -relevant_protocols: -- any string 1 -- any string 2 -specific_ecosystem: unconstrained text -title: Sample Exhaustive Biosample instance. Although all of these values should pass - validation, that does not mean that any Biosample of any type would necessarily - have this particular combination of values. -type: any string -websites: -- https://w3id.org/nmdc -- https://w3id.org/linkml + - https://w3id.org/nmdc + - https://w3id.org/linkml ``` -## Biosample-invalid-embargoed +## Database-invalid-functional-annotations ### Input ```yaml -embargoed: 999 -env_broad_scale: - has_raw_value: ENVO:00002030 - term: - id: ENVO:00002030 -env_local_scale: - has_raw_value: ENVO:00002169 - term: - id: ENVO:00002169 -env_medium: - has_raw_value: ENVO:00005792 - term: - id: ENVO:00005792 -id: nmdc:bsm-99-dtTMNb -part_of: -- gold:Gs0110115 +functional_annotation_set: +- has_function: KEGG_PATHWAY:XOXOXOXO +- has_function: KEGG_PATHWAY:iIiIiIiI ``` ## DataObject-invalid-data_object_type @@ -5856,18 +5871,3 @@ url: http://example.com was_generated_by: nmdc:invalid_id ``` -## Database-study_set-bad-emsl-doi-slot-name -### Input -```yaml -study_set: -- emsl_proposal_dois: - - doi:10.46936/intm.proj.2021.60141/60000423 - id: nmdc:sty-11-ab - -``` -## DataObject-no-id-or-name -### Input -```yaml -description: Crispr Terms for nmdc:ann0vx38 - -``` diff --git a/nmdc_schema/list_used_ranges.py b/nmdc_schema/list_used_ranges.py new file mode 100644 index 0000000000..d13ef1d7d7 --- /dev/null +++ b/nmdc_schema/list_used_ranges.py @@ -0,0 +1,13 @@ +from linkml_runtime import SchemaView + +schema_file = "../src/schema/nmdc.yaml" + +schema_view = SchemaView(schema_file) + +schema_classes = schema_view.all_classes() + +for ck, _ in schema_classes.items(): + induced_slots = schema_view.class_induced_slots(ck) + for induced_slot in induced_slots: + if induced_slot.name == 'used': + print(f"In class {ck}, slot used has range {induced_slot.range}") diff --git a/nmdc_schema/migration_recursion.py b/nmdc_schema/migration_recursion.py index fa37830c39..87b804df8b 100644 --- a/nmdc_schema/migration_recursion.py +++ b/nmdc_schema/migration_recursion.py @@ -228,26 +228,6 @@ def main(schema_path, input_path, output_path, salvage_prefix): logger.info(f"Starting migration of {tdk}") end_dict[tdk] = migrator.apply_changes_recursively_by_key(tdv, set(migrateable_slots)) - # if tdk == "study_set": - # logger.info(f"Starting {tdk}-specific migrations") - # for current_study in tdv: - # migrator.replace_doi_field_with_award_dois_list_field(current_study) - # if tdk == "extraction_set": - # logger.info(f"Starting {tdk}-specific migrations") - # for current_extraction in tdv: - # migrator.rename_sample_mass_field(current_extraction) - # if tdk == "omics_processing_set": - # logger.info(f"Starting {tdk}-specific migrations") - # for current_omics_processing in tdv: - # migrator.standardize_letter_casing_of_gold_sequencing_project_identifiers(current_omics_processing) - # if tdk == "biosample_set": - # logger.info(f"Starting {tdk}-specific migrations") - # for current_biosample in tdv: - # migrator.standardize_letter_casing_of_gold_biosample_identifiers(current_biosample) - # if tdk == "study_set": - # logger.info(f"Starting {tdk}-specific migrations") - # for current_study in tdv: - # migrator.standardize_letter_casing_of_gold_study_identifier(current_study) # If the migration specifies a sequence of transformations for this collection, # apply that sequence of transformations to each document within this collection. diff --git a/nmdc_schema/mongo_dump_api_emph.py b/nmdc_schema/mongo_dump_api_emph.py index fd991af1a7..2012841cee 100644 --- a/nmdc_schema/mongo_dump_api_emph.py +++ b/nmdc_schema/mongo_dump_api_emph.py @@ -207,28 +207,35 @@ def get_class_slots(self, class_name, include_scalars=False): @click.command() @click_log.simple_verbosity_option(logger) -@click.option('--admin-db', default="admin", help='MongoDB authentication source') +@click.option('--admin-db', default="admin", show_default=True, help='MongoDB authentication source') @click.option('--env-file', type=click.Path(exists=True), default='local/.env', - help='Path to .env file') + show_default=True, help='Path to .env file') @click.option('--max-docs-per-coll', default=100, - help='Maximum number of documents to retrieve per collection') # was 100_000 -@click.option('--mongo-db-name', default="nmdc", help='MongoDB database name') -@click.option('--mongo-host', default="localhost", help='MongoDB host name/address') -@click.option('--mongo-port', default=27777, help='MongoDB port') + show_default=True, help='Maximum number of documents to retrieve per collection') # was 100_000 +@click.option('--mongo-db-name', default="nmdc", show_default=True, help='MongoDB database name') +@click.option('--mongo-host', default="localhost", show_default=True, + help='MongoDB host name/address. Use "localhost" if using an ssh tunnel to ' + + 'mongo-loadbalancer.nmdc.production.svc.spin.nersc.org ' + + 'or mongo-loadbalancer.nmdc-dev.production.svc.spin.nersc.org') +@click.option('--mongo-port', default=27777, show_default=True, help='MongoDB port') @click.option('--output-yaml', required=True, type=click.Path(), - help="Output file.") -@click.option('--root-class', default="Database", help='Schema class that corresponds to a Mongo Database') + show_default=True, help="Output file.") +@click.option('--root-class', default="Database", + show_default=True, help='Schema class that corresponds to a Mongo Database') @click.option('--schema-file', type=click.Path(exists=True), default='src/schema/nmdc.yaml', - help='Path to root YAML file in the nmdc-schema') -@click.option('--selected-collections', multiple=True, help='MongoDB collection name') + show_default=True, + help='Path to root YAML file in the nmdc-schema. ' + + 'For determining structure only. No validation in this step.') +@click.option('--selected-collections', multiple=True, show_default=True, help='MongoDB collection name') @click.option('--page-size', default=10, + show_default=True, help='Number of documents retrieved per FastAPI GET request') # how many is too many? for what reason? seems like there's some overhead @click.option('--client-base-url', default="https://api.microbiomedata.org", - help='HTTP(S) path to the FastAPI server') -@click.option('--client-base-url', default="https://api.microbiomedata.org", - help='HTTP(S) path to the FastAPI server') + show_default=True, + help='HTTP(S) path to the FastAPI server. ' + + 'https://api-dev.microbiomedata.org/docs or https://api.microbiomedata.org/docs') @click.option('--endpoint-prefix', default="nmdcschema", - help='FastAPI path component between the URL and the endpoint name') + show_default=True, help='FastAPI path component between the URL and the endpoint name') def cli( admin_db, env_file, diff --git a/nmdc_schema/nmdc.py b/nmdc_schema/nmdc.py index c6f8118425..5a5140347c 100644 --- a/nmdc_schema/nmdc.py +++ b/nmdc_schema/nmdc.py @@ -1,5 +1,5 @@ # Auto generated from nmdc.yaml by pythongen.py version: 0.0.1 -# Generation date: 2023-09-21T12:49:25 +# Generation date: 2023-10-03T12:25:46 # Schema: NMDC # # id: https://w3id.org/nmdc/nmdc @@ -31,7 +31,7 @@ from linkml_runtime.utils.metamodelcore import Bool, URIorCURIE metamodel_version = "1.7.0" -version = "v8.0.0" +version = "v8.1.0" # Overwrite dataclasses _init_fn to add **kwargs in __init__ dataclasses._init_fn = dataclasses_init_fn_with_kwargs @@ -5760,7 +5760,7 @@ class MetaproteomicsAnalysisActivity(WorkflowExecutionActivity): started_at_time: str = None ended_at_time: str = None has_peptide_quantifications: Optional[Union[Union[dict, PeptideQuantification], List[Union[dict, PeptideQuantification]]]] = empty_list() - used: Optional[Union[str, InstrumentId]] = None + used: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -5772,8 +5772,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.has_peptide_quantifications = [self.has_peptide_quantifications] if self.has_peptide_quantifications is not None else [] self.has_peptide_quantifications = [v if isinstance(v, PeptideQuantification) else PeptideQuantification(**as_dict(v)) for v in self.has_peptide_quantifications] - if self.used is not None and not isinstance(self.used, InstrumentId): - self.used = InstrumentId(self.used) + if self.used is not None and not isinstance(self.used, str): + self.used = str(self.used) super().__post_init__(**kwargs) @@ -6277,26 +6277,6 @@ class StudyCategoryEnum(EnumDefinitionImpl): name="StudyCategoryEnum", ) -class DoorDirectEnum(EnumDefinitionImpl): - - inward = PermissibleValue(text="inward") - outward = PermissibleValue(text="outward") - sideways = PermissibleValue(text="sideways") - - _defn = EnumDefinition( - name="DoorDirectEnum", - ) - -class OxyStatSampEnum(EnumDefinitionImpl): - - aerobic = PermissibleValue(text="aerobic") - anaerobic = PermissibleValue(text="anaerobic") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="OxyStatSampEnum", - ) - class SurfAirContEnum(EnumDefinitionImpl): dust = PermissibleValue(text="dust") @@ -6319,162 +6299,187 @@ def _addvals(cls): setattr(cls, "biological contaminants", PermissibleValue(text="biological contaminants")) -class WindowVertPosEnum(EnumDefinitionImpl): +class WaterFeatTypeEnum(EnumDefinitionImpl): - bottom = PermissibleValue(text="bottom") - middle = PermissibleValue(text="middle") - top = PermissibleValue(text="top") - low = PermissibleValue(text="low") - high = PermissibleValue(text="high") + fountain = PermissibleValue(text="fountain") + pool = PermissibleValue(text="pool") + stream = PermissibleValue(text="stream") + waterfall = PermissibleValue(text="waterfall") _defn = EnumDefinition( - name="WindowVertPosEnum", + name="WaterFeatTypeEnum", ) -class FilterTypeEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "standing feature", + PermissibleValue(text="standing feature")) - HEPA = PermissibleValue(text="HEPA") - electrostatic = PermissibleValue(text="electrostatic") +class SampCollectPointEnum(EnumDefinitionImpl): + + well = PermissibleValue(text="well") + wellhead = PermissibleValue(text="wellhead") + separator = PermissibleValue(text="separator") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="FilterTypeEnum", + name="SampCollectPointEnum", ) @classmethod def _addvals(cls): - setattr(cls, "particulate air filter", - PermissibleValue(text="particulate air filter")) - setattr(cls, "chemical air filter", - PermissibleValue(text="chemical air filter")) - setattr(cls, "low-MERV pleated media", - PermissibleValue(text="low-MERV pleated media")) - setattr(cls, "gas-phase or ultraviolet air treatments", - PermissibleValue(text="gas-phase or ultraviolet air treatments")) + setattr(cls, "test well", + PermissibleValue(text="test well")) + setattr(cls, "drilling rig", + PermissibleValue(text="drilling rig")) + setattr(cls, "storage tank", + PermissibleValue(text="storage tank")) -class RelSampLocEnum(EnumDefinitionImpl): +class FloorWaterMoldEnum(EnumDefinitionImpl): + + condensation = PermissibleValue(text="condensation") _defn = EnumDefinition( - name="RelSampLocEnum", + name="FloorWaterMoldEnum", ) @classmethod def _addvals(cls): - setattr(cls, "edge of car", - PermissibleValue(text="edge of car")) - setattr(cls, "center of car", - PermissibleValue(text="center of car")) - setattr(cls, "under a seat", - PermissibleValue(text="under a seat")) + setattr(cls, "mold odor", + PermissibleValue(text="mold odor")) + setattr(cls, "wet floor", + PermissibleValue(text="wet floor")) + setattr(cls, "water stains", + PermissibleValue(text="water stains")) + setattr(cls, "wall discoloration", + PermissibleValue(text="wall discoloration")) + setattr(cls, "floor discoloration", + PermissibleValue(text="floor discoloration")) + setattr(cls, "ceiling discoloration", + PermissibleValue(text="ceiling discoloration")) + setattr(cls, "peeling paint or wallpaper", + PermissibleValue(text="peeling paint or wallpaper")) + setattr(cls, "bulging walls", + PermissibleValue(text="bulging walls")) -class SedimentTypeEnum(EnumDefinitionImpl): +class WallTextureEnum(EnumDefinitionImpl): - biogenous = PermissibleValue(text="biogenous") - cosmogenous = PermissibleValue(text="cosmogenous") - hydrogenous = PermissibleValue(text="hydrogenous") - lithogenous = PermissibleValue(text="lithogenous") + knockdown = PermissibleValue(text="knockdown") + popcorn = PermissibleValue(text="popcorn") + smooth = PermissibleValue(text="smooth") + swirl = PermissibleValue(text="swirl") _defn = EnumDefinition( - name="SedimentTypeEnum", + name="WallTextureEnum", ) -class OccupDocumentEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "crows feet", + PermissibleValue(text="crows feet")) + setattr(cls, "crows-foot stomp", + PermissibleValue(text="crows-foot stomp")) + setattr(cls, "", + PermissibleValue(text="")) + setattr(cls, "double skip", + PermissibleValue(text="double skip")) + setattr(cls, "hawk and trowel", + PermissibleValue(text="hawk and trowel")) + setattr(cls, "orange peel", + PermissibleValue(text="orange peel")) + setattr(cls, "rosebud stomp", + PermissibleValue(text="rosebud stomp")) + setattr(cls, "Santa-Fe texture", + PermissibleValue(text="Santa-Fe texture")) + setattr(cls, "skip trowel", + PermissibleValue(text="skip trowel")) + setattr(cls, "stomp knockdown", + PermissibleValue(text="stomp knockdown")) - estimate = PermissibleValue(text="estimate") - videos = PermissibleValue(text="videos") +class SampSubtypeEnum(EnumDefinitionImpl): + + biofilm = PermissibleValue(text="biofilm") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="OccupDocumentEnum", + name="SampSubtypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "automated count", - PermissibleValue(text="automated count")) - setattr(cls, "manual count", - PermissibleValue(text="manual count")) + setattr(cls, "oil phase", + PermissibleValue(text="oil phase")) + setattr(cls, "water phase", + PermissibleValue(text="water phase")) + setattr(cls, "not applicable", + PermissibleValue(text="not applicable")) -class RoomConnectedEnum(EnumDefinitionImpl): +class DrainageClassEnum(EnumDefinitionImpl): - attic = PermissibleValue(text="attic") - bathroom = PermissibleValue(text="bathroom") - closet = PermissibleValue(text="closet") - elevator = PermissibleValue(text="elevator") - hallway = PermissibleValue(text="hallway") - kitchen = PermissibleValue(text="kitchen") - office = PermissibleValue(text="office") - stairwell = PermissibleValue(text="stairwell") + poorly = PermissibleValue(text="poorly") + well = PermissibleValue(text="well") _defn = EnumDefinition( - name="RoomConnectedEnum", + name="DrainageClassEnum", ) @classmethod def _addvals(cls): - setattr(cls, "conference room", - PermissibleValue(text="conference room")) - setattr(cls, "examining room", - PermissibleValue(text="examining room")) - setattr(cls, "mail room", - PermissibleValue(text="mail room")) + setattr(cls, "very poorly", + PermissibleValue(text="very poorly")) + setattr(cls, "somewhat poorly", + PermissibleValue(text="somewhat poorly")) + setattr(cls, "moderately well", + PermissibleValue(text="moderately well")) + setattr(cls, "excessively drained", + PermissibleValue(text="excessively drained")) -class QuadPosEnum(EnumDefinitionImpl): +class FreqCleanEnum(EnumDefinitionImpl): + + Daily = PermissibleValue(text="Daily") + Weekly = PermissibleValue(text="Weekly") + Monthly = PermissibleValue(text="Monthly") + Quarterly = PermissibleValue(text="Quarterly") + Annually = PermissibleValue(text="Annually") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="QuadPosEnum", + name="FreqCleanEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "North side", - PermissibleValue(text="North side")) - setattr(cls, "West side", - PermissibleValue(text="West side")) - setattr(cls, "South side", - PermissibleValue(text="South side")) - setattr(cls, "East side", - PermissibleValue(text="East side")) - -class SrGeolAgeEnum(EnumDefinitionImpl): +class BioticRelationshipEnum(EnumDefinitionImpl): - Archean = PermissibleValue(text="Archean") - Cambrian = PermissibleValue(text="Cambrian") - Carboniferous = PermissibleValue(text="Carboniferous") - Cenozoic = PermissibleValue(text="Cenozoic") - Cretaceous = PermissibleValue(text="Cretaceous") - Devonian = PermissibleValue(text="Devonian") - Jurassic = PermissibleValue(text="Jurassic") - Mesozoic = PermissibleValue(text="Mesozoic") - Neogene = PermissibleValue(text="Neogene") - Ordovician = PermissibleValue(text="Ordovician") - Paleogene = PermissibleValue(text="Paleogene") - Paleozoic = PermissibleValue(text="Paleozoic") - Permian = PermissibleValue(text="Permian") - Precambrian = PermissibleValue(text="Precambrian") - Proterozoic = PermissibleValue(text="Proterozoic") - Silurian = PermissibleValue(text="Silurian") - Triassic = PermissibleValue(text="Triassic") - other = PermissibleValue(text="other") + parasite = PermissibleValue(text="parasite") + commensal = PermissibleValue(text="commensal") + symbiont = PermissibleValue(text="symbiont") _defn = EnumDefinition( - name="SrGeolAgeEnum", + name="BioticRelationshipEnum", ) -class DoorMoveEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "free living", + PermissibleValue(text="free living")) - collapsible = PermissibleValue(text="collapsible") - folding = PermissibleValue(text="folding") - revolving = PermissibleValue(text="revolving") - sliding = PermissibleValue(text="sliding") - swinging = PermissibleValue(text="swinging") +class LightTypeEnum(EnumDefinitionImpl): + + none = PermissibleValue(text="none") _defn = EnumDefinition( - name="DoorMoveEnum", + name="LightTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "rolling shutter", - PermissibleValue(text="rolling shutter")) + setattr(cls, "natural light", + PermissibleValue(text="natural light")) + setattr(cls, "electric light", + PermissibleValue(text="electric light")) + setattr(cls, "desk lamp", + PermissibleValue(text="desk lamp")) + setattr(cls, "flourescent lights", + PermissibleValue(text="flourescent lights")) class CurLandUseEnum(EnumDefinitionImpl): @@ -6538,105 +6543,160 @@ def _addvals(cls): setattr(cls, "vine crops", PermissibleValue(text="vine crops")) -class HcrGeolAgeEnum(EnumDefinitionImpl): +class DrawingsEnum(EnumDefinitionImpl): + + operation = PermissibleValue(text="operation") + construction = PermissibleValue(text="construction") + bid = PermissibleValue(text="bid") + design = PermissibleValue(text="design") + diagram = PermissibleValue(text="diagram") + sketch = PermissibleValue(text="sketch") + + _defn = EnumDefinition( + name="DrawingsEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "as built", + PermissibleValue(text="as built")) + setattr(cls, "building navigation map", + PermissibleValue(text="building navigation map")) + +class IndoorSurfEnum(EnumDefinitionImpl): + + cabinet = PermissibleValue(text="cabinet") + ceiling = PermissibleValue(text="ceiling") + door = PermissibleValue(text="door") + shelving = PermissibleValue(text="shelving") + window = PermissibleValue(text="window") + wall = PermissibleValue(text="wall") + + _defn = EnumDefinition( + name="IndoorSurfEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "counter top", + PermissibleValue(text="counter top")) + setattr(cls, "vent cover", + PermissibleValue(text="vent cover")) + +class SampCaptStatusEnum(EnumDefinitionImpl): - Archean = PermissibleValue(text="Archean") - Cambrian = PermissibleValue(text="Cambrian") - Carboniferous = PermissibleValue(text="Carboniferous") - Cenozoic = PermissibleValue(text="Cenozoic") - Cretaceous = PermissibleValue(text="Cretaceous") - Devonian = PermissibleValue(text="Devonian") - Jurassic = PermissibleValue(text="Jurassic") - Mesozoic = PermissibleValue(text="Mesozoic") - Neogene = PermissibleValue(text="Neogene") - Ordovician = PermissibleValue(text="Ordovician") - Paleogene = PermissibleValue(text="Paleogene") - Paleozoic = PermissibleValue(text="Paleozoic") - Permian = PermissibleValue(text="Permian") - Precambrian = PermissibleValue(text="Precambrian") - Proterozoic = PermissibleValue(text="Proterozoic") - Silurian = PermissibleValue(text="Silurian") - Triassic = PermissibleValue(text="Triassic") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="HcrGeolAgeEnum", + name="SampCaptStatusEnum", ) -class WallConstTypeEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "active surveillance in response to an outbreak", + PermissibleValue(text="active surveillance in response to an outbreak")) + setattr(cls, "active surveillance not initiated by an outbreak", + PermissibleValue(text="active surveillance not initiated by an outbreak")) + setattr(cls, "farm sample", + PermissibleValue(text="farm sample")) + setattr(cls, "market sample", + PermissibleValue(text="market sample")) + +class RoomLocEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="WallConstTypeEnum", + name="RoomLocEnum", ) @classmethod def _addvals(cls): - setattr(cls, "frame construction", - PermissibleValue(text="frame construction")) - setattr(cls, "joisted masonry", - PermissibleValue(text="joisted masonry")) - setattr(cls, "light noncombustible", - PermissibleValue(text="light noncombustible")) - setattr(cls, "masonry noncombustible", - PermissibleValue(text="masonry noncombustible")) - setattr(cls, "modified fire resistive", - PermissibleValue(text="modified fire resistive")) - setattr(cls, "fire resistive", - PermissibleValue(text="fire resistive")) + setattr(cls, "corner room", + PermissibleValue(text="corner room")) + setattr(cls, "interior room", + PermissibleValue(text="interior room")) + setattr(cls, "exterior wall", + PermissibleValue(text="exterior wall")) -class PlantSexEnum(EnumDefinitionImpl): +class OccupDocumentEnum(EnumDefinitionImpl): - Androdioecious = PermissibleValue(text="Androdioecious") - Androecious = PermissibleValue(text="Androecious") - Androgynous = PermissibleValue(text="Androgynous") - Androgynomonoecious = PermissibleValue(text="Androgynomonoecious") - Andromonoecious = PermissibleValue(text="Andromonoecious") - Bisexual = PermissibleValue(text="Bisexual") - Dichogamous = PermissibleValue(text="Dichogamous") - Diclinous = PermissibleValue(text="Diclinous") - Dioecious = PermissibleValue(text="Dioecious") - Gynodioecious = PermissibleValue(text="Gynodioecious") - Gynoecious = PermissibleValue(text="Gynoecious") - Gynomonoecious = PermissibleValue(text="Gynomonoecious") - Hermaphroditic = PermissibleValue(text="Hermaphroditic") - Imperfect = PermissibleValue(text="Imperfect") - Monoclinous = PermissibleValue(text="Monoclinous") - Monoecious = PermissibleValue(text="Monoecious") - Perfect = PermissibleValue(text="Perfect") - Polygamodioecious = PermissibleValue(text="Polygamodioecious") - Polygamomonoecious = PermissibleValue(text="Polygamomonoecious") - Polygamous = PermissibleValue(text="Polygamous") - Protandrous = PermissibleValue(text="Protandrous") - Protogynous = PermissibleValue(text="Protogynous") - Subandroecious = PermissibleValue(text="Subandroecious") - Subdioecious = PermissibleValue(text="Subdioecious") - Subgynoecious = PermissibleValue(text="Subgynoecious") - Synoecious = PermissibleValue(text="Synoecious") - Trimonoecious = PermissibleValue(text="Trimonoecious") - Trioecious = PermissibleValue(text="Trioecious") - Unisexual = PermissibleValue(text="Unisexual") + estimate = PermissibleValue(text="estimate") + videos = PermissibleValue(text="videos") _defn = EnumDefinition( - name="PlantSexEnum", + name="OccupDocumentEnum", ) -class CeilTypeEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "automated count", + PermissibleValue(text="automated count")) + setattr(cls, "manual count", + PermissibleValue(text="manual count")) - cathedral = PermissibleValue(text="cathedral") - dropped = PermissibleValue(text="dropped") - concave = PermissibleValue(text="concave") - coffered = PermissibleValue(text="coffered") - cove = PermissibleValue(text="cove") - stretched = PermissibleValue(text="stretched") +class ArchStrucEnum(EnumDefinitionImpl): + + building = PermissibleValue(text="building") + shed = PermissibleValue(text="shed") + home = PermissibleValue(text="home") _defn = EnumDefinition( - name="CeilTypeEnum", + name="ArchStrucEnum", + ) + +class WallFinishMatEnum(EnumDefinitionImpl): + + plaster = PermissibleValue(text="plaster") + tile = PermissibleValue(text="tile") + terrazzo = PermissibleValue(text="terrazzo") + wood = PermissibleValue(text="wood") + metal = PermissibleValue(text="metal") + masonry = PermissibleValue(text="masonry") + + _defn = EnumDefinition( + name="WallFinishMatEnum", ) @classmethod def _addvals(cls): - setattr(cls, "barrel-shaped", - PermissibleValue(text="barrel-shaped")) + setattr(cls, "gypsum plaster", + PermissibleValue(text="gypsum plaster")) + setattr(cls, "veneer plaster", + PermissibleValue(text="veneer plaster")) + setattr(cls, "gypsum board", + PermissibleValue(text="gypsum board")) + setattr(cls, "stone facing", + PermissibleValue(text="stone facing")) + setattr(cls, "acoustical treatment", + PermissibleValue(text="acoustical treatment")) + +class WindowMatEnum(EnumDefinitionImpl): + + clad = PermissibleValue(text="clad") + fiberglass = PermissibleValue(text="fiberglass") + metal = PermissibleValue(text="metal") + vinyl = PermissibleValue(text="vinyl") + wood = PermissibleValue(text="wood") + + _defn = EnumDefinition( + name="WindowMatEnum", + ) + +class IntWallCondEnum(EnumDefinitionImpl): + + new = PermissibleValue(text="new") + damaged = PermissibleValue(text="damaged") + rupture = PermissibleValue(text="rupture") + + _defn = EnumDefinition( + name="IntWallCondEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) class FloorFinishMatEnum(EnumDefinitionImpl): @@ -6672,391 +6732,400 @@ def _addvals(cls): setattr(cls, "none or unfinished", PermissibleValue(text="none or unfinished")) -class WallLocEnum(EnumDefinitionImpl): +class BuildDocsEnum(EnumDefinitionImpl): - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") + schedule = PermissibleValue(text="schedule") + sections = PermissibleValue(text="sections") + submittals = PermissibleValue(text="submittals") + windows = PermissibleValue(text="windows") _defn = EnumDefinition( - name="WallLocEnum", + name="BuildDocsEnum", ) -class WallSurfTreatmentEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "building information model", + PermissibleValue(text="building information model")) + setattr(cls, "commissioning report", + PermissibleValue(text="commissioning report")) + setattr(cls, "complaint logs", + PermissibleValue(text="complaint logs")) + setattr(cls, "contract administration", + PermissibleValue(text="contract administration")) + setattr(cls, "cost estimate", + PermissibleValue(text="cost estimate")) + setattr(cls, "janitorial schedules or logs", + PermissibleValue(text="janitorial schedules or logs")) + setattr(cls, "maintenance plans", + PermissibleValue(text="maintenance plans")) + setattr(cls, "shop drawings", + PermissibleValue(text="shop drawings")) + setattr(cls, "ventilation system", + PermissibleValue(text="ventilation system")) - painted = PermissibleValue(text="painted") - paneling = PermissibleValue(text="paneling") +class SurfMaterialEnum(EnumDefinitionImpl): + + adobe = PermissibleValue(text="adobe") + carpet = PermissibleValue(text="carpet") + concrete = PermissibleValue(text="concrete") + glass = PermissibleValue(text="glass") + metal = PermissibleValue(text="metal") + paint = PermissibleValue(text="paint") + plastic = PermissibleValue(text="plastic") + stone = PermissibleValue(text="stone") stucco = PermissibleValue(text="stucco") - fabric = PermissibleValue(text="fabric") + tile = PermissibleValue(text="tile") + vinyl = PermissibleValue(text="vinyl") + wood = PermissibleValue(text="wood") _defn = EnumDefinition( - name="WallSurfTreatmentEnum", + name="SurfMaterialEnum", ) @classmethod def _addvals(cls): - setattr(cls, "wall paper", - PermissibleValue(text="wall paper")) - setattr(cls, "no treatment", - PermissibleValue(text="no treatment")) + setattr(cls, "cinder blocks", + PermissibleValue(text="cinder blocks")) + setattr(cls, "hay bales", + PermissibleValue(text="hay bales")) + setattr(cls, "stainless steel", + PermissibleValue(text="stainless steel")) -class WindowCondEnum(EnumDefinitionImpl): - - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") +class TidalStageEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="WindowCondEnum", + name="TidalStageEnum", ) @classmethod def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) + setattr(cls, "low tide", + PermissibleValue(text="low tide")) + setattr(cls, "ebb tide", + PermissibleValue(text="ebb tide")) + setattr(cls, "flood tide", + PermissibleValue(text="flood tide")) + setattr(cls, "high tide", + PermissibleValue(text="high tide")) -class DoorMatEnum(EnumDefinitionImpl): +class WindowHorizPosEnum(EnumDefinitionImpl): - aluminum = PermissibleValue(text="aluminum") - fiberboard = PermissibleValue(text="fiberboard") - fiberglass = PermissibleValue(text="fiberglass") - metal = PermissibleValue(text="metal") - vinyl = PermissibleValue(text="vinyl") - wood = PermissibleValue(text="wood") + left = PermissibleValue(text="left") + middle = PermissibleValue(text="middle") + right = PermissibleValue(text="right") _defn = EnumDefinition( - name="DoorMatEnum", + name="WindowHorizPosEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "cellular PVC", - PermissibleValue(text="cellular PVC")) - setattr(cls, "engineered plastic", - PermissibleValue(text="engineered plastic")) - setattr(cls, "thermoplastic alloy", - PermissibleValue(text="thermoplastic alloy")) - setattr(cls, "wood/plastic composite", - PermissibleValue(text="wood/plastic composite")) - -class SoilHorizonEnum(EnumDefinitionImpl): +class TrainStopLocEnum(EnumDefinitionImpl): - Permafrost = PermissibleValue(text="Permafrost") + end = PermissibleValue(text="end") + mid = PermissibleValue(text="mid") + downtown = PermissibleValue(text="downtown") _defn = EnumDefinition( - name="SoilHorizonEnum", + name="TrainStopLocEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "O horizon", - PermissibleValue(text="O horizon")) - setattr(cls, "A horizon", - PermissibleValue(text="A horizon")) - setattr(cls, "E horizon", - PermissibleValue(text="E horizon")) - setattr(cls, "B horizon", - PermissibleValue(text="B horizon")) - setattr(cls, "C horizon", - PermissibleValue(text="C horizon")) - setattr(cls, "R layer", - PermissibleValue(text="R layer")) - setattr(cls, "M horizon", - PermissibleValue(text="M horizon")) - -class CeilFinishMatEnum(EnumDefinitionImpl): +class TrainLineEnum(EnumDefinitionImpl): - drywall = PermissibleValue(text="drywall") - tiles = PermissibleValue(text="tiles") - PVC = PermissibleValue(text="PVC") - plasterboard = PermissibleValue(text="plasterboard") - metal = PermissibleValue(text="metal") - fiberglass = PermissibleValue(text="fiberglass") - stucco = PermissibleValue(text="stucco") - wood = PermissibleValue(text="wood") + red = PermissibleValue(text="red") + green = PermissibleValue(text="green") + orange = PermissibleValue(text="orange") _defn = EnumDefinition( - name="CeilFinishMatEnum", + name="TrainLineEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "mineral fibre", - PermissibleValue(text="mineral fibre")) - setattr(cls, "mineral wool/calcium silicate", - PermissibleValue(text="mineral wool/calcium silicate")) - -class ShadingDeviceCondEnum(EnumDefinitionImpl): +class TrainStatLocEnum(EnumDefinitionImpl): - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") + riverside = PermissibleValue(text="riverside") _defn = EnumDefinition( - name="ShadingDeviceCondEnum", + name="TrainStatLocEnum", ) @classmethod def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) + setattr(cls, "south station above ground", + PermissibleValue(text="south station above ground")) + setattr(cls, "south station underground", + PermissibleValue(text="south station underground")) + setattr(cls, "south station amtrak", + PermissibleValue(text="south station amtrak")) + setattr(cls, "forest hills", + PermissibleValue(text="forest hills")) -class HcProducedEnum(EnumDefinitionImpl): +class SrDepEnvEnum(EnumDefinitionImpl): - Oil = PermissibleValue(text="Oil") - Gas = PermissibleValue(text="Gas") - Bitumen = PermissibleValue(text="Bitumen") + Lacustine = PermissibleValue(text="Lacustine") + Fluvioldeltaic = PermissibleValue(text="Fluvioldeltaic") + Fluviomarine = PermissibleValue(text="Fluviomarine") + Marine = PermissibleValue(text="Marine") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="HcProducedEnum", + name="SrDepEnvEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "Gas-Condensate", - PermissibleValue(text="Gas-Condensate")) - setattr(cls, "Coalbed Methane", - PermissibleValue(text="Coalbed Methane")) - -class DoorCompTypeEnum(EnumDefinitionImpl): +class SampWeatherEnum(EnumDefinitionImpl): - revolving = PermissibleValue(text="revolving") - sliding = PermissibleValue(text="sliding") - telescopic = PermissibleValue(text="telescopic") + cloudy = PermissibleValue(text="cloudy") + foggy = PermissibleValue(text="foggy") + hail = PermissibleValue(text="hail") + rain = PermissibleValue(text="rain") + snow = PermissibleValue(text="snow") + sleet = PermissibleValue(text="sleet") + sunny = PermissibleValue(text="sunny") + windy = PermissibleValue(text="windy") _defn = EnumDefinition( - name="DoorCompTypeEnum", + name="SampWeatherEnum", ) @classmethod def _addvals(cls): - setattr(cls, "metal covered", - PermissibleValue(text="metal covered")) - -class WindowLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="WindowLocEnum", - ) + setattr(cls, "clear sky", + PermissibleValue(text="clear sky")) -class SrLithologyEnum(EnumDefinitionImpl): +class WindowCoverEnum(EnumDefinitionImpl): - Clastic = PermissibleValue(text="Clastic") - Carbonate = PermissibleValue(text="Carbonate") - Coal = PermissibleValue(text="Coal") - Biosilicieous = PermissibleValue(text="Biosilicieous") - other = PermissibleValue(text="other") + blinds = PermissibleValue(text="blinds") + curtains = PermissibleValue(text="curtains") + none = PermissibleValue(text="none") _defn = EnumDefinition( - name="SrLithologyEnum", + name="WindowCoverEnum", ) -class PlantGrowthMedEnum(EnumDefinitionImpl): +class RoomTypeEnum(EnumDefinitionImpl): - perlite = PermissibleValue(text="perlite") - pumice = PermissibleValue(text="pumice") - sand = PermissibleValue(text="sand") - soil = PermissibleValue(text="soil") - vermiculite = PermissibleValue(text="vermiculite") - water = PermissibleValue(text="water") + attic = PermissibleValue(text="attic") + bathroom = PermissibleValue(text="bathroom") + closet = PermissibleValue(text="closet") + elevator = PermissibleValue(text="elevator") + hallway = PermissibleValue(text="hallway") + kitchen = PermissibleValue(text="kitchen") + stairwell = PermissibleValue(text="stairwell") + lobby = PermissibleValue(text="lobby") + vestibule = PermissibleValue(text="vestibule") + laboratory_wet = PermissibleValue(text="laboratory_wet") + laboratory_dry = PermissibleValue(text="laboratory_dry") + gymnasium = PermissibleValue(text="gymnasium") + natatorium = PermissibleValue(text="natatorium") + auditorium = PermissibleValue(text="auditorium") + lockers = PermissibleValue(text="lockers") + cafe = PermissibleValue(text="cafe") + warehouse = PermissibleValue(text="warehouse") _defn = EnumDefinition( - name="PlantGrowthMedEnum", + name="RoomTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "other artificial liquid medium", - PermissibleValue(text="other artificial liquid medium")) - setattr(cls, "other artificial solid medium", - PermissibleValue(text="other artificial solid medium")) - setattr(cls, "peat moss", - PermissibleValue(text="peat moss")) + setattr(cls, "conference room", + PermissibleValue(text="conference room")) + setattr(cls, "examining room", + PermissibleValue(text="examining room")) + setattr(cls, "mail room", + PermissibleValue(text="mail room")) + setattr(cls, "private office", + PermissibleValue(text="private office")) + setattr(cls, "open office", + PermissibleValue(text="open office")) + setattr(cls, ",restroom", + PermissibleValue(text=",restroom")) + setattr(cls, "mechanical or electrical room", + PermissibleValue(text="mechanical or electrical room")) + setattr(cls, "data center", + PermissibleValue(text="data center")) -class SurfMaterialEnum(EnumDefinitionImpl): +class SedimentTypeEnum(EnumDefinitionImpl): - adobe = PermissibleValue(text="adobe") - carpet = PermissibleValue(text="carpet") - concrete = PermissibleValue(text="concrete") - glass = PermissibleValue(text="glass") - metal = PermissibleValue(text="metal") - paint = PermissibleValue(text="paint") - plastic = PermissibleValue(text="plastic") - stone = PermissibleValue(text="stone") - stucco = PermissibleValue(text="stucco") - tile = PermissibleValue(text="tile") - vinyl = PermissibleValue(text="vinyl") - wood = PermissibleValue(text="wood") + biogenous = PermissibleValue(text="biogenous") + cosmogenous = PermissibleValue(text="cosmogenous") + hydrogenous = PermissibleValue(text="hydrogenous") + lithogenous = PermissibleValue(text="lithogenous") _defn = EnumDefinition( - name="SurfMaterialEnum", + name="SedimentTypeEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "cinder blocks", - PermissibleValue(text="cinder blocks")) - setattr(cls, "hay bales", - PermissibleValue(text="hay bales")) - setattr(cls, "stainless steel", - PermissibleValue(text="stainless steel")) - -class CeilCondEnum(EnumDefinitionImpl): - - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") +class FaoClassEnum(EnumDefinitionImpl): - _defn = EnumDefinition( - name="CeilCondEnum", - ) + Acrisols = PermissibleValue(text="Acrisols") + Andosols = PermissibleValue(text="Andosols") + Arenosols = PermissibleValue(text="Arenosols") + Cambisols = PermissibleValue(text="Cambisols") + Chernozems = PermissibleValue(text="Chernozems") + Ferralsols = PermissibleValue(text="Ferralsols") + Fluvisols = PermissibleValue(text="Fluvisols") + Gleysols = PermissibleValue(text="Gleysols") + Greyzems = PermissibleValue(text="Greyzems") + Gypsisols = PermissibleValue(text="Gypsisols") + Histosols = PermissibleValue(text="Histosols") + Kastanozems = PermissibleValue(text="Kastanozems") + Lithosols = PermissibleValue(text="Lithosols") + Luvisols = PermissibleValue(text="Luvisols") + Nitosols = PermissibleValue(text="Nitosols") + Phaeozems = PermissibleValue(text="Phaeozems") + Planosols = PermissibleValue(text="Planosols") + Podzols = PermissibleValue(text="Podzols") + Podzoluvisols = PermissibleValue(text="Podzoluvisols") + Rankers = PermissibleValue(text="Rankers") + Regosols = PermissibleValue(text="Regosols") + Rendzinas = PermissibleValue(text="Rendzinas") + Solonchaks = PermissibleValue(text="Solonchaks") + Solonetz = PermissibleValue(text="Solonetz") + Vertisols = PermissibleValue(text="Vertisols") + Yermosols = PermissibleValue(text="Yermosols") - @classmethod - def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) + _defn = EnumDefinition( + name="FaoClassEnum", + ) -class BuildingSettingEnum(EnumDefinitionImpl): +class ExtWindowOrientEnum(EnumDefinitionImpl): - urban = PermissibleValue(text="urban") - suburban = PermissibleValue(text="suburban") - exurban = PermissibleValue(text="exurban") - rural = PermissibleValue(text="rural") + north = PermissibleValue(text="north") + south = PermissibleValue(text="south") + east = PermissibleValue(text="east") + west = PermissibleValue(text="west") + northeast = PermissibleValue(text="northeast") + southeast = PermissibleValue(text="southeast") + southwest = PermissibleValue(text="southwest") + northwest = PermissibleValue(text="northwest") _defn = EnumDefinition( - name="BuildingSettingEnum", + name="ExtWindowOrientEnum", ) -class BuildOccupTypeEnum(EnumDefinitionImpl): +class SrGeolAgeEnum(EnumDefinitionImpl): - office = PermissibleValue(text="office") - market = PermissibleValue(text="market") - restaurant = PermissibleValue(text="restaurant") - residence = PermissibleValue(text="residence") - school = PermissibleValue(text="school") - residential = PermissibleValue(text="residential") - commercial = PermissibleValue(text="commercial") - airport = PermissibleValue(text="airport") + Archean = PermissibleValue(text="Archean") + Cambrian = PermissibleValue(text="Cambrian") + Carboniferous = PermissibleValue(text="Carboniferous") + Cenozoic = PermissibleValue(text="Cenozoic") + Cretaceous = PermissibleValue(text="Cretaceous") + Devonian = PermissibleValue(text="Devonian") + Jurassic = PermissibleValue(text="Jurassic") + Mesozoic = PermissibleValue(text="Mesozoic") + Neogene = PermissibleValue(text="Neogene") + Ordovician = PermissibleValue(text="Ordovician") + Paleogene = PermissibleValue(text="Paleogene") + Paleozoic = PermissibleValue(text="Paleozoic") + Permian = PermissibleValue(text="Permian") + Precambrian = PermissibleValue(text="Precambrian") + Proterozoic = PermissibleValue(text="Proterozoic") + Silurian = PermissibleValue(text="Silurian") + Triassic = PermissibleValue(text="Triassic") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="BuildOccupTypeEnum", + name="SrGeolAgeEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "low rise", - PermissibleValue(text="low rise")) - setattr(cls, "high rise", - PermissibleValue(text="high rise")) - setattr(cls, "wood framed", - PermissibleValue(text="wood framed")) - setattr(cls, "health care", - PermissibleValue(text="health care")) - setattr(cls, "sports complex", - PermissibleValue(text="sports complex")) - -class DeposEnvEnum(EnumDefinitionImpl): +class DoorMoveEnum(EnumDefinitionImpl): - other = PermissibleValue(text="other") + collapsible = PermissibleValue(text="collapsible") + folding = PermissibleValue(text="folding") + revolving = PermissibleValue(text="revolving") + sliding = PermissibleValue(text="sliding") + swinging = PermissibleValue(text="swinging") _defn = EnumDefinition( - name="DeposEnvEnum", + name="DoorMoveEnum", ) @classmethod def _addvals(cls): - setattr(cls, "Continental - Alluvial", - PermissibleValue(text="Continental - Alluvial")) - setattr(cls, "Continental - Aeolian", - PermissibleValue(text="Continental - Aeolian")) - setattr(cls, "Continental - Fluvial", - PermissibleValue(text="Continental - Fluvial")) - setattr(cls, "Continental - Lacustrine", - PermissibleValue(text="Continental - Lacustrine")) - setattr(cls, "Transitional - Deltaic", - PermissibleValue(text="Transitional - Deltaic")) - setattr(cls, "Transitional - Tidal", - PermissibleValue(text="Transitional - Tidal")) - setattr(cls, "Transitional - Lagoonal", - PermissibleValue(text="Transitional - Lagoonal")) - setattr(cls, "Transitional - Beach", - PermissibleValue(text="Transitional - Beach")) - setattr(cls, "Transitional - Lake", - PermissibleValue(text="Transitional - Lake")) - setattr(cls, "Marine - Shallow", - PermissibleValue(text="Marine - Shallow")) - setattr(cls, "Marine - Deep", - PermissibleValue(text="Marine - Deep")) - setattr(cls, "Marine - Reef", - PermissibleValue(text="Marine - Reef")) - setattr(cls, "Other - Evaporite", - PermissibleValue(text="Other - Evaporite")) - setattr(cls, "Other - Glacial", - PermissibleValue(text="Other - Glacial")) - setattr(cls, "Other - Volcanic", - PermissibleValue(text="Other - Volcanic")) + setattr(cls, "rolling shutter", + PermissibleValue(text="rolling shutter")) -class ProfilePositionEnum(EnumDefinitionImpl): +class DoorDirectEnum(EnumDefinitionImpl): - summit = PermissibleValue(text="summit") - shoulder = PermissibleValue(text="shoulder") - backslope = PermissibleValue(text="backslope") - footslope = PermissibleValue(text="footslope") - toeslope = PermissibleValue(text="toeslope") + inward = PermissibleValue(text="inward") + outward = PermissibleValue(text="outward") + sideways = PermissibleValue(text="sideways") _defn = EnumDefinition( - name="ProfilePositionEnum", + name="DoorDirectEnum", ) -class FurnitureEnum(EnumDefinitionImpl): +class CeilTextureEnum(EnumDefinitionImpl): - cabinet = PermissibleValue(text="cabinet") - chair = PermissibleValue(text="chair") - desks = PermissibleValue(text="desks") + knockdown = PermissibleValue(text="knockdown") + popcorn = PermissibleValue(text="popcorn") + smooth = PermissibleValue(text="smooth") + swirl = PermissibleValue(text="swirl") _defn = EnumDefinition( - name="FurnitureEnum", + name="CeilTextureEnum", ) -class DoorTypeEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "crows feet", + PermissibleValue(text="crows feet")) + setattr(cls, "crows-foot stomp", + PermissibleValue(text="crows-foot stomp")) + setattr(cls, "double skip", + PermissibleValue(text="double skip")) + setattr(cls, "hawk and trowel", + PermissibleValue(text="hawk and trowel")) + setattr(cls, "orange peel", + PermissibleValue(text="orange peel")) + setattr(cls, "rosebud stomp", + PermissibleValue(text="rosebud stomp")) + setattr(cls, "Santa-Fe texture", + PermissibleValue(text="Santa-Fe texture")) + setattr(cls, "skip trowel", + PermissibleValue(text="skip trowel")) + setattr(cls, "stomp knockdown", + PermissibleValue(text="stomp knockdown")) - composite = PermissibleValue(text="composite") - metal = PermissibleValue(text="metal") - wooden = PermissibleValue(text="wooden") +class SampMdEnum(EnumDefinitionImpl): + + DF = PermissibleValue(text="DF") + RT = PermissibleValue(text="RT") + KB = PermissibleValue(text="KB") + MSL = PermissibleValue(text="MSL") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="DoorTypeEnum", + name="SampMdEnum", ) -class TidalStageEnum(EnumDefinitionImpl): +class CeilTypeEnum(EnumDefinitionImpl): + + cathedral = PermissibleValue(text="cathedral") + dropped = PermissibleValue(text="dropped") + concave = PermissibleValue(text="concave") + coffered = PermissibleValue(text="coffered") + cove = PermissibleValue(text="cove") + stretched = PermissibleValue(text="stretched") _defn = EnumDefinition( - name="TidalStageEnum", + name="CeilTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "low tide", - PermissibleValue(text="low tide")) - setattr(cls, "ebb tide", - PermissibleValue(text="ebb tide")) - setattr(cls, "flood tide", - PermissibleValue(text="flood tide")) - setattr(cls, "high tide", - PermissibleValue(text="high tide")) + setattr(cls, "barrel-shaped", + PermissibleValue(text="barrel-shaped")) + +class WallLocEnum(EnumDefinitionImpl): + + north = PermissibleValue(text="north") + south = PermissibleValue(text="south") + east = PermissibleValue(text="east") + west = PermissibleValue(text="west") + + _defn = EnumDefinition( + name="WallLocEnum", + ) class DoorTypeMetalEnum(EnumDefinitionImpl): @@ -7076,150 +7145,80 @@ def _addvals(cls): setattr(cls, "steel plate", PermissibleValue(text="steel plate")) -class HandidnessEnum(EnumDefinitionImpl): +class GenderRestroomEnum(EnumDefinitionImpl): - ambidexterity = PermissibleValue(text="ambidexterity") + female = PermissibleValue(text="female") + male = PermissibleValue(text="male") + unisex = PermissibleValue(text="unisex") _defn = EnumDefinition( - name="HandidnessEnum", + name="GenderRestroomEnum", ) @classmethod def _addvals(cls): - setattr(cls, "left handedness", - PermissibleValue(text="left handedness")) - setattr(cls, "mixed-handedness", - PermissibleValue(text="mixed-handedness")) - setattr(cls, "right handedness", - PermissibleValue(text="right handedness")) + setattr(cls, "all gender", + PermissibleValue(text="all gender")) + setattr(cls, "gender neurtral", + PermissibleValue(text="gender neurtral")) + setattr(cls, "male and female", + PermissibleValue(text="male and female")) -class TillageEnum(EnumDefinitionImpl): +class VisMediaEnum(EnumDefinitionImpl): - drill = PermissibleValue(text="drill") - chisel = PermissibleValue(text="chisel") - tined = PermissibleValue(text="tined") - mouldboard = PermissibleValue(text="mouldboard") + photos = PermissibleValue(text="photos") + videos = PermissibleValue(text="videos") + interiors = PermissibleValue(text="interiors") + equipment = PermissibleValue(text="equipment") _defn = EnumDefinition( - name="TillageEnum", + name="VisMediaEnum", ) @classmethod def _addvals(cls): - setattr(cls, "cutting disc", - PermissibleValue(text="cutting disc")) - setattr(cls, "ridge till", - PermissibleValue(text="ridge till")) - setattr(cls, "strip tillage", - PermissibleValue(text="strip tillage")) - setattr(cls, "zonal tillage", - PermissibleValue(text="zonal tillage")) - setattr(cls, "disc plough", - PermissibleValue(text="disc plough")) - -class HcrEnum(EnumDefinitionImpl): - - Coalbed = PermissibleValue(text="Coalbed") - Shale = PermissibleValue(text="Shale") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="HcrEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "Oil Reservoir", - PermissibleValue(text="Oil Reservoir")) - setattr(cls, "Gas Reservoir", - PermissibleValue(text="Gas Reservoir")) - setattr(cls, "Oil Sand", - PermissibleValue(text="Oil Sand")) - setattr(cls, "Tight Oil Reservoir", - PermissibleValue(text="Tight Oil Reservoir")) - setattr(cls, "Tight Gas Reservoir", - PermissibleValue(text="Tight Gas Reservoir")) - -class FreqCleanEnum(EnumDefinitionImpl): - - Daily = PermissibleValue(text="Daily") - Weekly = PermissibleValue(text="Weekly") - Monthly = PermissibleValue(text="Monthly") - Quarterly = PermissibleValue(text="Quarterly") - Annually = PermissibleValue(text="Annually") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="FreqCleanEnum", - ) - -class GrowthHabitEnum(EnumDefinitionImpl): - - erect = PermissibleValue(text="erect") - spreading = PermissibleValue(text="spreading") - prostrate = PermissibleValue(text="prostrate") - - _defn = EnumDefinition( - name="GrowthHabitEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "semi-erect", - PermissibleValue(text="semi-erect")) - -class SeasonUseEnum(EnumDefinitionImpl): - - Spring = PermissibleValue(text="Spring") - Summer = PermissibleValue(text="Summer") - Fall = PermissibleValue(text="Fall") - Winter = PermissibleValue(text="Winter") - - _defn = EnumDefinition( - name="SeasonUseEnum", - ) - -class SrDepEnvEnum(EnumDefinitionImpl): - - Lacustine = PermissibleValue(text="Lacustine") - Fluvioldeltaic = PermissibleValue(text="Fluvioldeltaic") - Fluviomarine = PermissibleValue(text="Fluviomarine") - Marine = PermissibleValue(text="Marine") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SrDepEnvEnum", - ) + setattr(cls, "commonly of the building", + PermissibleValue(text="commonly of the building")) + setattr(cls, "site context (adjacent buildings, vegetation, terrain, streets)", + PermissibleValue(text="site context (adjacent buildings, vegetation, terrain, streets)")) + setattr(cls, "3D scans", + PermissibleValue(text="3D scans")) -class WaterFeatTypeEnum(EnumDefinitionImpl): +class WindowLocEnum(EnumDefinitionImpl): - fountain = PermissibleValue(text="fountain") - pool = PermissibleValue(text="pool") - stream = PermissibleValue(text="stream") - waterfall = PermissibleValue(text="waterfall") + north = PermissibleValue(text="north") + south = PermissibleValue(text="south") + east = PermissibleValue(text="east") + west = PermissibleValue(text="west") _defn = EnumDefinition( - name="WaterFeatTypeEnum", + name="WindowLocEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "standing feature", - PermissibleValue(text="standing feature")) - -class SubstructureTypeEnum(EnumDefinitionImpl): +class SoilHorizonEnum(EnumDefinitionImpl): - crawlspace = PermissibleValue(text="crawlspace") - basement = PermissibleValue(text="basement") + Permafrost = PermissibleValue(text="Permafrost") _defn = EnumDefinition( - name="SubstructureTypeEnum", + name="SoilHorizonEnum", ) @classmethod def _addvals(cls): - setattr(cls, "slab on grade", - PermissibleValue(text="slab on grade")) + setattr(cls, "O horizon", + PermissibleValue(text="O horizon")) + setattr(cls, "A horizon", + PermissibleValue(text="A horizon")) + setattr(cls, "E horizon", + PermissibleValue(text="E horizon")) + setattr(cls, "B horizon", + PermissibleValue(text="B horizon")) + setattr(cls, "C horizon", + PermissibleValue(text="C horizon")) + setattr(cls, "R layer", + PermissibleValue(text="R layer")) + setattr(cls, "M horizon", + PermissibleValue(text="M horizon")) class IndoorSpaceEnum(EnumDefinitionImpl): @@ -7240,256 +7239,121 @@ def _addvals(cls): setattr(cls, "locker room", PermissibleValue(text="locker room")) -class HostSexEnum(EnumDefinitionImpl): - - female = PermissibleValue(text="female") - hermaphrodite = PermissibleValue(text="hermaphrodite") - male = PermissibleValue(text="male") - neuter = PermissibleValue(text="neuter") - - _defn = EnumDefinition( - name="HostSexEnum", - ) - -class WindowTypeEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="WindowTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "single-hung sash window", - PermissibleValue(text="single-hung sash window")) - setattr(cls, "horizontal sash window", - PermissibleValue(text="horizontal sash window")) - setattr(cls, "fixed window", - PermissibleValue(text="fixed window")) - -class SpecificEnum(EnumDefinitionImpl): - - operation = PermissibleValue(text="operation") - construction = PermissibleValue(text="construction") - bid = PermissibleValue(text="bid") - design = PermissibleValue(text="design") - photos = PermissibleValue(text="photos") - - _defn = EnumDefinition( - name="SpecificEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "as built", - PermissibleValue(text="as built")) - -class FaoClassEnum(EnumDefinitionImpl): - - Acrisols = PermissibleValue(text="Acrisols") - Andosols = PermissibleValue(text="Andosols") - Arenosols = PermissibleValue(text="Arenosols") - Cambisols = PermissibleValue(text="Cambisols") - Chernozems = PermissibleValue(text="Chernozems") - Ferralsols = PermissibleValue(text="Ferralsols") - Fluvisols = PermissibleValue(text="Fluvisols") - Gleysols = PermissibleValue(text="Gleysols") - Greyzems = PermissibleValue(text="Greyzems") - Gypsisols = PermissibleValue(text="Gypsisols") - Histosols = PermissibleValue(text="Histosols") - Kastanozems = PermissibleValue(text="Kastanozems") - Lithosols = PermissibleValue(text="Lithosols") - Luvisols = PermissibleValue(text="Luvisols") - Nitosols = PermissibleValue(text="Nitosols") - Phaeozems = PermissibleValue(text="Phaeozems") - Planosols = PermissibleValue(text="Planosols") - Podzols = PermissibleValue(text="Podzols") - Podzoluvisols = PermissibleValue(text="Podzoluvisols") - Rankers = PermissibleValue(text="Rankers") - Regosols = PermissibleValue(text="Regosols") - Rendzinas = PermissibleValue(text="Rendzinas") - Solonchaks = PermissibleValue(text="Solonchaks") - Solonetz = PermissibleValue(text="Solonetz") - Vertisols = PermissibleValue(text="Vertisols") - Yermosols = PermissibleValue(text="Yermosols") - - _defn = EnumDefinition( - name="FaoClassEnum", - ) - -class FloorStrucEnum(EnumDefinitionImpl): - - balcony = PermissibleValue(text="balcony") - concrete = PermissibleValue(text="concrete") - - _defn = EnumDefinition( - name="FloorStrucEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "floating floor", - PermissibleValue(text="floating floor")) - setattr(cls, "glass floor", - PermissibleValue(text="glass floor")) - setattr(cls, "raised floor", - PermissibleValue(text="raised floor")) - setattr(cls, "sprung floor", - PermissibleValue(text="sprung floor")) - setattr(cls, "wood-framed", - PermissibleValue(text="wood-framed")) - -class WallTextureEnum(EnumDefinitionImpl): - - knockdown = PermissibleValue(text="knockdown") - popcorn = PermissibleValue(text="popcorn") - smooth = PermissibleValue(text="smooth") - swirl = PermissibleValue(text="swirl") - - _defn = EnumDefinition( - name="WallTextureEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "crows feet", - PermissibleValue(text="crows feet")) - setattr(cls, "crows-foot stomp", - PermissibleValue(text="crows-foot stomp")) - setattr(cls, "", - PermissibleValue(text="")) - setattr(cls, "double skip", - PermissibleValue(text="double skip")) - setattr(cls, "hawk and trowel", - PermissibleValue(text="hawk and trowel")) - setattr(cls, "orange peel", - PermissibleValue(text="orange peel")) - setattr(cls, "rosebud stomp", - PermissibleValue(text="rosebud stomp")) - setattr(cls, "Santa-Fe texture", - PermissibleValue(text="Santa-Fe texture")) - setattr(cls, "skip trowel", - PermissibleValue(text="skip trowel")) - setattr(cls, "stomp knockdown", - PermissibleValue(text="stomp knockdown")) - -class TrainStopLocEnum(EnumDefinitionImpl): - - end = PermissibleValue(text="end") - mid = PermissibleValue(text="mid") - downtown = PermissibleValue(text="downtown") - - _defn = EnumDefinition( - name="TrainStopLocEnum", - ) - -class DrawingsEnum(EnumDefinitionImpl): +class DoorTypeEnum(EnumDefinitionImpl): - operation = PermissibleValue(text="operation") - construction = PermissibleValue(text="construction") - bid = PermissibleValue(text="bid") - design = PermissibleValue(text="design") - diagram = PermissibleValue(text="diagram") - sketch = PermissibleValue(text="sketch") + composite = PermissibleValue(text="composite") + metal = PermissibleValue(text="metal") + wooden = PermissibleValue(text="wooden") _defn = EnumDefinition( - name="DrawingsEnum", + name="DoorTypeEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "as built", - PermissibleValue(text="as built")) - setattr(cls, "building navigation map", - PermissibleValue(text="building navigation map")) +class DeposEnvEnum(EnumDefinitionImpl): -class RoomLocEnum(EnumDefinitionImpl): + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="RoomLocEnum", + name="DeposEnvEnum", ) @classmethod def _addvals(cls): - setattr(cls, "corner room", - PermissibleValue(text="corner room")) - setattr(cls, "interior room", - PermissibleValue(text="interior room")) - setattr(cls, "exterior wall", - PermissibleValue(text="exterior wall")) + setattr(cls, "Continental - Alluvial", + PermissibleValue(text="Continental - Alluvial")) + setattr(cls, "Continental - Aeolian", + PermissibleValue(text="Continental - Aeolian")) + setattr(cls, "Continental - Fluvial", + PermissibleValue(text="Continental - Fluvial")) + setattr(cls, "Continental - Lacustrine", + PermissibleValue(text="Continental - Lacustrine")) + setattr(cls, "Transitional - Deltaic", + PermissibleValue(text="Transitional - Deltaic")) + setattr(cls, "Transitional - Tidal", + PermissibleValue(text="Transitional - Tidal")) + setattr(cls, "Transitional - Lagoonal", + PermissibleValue(text="Transitional - Lagoonal")) + setattr(cls, "Transitional - Beach", + PermissibleValue(text="Transitional - Beach")) + setattr(cls, "Transitional - Lake", + PermissibleValue(text="Transitional - Lake")) + setattr(cls, "Marine - Shallow", + PermissibleValue(text="Marine - Shallow")) + setattr(cls, "Marine - Deep", + PermissibleValue(text="Marine - Deep")) + setattr(cls, "Marine - Reef", + PermissibleValue(text="Marine - Reef")) + setattr(cls, "Other - Evaporite", + PermissibleValue(text="Other - Evaporite")) + setattr(cls, "Other - Glacial", + PermissibleValue(text="Other - Glacial")) + setattr(cls, "Other - Volcanic", + PermissibleValue(text="Other - Volcanic")) -class LightTypeEnum(EnumDefinitionImpl): +class SrLithologyEnum(EnumDefinitionImpl): - none = PermissibleValue(text="none") + Clastic = PermissibleValue(text="Clastic") + Carbonate = PermissibleValue(text="Carbonate") + Coal = PermissibleValue(text="Coal") + Biosilicieous = PermissibleValue(text="Biosilicieous") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="LightTypeEnum", + name="SrLithologyEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "natural light", - PermissibleValue(text="natural light")) - setattr(cls, "electric light", - PermissibleValue(text="electric light")) - setattr(cls, "desk lamp", - PermissibleValue(text="desk lamp")) - setattr(cls, "flourescent lights", - PermissibleValue(text="flourescent lights")) - -class WeekdayEnum(EnumDefinitionImpl): +class PlantSexEnum(EnumDefinitionImpl): - Monday = PermissibleValue(text="Monday") - Tuesday = PermissibleValue(text="Tuesday") - Wednesday = PermissibleValue(text="Wednesday") - Thursday = PermissibleValue(text="Thursday") - Friday = PermissibleValue(text="Friday") - Saturday = PermissibleValue(text="Saturday") - Sunday = PermissibleValue(text="Sunday") + Androdioecious = PermissibleValue(text="Androdioecious") + Androecious = PermissibleValue(text="Androecious") + Androgynous = PermissibleValue(text="Androgynous") + Androgynomonoecious = PermissibleValue(text="Androgynomonoecious") + Andromonoecious = PermissibleValue(text="Andromonoecious") + Bisexual = PermissibleValue(text="Bisexual") + Dichogamous = PermissibleValue(text="Dichogamous") + Diclinous = PermissibleValue(text="Diclinous") + Dioecious = PermissibleValue(text="Dioecious") + Gynodioecious = PermissibleValue(text="Gynodioecious") + Gynoecious = PermissibleValue(text="Gynoecious") + Gynomonoecious = PermissibleValue(text="Gynomonoecious") + Hermaphroditic = PermissibleValue(text="Hermaphroditic") + Imperfect = PermissibleValue(text="Imperfect") + Monoclinous = PermissibleValue(text="Monoclinous") + Monoecious = PermissibleValue(text="Monoecious") + Perfect = PermissibleValue(text="Perfect") + Polygamodioecious = PermissibleValue(text="Polygamodioecious") + Polygamomonoecious = PermissibleValue(text="Polygamomonoecious") + Polygamous = PermissibleValue(text="Polygamous") + Protandrous = PermissibleValue(text="Protandrous") + Protogynous = PermissibleValue(text="Protogynous") + Subandroecious = PermissibleValue(text="Subandroecious") + Subdioecious = PermissibleValue(text="Subdioecious") + Subgynoecious = PermissibleValue(text="Subgynoecious") + Synoecious = PermissibleValue(text="Synoecious") + Trimonoecious = PermissibleValue(text="Trimonoecious") + Trioecious = PermissibleValue(text="Trioecious") + Unisexual = PermissibleValue(text="Unisexual") _defn = EnumDefinition( - name="WeekdayEnum", + name="PlantSexEnum", ) -class ArchStrucEnum(EnumDefinitionImpl): - - building = PermissibleValue(text="building") - shed = PermissibleValue(text="shed") - home = PermissibleValue(text="home") - - _defn = EnumDefinition( - name="ArchStrucEnum", - ) +class SpecificEnum(EnumDefinitionImpl): -class HeatCoolTypeEnum(EnumDefinitionImpl): + operation = PermissibleValue(text="operation") + construction = PermissibleValue(text="construction") + bid = PermissibleValue(text="bid") + design = PermissibleValue(text="design") + photos = PermissibleValue(text="photos") _defn = EnumDefinition( - name="HeatCoolTypeEnum", + name="SpecificEnum", ) @classmethod def _addvals(cls): - setattr(cls, "radiant system", - PermissibleValue(text="radiant system")) - setattr(cls, "heat pump", - PermissibleValue(text="heat pump")) - setattr(cls, "forced air system", - PermissibleValue(text="forced air system")) - setattr(cls, "steam forced heat", - PermissibleValue(text="steam forced heat")) - setattr(cls, "wood stove", - PermissibleValue(text="wood stove")) - -class SampMdEnum(EnumDefinitionImpl): - - DF = PermissibleValue(text="DF") - RT = PermissibleValue(text="RT") - KB = PermissibleValue(text="KB") - MSL = PermissibleValue(text="MSL") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SampMdEnum", - ) + setattr(cls, "as built", + PermissibleValue(text="as built")) class ExtWallOrientEnum(EnumDefinitionImpl): @@ -7506,203 +7370,224 @@ class ExtWallOrientEnum(EnumDefinitionImpl): name="ExtWallOrientEnum", ) -class MechStrucEnum(EnumDefinitionImpl): - - subway = PermissibleValue(text="subway") - coach = PermissibleValue(text="coach") - carriage = PermissibleValue(text="carriage") - elevator = PermissibleValue(text="elevator") - escalator = PermissibleValue(text="escalator") - boat = PermissibleValue(text="boat") - train = PermissibleValue(text="train") - car = PermissibleValue(text="car") - bus = PermissibleValue(text="bus") - - _defn = EnumDefinition( - name="MechStrucEnum", - ) - -class ExtWindowOrientEnum(EnumDefinitionImpl): +class DoorLocEnum(EnumDefinitionImpl): north = PermissibleValue(text="north") south = PermissibleValue(text="south") east = PermissibleValue(text="east") west = PermissibleValue(text="west") - northeast = PermissibleValue(text="northeast") - southeast = PermissibleValue(text="southeast") - southwest = PermissibleValue(text="southwest") - northwest = PermissibleValue(text="northwest") _defn = EnumDefinition( - name="ExtWindowOrientEnum", + name="DoorLocEnum", ) -class WindowCoverEnum(EnumDefinitionImpl): +class ProfilePositionEnum(EnumDefinitionImpl): - blinds = PermissibleValue(text="blinds") - curtains = PermissibleValue(text="curtains") - none = PermissibleValue(text="none") + summit = PermissibleValue(text="summit") + shoulder = PermissibleValue(text="shoulder") + backslope = PermissibleValue(text="backslope") + footslope = PermissibleValue(text="footslope") + toeslope = PermissibleValue(text="toeslope") _defn = EnumDefinition( - name="WindowCoverEnum", + name="ProfilePositionEnum", ) -class DrainageClassEnum(EnumDefinitionImpl): +class GrowthHabitEnum(EnumDefinitionImpl): - poorly = PermissibleValue(text="poorly") - well = PermissibleValue(text="well") + erect = PermissibleValue(text="erect") + spreading = PermissibleValue(text="spreading") + prostrate = PermissibleValue(text="prostrate") _defn = EnumDefinition( - name="DrainageClassEnum", + name="GrowthHabitEnum", ) @classmethod def _addvals(cls): - setattr(cls, "very poorly", - PermissibleValue(text="very poorly")) - setattr(cls, "somewhat poorly", - PermissibleValue(text="somewhat poorly")) - setattr(cls, "moderately well", - PermissibleValue(text="moderately well")) - setattr(cls, "excessively drained", - PermissibleValue(text="excessively drained")) + setattr(cls, "semi-erect", + PermissibleValue(text="semi-erect")) -class WindowHorizPosEnum(EnumDefinitionImpl): +class SeasonUseEnum(EnumDefinitionImpl): - left = PermissibleValue(text="left") - middle = PermissibleValue(text="middle") - right = PermissibleValue(text="right") + Spring = PermissibleValue(text="Spring") + Summer = PermissibleValue(text="Summer") + Fall = PermissibleValue(text="Fall") + Winter = PermissibleValue(text="Winter") _defn = EnumDefinition( - name="WindowHorizPosEnum", + name="SeasonUseEnum", ) -class SampSubtypeEnum(EnumDefinitionImpl): +class CeilFinishMatEnum(EnumDefinitionImpl): - biofilm = PermissibleValue(text="biofilm") - other = PermissibleValue(text="other") + drywall = PermissibleValue(text="drywall") + tiles = PermissibleValue(text="tiles") + PVC = PermissibleValue(text="PVC") + plasterboard = PermissibleValue(text="plasterboard") + metal = PermissibleValue(text="metal") + fiberglass = PermissibleValue(text="fiberglass") + stucco = PermissibleValue(text="stucco") + wood = PermissibleValue(text="wood") _defn = EnumDefinition( - name="SampSubtypeEnum", + name="CeilFinishMatEnum", ) @classmethod def _addvals(cls): - setattr(cls, "oil phase", - PermissibleValue(text="oil phase")) - setattr(cls, "water phase", - PermissibleValue(text="water phase")) - setattr(cls, "not applicable", - PermissibleValue(text="not applicable")) + setattr(cls, "mineral fibre", + PermissibleValue(text="mineral fibre")) + setattr(cls, "mineral wool/calcium silicate", + PermissibleValue(text="mineral wool/calcium silicate")) -class CeilTextureEnum(EnumDefinitionImpl): +class TillageEnum(EnumDefinitionImpl): - knockdown = PermissibleValue(text="knockdown") - popcorn = PermissibleValue(text="popcorn") - smooth = PermissibleValue(text="smooth") - swirl = PermissibleValue(text="swirl") + drill = PermissibleValue(text="drill") + chisel = PermissibleValue(text="chisel") + tined = PermissibleValue(text="tined") + mouldboard = PermissibleValue(text="mouldboard") _defn = EnumDefinition( - name="CeilTextureEnum", + name="TillageEnum", ) @classmethod def _addvals(cls): - setattr(cls, "crows feet", - PermissibleValue(text="crows feet")) - setattr(cls, "crows-foot stomp", - PermissibleValue(text="crows-foot stomp")) - setattr(cls, "double skip", - PermissibleValue(text="double skip")) - setattr(cls, "hawk and trowel", - PermissibleValue(text="hawk and trowel")) - setattr(cls, "orange peel", - PermissibleValue(text="orange peel")) - setattr(cls, "rosebud stomp", - PermissibleValue(text="rosebud stomp")) - setattr(cls, "Santa-Fe texture", - PermissibleValue(text="Santa-Fe texture")) - setattr(cls, "skip trowel", - PermissibleValue(text="skip trowel")) - setattr(cls, "stomp knockdown", - PermissibleValue(text="stomp knockdown")) + setattr(cls, "cutting disc", + PermissibleValue(text="cutting disc")) + setattr(cls, "ridge till", + PermissibleValue(text="ridge till")) + setattr(cls, "strip tillage", + PermissibleValue(text="strip tillage")) + setattr(cls, "zonal tillage", + PermissibleValue(text="zonal tillage")) + setattr(cls, "disc plough", + PermissibleValue(text="disc plough")) -class RoomSampPosEnum(EnumDefinitionImpl): +class WindowTypeEnum(EnumDefinitionImpl): - center = PermissibleValue(text="center") + _defn = EnumDefinition( + name="WindowTypeEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "single-hung sash window", + PermissibleValue(text="single-hung sash window")) + setattr(cls, "horizontal sash window", + PermissibleValue(text="horizontal sash window")) + setattr(cls, "fixed window", + PermissibleValue(text="fixed window")) + +class CeilCondEnum(EnumDefinitionImpl): + + new = PermissibleValue(text="new") + damaged = PermissibleValue(text="damaged") + rupture = PermissibleValue(text="rupture") _defn = EnumDefinition( - name="RoomSampPosEnum", + name="CeilCondEnum", ) @classmethod def _addvals(cls): - setattr(cls, "north corner", - PermissibleValue(text="north corner")) - setattr(cls, "south corner", - PermissibleValue(text="south corner")) - setattr(cls, "west corner", - PermissibleValue(text="west corner")) - setattr(cls, "east corner", - PermissibleValue(text="east corner")) - setattr(cls, "northeast corner", - PermissibleValue(text="northeast corner")) - setattr(cls, "northwest corner", - PermissibleValue(text="northwest corner")) - setattr(cls, "southeast corner", - PermissibleValue(text="southeast corner")) - setattr(cls, "southwest corner", - PermissibleValue(text="southwest corner")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) -class IndoorSurfEnum(EnumDefinitionImpl): +class HcrGeolAgeEnum(EnumDefinitionImpl): - cabinet = PermissibleValue(text="cabinet") - ceiling = PermissibleValue(text="ceiling") - door = PermissibleValue(text="door") - shelving = PermissibleValue(text="shelving") - window = PermissibleValue(text="window") - wall = PermissibleValue(text="wall") + Archean = PermissibleValue(text="Archean") + Cambrian = PermissibleValue(text="Cambrian") + Carboniferous = PermissibleValue(text="Carboniferous") + Cenozoic = PermissibleValue(text="Cenozoic") + Cretaceous = PermissibleValue(text="Cretaceous") + Devonian = PermissibleValue(text="Devonian") + Jurassic = PermissibleValue(text="Jurassic") + Mesozoic = PermissibleValue(text="Mesozoic") + Neogene = PermissibleValue(text="Neogene") + Ordovician = PermissibleValue(text="Ordovician") + Paleogene = PermissibleValue(text="Paleogene") + Paleozoic = PermissibleValue(text="Paleozoic") + Permian = PermissibleValue(text="Permian") + Precambrian = PermissibleValue(text="Precambrian") + Proterozoic = PermissibleValue(text="Proterozoic") + Silurian = PermissibleValue(text="Silurian") + Triassic = PermissibleValue(text="Triassic") + other = PermissibleValue(text="other") + + _defn = EnumDefinition( + name="HcrGeolAgeEnum", + ) + +class DoorCondEnum(EnumDefinitionImpl): + + damaged = PermissibleValue(text="damaged") + new = PermissibleValue(text="new") + rupture = PermissibleValue(text="rupture") _defn = EnumDefinition( - name="IndoorSurfEnum", + name="DoorCondEnum", ) @classmethod def _addvals(cls): - setattr(cls, "counter top", - PermissibleValue(text="counter top")) - setattr(cls, "vent cover", - PermissibleValue(text="vent cover")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) -class OrganismCountEnum(EnumDefinitionImpl): +class LithologyEnum(EnumDefinitionImpl): - ATP = PermissibleValue(text="ATP") - MPN = PermissibleValue(text="MPN") + Basement = PermissibleValue(text="Basement") + Chalk = PermissibleValue(text="Chalk") + Chert = PermissibleValue(text="Chert") + Coal = PermissibleValue(text="Coal") + Conglomerate = PermissibleValue(text="Conglomerate") + Diatomite = PermissibleValue(text="Diatomite") + Dolomite = PermissibleValue(text="Dolomite") + Limestone = PermissibleValue(text="Limestone") + Sandstone = PermissibleValue(text="Sandstone") + Shale = PermissibleValue(text="Shale") + Siltstone = PermissibleValue(text="Siltstone") + Volcanic = PermissibleValue(text="Volcanic") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="OrganismCountEnum", + name="LithologyEnum", ) -class VisMediaEnum(EnumDefinitionImpl): - - photos = PermissibleValue(text="photos") - videos = PermissibleValue(text="videos") - interiors = PermissibleValue(text="interiors") - equipment = PermissibleValue(text="equipment") +class HeatCoolTypeEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="VisMediaEnum", + name="HeatCoolTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "commonly of the building", - PermissibleValue(text="commonly of the building")) - setattr(cls, "site context (adjacent buildings, vegetation, terrain, streets)", - PermissibleValue(text="site context (adjacent buildings, vegetation, terrain, streets)")) - setattr(cls, "3D scans", - PermissibleValue(text="3D scans")) + setattr(cls, "radiant system", + PermissibleValue(text="radiant system")) + setattr(cls, "heat pump", + PermissibleValue(text="heat pump")) + setattr(cls, "forced air system", + PermissibleValue(text="forced air system")) + setattr(cls, "steam forced heat", + PermissibleValue(text="steam forced heat")) + setattr(cls, "wood stove", + PermissibleValue(text="wood stove")) + +class BuildingSettingEnum(EnumDefinitionImpl): + + urban = PermissibleValue(text="urban") + suburban = PermissibleValue(text="suburban") + exurban = PermissibleValue(text="exurban") + rural = PermissibleValue(text="rural") + + _defn = EnumDefinition( + name="BuildingSettingEnum", + ) class RoomCondtEnum(EnumDefinitionImpl): @@ -7723,46 +7608,40 @@ def _addvals(cls): setattr(cls, "visible signs of mold/mildew", PermissibleValue(text="visible signs of mold/mildew")) -class SampCollectPointEnum(EnumDefinitionImpl): - - well = PermissibleValue(text="well") - wellhead = PermissibleValue(text="wellhead") - separator = PermissibleValue(text="separator") - other = PermissibleValue(text="other") +class RelSampLocEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="SampCollectPointEnum", + name="RelSampLocEnum", ) @classmethod def _addvals(cls): - setattr(cls, "test well", - PermissibleValue(text="test well")) - setattr(cls, "drilling rig", - PermissibleValue(text="drilling rig")) - setattr(cls, "storage tank", - PermissibleValue(text="storage tank")) + setattr(cls, "edge of car", + PermissibleValue(text="edge of car")) + setattr(cls, "center of car", + PermissibleValue(text="center of car")) + setattr(cls, "under a seat", + PermissibleValue(text="under a seat")) -class SampCaptStatusEnum(EnumDefinitionImpl): +class WallSurfTreatmentEnum(EnumDefinitionImpl): - other = PermissibleValue(text="other") + painted = PermissibleValue(text="painted") + paneling = PermissibleValue(text="paneling") + stucco = PermissibleValue(text="stucco") + fabric = PermissibleValue(text="fabric") _defn = EnumDefinition( - name="SampCaptStatusEnum", + name="WallSurfTreatmentEnum", ) @classmethod def _addvals(cls): - setattr(cls, "active surveillance in response to an outbreak", - PermissibleValue(text="active surveillance in response to an outbreak")) - setattr(cls, "active surveillance not initiated by an outbreak", - PermissibleValue(text="active surveillance not initiated by an outbreak")) - setattr(cls, "farm sample", - PermissibleValue(text="farm sample")) - setattr(cls, "market sample", - PermissibleValue(text="market sample")) + setattr(cls, "wall paper", + PermissibleValue(text="wall paper")) + setattr(cls, "no treatment", + PermissibleValue(text="no treatment")) -class RoomTypeEnum(EnumDefinitionImpl): +class RoomConnectedEnum(EnumDefinitionImpl): attic = PermissibleValue(text="attic") bathroom = PermissibleValue(text="bathroom") @@ -7770,20 +7649,11 @@ class RoomTypeEnum(EnumDefinitionImpl): elevator = PermissibleValue(text="elevator") hallway = PermissibleValue(text="hallway") kitchen = PermissibleValue(text="kitchen") + office = PermissibleValue(text="office") stairwell = PermissibleValue(text="stairwell") - lobby = PermissibleValue(text="lobby") - vestibule = PermissibleValue(text="vestibule") - laboratory_wet = PermissibleValue(text="laboratory_wet") - laboratory_dry = PermissibleValue(text="laboratory_dry") - gymnasium = PermissibleValue(text="gymnasium") - natatorium = PermissibleValue(text="natatorium") - auditorium = PermissibleValue(text="auditorium") - lockers = PermissibleValue(text="lockers") - cafe = PermissibleValue(text="cafe") - warehouse = PermissibleValue(text="warehouse") _defn = EnumDefinition( - name="RoomTypeEnum", + name="RoomConnectedEnum", ) @classmethod @@ -7794,71 +7664,128 @@ def _addvals(cls): PermissibleValue(text="examining room")) setattr(cls, "mail room", PermissibleValue(text="mail room")) - setattr(cls, "private office", - PermissibleValue(text="private office")) - setattr(cls, "open office", - PermissibleValue(text="open office")) - setattr(cls, ",restroom", - PermissibleValue(text=",restroom")) - setattr(cls, "mechanical or electrical room", - PermissibleValue(text="mechanical or electrical room")) - setattr(cls, "data center", - PermissibleValue(text="data center")) -class SampDisStageEnum(EnumDefinitionImpl): +class WindowVertPosEnum(EnumDefinitionImpl): - dissemination = PermissibleValue(text="dissemination") - infection = PermissibleValue(text="infection") - inoculation = PermissibleValue(text="inoculation") - penetration = PermissibleValue(text="penetration") - other = PermissibleValue(text="other") + bottom = PermissibleValue(text="bottom") + middle = PermissibleValue(text="middle") + top = PermissibleValue(text="top") + low = PermissibleValue(text="low") + high = PermissibleValue(text="high") _defn = EnumDefinition( - name="SampDisStageEnum", + name="WindowVertPosEnum", + ) + +class WeekdayEnum(EnumDefinitionImpl): + + Monday = PermissibleValue(text="Monday") + Tuesday = PermissibleValue(text="Tuesday") + Wednesday = PermissibleValue(text="Wednesday") + Thursday = PermissibleValue(text="Thursday") + Friday = PermissibleValue(text="Friday") + Saturday = PermissibleValue(text="Saturday") + Sunday = PermissibleValue(text="Sunday") + + _defn = EnumDefinition( + name="WeekdayEnum", + ) + +class RoomSampPosEnum(EnumDefinitionImpl): + + center = PermissibleValue(text="center") + + _defn = EnumDefinition( + name="RoomSampPosEnum", ) @classmethod def _addvals(cls): - setattr(cls, "growth and reproduction", - PermissibleValue(text="growth and reproduction")) + setattr(cls, "north corner", + PermissibleValue(text="north corner")) + setattr(cls, "south corner", + PermissibleValue(text="south corner")) + setattr(cls, "west corner", + PermissibleValue(text="west corner")) + setattr(cls, "east corner", + PermissibleValue(text="east corner")) + setattr(cls, "northeast corner", + PermissibleValue(text="northeast corner")) + setattr(cls, "northwest corner", + PermissibleValue(text="northwest corner")) + setattr(cls, "southeast corner", + PermissibleValue(text="southeast corner")) + setattr(cls, "southwest corner", + PermissibleValue(text="southwest corner")) -class FloorCondEnum(EnumDefinitionImpl): +class DoorMatEnum(EnumDefinitionImpl): - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") + aluminum = PermissibleValue(text="aluminum") + fiberboard = PermissibleValue(text="fiberboard") + fiberglass = PermissibleValue(text="fiberglass") + metal = PermissibleValue(text="metal") + vinyl = PermissibleValue(text="vinyl") + wood = PermissibleValue(text="wood") _defn = EnumDefinition( - name="FloorCondEnum", + name="DoorMatEnum", ) @classmethod def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) + setattr(cls, "cellular PVC", + PermissibleValue(text="cellular PVC")) + setattr(cls, "engineered plastic", + PermissibleValue(text="engineered plastic")) + setattr(cls, "thermoplastic alloy", + PermissibleValue(text="thermoplastic alloy")) + setattr(cls, "wood/plastic composite", + PermissibleValue(text="wood/plastic composite")) -class LithologyEnum(EnumDefinitionImpl): +class BiolStatEnum(EnumDefinitionImpl): - Basement = PermissibleValue(text="Basement") - Chalk = PermissibleValue(text="Chalk") - Chert = PermissibleValue(text="Chert") - Coal = PermissibleValue(text="Coal") - Conglomerate = PermissibleValue(text="Conglomerate") - Diatomite = PermissibleValue(text="Diatomite") - Dolomite = PermissibleValue(text="Dolomite") - Limestone = PermissibleValue(text="Limestone") - Sandstone = PermissibleValue(text="Sandstone") - Shale = PermissibleValue(text="Shale") - Siltstone = PermissibleValue(text="Siltstone") - Volcanic = PermissibleValue(text="Volcanic") - other = PermissibleValue(text="other") + wild = PermissibleValue(text="wild") + natural = PermissibleValue(text="natural") + hybrid = PermissibleValue(text="hybrid") + mutant = PermissibleValue(text="mutant") + + _defn = EnumDefinition( + name="BiolStatEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "semi-natural", + PermissibleValue(text="semi-natural")) + setattr(cls, "inbred line", + PermissibleValue(text="inbred line")) + setattr(cls, "breeder's line", + PermissibleValue(text="breeder's line")) + setattr(cls, "clonal selection", + PermissibleValue(text="clonal selection")) + +class FloorStrucEnum(EnumDefinitionImpl): + + balcony = PermissibleValue(text="balcony") + concrete = PermissibleValue(text="concrete") _defn = EnumDefinition( - name="LithologyEnum", + name="FloorStrucEnum", ) + @classmethod + def _addvals(cls): + setattr(cls, "floating floor", + PermissibleValue(text="floating floor")) + setattr(cls, "glass floor", + PermissibleValue(text="glass floor")) + setattr(cls, "raised floor", + PermissibleValue(text="raised floor")) + setattr(cls, "sprung floor", + PermissibleValue(text="sprung floor")) + setattr(cls, "wood-framed", + PermissibleValue(text="wood-framed")) + class DoorTypeWoodEnum(EnumDefinitionImpl): battened = PermissibleValue(text="battened") @@ -7886,110 +7813,174 @@ def _addvals(cls): setattr(cls, "wire gauged", PermissibleValue(text="wire gauged")) -class WallFinishMatEnum(EnumDefinitionImpl): +class OrganismCountEnum(EnumDefinitionImpl): - plaster = PermissibleValue(text="plaster") - tile = PermissibleValue(text="tile") - terrazzo = PermissibleValue(text="terrazzo") - wood = PermissibleValue(text="wood") - metal = PermissibleValue(text="metal") - masonry = PermissibleValue(text="masonry") + ATP = PermissibleValue(text="ATP") + MPN = PermissibleValue(text="MPN") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="WallFinishMatEnum", + name="OrganismCountEnum", + ) + +class ShadingDeviceCondEnum(EnumDefinitionImpl): + + damaged = PermissibleValue(text="damaged") + new = PermissibleValue(text="new") + rupture = PermissibleValue(text="rupture") + + _defn = EnumDefinition( + name="ShadingDeviceCondEnum", ) @classmethod def _addvals(cls): - setattr(cls, "gypsum plaster", - PermissibleValue(text="gypsum plaster")) - setattr(cls, "veneer plaster", - PermissibleValue(text="veneer plaster")) - setattr(cls, "gypsum board", - PermissibleValue(text="gypsum board")) - setattr(cls, "stone facing", - PermissibleValue(text="stone facing")) - setattr(cls, "acoustical treatment", - PermissibleValue(text="acoustical treatment")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) -class GenderRestroomEnum(EnumDefinitionImpl): +class HcrEnum(EnumDefinitionImpl): - female = PermissibleValue(text="female") - male = PermissibleValue(text="male") - unisex = PermissibleValue(text="unisex") + Coalbed = PermissibleValue(text="Coalbed") + Shale = PermissibleValue(text="Shale") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="GenderRestroomEnum", + name="HcrEnum", ) @classmethod def _addvals(cls): - setattr(cls, "all gender", - PermissibleValue(text="all gender")) - setattr(cls, "gender neurtral", - PermissibleValue(text="gender neurtral")) - setattr(cls, "male and female", - PermissibleValue(text="male and female")) + setattr(cls, "Oil Reservoir", + PermissibleValue(text="Oil Reservoir")) + setattr(cls, "Gas Reservoir", + PermissibleValue(text="Gas Reservoir")) + setattr(cls, "Oil Sand", + PermissibleValue(text="Oil Sand")) + setattr(cls, "Tight Oil Reservoir", + PermissibleValue(text="Tight Oil Reservoir")) + setattr(cls, "Tight Gas Reservoir", + PermissibleValue(text="Tight Gas Reservoir")) -class IntWallCondEnum(EnumDefinitionImpl): +class MechStrucEnum(EnumDefinitionImpl): - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") + subway = PermissibleValue(text="subway") + coach = PermissibleValue(text="coach") + carriage = PermissibleValue(text="carriage") + elevator = PermissibleValue(text="elevator") + escalator = PermissibleValue(text="escalator") + boat = PermissibleValue(text="boat") + train = PermissibleValue(text="train") + car = PermissibleValue(text="car") + bus = PermissibleValue(text="bus") _defn = EnumDefinition( - name="IntWallCondEnum", + name="MechStrucEnum", + ) + +class HcProducedEnum(EnumDefinitionImpl): + + Oil = PermissibleValue(text="Oil") + Gas = PermissibleValue(text="Gas") + Bitumen = PermissibleValue(text="Bitumen") + other = PermissibleValue(text="other") + + _defn = EnumDefinition( + name="HcProducedEnum", ) @classmethod def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) + setattr(cls, "Gas-Condensate", + PermissibleValue(text="Gas-Condensate")) + setattr(cls, "Coalbed Methane", + PermissibleValue(text="Coalbed Methane")) -class FloorWaterMoldEnum(EnumDefinitionImpl): +class ShadingDeviceTypeEnum(EnumDefinitionImpl): - condensation = PermissibleValue(text="condensation") + tree = PermissibleValue(text="tree") + trellis = PermissibleValue(text="trellis") _defn = EnumDefinition( - name="FloorWaterMoldEnum", + name="ShadingDeviceTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "mold odor", - PermissibleValue(text="mold odor")) - setattr(cls, "wet floor", - PermissibleValue(text="wet floor")) - setattr(cls, "water stains", - PermissibleValue(text="water stains")) - setattr(cls, "wall discoloration", - PermissibleValue(text="wall discoloration")) - setattr(cls, "floor discoloration", - PermissibleValue(text="floor discoloration")) - setattr(cls, "ceiling discoloration", - PermissibleValue(text="ceiling discoloration")) - setattr(cls, "peeling paint or wallpaper", - PermissibleValue(text="peeling paint or wallpaper")) - setattr(cls, "bulging walls", - PermissibleValue(text="bulging walls")) + setattr(cls, "bahama shutters", + PermissibleValue(text="bahama shutters")) + setattr(cls, "exterior roll blind", + PermissibleValue(text="exterior roll blind")) + setattr(cls, "gambrel awning", + PermissibleValue(text="gambrel awning")) + setattr(cls, "hood awning", + PermissibleValue(text="hood awning")) + setattr(cls, "porchroller awning", + PermissibleValue(text="porchroller awning")) + setattr(cls, "sarasota shutters", + PermissibleValue(text="sarasota shutters")) + setattr(cls, "slatted aluminum", + PermissibleValue(text="slatted aluminum")) + setattr(cls, "solid aluminum awning", + PermissibleValue(text="solid aluminum awning")) + setattr(cls, "sun screen", + PermissibleValue(text="sun screen")) + setattr(cls, "venetian awning", + PermissibleValue(text="venetian awning")) -class SampFloorEnum(EnumDefinitionImpl): +class QuadPosEnum(EnumDefinitionImpl): - basement = PermissibleValue(text="basement") - lobby = PermissibleValue(text="lobby") + _defn = EnumDefinition( + name="QuadPosEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "North side", + PermissibleValue(text="North side")) + setattr(cls, "West side", + PermissibleValue(text="West side")) + setattr(cls, "South side", + PermissibleValue(text="South side")) + setattr(cls, "East side", + PermissibleValue(text="East side")) + +class SrKerogTypeEnum(EnumDefinitionImpl): + + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="SampFloorEnum", + name="SrKerogTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "1st floor", - PermissibleValue(text="1st floor")) - setattr(cls, "2nd floor", - PermissibleValue(text="2nd floor")) + setattr(cls, "Type I", + PermissibleValue(text="Type I")) + setattr(cls, "Type II", + PermissibleValue(text="Type II")) + setattr(cls, "Type III", + PermissibleValue(text="Type III")) + setattr(cls, "Type IV", + PermissibleValue(text="Type IV")) + +class FloorCondEnum(EnumDefinitionImpl): + + new = PermissibleValue(text="new") + damaged = PermissibleValue(text="damaged") + rupture = PermissibleValue(text="rupture") + + _defn = EnumDefinition( + name="FloorCondEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) class HeatDelivLocEnum(EnumDefinitionImpl): @@ -8002,214 +7993,223 @@ class HeatDelivLocEnum(EnumDefinitionImpl): name="HeatDelivLocEnum", ) -class BiolStatEnum(EnumDefinitionImpl): +class HostSexEnum(EnumDefinitionImpl): - wild = PermissibleValue(text="wild") - natural = PermissibleValue(text="natural") - hybrid = PermissibleValue(text="hybrid") - mutant = PermissibleValue(text="mutant") + female = PermissibleValue(text="female") + hermaphrodite = PermissibleValue(text="hermaphrodite") + male = PermissibleValue(text="male") + neuter = PermissibleValue(text="neuter") _defn = EnumDefinition( - name="BiolStatEnum", + name="HostSexEnum", + ) + +class WindowCondEnum(EnumDefinitionImpl): + + damaged = PermissibleValue(text="damaged") + new = PermissibleValue(text="new") + rupture = PermissibleValue(text="rupture") + + _defn = EnumDefinition( + name="WindowCondEnum", ) @classmethod def _addvals(cls): - setattr(cls, "semi-natural", - PermissibleValue(text="semi-natural")) - setattr(cls, "inbred line", - PermissibleValue(text="inbred line")) - setattr(cls, "breeder's line", - PermissibleValue(text="breeder's line")) - setattr(cls, "clonal selection", - PermissibleValue(text="clonal selection")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) -class ShadingDeviceTypeEnum(EnumDefinitionImpl): +class HandidnessEnum(EnumDefinitionImpl): + + ambidexterity = PermissibleValue(text="ambidexterity") + + _defn = EnumDefinition( + name="HandidnessEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "left handedness", + PermissibleValue(text="left handedness")) + setattr(cls, "mixed-handedness", + PermissibleValue(text="mixed-handedness")) + setattr(cls, "right handedness", + PermissibleValue(text="right handedness")) - tree = PermissibleValue(text="tree") - trellis = PermissibleValue(text="trellis") +class WallConstTypeEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="ShadingDeviceTypeEnum", + name="WallConstTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "bahama shutters", - PermissibleValue(text="bahama shutters")) - setattr(cls, "exterior roll blind", - PermissibleValue(text="exterior roll blind")) - setattr(cls, "gambrel awning", - PermissibleValue(text="gambrel awning")) - setattr(cls, "hood awning", - PermissibleValue(text="hood awning")) - setattr(cls, "porchroller awning", - PermissibleValue(text="porchroller awning")) - setattr(cls, "sarasota shutters", - PermissibleValue(text="sarasota shutters")) - setattr(cls, "slatted aluminum", - PermissibleValue(text="slatted aluminum")) - setattr(cls, "solid aluminum awning", - PermissibleValue(text="solid aluminum awning")) - setattr(cls, "sun screen", - PermissibleValue(text="sun screen")) - setattr(cls, "venetian awning", - PermissibleValue(text="venetian awning")) + setattr(cls, "frame construction", + PermissibleValue(text="frame construction")) + setattr(cls, "joisted masonry", + PermissibleValue(text="joisted masonry")) + setattr(cls, "light noncombustible", + PermissibleValue(text="light noncombustible")) + setattr(cls, "masonry noncombustible", + PermissibleValue(text="masonry noncombustible")) + setattr(cls, "modified fire resistive", + PermissibleValue(text="modified fire resistive")) + setattr(cls, "fire resistive", + PermissibleValue(text="fire resistive")) -class TrainStatLocEnum(EnumDefinitionImpl): +class BuildOccupTypeEnum(EnumDefinitionImpl): - riverside = PermissibleValue(text="riverside") + office = PermissibleValue(text="office") + market = PermissibleValue(text="market") + restaurant = PermissibleValue(text="restaurant") + residence = PermissibleValue(text="residence") + school = PermissibleValue(text="school") + residential = PermissibleValue(text="residential") + commercial = PermissibleValue(text="commercial") + airport = PermissibleValue(text="airport") _defn = EnumDefinition( - name="TrainStatLocEnum", + name="BuildOccupTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "south station above ground", - PermissibleValue(text="south station above ground")) - setattr(cls, "south station underground", - PermissibleValue(text="south station underground")) - setattr(cls, "south station amtrak", - PermissibleValue(text="south station amtrak")) - setattr(cls, "forest hills", - PermissibleValue(text="forest hills")) + setattr(cls, "low rise", + PermissibleValue(text="low rise")) + setattr(cls, "high rise", + PermissibleValue(text="high rise")) + setattr(cls, "wood framed", + PermissibleValue(text="wood framed")) + setattr(cls, "health care", + PermissibleValue(text="health care")) + setattr(cls, "sports complex", + PermissibleValue(text="sports complex")) -class WindowMatEnum(EnumDefinitionImpl): +class OxyStatSampEnum(EnumDefinitionImpl): - clad = PermissibleValue(text="clad") - fiberglass = PermissibleValue(text="fiberglass") - metal = PermissibleValue(text="metal") - vinyl = PermissibleValue(text="vinyl") - wood = PermissibleValue(text="wood") + aerobic = PermissibleValue(text="aerobic") + anaerobic = PermissibleValue(text="anaerobic") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="WindowMatEnum", + name="OxyStatSampEnum", ) -class SampWeatherEnum(EnumDefinitionImpl): +class FilterTypeEnum(EnumDefinitionImpl): - cloudy = PermissibleValue(text="cloudy") - foggy = PermissibleValue(text="foggy") - hail = PermissibleValue(text="hail") - rain = PermissibleValue(text="rain") - snow = PermissibleValue(text="snow") - sleet = PermissibleValue(text="sleet") - sunny = PermissibleValue(text="sunny") - windy = PermissibleValue(text="windy") + HEPA = PermissibleValue(text="HEPA") + electrostatic = PermissibleValue(text="electrostatic") _defn = EnumDefinition( - name="SampWeatherEnum", + name="FilterTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "clear sky", - PermissibleValue(text="clear sky")) + setattr(cls, "particulate air filter", + PermissibleValue(text="particulate air filter")) + setattr(cls, "chemical air filter", + PermissibleValue(text="chemical air filter")) + setattr(cls, "low-MERV pleated media", + PermissibleValue(text="low-MERV pleated media")) + setattr(cls, "gas-phase or ultraviolet air treatments", + PermissibleValue(text="gas-phase or ultraviolet air treatments")) -class BioticRelationshipEnum(EnumDefinitionImpl): +class SampFloorEnum(EnumDefinitionImpl): - parasite = PermissibleValue(text="parasite") - commensal = PermissibleValue(text="commensal") - symbiont = PermissibleValue(text="symbiont") + basement = PermissibleValue(text="basement") + lobby = PermissibleValue(text="lobby") _defn = EnumDefinition( - name="BioticRelationshipEnum", + name="SampFloorEnum", ) @classmethod def _addvals(cls): - setattr(cls, "free living", - PermissibleValue(text="free living")) + setattr(cls, "1st floor", + PermissibleValue(text="1st floor")) + setattr(cls, "2nd floor", + PermissibleValue(text="2nd floor")) -class DoorCondEnum(EnumDefinitionImpl): +class FurnitureEnum(EnumDefinitionImpl): - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") + cabinet = PermissibleValue(text="cabinet") + chair = PermissibleValue(text="chair") + desks = PermissibleValue(text="desks") _defn = EnumDefinition( - name="DoorCondEnum", + name="FurnitureEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - -class TrainLineEnum(EnumDefinitionImpl): +class SampDisStageEnum(EnumDefinitionImpl): - red = PermissibleValue(text="red") - green = PermissibleValue(text="green") - orange = PermissibleValue(text="orange") + dissemination = PermissibleValue(text="dissemination") + infection = PermissibleValue(text="infection") + inoculation = PermissibleValue(text="inoculation") + penetration = PermissibleValue(text="penetration") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="TrainLineEnum", + name="SampDisStageEnum", ) -class BuildDocsEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "growth and reproduction", + PermissibleValue(text="growth and reproduction")) - schedule = PermissibleValue(text="schedule") - sections = PermissibleValue(text="sections") - submittals = PermissibleValue(text="submittals") - windows = PermissibleValue(text="windows") +class SubstructureTypeEnum(EnumDefinitionImpl): + + crawlspace = PermissibleValue(text="crawlspace") + basement = PermissibleValue(text="basement") _defn = EnumDefinition( - name="BuildDocsEnum", + name="SubstructureTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "building information model", - PermissibleValue(text="building information model")) - setattr(cls, "commissioning report", - PermissibleValue(text="commissioning report")) - setattr(cls, "complaint logs", - PermissibleValue(text="complaint logs")) - setattr(cls, "contract administration", - PermissibleValue(text="contract administration")) - setattr(cls, "cost estimate", - PermissibleValue(text="cost estimate")) - setattr(cls, "janitorial schedules or logs", - PermissibleValue(text="janitorial schedules or logs")) - setattr(cls, "maintenance plans", - PermissibleValue(text="maintenance plans")) - setattr(cls, "shop drawings", - PermissibleValue(text="shop drawings")) - setattr(cls, "ventilation system", - PermissibleValue(text="ventilation system")) + setattr(cls, "slab on grade", + PermissibleValue(text="slab on grade")) -class DoorLocEnum(EnumDefinitionImpl): +class DoorCompTypeEnum(EnumDefinitionImpl): - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") + revolving = PermissibleValue(text="revolving") + sliding = PermissibleValue(text="sliding") + telescopic = PermissibleValue(text="telescopic") _defn = EnumDefinition( - name="DoorLocEnum", + name="DoorCompTypeEnum", ) -class SrKerogTypeEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "metal covered", + PermissibleValue(text="metal covered")) - other = PermissibleValue(text="other") +class PlantGrowthMedEnum(EnumDefinitionImpl): + + perlite = PermissibleValue(text="perlite") + pumice = PermissibleValue(text="pumice") + sand = PermissibleValue(text="sand") + soil = PermissibleValue(text="soil") + vermiculite = PermissibleValue(text="vermiculite") + water = PermissibleValue(text="water") _defn = EnumDefinition( - name="SrKerogTypeEnum", + name="PlantGrowthMedEnum", ) @classmethod def _addvals(cls): - setattr(cls, "Type I", - PermissibleValue(text="Type I")) - setattr(cls, "Type II", - PermissibleValue(text="Type II")) - setattr(cls, "Type III", - PermissibleValue(text="Type III")) - setattr(cls, "Type IV", - PermissibleValue(text="Type IV")) + setattr(cls, "other artificial liquid medium", + PermissibleValue(text="other artificial liquid medium")) + setattr(cls, "other artificial solid medium", + PermissibleValue(text="other artificial solid medium")) + setattr(cls, "peat moss", + PermissibleValue(text="peat moss")) class SampleTypeEnum(EnumDefinitionImpl): @@ -10502,29 +10502,29 @@ class slots: slots.xylene = Slot(uri=MIXS['0000156'], name="xylene", curie=MIXS.curie('0000156'), model_uri=NMDC.xylene, domain=None, range=Optional[Union[dict, QuantityValue]]) -slots.investigation_field = Slot(uri=MIXS.investigation_field, name="investigation field", curie=MIXS.curie('investigation_field'), - model_uri=NMDC.investigation_field, domain=None, range=Optional[str]) +slots.has_unit = Slot(uri=MIXS.has_unit, name="has unit", curie=MIXS.curie('has_unit'), + model_uri=NMDC.has_unit, domain=None, range=Optional[str]) -slots.core_field = Slot(uri=MIXS.core_field, name="core field", curie=MIXS.curie('core_field'), - model_uri=NMDC.core_field, domain=None, range=Optional[str]) +slots.sequencing_field = Slot(uri=MIXS.sequencing_field, name="sequencing field", curie=MIXS.curie('sequencing_field'), + model_uri=NMDC.sequencing_field, domain=None, range=Optional[str]) -slots.nucleic_acid_sequence_source_field = Slot(uri=MIXS.nucleic_acid_sequence_source_field, name="nucleic acid sequence source field", curie=MIXS.curie('nucleic_acid_sequence_source_field'), - model_uri=NMDC.nucleic_acid_sequence_source_field, domain=None, range=Optional[str]) +slots.has_raw_value = Slot(uri=MIXS.has_raw_value, name="has raw value", curie=MIXS.curie('has_raw_value'), + model_uri=NMDC.has_raw_value, domain=None, range=Optional[str]) -slots.has_numeric_value = Slot(uri=MIXS.has_numeric_value, name="has numeric value", curie=MIXS.curie('has_numeric_value'), - model_uri=NMDC.has_numeric_value, domain=None, range=Optional[float]) +slots.core_field = Slot(uri=MIXS.core_field, name="core field", curie=MIXS.curie('core_field'), + model_uri=NMDC.core_field, domain=None, range=Optional[str]) slots.environment_field = Slot(uri=MIXS.environment_field, name="environment field", curie=MIXS.curie('environment_field'), model_uri=NMDC.environment_field, domain=None, range=Optional[str]) -slots.has_unit = Slot(uri=MIXS.has_unit, name="has unit", curie=MIXS.curie('has_unit'), - model_uri=NMDC.has_unit, domain=None, range=Optional[str]) +slots.has_numeric_value = Slot(uri=MIXS.has_numeric_value, name="has numeric value", curie=MIXS.curie('has_numeric_value'), + model_uri=NMDC.has_numeric_value, domain=None, range=Optional[float]) -slots.sequencing_field = Slot(uri=MIXS.sequencing_field, name="sequencing field", curie=MIXS.curie('sequencing_field'), - model_uri=NMDC.sequencing_field, domain=None, range=Optional[str]) +slots.nucleic_acid_sequence_source_field = Slot(uri=MIXS.nucleic_acid_sequence_source_field, name="nucleic acid sequence source field", curie=MIXS.curie('nucleic_acid_sequence_source_field'), + model_uri=NMDC.nucleic_acid_sequence_source_field, domain=None, range=Optional[str]) -slots.has_raw_value = Slot(uri=MIXS.has_raw_value, name="has raw value", curie=MIXS.curie('has_raw_value'), - model_uri=NMDC.has_raw_value, domain=None, range=Optional[str]) +slots.investigation_field = Slot(uri=MIXS.investigation_field, name="investigation field", curie=MIXS.curie('investigation_field'), + model_uri=NMDC.investigation_field, domain=None, range=Optional[str]) slots.emsl_store_temp = Slot(uri=NMDC.emsl_store_temp, name="emsl_store_temp", curie=NMDC.curie('emsl_store_temp'), model_uri=NMDC.emsl_store_temp, domain=None, range=Optional[str]) @@ -11378,7 +11378,7 @@ class slots: pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$')) slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), - model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) + model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[str], mappings = [PROV.used]) slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], diff --git a/nmdc_schema/nmdc.schema.json b/nmdc_schema/nmdc.schema.json index b3d909ce11..9fc084fa4f 100644 --- a/nmdc_schema/nmdc.schema.json +++ b/nmdc_schema/nmdc.schema.json @@ -1400,7 +1400,7 @@ }, "lat_lon": { "$ref": "#/$defs/GeolocationValue", - "description": "This is currently a required field but it's not clear if this should be required for human hosts" + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system" }, "lbc_thirty": { "$ref": "#/$defs/QuantityValue", @@ -8152,5 +8152,5 @@ }, "title": "NMDC", "type": "object", - "version": "v8.0.0" + "version": "v8.1.0" } \ No newline at end of file diff --git a/nmdc_schema/nmdc_materialized_patterns.schema.json b/nmdc_schema/nmdc_materialized_patterns.schema.json index e9eb9b8fc2..e9e80fa399 100644 --- a/nmdc_schema/nmdc_materialized_patterns.schema.json +++ b/nmdc_schema/nmdc_materialized_patterns.schema.json @@ -1400,7 +1400,7 @@ }, "lat_lon": { "$ref": "#/$defs/GeolocationValue", - "description": "This is currently a required field but it's not clear if this should be required for human hosts" + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system" }, "lbc_thirty": { "$ref": "#/$defs/QuantityValue", @@ -8152,5 +8152,5 @@ }, "title": "NMDC", "type": "object", - "version": "v8.0.0" + "version": "v8.1.0" } diff --git a/nmdc_schema/nmdc_materialized_patterns.yaml b/nmdc_schema/nmdc_materialized_patterns.yaml index 2f26913595..0c1b992946 100644 --- a/nmdc_schema/nmdc_materialized_patterns.yaml +++ b/nmdc_schema/nmdc_materialized_patterns.yaml @@ -11,7 +11,7 @@ notes: - not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1 id: https://w3id.org/nmdc/nmdc -version: v8.0.0 +version: v8.1.0 license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: CATH: @@ -347,6 +347,10 @@ types: string: name: string description: A character string + notes: + - In RDF serializations, a slot with range of string is treated as a literal or + type xsd:string. If you are authoring schemas in LinkML YAML, the type is + referenced with the lower case "string". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Text @@ -355,6 +359,9 @@ types: integer: name: integer description: An integer + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "integer". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Integer @@ -363,6 +370,9 @@ types: boolean: name: boolean description: A binary (true or false) value + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "boolean". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Boolean @@ -372,6 +382,9 @@ types: float: name: float description: A real number that conforms to the xsd:float specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "float". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Float @@ -380,6 +393,9 @@ types: double: name: double description: A real number that conforms to the xsd:double specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "double". from_schema: https://w3id.org/nmdc/nmdc close_mappings: - schema:Float @@ -389,6 +405,9 @@ types: name: decimal description: A real number with arbitrary precision that conforms to the xsd:decimal specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "decimal". from_schema: https://w3id.org/nmdc/nmdc broad_mappings: - schema:Number @@ -400,17 +419,21 @@ types: particular day notes: - URI is dateTime because OWL reasoners do not work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "time". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Time base: XSDTime - uri: xsd:dateTime + uri: xsd:time repr: str date: name: date description: a date (year, month and day) in an idealized calendar notes: - URI is dateTime because OWL reasoners don't work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Date @@ -420,6 +443,9 @@ types: datetime: name: datetime description: The combination of a date and time + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "datetime". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:DateTime @@ -429,6 +455,9 @@ types: date_or_datetime: name: date_or_datetime description: Either a date or a datetime + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date_or_datetime". from_schema: https://w3id.org/nmdc/nmdc base: str uri: linkml:DateOrDatetime @@ -436,6 +465,9 @@ types: uriorcurie: name: uriorcurie description: a URI or a CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uriorcurie". from_schema: https://w3id.org/nmdc/nmdc base: URIorCURIE uri: xsd:anyURI @@ -444,6 +476,9 @@ types: name: curie conforms_to: https://www.w3.org/TR/curie/ description: a compact URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "curie". comments: - in RDF serializations this MUST be expanded to a URI - in non-RDF serializations MAY be serialized as the compact representation @@ -455,6 +490,9 @@ types: name: uri conforms_to: https://www.ietf.org/rfc/rfc3987.txt description: a complete URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uri". comments: - in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which @@ -468,6 +506,9 @@ types: ncname: name: ncname description: Prefix part of CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "ncname". from_schema: https://w3id.org/nmdc/nmdc base: NCName uri: xsd:string @@ -475,8 +516,11 @@ types: objectidentifier: name: objectidentifier description: A URI or CURIE that represents an object in the model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "objectidentifier". comments: - - Used for inheritence and type checking + - Used for inheritance and type checking from_schema: https://w3id.org/nmdc/nmdc base: ElementIdentifier uri: shex:iri @@ -484,10 +528,52 @@ types: nodeidentifier: name: nodeidentifier description: A URI, CURIE or BNODE that represents a node in a model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "nodeidentifier". from_schema: https://w3id.org/nmdc/nmdc base: NodeIdentifier uri: shex:nonLiteral repr: str + jsonpointer: + name: jsonpointer + conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 + description: A string encoding a JSON Pointer. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to a valid object within the current + instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpointer". + from_schema: https://w3id.org/nmdc/nmdc + base: str + uri: xsd:string + repr: str + jsonpath: + name: jsonpath + conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html + description: A string encoding a JSON Path. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to zero or more valid objects within + the current instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpath". + from_schema: https://w3id.org/nmdc/nmdc + base: str + uri: xsd:string + repr: str + sparqlpath: + name: sparqlpath + conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths + description: A string encoding a SPARQL Property Path. The value of the string + MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects + within the current instance document when encoded as RDF. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "sparqlpath". + from_schema: https://w3id.org/nmdc/nmdc + base: str + uri: xsd:string + repr: str enums: StatusEnum: name: StatusEnum @@ -1190,26 +1276,6 @@ enums: text: soil water_extract_soil: text: water_extract_soil - door_direct_enum: - name: door_direct_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - inward: - text: inward - outward: - text: outward - sideways: - text: sideways - oxy_stat_samp_enum: - name: oxy_stat_samp_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - aerobic: - text: aerobic - anaerobic: - text: anaerobic - other: - text: other surf_air_cont_enum: name: surf_air_cont_enum from_schema: https://w3id.org/nmdc/nmdc @@ -1230,164 +1296,164 @@ enums: text: nutrients biocides: text: biocides - window_vert_pos_enum: - name: window_vert_pos_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - bottom: - text: bottom - middle: - text: middle - top: - text: top - low: - text: low - high: - text: high - filter_type_enum: - name: filter_type_enum + water_feat_type_enum: + name: water_feat_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - particulate air filter: - text: particulate air filter - chemical air filter: - text: chemical air filter - low-MERV pleated media: - text: low-MERV pleated media - HEPA: - text: HEPA - electrostatic: - text: electrostatic - gas-phase or ultraviolet air treatments: - text: gas-phase or ultraviolet air treatments - rel_samp_loc_enum: - name: rel_samp_loc_enum + fountain: + text: fountain + pool: + text: pool + standing feature: + text: standing feature + stream: + text: stream + waterfall: + text: waterfall + samp_collect_point_enum: + name: samp_collect_point_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - edge of car: - text: edge of car - center of car: - text: center of car - under a seat: - text: under a seat - sediment_type_enum: - name: sediment_type_enum + well: + text: well + test well: + text: test well + drilling rig: + text: drilling rig + wellhead: + text: wellhead + separator: + text: separator + storage tank: + text: storage tank + other: + text: other + floor_water_mold_enum: + name: floor_water_mold_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - biogenous: - text: biogenous - cosmogenous: - text: cosmogenous - hydrogenous: - text: hydrogenous - lithogenous: - text: lithogenous - occup_document_enum: - name: occup_document_enum + mold odor: + text: mold odor + wet floor: + text: wet floor + water stains: + text: water stains + wall discoloration: + text: wall discoloration + floor discoloration: + text: floor discoloration + ceiling discoloration: + text: ceiling discoloration + peeling paint or wallpaper: + text: peeling paint or wallpaper + bulging walls: + text: bulging walls + condensation: + text: condensation + wall_texture_enum: + name: wall_texture_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - automated count: - text: automated count - estimate: - text: estimate - manual count: - text: manual count - videos: - text: videos - room_connected_enum: - name: room_connected_enum + crows feet: + text: crows feet + crows-foot stomp: + text: crows-foot stomp + ? '' + : text: '' + double skip: + text: double skip + hawk and trowel: + text: hawk and trowel + knockdown: + text: knockdown + popcorn: + text: popcorn + orange peel: + text: orange peel + rosebud stomp: + text: rosebud stomp + Santa-Fe texture: + text: Santa-Fe texture + skip trowel: + text: skip trowel + smooth: + text: smooth + stomp knockdown: + text: stomp knockdown + swirl: + text: swirl + samp_subtype_enum: + name: samp_subtype_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - attic: - text: attic - bathroom: - text: bathroom - closet: - text: closet - conference room: - text: conference room - elevator: - text: elevator - examining room: - text: examining room - hallway: - text: hallway - kitchen: - text: kitchen - mail room: - text: mail room - office: - text: office - stairwell: - text: stairwell - quad_pos_enum: - name: quad_pos_enum + oil phase: + text: oil phase + water phase: + text: water phase + biofilm: + text: biofilm + not applicable: + text: not applicable + other: + text: other + drainage_class_enum: + name: drainage_class_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - North side: - text: North side - West side: - text: West side - South side: - text: South side - East side: - text: East side - sr_geol_age_enum: - name: sr_geol_age_enum + very poorly: + text: very poorly + poorly: + text: poorly + somewhat poorly: + text: somewhat poorly + moderately well: + text: moderately well + well: + text: well + excessively drained: + text: excessively drained + freq_clean_enum: + name: freq_clean_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Archean: - text: Archean - Cambrian: - text: Cambrian - Carboniferous: - text: Carboniferous - Cenozoic: - text: Cenozoic - Cretaceous: - text: Cretaceous - Devonian: - text: Devonian - Jurassic: - text: Jurassic - Mesozoic: - text: Mesozoic - Neogene: - text: Neogene - Ordovician: - text: Ordovician - Paleogene: - text: Paleogene - Paleozoic: - text: Paleozoic - Permian: - text: Permian - Precambrian: - text: Precambrian - Proterozoic: - text: Proterozoic - Silurian: - text: Silurian - Triassic: - text: Triassic + Daily: + text: Daily + Weekly: + text: Weekly + Monthly: + text: Monthly + Quarterly: + text: Quarterly + Annually: + text: Annually other: text: other - door_move_enum: - name: door_move_enum + biotic_relationship_enum: + name: biotic_relationship_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - collapsible: - text: collapsible - folding: - text: folding - revolving: - text: revolving - rolling shutter: - text: rolling shutter - sliding: - text: sliding - swinging: - text: swinging + free living: + text: free living + parasite: + text: parasite + commensal: + text: commensal + symbiont: + text: symbiont + light_type_enum: + name: light_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + natural light: + text: natural light + electric light: + text: electric light + desk lamp: + text: desk lamp + flourescent lights: + text: flourescent lights + none: + text: none cur_land_use_enum: name: cur_land_use_enum from_schema: https://w3id.org/nmdc/nmdc @@ -1583,142 +1649,146 @@ enums: value: vine crops (grapes) examples: - value: grapes - hcr_geol_age_enum: - name: hcr_geol_age_enum + drawings_enum: + name: drawings_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Archean: - text: Archean - Cambrian: - text: Cambrian - Carboniferous: - text: Carboniferous - Cenozoic: - text: Cenozoic - Cretaceous: - text: Cretaceous - Devonian: - text: Devonian - Jurassic: - text: Jurassic - Mesozoic: - text: Mesozoic - Neogene: - text: Neogene - Ordovician: - text: Ordovician - Paleogene: - text: Paleogene - Paleozoic: - text: Paleozoic - Permian: - text: Permian - Precambrian: - text: Precambrian - Proterozoic: - text: Proterozoic - Silurian: - text: Silurian - Triassic: - text: Triassic + operation: + text: operation + as built: + text: as built + construction: + text: construction + bid: + text: bid + design: + text: design + building navigation map: + text: building navigation map + diagram: + text: diagram + sketch: + text: sketch + indoor_surf_enum: + name: indoor_surf_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + cabinet: + text: cabinet + ceiling: + text: ceiling + counter top: + text: counter top + door: + text: door + shelving: + text: shelving + vent cover: + text: vent cover + window: + text: window + wall: + text: wall + samp_capt_status_enum: + name: samp_capt_status_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + active surveillance in response to an outbreak: + text: active surveillance in response to an outbreak + active surveillance not initiated by an outbreak: + text: active surveillance not initiated by an outbreak + farm sample: + text: farm sample + market sample: + text: market sample other: text: other - wall_const_type_enum: - name: wall_const_type_enum + room_loc_enum: + name: room_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - frame construction: - text: frame construction - joisted masonry: - text: joisted masonry - light noncombustible: - text: light noncombustible - masonry noncombustible: - text: masonry noncombustible - modified fire resistive: - text: modified fire resistive - fire resistive: - text: fire resistive - plant_sex_enum: - name: plant_sex_enum + corner room: + text: corner room + interior room: + text: interior room + exterior wall: + text: exterior wall + occup_document_enum: + name: occup_document_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Androdioecious: - text: Androdioecious - Androecious: - text: Androecious - Androgynous: - text: Androgynous - Androgynomonoecious: - text: Androgynomonoecious - Andromonoecious: - text: Andromonoecious - Bisexual: - text: Bisexual - Dichogamous: - text: Dichogamous - Diclinous: - text: Diclinous - Dioecious: - text: Dioecious - Gynodioecious: - text: Gynodioecious - Gynoecious: - text: Gynoecious - Gynomonoecious: - text: Gynomonoecious - Hermaphroditic: - text: Hermaphroditic - Imperfect: - text: Imperfect - Monoclinous: - text: Monoclinous - Monoecious: - text: Monoecious - Perfect: - text: Perfect - Polygamodioecious: - text: Polygamodioecious - Polygamomonoecious: - text: Polygamomonoecious - Polygamous: - text: Polygamous - Protandrous: - text: Protandrous - Protogynous: - text: Protogynous - Subandroecious: - text: Subandroecious - Subdioecious: - text: Subdioecious - Subgynoecious: - text: Subgynoecious - Synoecious: - text: Synoecious - Trimonoecious: - text: Trimonoecious - Trioecious: - text: Trioecious - Unisexual: - text: Unisexual - ceil_type_enum: - name: ceil_type_enum + automated count: + text: automated count + estimate: + text: estimate + manual count: + text: manual count + videos: + text: videos + arch_struc_enum: + name: arch_struc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - cathedral: - text: cathedral - dropped: - text: dropped - concave: - text: concave - barrel-shaped: - text: barrel-shaped - coffered: - text: coffered - cove: - text: cove - stretched: - text: stretched + building: + text: building + shed: + text: shed + home: + text: home + wall_finish_mat_enum: + name: wall_finish_mat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + plaster: + text: plaster + gypsum plaster: + text: gypsum plaster + veneer plaster: + text: veneer plaster + gypsum board: + text: gypsum board + tile: + text: tile + terrazzo: + text: terrazzo + stone facing: + text: stone facing + acoustical treatment: + text: acoustical treatment + wood: + text: wood + metal: + text: metal + masonry: + text: masonry + window_mat_enum: + name: window_mat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + clad: + text: clad + fiberglass: + text: fiberglass + metal: + text: metal + vinyl: + text: vinyl + wood: + text: wood + int_wall_cond_enum: + name: int_wall_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture floor_finish_mat_enum: name: floor_finish_mat_enum from_schema: https://w3id.org/nmdc/nmdc @@ -1759,584 +1829,240 @@ enums: text: paint none or unfinished: text: none or unfinished - wall_loc_enum: - name: wall_loc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - wall_surf_treatment_enum: - name: wall_surf_treatment_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - painted: - text: painted - wall paper: - text: wall paper - no treatment: - text: no treatment - paneling: - text: paneling - stucco: - text: stucco - fabric: - text: fabric - window_cond_enum: - name: window_cond_enum + build_docs_enum: + name: build_docs_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - door_mat_enum: - name: door_mat_enum + building information model: + text: building information model + commissioning report: + text: commissioning report + complaint logs: + text: complaint logs + contract administration: + text: contract administration + cost estimate: + text: cost estimate + janitorial schedules or logs: + text: janitorial schedules or logs + maintenance plans: + text: maintenance plans + schedule: + text: schedule + sections: + text: sections + shop drawings: + text: shop drawings + submittals: + text: submittals + ventilation system: + text: ventilation system + windows: + text: windows + surf_material_enum: + name: surf_material_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - aluminum: - text: aluminum - cellular PVC: - text: cellular PVC - engineered plastic: - text: engineered plastic - fiberboard: - text: fiberboard - fiberglass: - text: fiberglass + adobe: + text: adobe + carpet: + text: carpet + cinder blocks: + text: cinder blocks + concrete: + text: concrete + hay bales: + text: hay bales + glass: + text: glass metal: text: metal - thermoplastic alloy: - text: thermoplastic alloy + paint: + text: paint + plastic: + text: plastic + stainless steel: + text: stainless steel + stone: + text: stone + stucco: + text: stucco + tile: + text: tile vinyl: text: vinyl wood: text: wood - wood/plastic composite: - text: wood/plastic composite - soil_horizon_enum: - name: soil_horizon_enum + tidal_stage_enum: + name: tidal_stage_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - O horizon: - text: O horizon - A horizon: - text: A horizon - E horizon: - text: E horizon - B horizon: - text: B horizon - C horizon: - text: C horizon - R layer: - text: R layer - Permafrost: - text: Permafrost - M horizon: - text: M horizon - ceil_finish_mat_enum: - name: ceil_finish_mat_enum + low tide: + text: low tide + ebb tide: + text: ebb tide + flood tide: + text: flood tide + high tide: + text: high tide + window_horiz_pos_enum: + name: window_horiz_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - drywall: - text: drywall - mineral fibre: - text: mineral fibre - tiles: - text: tiles - PVC: - text: PVC - plasterboard: - text: plasterboard - metal: - text: metal - fiberglass: - text: fiberglass - stucco: - text: stucco - mineral wool/calcium silicate: - text: mineral wool/calcium silicate - wood: - text: wood - shading_device_cond_enum: - name: shading_device_cond_enum + left: + text: left + middle: + text: middle + right: + text: right + train_stop_loc_enum: + name: train_stop_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - hc_produced_enum: - name: hc_produced_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Oil: - text: Oil - Gas-Condensate: - text: Gas-Condensate - Gas: - text: Gas - Bitumen: - text: Bitumen - Coalbed Methane: - text: Coalbed Methane - other: - text: other - door_comp_type_enum: - name: door_comp_type_enum + end: + text: end + mid: + text: mid + downtown: + text: downtown + train_line_enum: + name: train_line_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - metal covered: - text: metal covered - revolving: - text: revolving - sliding: - text: sliding - telescopic: - text: telescopic - window_loc_enum: - name: window_loc_enum + red: + text: red + green: + text: green + orange: + text: orange + train_stat_loc_enum: + name: train_stat_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - sr_lithology_enum: - name: sr_lithology_enum + south station above ground: + text: south station above ground + south station underground: + text: south station underground + south station amtrak: + text: south station amtrak + forest hills: + text: forest hills + riverside: + text: riverside + sr_dep_env_enum: + name: sr_dep_env_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Clastic: - text: Clastic - Carbonate: - text: Carbonate - Coal: - text: Coal - Biosilicieous: - text: Biosilicieous + Lacustine: + text: Lacustine + Fluvioldeltaic: + text: Fluvioldeltaic + Fluviomarine: + text: Fluviomarine + Marine: + text: Marine other: text: other - plant_growth_med_enum: - name: plant_growth_med_enum + samp_weather_enum: + name: samp_weather_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - other artificial liquid medium: - text: other artificial liquid medium - other artificial solid medium: - text: other artificial solid medium - peat moss: - text: peat moss - perlite: - text: perlite - pumice: - text: pumice - sand: - text: sand - soil: - text: soil - vermiculite: - text: vermiculite - water: - text: water - surf_material_enum: - name: surf_material_enum + clear sky: + text: clear sky + cloudy: + text: cloudy + foggy: + text: foggy + hail: + text: hail + rain: + text: rain + snow: + text: snow + sleet: + text: sleet + sunny: + text: sunny + windy: + text: windy + window_cover_enum: + name: window_cover_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - adobe: - text: adobe - carpet: - text: carpet - cinder blocks: - text: cinder blocks - concrete: - text: concrete - hay bales: - text: hay bales - glass: - text: glass - metal: - text: metal - paint: - text: paint - plastic: - text: plastic - stainless steel: - text: stainless steel - stone: - text: stone - stucco: - text: stucco - tile: - text: tile - vinyl: - text: vinyl - wood: - text: wood - ceil_cond_enum: - name: ceil_cond_enum + blinds: + text: blinds + curtains: + text: curtains + none: + text: none + room_type_enum: + name: room_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - building_setting_enum: - name: building_setting_enum + attic: + text: attic + bathroom: + text: bathroom + closet: + text: closet + conference room: + text: conference room + elevator: + text: elevator + examining room: + text: examining room + hallway: + text: hallway + kitchen: + text: kitchen + mail room: + text: mail room + private office: + text: private office + open office: + text: open office + stairwell: + text: stairwell + ',restroom': + text: ',restroom' + lobby: + text: lobby + vestibule: + text: vestibule + mechanical or electrical room: + text: mechanical or electrical room + data center: + text: data center + laboratory_wet: + text: laboratory_wet + laboratory_dry: + text: laboratory_dry + gymnasium: + text: gymnasium + natatorium: + text: natatorium + auditorium: + text: auditorium + lockers: + text: lockers + cafe: + text: cafe + warehouse: + text: warehouse + sediment_type_enum: + name: sediment_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - urban: - text: urban - suburban: - text: suburban - exurban: - text: exurban - rural: - text: rural - build_occup_type_enum: - name: build_occup_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - office: - text: office - market: - text: market - restaurant: - text: restaurant - residence: - text: residence - school: - text: school - residential: - text: residential - commercial: - text: commercial - low rise: - text: low rise - high rise: - text: high rise - wood framed: - text: wood framed - health care: - text: health care - airport: - text: airport - sports complex: - text: sports complex - depos_env_enum: - name: depos_env_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Continental - Alluvial: - text: Continental - Alluvial - Continental - Aeolian: - text: Continental - Aeolian - Continental - Fluvial: - text: Continental - Fluvial - Continental - Lacustrine: - text: Continental - Lacustrine - Transitional - Deltaic: - text: Transitional - Deltaic - Transitional - Tidal: - text: Transitional - Tidal - Transitional - Lagoonal: - text: Transitional - Lagoonal - Transitional - Beach: - text: Transitional - Beach - Transitional - Lake: - text: Transitional - Lake - Marine - Shallow: - text: Marine - Shallow - Marine - Deep: - text: Marine - Deep - Marine - Reef: - text: Marine - Reef - Other - Evaporite: - text: Other - Evaporite - Other - Glacial: - text: Other - Glacial - Other - Volcanic: - text: Other - Volcanic - other: - text: other - profile_position_enum: - name: profile_position_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - summit: - text: summit - shoulder: - text: shoulder - backslope: - text: backslope - footslope: - text: footslope - toeslope: - text: toeslope - furniture_enum: - name: furniture_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - cabinet: - text: cabinet - chair: - text: chair - desks: - text: desks - door_type_enum: - name: door_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - composite: - text: composite - metal: - text: metal - wooden: - text: wooden - tidal_stage_enum: - name: tidal_stage_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - low tide: - text: low tide - ebb tide: - text: ebb tide - flood tide: - text: flood tide - high tide: - text: high tide - door_type_metal_enum: - name: door_type_metal_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - collapsible: - text: collapsible - corrugated steel: - text: corrugated steel - hollow: - text: hollow - rolling shutters: - text: rolling shutters - steel plate: - text: steel plate - handidness_enum: - name: handidness_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - ambidexterity: - text: ambidexterity - left handedness: - text: left handedness - mixed-handedness: - text: mixed-handedness - right handedness: - text: right handedness - tillage_enum: - name: tillage_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - drill: - text: drill - cutting disc: - text: cutting disc - ridge till: - text: ridge till - strip tillage: - text: strip tillage - zonal tillage: - text: zonal tillage - chisel: - text: chisel - tined: - text: tined - mouldboard: - text: mouldboard - disc plough: - text: disc plough - hcr_enum: - name: hcr_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Oil Reservoir: - text: Oil Reservoir - Gas Reservoir: - text: Gas Reservoir - Oil Sand: - text: Oil Sand - Coalbed: - text: Coalbed - Shale: - text: Shale - Tight Oil Reservoir: - text: Tight Oil Reservoir - Tight Gas Reservoir: - text: Tight Gas Reservoir - other: - text: other - freq_clean_enum: - name: freq_clean_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Daily: - text: Daily - Weekly: - text: Weekly - Monthly: - text: Monthly - Quarterly: - text: Quarterly - Annually: - text: Annually - other: - text: other - growth_habit_enum: - name: growth_habit_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - erect: - text: erect - semi-erect: - text: semi-erect - spreading: - text: spreading - prostrate: - text: prostrate - season_use_enum: - name: season_use_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Spring: - text: Spring - Summer: - text: Summer - Fall: - text: Fall - Winter: - text: Winter - sr_dep_env_enum: - name: sr_dep_env_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Lacustine: - text: Lacustine - Fluvioldeltaic: - text: Fluvioldeltaic - Fluviomarine: - text: Fluviomarine - Marine: - text: Marine - other: - text: other - water_feat_type_enum: - name: water_feat_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - fountain: - text: fountain - pool: - text: pool - standing feature: - text: standing feature - stream: - text: stream - waterfall: - text: waterfall - substructure_type_enum: - name: substructure_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - crawlspace: - text: crawlspace - slab on grade: - text: slab on grade - basement: - text: basement - indoor_space_enum: - name: indoor_space_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - bedroom: - text: bedroom - office: - text: office - bathroom: - text: bathroom - foyer: - text: foyer - kitchen: - text: kitchen - locker room: - text: locker room - hallway: - text: hallway - elevator: - text: elevator - host_sex_enum: - name: host_sex_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - female: - text: female - hermaphrodite: - text: hermaphrodite - male: - text: male - neuter: - text: neuter - window_type_enum: - name: window_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - single-hung sash window: - text: single-hung sash window - horizontal sash window: - text: horizontal sash window - fixed window: - text: fixed window - specific_enum: - name: specific_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - photos: - text: photos - fao_class_enum: - name: fao_class_enum + biogenous: + text: biogenous + cosmogenous: + text: cosmogenous + hydrogenous: + text: hydrogenous + lithogenous: + text: lithogenous + fao_class_enum: + name: fao_class_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: Acrisols: @@ -2391,166 +2117,404 @@ enums: text: Vertisols Yermosols: text: Yermosols - floor_struc_enum: - name: floor_struc_enum + ext_window_orient_enum: + name: ext_window_orient_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - balcony: - text: balcony - floating floor: - text: floating floor - glass floor: - text: glass floor - raised floor: - text: raised floor - sprung floor: - text: sprung floor - wood-framed: - text: wood-framed - concrete: - text: concrete - wall_texture_enum: - name: wall_texture_enum + north: + text: north + south: + text: south + east: + text: east + west: + text: west + northeast: + text: northeast + southeast: + text: southeast + southwest: + text: southwest + northwest: + text: northwest + sr_geol_age_enum: + name: sr_geol_age_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + Archean: + text: Archean + Cambrian: + text: Cambrian + Carboniferous: + text: Carboniferous + Cenozoic: + text: Cenozoic + Cretaceous: + text: Cretaceous + Devonian: + text: Devonian + Jurassic: + text: Jurassic + Mesozoic: + text: Mesozoic + Neogene: + text: Neogene + Ordovician: + text: Ordovician + Paleogene: + text: Paleogene + Paleozoic: + text: Paleozoic + Permian: + text: Permian + Precambrian: + text: Precambrian + Proterozoic: + text: Proterozoic + Silurian: + text: Silurian + Triassic: + text: Triassic + other: + text: other + door_move_enum: + name: door_move_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + collapsible: + text: collapsible + folding: + text: folding + revolving: + text: revolving + rolling shutter: + text: rolling shutter + sliding: + text: sliding + swinging: + text: swinging + door_direct_enum: + name: door_direct_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + inward: + text: inward + outward: + text: outward + sideways: + text: sideways + ceil_texture_enum: + name: ceil_texture_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + crows feet: + text: crows feet + crows-foot stomp: + text: crows-foot stomp + double skip: + text: double skip + hawk and trowel: + text: hawk and trowel + knockdown: + text: knockdown + popcorn: + text: popcorn + orange peel: + text: orange peel + rosebud stomp: + text: rosebud stomp + Santa-Fe texture: + text: Santa-Fe texture + skip trowel: + text: skip trowel + smooth: + text: smooth + stomp knockdown: + text: stomp knockdown + swirl: + text: swirl + samp_md_enum: + name: samp_md_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + DF: + text: DF + RT: + text: RT + KB: + text: KB + MSL: + text: MSL + other: + text: other + ceil_type_enum: + name: ceil_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + cathedral: + text: cathedral + dropped: + text: dropped + concave: + text: concave + barrel-shaped: + text: barrel-shaped + coffered: + text: coffered + cove: + text: cove + stretched: + text: stretched + wall_loc_enum: + name: wall_loc_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + north: + text: north + south: + text: south + east: + text: east + west: + text: west + door_type_metal_enum: + name: door_type_metal_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + collapsible: + text: collapsible + corrugated steel: + text: corrugated steel + hollow: + text: hollow + rolling shutters: + text: rolling shutters + steel plate: + text: steel plate + gender_restroom_enum: + name: gender_restroom_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + all gender: + text: all gender + female: + text: female + gender neurtral: + text: gender neurtral + male: + text: male + male and female: + text: male and female + unisex: + text: unisex + vis_media_enum: + name: vis_media_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - ? '' - : text: '' - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - train_stop_loc_enum: - name: train_stop_loc_enum + photos: + text: photos + videos: + text: videos + commonly of the building: + text: commonly of the building + site context (adjacent buildings, vegetation, terrain, streets): + text: site context (adjacent buildings, vegetation, terrain, streets) + interiors: + text: interiors + equipment: + text: equipment + 3D scans: + text: 3D scans + window_loc_enum: + name: window_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - end: - text: end - mid: - text: mid - downtown: - text: downtown - drawings_enum: - name: drawings_enum + north: + text: north + south: + text: south + east: + text: east + west: + text: west + soil_horizon_enum: + name: soil_horizon_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - building navigation map: - text: building navigation map - diagram: - text: diagram - sketch: - text: sketch - room_loc_enum: - name: room_loc_enum + O horizon: + text: O horizon + A horizon: + text: A horizon + E horizon: + text: E horizon + B horizon: + text: B horizon + C horizon: + text: C horizon + R layer: + text: R layer + Permafrost: + text: Permafrost + M horizon: + text: M horizon + indoor_space_enum: + name: indoor_space_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - corner room: - text: corner room - interior room: - text: interior room - exterior wall: - text: exterior wall - light_type_enum: - name: light_type_enum + bedroom: + text: bedroom + office: + text: office + bathroom: + text: bathroom + foyer: + text: foyer + kitchen: + text: kitchen + locker room: + text: locker room + hallway: + text: hallway + elevator: + text: elevator + door_type_enum: + name: door_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - natural light: - text: natural light - electric light: - text: electric light - desk lamp: - text: desk lamp - flourescent lights: - text: flourescent lights - none: - text: none - weekday_enum: - name: weekday_enum + composite: + text: composite + metal: + text: metal + wooden: + text: wooden + depos_env_enum: + name: depos_env_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Monday: - text: Monday - Tuesday: - text: Tuesday - Wednesday: - text: Wednesday - Thursday: - text: Thursday - Friday: - text: Friday - Saturday: - text: Saturday - Sunday: - text: Sunday - arch_struc_enum: - name: arch_struc_enum + Continental - Alluvial: + text: Continental - Alluvial + Continental - Aeolian: + text: Continental - Aeolian + Continental - Fluvial: + text: Continental - Fluvial + Continental - Lacustrine: + text: Continental - Lacustrine + Transitional - Deltaic: + text: Transitional - Deltaic + Transitional - Tidal: + text: Transitional - Tidal + Transitional - Lagoonal: + text: Transitional - Lagoonal + Transitional - Beach: + text: Transitional - Beach + Transitional - Lake: + text: Transitional - Lake + Marine - Shallow: + text: Marine - Shallow + Marine - Deep: + text: Marine - Deep + Marine - Reef: + text: Marine - Reef + Other - Evaporite: + text: Other - Evaporite + Other - Glacial: + text: Other - Glacial + Other - Volcanic: + text: Other - Volcanic + other: + text: other + sr_lithology_enum: + name: sr_lithology_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - building: - text: building - shed: - text: shed - home: - text: home - heat_cool_type_enum: - name: heat_cool_type_enum + Clastic: + text: Clastic + Carbonate: + text: Carbonate + Coal: + text: Coal + Biosilicieous: + text: Biosilicieous + other: + text: other + plant_sex_enum: + name: plant_sex_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - radiant system: - text: radiant system - heat pump: - text: heat pump - forced air system: - text: forced air system - steam forced heat: - text: steam forced heat - wood stove: - text: wood stove - samp_md_enum: - name: samp_md_enum + Androdioecious: + text: Androdioecious + Androecious: + text: Androecious + Androgynous: + text: Androgynous + Androgynomonoecious: + text: Androgynomonoecious + Andromonoecious: + text: Andromonoecious + Bisexual: + text: Bisexual + Dichogamous: + text: Dichogamous + Diclinous: + text: Diclinous + Dioecious: + text: Dioecious + Gynodioecious: + text: Gynodioecious + Gynoecious: + text: Gynoecious + Gynomonoecious: + text: Gynomonoecious + Hermaphroditic: + text: Hermaphroditic + Imperfect: + text: Imperfect + Monoclinous: + text: Monoclinous + Monoecious: + text: Monoecious + Perfect: + text: Perfect + Polygamodioecious: + text: Polygamodioecious + Polygamomonoecious: + text: Polygamomonoecious + Polygamous: + text: Polygamous + Protandrous: + text: Protandrous + Protogynous: + text: Protogynous + Subandroecious: + text: Subandroecious + Subdioecious: + text: Subdioecious + Subgynoecious: + text: Subgynoecious + Synoecious: + text: Synoecious + Trimonoecious: + text: Trimonoecious + Trioecious: + text: Trioecious + Unisexual: + text: Unisexual + specific_enum: + name: specific_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - DF: - text: DF - RT: - text: RT - KB: - text: KB - MSL: - text: MSL - other: - text: other + operation: + text: operation + as built: + text: as built + construction: + text: construction + bid: + text: bid + design: + text: design + photos: + text: photos ext_wall_orient_enum: name: ext_wall_orient_enum from_schema: https://w3id.org/nmdc/nmdc @@ -2571,30 +2535,8 @@ enums: text: southwest northwest: text: northwest - mech_struc_enum: - name: mech_struc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - subway: - text: subway - coach: - text: coach - carriage: - text: carriage - elevator: - text: elevator - escalator: - text: escalator - boat: - text: boat - train: - text: train - car: - text: car - bus: - text: bus - ext_window_orient_enum: - name: ext_window_orient_enum + door_loc_enum: + name: door_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: north: @@ -2605,164 +2547,224 @@ enums: text: east west: text: west - northeast: - text: northeast - southeast: - text: southeast - southwest: - text: southwest - northwest: - text: northwest - window_cover_enum: - name: window_cover_enum + profile_position_enum: + name: profile_position_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - blinds: - text: blinds - curtains: - text: curtains - none: - text: none - drainage_class_enum: - name: drainage_class_enum + summit: + text: summit + shoulder: + text: shoulder + backslope: + text: backslope + footslope: + text: footslope + toeslope: + text: toeslope + growth_habit_enum: + name: growth_habit_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - very poorly: - text: very poorly - poorly: - text: poorly - somewhat poorly: - text: somewhat poorly - moderately well: - text: moderately well - well: - text: well - excessively drained: - text: excessively drained - window_horiz_pos_enum: - name: window_horiz_pos_enum + erect: + text: erect + semi-erect: + text: semi-erect + spreading: + text: spreading + prostrate: + text: prostrate + season_use_enum: + name: season_use_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - left: - text: left - middle: - text: middle - right: - text: right - samp_subtype_enum: - name: samp_subtype_enum + Spring: + text: Spring + Summer: + text: Summer + Fall: + text: Fall + Winter: + text: Winter + ceil_finish_mat_enum: + name: ceil_finish_mat_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - oil phase: - text: oil phase - water phase: - text: water phase - biofilm: - text: biofilm - not applicable: - text: not applicable - other: - text: other - ceil_texture_enum: - name: ceil_texture_enum + drywall: + text: drywall + mineral fibre: + text: mineral fibre + tiles: + text: tiles + PVC: + text: PVC + plasterboard: + text: plasterboard + metal: + text: metal + fiberglass: + text: fiberglass + stucco: + text: stucco + mineral wool/calcium silicate: + text: mineral wool/calcium silicate + wood: + text: wood + tillage_enum: + name: tillage_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - room_samp_pos_enum: - name: room_samp_pos_enum + drill: + text: drill + cutting disc: + text: cutting disc + ridge till: + text: ridge till + strip tillage: + text: strip tillage + zonal tillage: + text: zonal tillage + chisel: + text: chisel + tined: + text: tined + mouldboard: + text: mouldboard + disc plough: + text: disc plough + window_type_enum: + name: window_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + single-hung sash window: + text: single-hung sash window + horizontal sash window: + text: horizontal sash window + fixed window: + text: fixed window + ceil_cond_enum: + name: ceil_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture + hcr_geol_age_enum: + name: hcr_geol_age_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north corner: - text: north corner - south corner: - text: south corner - west corner: - text: west corner - east corner: - text: east corner - northeast corner: - text: northeast corner - northwest corner: - text: northwest corner - southeast corner: - text: southeast corner - southwest corner: - text: southwest corner - center: - text: center - indoor_surf_enum: - name: indoor_surf_enum + Archean: + text: Archean + Cambrian: + text: Cambrian + Carboniferous: + text: Carboniferous + Cenozoic: + text: Cenozoic + Cretaceous: + text: Cretaceous + Devonian: + text: Devonian + Jurassic: + text: Jurassic + Mesozoic: + text: Mesozoic + Neogene: + text: Neogene + Ordovician: + text: Ordovician + Paleogene: + text: Paleogene + Paleozoic: + text: Paleozoic + Permian: + text: Permian + Precambrian: + text: Precambrian + Proterozoic: + text: Proterozoic + Silurian: + text: Silurian + Triassic: + text: Triassic + other: + text: other + door_cond_enum: + name: door_cond_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - cabinet: - text: cabinet - ceiling: - text: ceiling - counter top: - text: counter top - door: - text: door - shelving: - text: shelving - vent cover: - text: vent cover - window: - text: window - wall: - text: wall - organism_count_enum: - name: organism_count_enum + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + lithology_enum: + name: lithology_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - ATP: - text: ATP - MPN: - text: MPN + Basement: + text: Basement + Chalk: + text: Chalk + Chert: + text: Chert + Coal: + text: Coal + Conglomerate: + text: Conglomerate + Diatomite: + text: Diatomite + Dolomite: + text: Dolomite + Limestone: + text: Limestone + Sandstone: + text: Sandstone + Shale: + text: Shale + Siltstone: + text: Siltstone + Volcanic: + text: Volcanic other: text: other - vis_media_enum: - name: vis_media_enum + heat_cool_type_enum: + name: heat_cool_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - photos: - text: photos - videos: - text: videos - commonly of the building: - text: commonly of the building - site context (adjacent buildings, vegetation, terrain, streets): - text: site context (adjacent buildings, vegetation, terrain, streets) - interiors: - text: interiors - equipment: - text: equipment - 3D scans: - text: 3D scans + radiant system: + text: radiant system + heat pump: + text: heat pump + forced air system: + text: forced air system + steam forced heat: + text: steam forced heat + wood stove: + text: wood stove + building_setting_enum: + name: building_setting_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + urban: + text: urban + suburban: + text: suburban + exurban: + text: exurban + rural: + text: rural room_condt_enum: name: room_condt_enum from_schema: https://w3id.org/nmdc/nmdc @@ -2779,40 +2781,34 @@ enums: text: rupture visible signs of mold/mildew: text: visible signs of mold/mildew - samp_collect_point_enum: - name: samp_collect_point_enum + rel_samp_loc_enum: + name: rel_samp_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - well: - text: well - test well: - text: test well - drilling rig: - text: drilling rig - wellhead: - text: wellhead - separator: - text: separator - storage tank: - text: storage tank - other: - text: other - samp_capt_status_enum: - name: samp_capt_status_enum + edge of car: + text: edge of car + center of car: + text: center of car + under a seat: + text: under a seat + wall_surf_treatment_enum: + name: wall_surf_treatment_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - active surveillance in response to an outbreak: - text: active surveillance in response to an outbreak - active surveillance not initiated by an outbreak: - text: active surveillance not initiated by an outbreak - farm sample: - text: farm sample - market sample: - text: market sample - other: - text: other - room_type_enum: - name: room_type_enum + painted: + text: painted + wall paper: + text: wall paper + no treatment: + text: no treatment + paneling: + text: paneling + stucco: + text: stucco + fabric: + text: fabric + room_connected_enum: + name: room_connected_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: attic: @@ -2829,102 +2825,130 @@ enums: text: examining room hallway: text: hallway - kitchen: - text: kitchen - mail room: - text: mail room - private office: - text: private office - open office: - text: open office - stairwell: - text: stairwell - ',restroom': - text: ',restroom' - lobby: - text: lobby - vestibule: - text: vestibule - mechanical or electrical room: - text: mechanical or electrical room - data center: - text: data center - laboratory_wet: - text: laboratory_wet - laboratory_dry: - text: laboratory_dry - gymnasium: - text: gymnasium - natatorium: - text: natatorium - auditorium: - text: auditorium - lockers: - text: lockers - cafe: - text: cafe - warehouse: - text: warehouse - samp_dis_stage_enum: - name: samp_dis_stage_enum + kitchen: + text: kitchen + mail room: + text: mail room + office: + text: office + stairwell: + text: stairwell + window_vert_pos_enum: + name: window_vert_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - dissemination: - text: dissemination - growth and reproduction: - text: growth and reproduction - infection: - text: infection - inoculation: - text: inoculation - penetration: - text: penetration - other: - text: other - floor_cond_enum: - name: floor_cond_enum + bottom: + text: bottom + middle: + text: middle + top: + text: top + low: + text: low + high: + text: high + weekday_enum: + name: weekday_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - lithology_enum: - name: lithology_enum + Monday: + text: Monday + Tuesday: + text: Tuesday + Wednesday: + text: Wednesday + Thursday: + text: Thursday + Friday: + text: Friday + Saturday: + text: Saturday + Sunday: + text: Sunday + room_samp_pos_enum: + name: room_samp_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Basement: - text: Basement - Chalk: - text: Chalk - Chert: - text: Chert - Coal: - text: Coal - Conglomerate: - text: Conglomerate - Diatomite: - text: Diatomite - Dolomite: - text: Dolomite - Limestone: - text: Limestone - Sandstone: - text: Sandstone - Shale: - text: Shale - Siltstone: - text: Siltstone - Volcanic: - text: Volcanic - other: - text: other + north corner: + text: north corner + south corner: + text: south corner + west corner: + text: west corner + east corner: + text: east corner + northeast corner: + text: northeast corner + northwest corner: + text: northwest corner + southeast corner: + text: southeast corner + southwest corner: + text: southwest corner + center: + text: center + door_mat_enum: + name: door_mat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + aluminum: + text: aluminum + cellular PVC: + text: cellular PVC + engineered plastic: + text: engineered plastic + fiberboard: + text: fiberboard + fiberglass: + text: fiberglass + metal: + text: metal + thermoplastic alloy: + text: thermoplastic alloy + vinyl: + text: vinyl + wood: + text: wood + wood/plastic composite: + text: wood/plastic composite + biol_stat_enum: + name: biol_stat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + wild: + text: wild + natural: + text: natural + semi-natural: + text: semi-natural + inbred line: + text: inbred line + breeder's line: + text: breeder's line + hybrid: + text: hybrid + clonal selection: + text: clonal selection + mutant: + text: mutant + floor_struc_enum: + name: floor_struc_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + balcony: + text: balcony + floating floor: + text: floating floor + glass floor: + text: glass floor + raised floor: + text: raised floor + sprung floor: + text: sprung floor + wood-framed: + text: wood-framed + concrete: + text: concrete door_type_wood_enum: name: door_type_wood_enum from_schema: https://w3id.org/nmdc/nmdc @@ -2949,128 +2973,88 @@ enums: text: louvered wire gauged: text: wire gauged - wall_finish_mat_enum: - name: wall_finish_mat_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - plaster: - text: plaster - gypsum plaster: - text: gypsum plaster - veneer plaster: - text: veneer plaster - gypsum board: - text: gypsum board - tile: - text: tile - terrazzo: - text: terrazzo - stone facing: - text: stone facing - acoustical treatment: - text: acoustical treatment - wood: - text: wood - metal: - text: metal - masonry: - text: masonry - gender_restroom_enum: - name: gender_restroom_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - all gender: - text: all gender - female: - text: female - gender neurtral: - text: gender neurtral - male: - text: male - male and female: - text: male and female - unisex: - text: unisex - int_wall_cond_enum: - name: int_wall_cond_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - floor_water_mold_enum: - name: floor_water_mold_enum + organism_count_enum: + name: organism_count_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - mold odor: - text: mold odor - wet floor: - text: wet floor - water stains: - text: water stains - wall discoloration: - text: wall discoloration - floor discoloration: - text: floor discoloration - ceiling discoloration: - text: ceiling discoloration - peeling paint or wallpaper: - text: peeling paint or wallpaper - bulging walls: - text: bulging walls - condensation: - text: condensation - samp_floor_enum: - name: samp_floor_enum + ATP: + text: ATP + MPN: + text: MPN + other: + text: other + shading_device_cond_enum: + name: shading_device_cond_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - 1st floor: - text: 1st floor - 2nd floor: - text: 2nd floor - basement: - text: basement - lobby: - text: lobby - heat_deliv_loc_enum: - name: heat_deliv_loc_enum + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + hcr_enum: + name: hcr_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - biol_stat_enum: - name: biol_stat_enum + Oil Reservoir: + text: Oil Reservoir + Gas Reservoir: + text: Gas Reservoir + Oil Sand: + text: Oil Sand + Coalbed: + text: Coalbed + Shale: + text: Shale + Tight Oil Reservoir: + text: Tight Oil Reservoir + Tight Gas Reservoir: + text: Tight Gas Reservoir + other: + text: other + mech_struc_enum: + name: mech_struc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - wild: - text: wild - natural: - text: natural - semi-natural: - text: semi-natural - inbred line: - text: inbred line - breeder's line: - text: breeder's line - hybrid: - text: hybrid - clonal selection: - text: clonal selection - mutant: - text: mutant + subway: + text: subway + coach: + text: coach + carriage: + text: carriage + elevator: + text: elevator + escalator: + text: escalator + boat: + text: boat + train: + text: train + car: + text: car + bus: + text: bus + hc_produced_enum: + name: hc_produced_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + Oil: + text: Oil + Gas-Condensate: + text: Gas-Condensate + Gas: + text: Gas + Bitumen: + text: Bitumen + Coalbed Methane: + text: Coalbed Methane + other: + text: other shading_device_type_enum: name: shading_device_type_enum from_schema: https://w3id.org/nmdc/nmdc @@ -3099,148 +3083,250 @@ enums: text: trellis venetian awning: text: venetian awning - train_stat_loc_enum: - name: train_stat_loc_enum + quad_pos_enum: + name: quad_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - south station above ground: - text: south station above ground - south station underground: - text: south station underground - south station amtrak: - text: south station amtrak - forest hills: - text: forest hills - riverside: - text: riverside - window_mat_enum: - name: window_mat_enum + North side: + text: North side + West side: + text: West side + South side: + text: South side + East side: + text: East side + sr_kerog_type_enum: + name: sr_kerog_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - clad: - text: clad - fiberglass: - text: fiberglass - metal: - text: metal - vinyl: - text: vinyl - wood: - text: wood - samp_weather_enum: - name: samp_weather_enum + Type I: + text: Type I + Type II: + text: Type II + Type III: + text: Type III + Type IV: + text: Type IV + other: + text: other + floor_cond_enum: + name: floor_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture + heat_deliv_loc_enum: + name: heat_deliv_loc_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + north: + text: north + south: + text: south + east: + text: east + west: + text: west + host_sex_enum: + name: host_sex_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + female: + text: female + hermaphrodite: + text: hermaphrodite + male: + text: male + neuter: + text: neuter + window_cond_enum: + name: window_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + handidness_enum: + name: handidness_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + ambidexterity: + text: ambidexterity + left handedness: + text: left handedness + mixed-handedness: + text: mixed-handedness + right handedness: + text: right handedness + wall_const_type_enum: + name: wall_const_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + frame construction: + text: frame construction + joisted masonry: + text: joisted masonry + light noncombustible: + text: light noncombustible + masonry noncombustible: + text: masonry noncombustible + modified fire resistive: + text: modified fire resistive + fire resistive: + text: fire resistive + build_occup_type_enum: + name: build_occup_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + office: + text: office + market: + text: market + restaurant: + text: restaurant + residence: + text: residence + school: + text: school + residential: + text: residential + commercial: + text: commercial + low rise: + text: low rise + high rise: + text: high rise + wood framed: + text: wood framed + health care: + text: health care + airport: + text: airport + sports complex: + text: sports complex + oxy_stat_samp_enum: + name: oxy_stat_samp_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - clear sky: - text: clear sky - cloudy: - text: cloudy - foggy: - text: foggy - hail: - text: hail - rain: - text: rain - snow: - text: snow - sleet: - text: sleet - sunny: - text: sunny - windy: - text: windy - biotic_relationship_enum: - name: biotic_relationship_enum + aerobic: + text: aerobic + anaerobic: + text: anaerobic + other: + text: other + filter_type_enum: + name: filter_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - free living: - text: free living - parasite: - text: parasite - commensal: - text: commensal - symbiont: - text: symbiont - door_cond_enum: - name: door_cond_enum + particulate air filter: + text: particulate air filter + chemical air filter: + text: chemical air filter + low-MERV pleated media: + text: low-MERV pleated media + HEPA: + text: HEPA + electrostatic: + text: electrostatic + gas-phase or ultraviolet air treatments: + text: gas-phase or ultraviolet air treatments + samp_floor_enum: + name: samp_floor_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - train_line_enum: - name: train_line_enum + 1st floor: + text: 1st floor + 2nd floor: + text: 2nd floor + basement: + text: basement + lobby: + text: lobby + furniture_enum: + name: furniture_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - red: - text: red - green: - text: green - orange: - text: orange - build_docs_enum: - name: build_docs_enum + cabinet: + text: cabinet + chair: + text: chair + desks: + text: desks + samp_dis_stage_enum: + name: samp_dis_stage_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - building information model: - text: building information model - commissioning report: - text: commissioning report - complaint logs: - text: complaint logs - contract administration: - text: contract administration - cost estimate: - text: cost estimate - janitorial schedules or logs: - text: janitorial schedules or logs - maintenance plans: - text: maintenance plans - schedule: - text: schedule - sections: - text: sections - shop drawings: - text: shop drawings - submittals: - text: submittals - ventilation system: - text: ventilation system - windows: - text: windows - door_loc_enum: - name: door_loc_enum + dissemination: + text: dissemination + growth and reproduction: + text: growth and reproduction + infection: + text: infection + inoculation: + text: inoculation + penetration: + text: penetration + other: + text: other + substructure_type_enum: + name: substructure_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - sr_kerog_type_enum: - name: sr_kerog_type_enum + crawlspace: + text: crawlspace + slab on grade: + text: slab on grade + basement: + text: basement + door_comp_type_enum: + name: door_comp_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Type I: - text: Type I - Type II: - text: Type II - Type III: - text: Type III - Type IV: - text: Type IV - other: - text: other + metal covered: + text: metal covered + revolving: + text: revolving + sliding: + text: sliding + telescopic: + text: telescopic + plant_growth_med_enum: + name: plant_growth_med_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + other artificial liquid medium: + text: other artificial liquid medium + other artificial solid medium: + text: other artificial solid medium + peat moss: + text: peat moss + perlite: + text: perlite + pumice: + text: pumice + sand: + text: sand + soil: + text: soil + vermiculite: + text: vermiculite + water: + text: water slots: metagenome_annotation_id: name: metagenome_annotation_id @@ -5531,8 +5617,6 @@ slots: examples: - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 2 string_serialization: '{date, arbitrary precision}' slot_group: MIxS Inspired @@ -5549,8 +5633,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 1 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -5568,8 +5650,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 3 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -5587,8 +5667,6 @@ slots: examples: - value: 'experimental treatment: value' from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:experimental_factor|additional_info rank: 7 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5603,8 +5681,6 @@ slots: - value: C18 - value: Basix PES, 13-100-106 FisherSci from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:filter_type rank: 6 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5622,8 +5698,6 @@ slots: - value: 13C glucose - value: H218O from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:chem_administration rank: 16 string_serialization: '{termLabel} {[termID]}; {timestamp}' slot_group: MIxS Inspired @@ -5640,8 +5714,6 @@ slots: - value: https://doi.org/10.1016/0038-0717(87)90052-6 - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:micro_biomass_meth rank: 11 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5656,8 +5728,6 @@ slots: - value: https://doi.org/10.1016/0038-0717(87)90052-6 - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:micro_biomass_meth rank: 13 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5672,8 +5742,6 @@ slots: examples: - value: 0.05 ug C/g dry soil from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:microbial_biomass rank: 10 string_serialization: '{float} {unit}' slot_group: MIxS Inspired @@ -5688,8 +5756,6 @@ slots: examples: - value: 0.05 ug N/g dry soil from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:microbial_biomass rank: 12 string_serialization: '{float} {unit}' slot_group: MIxS Inspired @@ -5702,8 +5768,6 @@ slots: examples: - value: insect 0.23 ug; plant 1g from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:biomass|microbial_biomass rank: 8 string_serialization: '{text};{float} {unit}' slot_group: MIxS Inspired @@ -5716,8 +5780,6 @@ slots: examples: - value: https://doi.org/10.1038/s41467-021-26181-3 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:microbial_biomass rank: 9 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5730,8 +5792,6 @@ slots: examples: - value: https://doi.org/10.1016/0038-0717(85)90144-0 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:org_nitro|tot_nitro_cont_meth rank: 14 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5744,8 +5804,6 @@ slots: - This is an open text field to provide any treatments that cannot be captured in the provided slots. from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:additional_info rank: 15 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5763,8 +5821,6 @@ slots: examples: - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 4 string_serialization: '{date, arbitrary precision}' slot_group: MIxS Inspired @@ -5781,8 +5837,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 5 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -17361,19 +17415,28 @@ slots: slot_uri: MIXS:0000156 multivalued: false range: QuantityValue - investigation field: - name: investigation field - description: field describing aspect of the investigation/study to which the sample - belongs + has unit: + name: has unit + description: Example "m" + from_schema: https://w3id.org/nmdc/nmdc + owner: QuantityValue + sequencing field: + name: sequencing field from_schema: https://w3id.org/nmdc/nmdc abstract: true + has raw value: + name: has raw value + from_schema: https://w3id.org/nmdc/nmdc + string_serialization: '{has numeric value} {has unit}' + owner: QuantityValue core field: name: core field description: basic fields from_schema: https://w3id.org/nmdc/nmdc abstract: true - nucleic acid sequence source field: - name: nucleic acid sequence source field + environment field: + name: environment field + description: field describing environmental aspect of a sample from_schema: https://w3id.org/nmdc/nmdc abstract: true has numeric value: @@ -17381,25 +17444,16 @@ slots: from_schema: https://w3id.org/nmdc/nmdc owner: QuantityValue range: double - environment field: - name: environment field - description: field describing environmental aspect of a sample + nucleic acid sequence source field: + name: nucleic acid sequence source field from_schema: https://w3id.org/nmdc/nmdc abstract: true - has unit: - name: has unit - description: Example "m" - from_schema: https://w3id.org/nmdc/nmdc - owner: QuantityValue - sequencing field: - name: sequencing field + investigation field: + name: investigation field + description: field describing aspect of the investigation/study to which the sample + belongs from_schema: https://w3id.org/nmdc/nmdc abstract: true - has raw value: - name: has raw value - from_schema: https://w3id.org/nmdc/nmdc - string_serialization: '{has numeric value} {has unit}' - owner: QuantityValue chemical: name: chemical description: from reaction participant class @@ -18486,10 +18540,9 @@ classes: Matches the entity that has been submitted to NMDC lat_lon: name: lat_lon - description: This is currently a required field but it's not clear if this - should be required for human hosts - notes: - - required where? + todos: + - This is currently a required field but it's not clear if this should be + required for human hosts env_broad_scale: name: env_broad_scale required: true @@ -19438,7 +19491,6 @@ classes: used: name: used description: The instrument used to collect the data used in the analysis - range: Instrument id: name: id required: true diff --git a/nmdc_schema/nmdc_schema_accepting_legacy_ids.py b/nmdc_schema/nmdc_schema_accepting_legacy_ids.py index c0beb2eb08..dcbaaf19c5 100644 --- a/nmdc_schema/nmdc_schema_accepting_legacy_ids.py +++ b/nmdc_schema/nmdc_schema_accepting_legacy_ids.py @@ -1,5 +1,5 @@ # Auto generated from nmdc_schema_accepting_legacy_ids.yaml by pythongen.py version: 0.0.1 -# Generation date: 2023-09-21T12:50:42 +# Generation date: 2023-10-03T12:26:28 # Schema: NMDC # # id: https://w3id.org/nmdc/nmdc @@ -30,7 +30,7 @@ from linkml_runtime.utils.metamodelcore import Bool, Curie, Decimal, ElementIdentifier, NCName, NodeIdentifier, URI, URIorCURIE, XSDDate, XSDDateTime, XSDTime metamodel_version = "1.7.0" -version = "v8.0.0" +version = "v8.1.0" # Overwrite dataclasses _init_fn to add **kwargs in __init__ dataclasses._init_fn = dataclasses_init_fn_with_kwargs @@ -196,8 +196,8 @@ class Decimal(Decimal): class Time(XSDTime): """ A time object represents a (local) time of day, independent of any particular day """ - type_class_uri = XSD.dateTime - type_class_curie = "xsd:dateTime" + type_class_uri = XSD.time + type_class_curie = "xsd:time" type_name = "time" type_model_uri = NMDC.Time @@ -274,6 +274,30 @@ class Nodeidentifier(NodeIdentifier): type_model_uri = NMDC.Nodeidentifier +class Jsonpointer(str): + """ A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. """ + type_class_uri = XSD.string + type_class_curie = "xsd:string" + type_name = "jsonpointer" + type_model_uri = NMDC.Jsonpointer + + +class Jsonpath(str): + """ A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. """ + type_class_uri = XSD.string + type_class_curie = "xsd:string" + type_name = "jsonpath" + type_model_uri = NMDC.Jsonpath + + +class Sparqlpath(str): + """ A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. """ + type_class_uri = XSD.string + type_class_curie = "xsd:string" + type_name = "sparqlpath" + type_model_uri = NMDC.Sparqlpath + + class ExternalIdentifier(Uriorcurie): """ A CURIE representing an external identifier """ type_class_uri = XSD.anyURI @@ -5471,7 +5495,7 @@ class MetaproteomicsAnalysisActivity(WorkflowExecutionActivity): started_at_time: str = None ended_at_time: str = None has_peptide_quantifications: Optional[Union[Union[dict, "PeptideQuantification"], List[Union[dict, "PeptideQuantification"]]]] = empty_list() - used: Optional[Union[str, InstrumentId]] = None + used: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -5483,8 +5507,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.has_peptide_quantifications = [self.has_peptide_quantifications] if self.has_peptide_quantifications is not None else [] self.has_peptide_quantifications = [v if isinstance(v, PeptideQuantification) else PeptideQuantification(**as_dict(v)) for v in self.has_peptide_quantifications] - if self.used is not None and not isinstance(self.used, InstrumentId): - self.used = InstrumentId(self.used) + if self.used is not None and not isinstance(self.used, str): + self.used = str(self.used) super().__post_init__(**kwargs) @@ -6524,26 +6548,6 @@ class SampleTypeEnum(EnumDefinitionImpl): name="SampleTypeEnum", ) -class DoorDirectEnum(EnumDefinitionImpl): - - inward = PermissibleValue(text="inward") - outward = PermissibleValue(text="outward") - sideways = PermissibleValue(text="sideways") - - _defn = EnumDefinition( - name="DoorDirectEnum", - ) - -class OxyStatSampEnum(EnumDefinitionImpl): - - aerobic = PermissibleValue(text="aerobic") - anaerobic = PermissibleValue(text="anaerobic") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="OxyStatSampEnum", - ) - class SurfAirContEnum(EnumDefinitionImpl): dust = PermissibleValue(text="dust") @@ -6566,176 +6570,201 @@ def _addvals(cls): setattr(cls, "biological contaminants", PermissibleValue(text="biological contaminants")) -class WindowVertPosEnum(EnumDefinitionImpl): - - bottom = PermissibleValue(text="bottom") - middle = PermissibleValue(text="middle") - top = PermissibleValue(text="top") - low = PermissibleValue(text="low") - high = PermissibleValue(text="high") - - _defn = EnumDefinition( - name="WindowVertPosEnum", - ) - -class FilterTypeEnum(EnumDefinitionImpl): +class WaterFeatTypeEnum(EnumDefinitionImpl): - HEPA = PermissibleValue(text="HEPA") - electrostatic = PermissibleValue(text="electrostatic") + fountain = PermissibleValue(text="fountain") + pool = PermissibleValue(text="pool") + stream = PermissibleValue(text="stream") + waterfall = PermissibleValue(text="waterfall") _defn = EnumDefinition( - name="FilterTypeEnum", + name="WaterFeatTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "particulate air filter", - PermissibleValue(text="particulate air filter")) - setattr(cls, "chemical air filter", - PermissibleValue(text="chemical air filter")) - setattr(cls, "low-MERV pleated media", - PermissibleValue(text="low-MERV pleated media")) - setattr(cls, "gas-phase or ultraviolet air treatments", - PermissibleValue(text="gas-phase or ultraviolet air treatments")) + setattr(cls, "standing feature", + PermissibleValue(text="standing feature")) -class RelSampLocEnum(EnumDefinitionImpl): +class SampCollectPointEnum(EnumDefinitionImpl): + + well = PermissibleValue(text="well") + wellhead = PermissibleValue(text="wellhead") + separator = PermissibleValue(text="separator") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="RelSampLocEnum", + name="SampCollectPointEnum", ) @classmethod def _addvals(cls): - setattr(cls, "edge of car", - PermissibleValue(text="edge of car")) - setattr(cls, "center of car", - PermissibleValue(text="center of car")) - setattr(cls, "under a seat", - PermissibleValue(text="under a seat")) + setattr(cls, "test well", + PermissibleValue(text="test well")) + setattr(cls, "drilling rig", + PermissibleValue(text="drilling rig")) + setattr(cls, "storage tank", + PermissibleValue(text="storage tank")) -class SedimentTypeEnum(EnumDefinitionImpl): +class FloorWaterMoldEnum(EnumDefinitionImpl): - biogenous = PermissibleValue(text="biogenous") - cosmogenous = PermissibleValue(text="cosmogenous") - hydrogenous = PermissibleValue(text="hydrogenous") - lithogenous = PermissibleValue(text="lithogenous") + condensation = PermissibleValue(text="condensation") _defn = EnumDefinition( - name="SedimentTypeEnum", + name="FloorWaterMoldEnum", ) -class OccupDocumentEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "mold odor", + PermissibleValue(text="mold odor")) + setattr(cls, "wet floor", + PermissibleValue(text="wet floor")) + setattr(cls, "water stains", + PermissibleValue(text="water stains")) + setattr(cls, "wall discoloration", + PermissibleValue(text="wall discoloration")) + setattr(cls, "floor discoloration", + PermissibleValue(text="floor discoloration")) + setattr(cls, "ceiling discoloration", + PermissibleValue(text="ceiling discoloration")) + setattr(cls, "peeling paint or wallpaper", + PermissibleValue(text="peeling paint or wallpaper")) + setattr(cls, "bulging walls", + PermissibleValue(text="bulging walls")) - estimate = PermissibleValue(text="estimate") - videos = PermissibleValue(text="videos") +class WallTextureEnum(EnumDefinitionImpl): + + knockdown = PermissibleValue(text="knockdown") + popcorn = PermissibleValue(text="popcorn") + smooth = PermissibleValue(text="smooth") + swirl = PermissibleValue(text="swirl") _defn = EnumDefinition( - name="OccupDocumentEnum", + name="WallTextureEnum", ) @classmethod def _addvals(cls): - setattr(cls, "automated count", - PermissibleValue(text="automated count")) - setattr(cls, "manual count", - PermissibleValue(text="manual count")) + setattr(cls, "crows feet", + PermissibleValue(text="crows feet")) + setattr(cls, "crows-foot stomp", + PermissibleValue(text="crows-foot stomp")) + setattr(cls, "", + PermissibleValue(text="")) + setattr(cls, "double skip", + PermissibleValue(text="double skip")) + setattr(cls, "hawk and trowel", + PermissibleValue(text="hawk and trowel")) + setattr(cls, "orange peel", + PermissibleValue(text="orange peel")) + setattr(cls, "rosebud stomp", + PermissibleValue(text="rosebud stomp")) + setattr(cls, "Santa-Fe texture", + PermissibleValue(text="Santa-Fe texture")) + setattr(cls, "skip trowel", + PermissibleValue(text="skip trowel")) + setattr(cls, "stomp knockdown", + PermissibleValue(text="stomp knockdown")) -class RoomConnectedEnum(EnumDefinitionImpl): +class SampSubtypeEnum(EnumDefinitionImpl): - attic = PermissibleValue(text="attic") - bathroom = PermissibleValue(text="bathroom") - closet = PermissibleValue(text="closet") - elevator = PermissibleValue(text="elevator") - hallway = PermissibleValue(text="hallway") - kitchen = PermissibleValue(text="kitchen") - office = PermissibleValue(text="office") - stairwell = PermissibleValue(text="stairwell") + biofilm = PermissibleValue(text="biofilm") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="RoomConnectedEnum", + name="SampSubtypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "conference room", - PermissibleValue(text="conference room")) - setattr(cls, "examining room", - PermissibleValue(text="examining room")) - setattr(cls, "mail room", - PermissibleValue(text="mail room")) + setattr(cls, "oil phase", + PermissibleValue(text="oil phase")) + setattr(cls, "water phase", + PermissibleValue(text="water phase")) + setattr(cls, "not applicable", + PermissibleValue(text="not applicable")) -class QuadPosEnum(EnumDefinitionImpl): +class DrainageClassEnum(EnumDefinitionImpl): + + poorly = PermissibleValue(text="poorly") + well = PermissibleValue(text="well") _defn = EnumDefinition( - name="QuadPosEnum", + name="DrainageClassEnum", ) @classmethod def _addvals(cls): - setattr(cls, "North side", - PermissibleValue(text="North side")) - setattr(cls, "West side", - PermissibleValue(text="West side")) - setattr(cls, "South side", - PermissibleValue(text="South side")) - setattr(cls, "East side", - PermissibleValue(text="East side")) + setattr(cls, "very poorly", + PermissibleValue(text="very poorly")) + setattr(cls, "somewhat poorly", + PermissibleValue(text="somewhat poorly")) + setattr(cls, "moderately well", + PermissibleValue(text="moderately well")) + setattr(cls, "excessively drained", + PermissibleValue(text="excessively drained")) -class SrGeolAgeEnum(EnumDefinitionImpl): +class FreqCleanEnum(EnumDefinitionImpl): - Archean = PermissibleValue(text="Archean") - Cambrian = PermissibleValue(text="Cambrian") - Carboniferous = PermissibleValue(text="Carboniferous") - Cenozoic = PermissibleValue(text="Cenozoic") - Cretaceous = PermissibleValue(text="Cretaceous") - Devonian = PermissibleValue(text="Devonian") - Jurassic = PermissibleValue(text="Jurassic") - Mesozoic = PermissibleValue(text="Mesozoic") - Neogene = PermissibleValue(text="Neogene") - Ordovician = PermissibleValue(text="Ordovician") - Paleogene = PermissibleValue(text="Paleogene") - Paleozoic = PermissibleValue(text="Paleozoic") - Permian = PermissibleValue(text="Permian") - Precambrian = PermissibleValue(text="Precambrian") - Proterozoic = PermissibleValue(text="Proterozoic") - Silurian = PermissibleValue(text="Silurian") - Triassic = PermissibleValue(text="Triassic") + Daily = PermissibleValue(text="Daily") + Weekly = PermissibleValue(text="Weekly") + Monthly = PermissibleValue(text="Monthly") + Quarterly = PermissibleValue(text="Quarterly") + Annually = PermissibleValue(text="Annually") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="SrGeolAgeEnum", + name="FreqCleanEnum", ) -class DoorMoveEnum(EnumDefinitionImpl): +class BioticRelationshipEnum(EnumDefinitionImpl): - collapsible = PermissibleValue(text="collapsible") - folding = PermissibleValue(text="folding") - revolving = PermissibleValue(text="revolving") - sliding = PermissibleValue(text="sliding") - swinging = PermissibleValue(text="swinging") + parasite = PermissibleValue(text="parasite") + commensal = PermissibleValue(text="commensal") + symbiont = PermissibleValue(text="symbiont") _defn = EnumDefinition( - name="DoorMoveEnum", + name="BioticRelationshipEnum", ) @classmethod def _addvals(cls): - setattr(cls, "rolling shutter", - PermissibleValue(text="rolling shutter")) + setattr(cls, "free living", + PermissibleValue(text="free living")) -class CurLandUseEnum(EnumDefinitionImpl): +class LightTypeEnum(EnumDefinitionImpl): - badlands = PermissibleValue(text="badlands") - cities = PermissibleValue(text="cities") - conifers = PermissibleValue(text="conifers") - farmstead = PermissibleValue(text="farmstead") - gravel = PermissibleValue(text="gravel") - hardwoods = PermissibleValue(text="hardwoods") - hayland = PermissibleValue(text="hayland") - marshlands = PermissibleValue(text="marshlands") - meadows = PermissibleValue(text="meadows") - mudflats = PermissibleValue(text="mudflats") - pastureland = PermissibleValue(text="pastureland") + none = PermissibleValue(text="none") + + _defn = EnumDefinition( + name="LightTypeEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "natural light", + PermissibleValue(text="natural light")) + setattr(cls, "electric light", + PermissibleValue(text="electric light")) + setattr(cls, "desk lamp", + PermissibleValue(text="desk lamp")) + setattr(cls, "flourescent lights", + PermissibleValue(text="flourescent lights")) + +class CurLandUseEnum(EnumDefinitionImpl): + + badlands = PermissibleValue(text="badlands") + cities = PermissibleValue(text="cities") + conifers = PermissibleValue(text="conifers") + farmstead = PermissibleValue(text="farmstead") + gravel = PermissibleValue(text="gravel") + hardwoods = PermissibleValue(text="hardwoods") + hayland = PermissibleValue(text="hayland") + marshlands = PermissibleValue(text="marshlands") + meadows = PermissibleValue(text="meadows") + mudflats = PermissibleValue(text="mudflats") + pastureland = PermissibleValue(text="pastureland") rainforest = PermissibleValue(text="rainforest") rangeland = PermissibleValue(text="rangeland") rock = PermissibleValue(text="rock") @@ -6785,105 +6814,160 @@ def _addvals(cls): setattr(cls, "vine crops", PermissibleValue(text="vine crops")) -class HcrGeolAgeEnum(EnumDefinitionImpl): +class DrawingsEnum(EnumDefinitionImpl): + + operation = PermissibleValue(text="operation") + construction = PermissibleValue(text="construction") + bid = PermissibleValue(text="bid") + design = PermissibleValue(text="design") + diagram = PermissibleValue(text="diagram") + sketch = PermissibleValue(text="sketch") + + _defn = EnumDefinition( + name="DrawingsEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "as built", + PermissibleValue(text="as built")) + setattr(cls, "building navigation map", + PermissibleValue(text="building navigation map")) + +class IndoorSurfEnum(EnumDefinitionImpl): + + cabinet = PermissibleValue(text="cabinet") + ceiling = PermissibleValue(text="ceiling") + door = PermissibleValue(text="door") + shelving = PermissibleValue(text="shelving") + window = PermissibleValue(text="window") + wall = PermissibleValue(text="wall") + + _defn = EnumDefinition( + name="IndoorSurfEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "counter top", + PermissibleValue(text="counter top")) + setattr(cls, "vent cover", + PermissibleValue(text="vent cover")) + +class SampCaptStatusEnum(EnumDefinitionImpl): - Archean = PermissibleValue(text="Archean") - Cambrian = PermissibleValue(text="Cambrian") - Carboniferous = PermissibleValue(text="Carboniferous") - Cenozoic = PermissibleValue(text="Cenozoic") - Cretaceous = PermissibleValue(text="Cretaceous") - Devonian = PermissibleValue(text="Devonian") - Jurassic = PermissibleValue(text="Jurassic") - Mesozoic = PermissibleValue(text="Mesozoic") - Neogene = PermissibleValue(text="Neogene") - Ordovician = PermissibleValue(text="Ordovician") - Paleogene = PermissibleValue(text="Paleogene") - Paleozoic = PermissibleValue(text="Paleozoic") - Permian = PermissibleValue(text="Permian") - Precambrian = PermissibleValue(text="Precambrian") - Proterozoic = PermissibleValue(text="Proterozoic") - Silurian = PermissibleValue(text="Silurian") - Triassic = PermissibleValue(text="Triassic") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="HcrGeolAgeEnum", + name="SampCaptStatusEnum", ) -class WallConstTypeEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "active surveillance in response to an outbreak", + PermissibleValue(text="active surveillance in response to an outbreak")) + setattr(cls, "active surveillance not initiated by an outbreak", + PermissibleValue(text="active surveillance not initiated by an outbreak")) + setattr(cls, "farm sample", + PermissibleValue(text="farm sample")) + setattr(cls, "market sample", + PermissibleValue(text="market sample")) + +class RoomLocEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="WallConstTypeEnum", + name="RoomLocEnum", ) @classmethod def _addvals(cls): - setattr(cls, "frame construction", - PermissibleValue(text="frame construction")) - setattr(cls, "joisted masonry", - PermissibleValue(text="joisted masonry")) - setattr(cls, "light noncombustible", - PermissibleValue(text="light noncombustible")) - setattr(cls, "masonry noncombustible", - PermissibleValue(text="masonry noncombustible")) - setattr(cls, "modified fire resistive", - PermissibleValue(text="modified fire resistive")) - setattr(cls, "fire resistive", - PermissibleValue(text="fire resistive")) + setattr(cls, "corner room", + PermissibleValue(text="corner room")) + setattr(cls, "interior room", + PermissibleValue(text="interior room")) + setattr(cls, "exterior wall", + PermissibleValue(text="exterior wall")) -class PlantSexEnum(EnumDefinitionImpl): +class OccupDocumentEnum(EnumDefinitionImpl): - Androdioecious = PermissibleValue(text="Androdioecious") - Androecious = PermissibleValue(text="Androecious") - Androgynous = PermissibleValue(text="Androgynous") - Androgynomonoecious = PermissibleValue(text="Androgynomonoecious") - Andromonoecious = PermissibleValue(text="Andromonoecious") - Bisexual = PermissibleValue(text="Bisexual") - Dichogamous = PermissibleValue(text="Dichogamous") - Diclinous = PermissibleValue(text="Diclinous") - Dioecious = PermissibleValue(text="Dioecious") - Gynodioecious = PermissibleValue(text="Gynodioecious") - Gynoecious = PermissibleValue(text="Gynoecious") - Gynomonoecious = PermissibleValue(text="Gynomonoecious") - Hermaphroditic = PermissibleValue(text="Hermaphroditic") - Imperfect = PermissibleValue(text="Imperfect") - Monoclinous = PermissibleValue(text="Monoclinous") - Monoecious = PermissibleValue(text="Monoecious") - Perfect = PermissibleValue(text="Perfect") - Polygamodioecious = PermissibleValue(text="Polygamodioecious") - Polygamomonoecious = PermissibleValue(text="Polygamomonoecious") - Polygamous = PermissibleValue(text="Polygamous") - Protandrous = PermissibleValue(text="Protandrous") - Protogynous = PermissibleValue(text="Protogynous") - Subandroecious = PermissibleValue(text="Subandroecious") - Subdioecious = PermissibleValue(text="Subdioecious") - Subgynoecious = PermissibleValue(text="Subgynoecious") - Synoecious = PermissibleValue(text="Synoecious") - Trimonoecious = PermissibleValue(text="Trimonoecious") - Trioecious = PermissibleValue(text="Trioecious") - Unisexual = PermissibleValue(text="Unisexual") + estimate = PermissibleValue(text="estimate") + videos = PermissibleValue(text="videos") _defn = EnumDefinition( - name="PlantSexEnum", + name="OccupDocumentEnum", ) -class CeilTypeEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "automated count", + PermissibleValue(text="automated count")) + setattr(cls, "manual count", + PermissibleValue(text="manual count")) - cathedral = PermissibleValue(text="cathedral") - dropped = PermissibleValue(text="dropped") - concave = PermissibleValue(text="concave") - coffered = PermissibleValue(text="coffered") - cove = PermissibleValue(text="cove") - stretched = PermissibleValue(text="stretched") +class ArchStrucEnum(EnumDefinitionImpl): + + building = PermissibleValue(text="building") + shed = PermissibleValue(text="shed") + home = PermissibleValue(text="home") _defn = EnumDefinition( - name="CeilTypeEnum", + name="ArchStrucEnum", + ) + +class WallFinishMatEnum(EnumDefinitionImpl): + + plaster = PermissibleValue(text="plaster") + tile = PermissibleValue(text="tile") + terrazzo = PermissibleValue(text="terrazzo") + wood = PermissibleValue(text="wood") + metal = PermissibleValue(text="metal") + masonry = PermissibleValue(text="masonry") + + _defn = EnumDefinition( + name="WallFinishMatEnum", ) @classmethod def _addvals(cls): - setattr(cls, "barrel-shaped", - PermissibleValue(text="barrel-shaped")) + setattr(cls, "gypsum plaster", + PermissibleValue(text="gypsum plaster")) + setattr(cls, "veneer plaster", + PermissibleValue(text="veneer plaster")) + setattr(cls, "gypsum board", + PermissibleValue(text="gypsum board")) + setattr(cls, "stone facing", + PermissibleValue(text="stone facing")) + setattr(cls, "acoustical treatment", + PermissibleValue(text="acoustical treatment")) + +class WindowMatEnum(EnumDefinitionImpl): + + clad = PermissibleValue(text="clad") + fiberglass = PermissibleValue(text="fiberglass") + metal = PermissibleValue(text="metal") + vinyl = PermissibleValue(text="vinyl") + wood = PermissibleValue(text="wood") + + _defn = EnumDefinition( + name="WindowMatEnum", + ) + +class IntWallCondEnum(EnumDefinitionImpl): + + new = PermissibleValue(text="new") + damaged = PermissibleValue(text="damaged") + rupture = PermissibleValue(text="rupture") + + _defn = EnumDefinition( + name="IntWallCondEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) class FloorFinishMatEnum(EnumDefinitionImpl): @@ -6919,617 +7003,228 @@ def _addvals(cls): setattr(cls, "none or unfinished", PermissibleValue(text="none or unfinished")) -class WallLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="WallLocEnum", - ) - -class WallSurfTreatmentEnum(EnumDefinitionImpl): +class BuildDocsEnum(EnumDefinitionImpl): - painted = PermissibleValue(text="painted") - paneling = PermissibleValue(text="paneling") - stucco = PermissibleValue(text="stucco") - fabric = PermissibleValue(text="fabric") + schedule = PermissibleValue(text="schedule") + sections = PermissibleValue(text="sections") + submittals = PermissibleValue(text="submittals") + windows = PermissibleValue(text="windows") _defn = EnumDefinition( - name="WallSurfTreatmentEnum", + name="BuildDocsEnum", ) @classmethod def _addvals(cls): - setattr(cls, "wall paper", - PermissibleValue(text="wall paper")) - setattr(cls, "no treatment", - PermissibleValue(text="no treatment")) - -class WindowCondEnum(EnumDefinitionImpl): - - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") - - _defn = EnumDefinition( - name="WindowCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) + setattr(cls, "building information model", + PermissibleValue(text="building information model")) + setattr(cls, "commissioning report", + PermissibleValue(text="commissioning report")) + setattr(cls, "complaint logs", + PermissibleValue(text="complaint logs")) + setattr(cls, "contract administration", + PermissibleValue(text="contract administration")) + setattr(cls, "cost estimate", + PermissibleValue(text="cost estimate")) + setattr(cls, "janitorial schedules or logs", + PermissibleValue(text="janitorial schedules or logs")) + setattr(cls, "maintenance plans", + PermissibleValue(text="maintenance plans")) + setattr(cls, "shop drawings", + PermissibleValue(text="shop drawings")) + setattr(cls, "ventilation system", + PermissibleValue(text="ventilation system")) -class DoorMatEnum(EnumDefinitionImpl): +class SurfMaterialEnum(EnumDefinitionImpl): - aluminum = PermissibleValue(text="aluminum") - fiberboard = PermissibleValue(text="fiberboard") - fiberglass = PermissibleValue(text="fiberglass") + adobe = PermissibleValue(text="adobe") + carpet = PermissibleValue(text="carpet") + concrete = PermissibleValue(text="concrete") + glass = PermissibleValue(text="glass") metal = PermissibleValue(text="metal") + paint = PermissibleValue(text="paint") + plastic = PermissibleValue(text="plastic") + stone = PermissibleValue(text="stone") + stucco = PermissibleValue(text="stucco") + tile = PermissibleValue(text="tile") vinyl = PermissibleValue(text="vinyl") wood = PermissibleValue(text="wood") _defn = EnumDefinition( - name="DoorMatEnum", + name="SurfMaterialEnum", ) @classmethod def _addvals(cls): - setattr(cls, "cellular PVC", - PermissibleValue(text="cellular PVC")) - setattr(cls, "engineered plastic", - PermissibleValue(text="engineered plastic")) - setattr(cls, "thermoplastic alloy", - PermissibleValue(text="thermoplastic alloy")) - setattr(cls, "wood/plastic composite", - PermissibleValue(text="wood/plastic composite")) - -class SoilHorizonEnum(EnumDefinitionImpl): + setattr(cls, "cinder blocks", + PermissibleValue(text="cinder blocks")) + setattr(cls, "hay bales", + PermissibleValue(text="hay bales")) + setattr(cls, "stainless steel", + PermissibleValue(text="stainless steel")) - Permafrost = PermissibleValue(text="Permafrost") +class TidalStageEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="SoilHorizonEnum", + name="TidalStageEnum", ) @classmethod def _addvals(cls): - setattr(cls, "O horizon", - PermissibleValue(text="O horizon")) - setattr(cls, "A horizon", - PermissibleValue(text="A horizon")) - setattr(cls, "E horizon", - PermissibleValue(text="E horizon")) - setattr(cls, "B horizon", - PermissibleValue(text="B horizon")) - setattr(cls, "C horizon", - PermissibleValue(text="C horizon")) - setattr(cls, "R layer", - PermissibleValue(text="R layer")) - setattr(cls, "M horizon", - PermissibleValue(text="M horizon")) + setattr(cls, "low tide", + PermissibleValue(text="low tide")) + setattr(cls, "ebb tide", + PermissibleValue(text="ebb tide")) + setattr(cls, "flood tide", + PermissibleValue(text="flood tide")) + setattr(cls, "high tide", + PermissibleValue(text="high tide")) -class CeilFinishMatEnum(EnumDefinitionImpl): +class WindowHorizPosEnum(EnumDefinitionImpl): - drywall = PermissibleValue(text="drywall") - tiles = PermissibleValue(text="tiles") - PVC = PermissibleValue(text="PVC") - plasterboard = PermissibleValue(text="plasterboard") - metal = PermissibleValue(text="metal") - fiberglass = PermissibleValue(text="fiberglass") - stucco = PermissibleValue(text="stucco") - wood = PermissibleValue(text="wood") + left = PermissibleValue(text="left") + middle = PermissibleValue(text="middle") + right = PermissibleValue(text="right") _defn = EnumDefinition( - name="CeilFinishMatEnum", + name="WindowHorizPosEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "mineral fibre", - PermissibleValue(text="mineral fibre")) - setattr(cls, "mineral wool/calcium silicate", - PermissibleValue(text="mineral wool/calcium silicate")) - -class ShadingDeviceCondEnum(EnumDefinitionImpl): +class TrainStopLocEnum(EnumDefinitionImpl): - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") + end = PermissibleValue(text="end") + mid = PermissibleValue(text="mid") + downtown = PermissibleValue(text="downtown") _defn = EnumDefinition( - name="ShadingDeviceCondEnum", + name="TrainStopLocEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - -class HcProducedEnum(EnumDefinitionImpl): +class TrainLineEnum(EnumDefinitionImpl): - Oil = PermissibleValue(text="Oil") - Gas = PermissibleValue(text="Gas") - Bitumen = PermissibleValue(text="Bitumen") - other = PermissibleValue(text="other") + red = PermissibleValue(text="red") + green = PermissibleValue(text="green") + orange = PermissibleValue(text="orange") _defn = EnumDefinition( - name="HcProducedEnum", + name="TrainLineEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "Gas-Condensate", - PermissibleValue(text="Gas-Condensate")) - setattr(cls, "Coalbed Methane", - PermissibleValue(text="Coalbed Methane")) - -class DoorCompTypeEnum(EnumDefinitionImpl): +class TrainStatLocEnum(EnumDefinitionImpl): - revolving = PermissibleValue(text="revolving") - sliding = PermissibleValue(text="sliding") - telescopic = PermissibleValue(text="telescopic") + riverside = PermissibleValue(text="riverside") _defn = EnumDefinition( - name="DoorCompTypeEnum", + name="TrainStatLocEnum", ) @classmethod def _addvals(cls): - setattr(cls, "metal covered", - PermissibleValue(text="metal covered")) - -class WindowLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - - _defn = EnumDefinition( - name="WindowLocEnum", - ) + setattr(cls, "south station above ground", + PermissibleValue(text="south station above ground")) + setattr(cls, "south station underground", + PermissibleValue(text="south station underground")) + setattr(cls, "south station amtrak", + PermissibleValue(text="south station amtrak")) + setattr(cls, "forest hills", + PermissibleValue(text="forest hills")) -class SrLithologyEnum(EnumDefinitionImpl): +class SrDepEnvEnum(EnumDefinitionImpl): - Clastic = PermissibleValue(text="Clastic") - Carbonate = PermissibleValue(text="Carbonate") - Coal = PermissibleValue(text="Coal") - Biosilicieous = PermissibleValue(text="Biosilicieous") + Lacustine = PermissibleValue(text="Lacustine") + Fluvioldeltaic = PermissibleValue(text="Fluvioldeltaic") + Fluviomarine = PermissibleValue(text="Fluviomarine") + Marine = PermissibleValue(text="Marine") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="SrLithologyEnum", + name="SrDepEnvEnum", ) -class PlantGrowthMedEnum(EnumDefinitionImpl): +class SampWeatherEnum(EnumDefinitionImpl): - perlite = PermissibleValue(text="perlite") - pumice = PermissibleValue(text="pumice") - sand = PermissibleValue(text="sand") - soil = PermissibleValue(text="soil") - vermiculite = PermissibleValue(text="vermiculite") - water = PermissibleValue(text="water") + cloudy = PermissibleValue(text="cloudy") + foggy = PermissibleValue(text="foggy") + hail = PermissibleValue(text="hail") + rain = PermissibleValue(text="rain") + snow = PermissibleValue(text="snow") + sleet = PermissibleValue(text="sleet") + sunny = PermissibleValue(text="sunny") + windy = PermissibleValue(text="windy") _defn = EnumDefinition( - name="PlantGrowthMedEnum", + name="SampWeatherEnum", ) @classmethod def _addvals(cls): - setattr(cls, "other artificial liquid medium", - PermissibleValue(text="other artificial liquid medium")) - setattr(cls, "other artificial solid medium", - PermissibleValue(text="other artificial solid medium")) - setattr(cls, "peat moss", - PermissibleValue(text="peat moss")) + setattr(cls, "clear sky", + PermissibleValue(text="clear sky")) -class SurfMaterialEnum(EnumDefinitionImpl): +class WindowCoverEnum(EnumDefinitionImpl): - adobe = PermissibleValue(text="adobe") - carpet = PermissibleValue(text="carpet") - concrete = PermissibleValue(text="concrete") - glass = PermissibleValue(text="glass") - metal = PermissibleValue(text="metal") - paint = PermissibleValue(text="paint") - plastic = PermissibleValue(text="plastic") - stone = PermissibleValue(text="stone") - stucco = PermissibleValue(text="stucco") - tile = PermissibleValue(text="tile") - vinyl = PermissibleValue(text="vinyl") - wood = PermissibleValue(text="wood") + blinds = PermissibleValue(text="blinds") + curtains = PermissibleValue(text="curtains") + none = PermissibleValue(text="none") _defn = EnumDefinition( - name="SurfMaterialEnum", + name="WindowCoverEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "cinder blocks", - PermissibleValue(text="cinder blocks")) - setattr(cls, "hay bales", - PermissibleValue(text="hay bales")) - setattr(cls, "stainless steel", - PermissibleValue(text="stainless steel")) - -class CeilCondEnum(EnumDefinitionImpl): - - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") +class RoomTypeEnum(EnumDefinitionImpl): - _defn = EnumDefinition( - name="CeilCondEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) - -class BuildingSettingEnum(EnumDefinitionImpl): - - urban = PermissibleValue(text="urban") - suburban = PermissibleValue(text="suburban") - exurban = PermissibleValue(text="exurban") - rural = PermissibleValue(text="rural") - - _defn = EnumDefinition( - name="BuildingSettingEnum", - ) - -class BuildOccupTypeEnum(EnumDefinitionImpl): - - office = PermissibleValue(text="office") - market = PermissibleValue(text="market") - restaurant = PermissibleValue(text="restaurant") - residence = PermissibleValue(text="residence") - school = PermissibleValue(text="school") - residential = PermissibleValue(text="residential") - commercial = PermissibleValue(text="commercial") - airport = PermissibleValue(text="airport") - - _defn = EnumDefinition( - name="BuildOccupTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "low rise", - PermissibleValue(text="low rise")) - setattr(cls, "high rise", - PermissibleValue(text="high rise")) - setattr(cls, "wood framed", - PermissibleValue(text="wood framed")) - setattr(cls, "health care", - PermissibleValue(text="health care")) - setattr(cls, "sports complex", - PermissibleValue(text="sports complex")) - -class DeposEnvEnum(EnumDefinitionImpl): - - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="DeposEnvEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "Continental - Alluvial", - PermissibleValue(text="Continental - Alluvial")) - setattr(cls, "Continental - Aeolian", - PermissibleValue(text="Continental - Aeolian")) - setattr(cls, "Continental - Fluvial", - PermissibleValue(text="Continental - Fluvial")) - setattr(cls, "Continental - Lacustrine", - PermissibleValue(text="Continental - Lacustrine")) - setattr(cls, "Transitional - Deltaic", - PermissibleValue(text="Transitional - Deltaic")) - setattr(cls, "Transitional - Tidal", - PermissibleValue(text="Transitional - Tidal")) - setattr(cls, "Transitional - Lagoonal", - PermissibleValue(text="Transitional - Lagoonal")) - setattr(cls, "Transitional - Beach", - PermissibleValue(text="Transitional - Beach")) - setattr(cls, "Transitional - Lake", - PermissibleValue(text="Transitional - Lake")) - setattr(cls, "Marine - Shallow", - PermissibleValue(text="Marine - Shallow")) - setattr(cls, "Marine - Deep", - PermissibleValue(text="Marine - Deep")) - setattr(cls, "Marine - Reef", - PermissibleValue(text="Marine - Reef")) - setattr(cls, "Other - Evaporite", - PermissibleValue(text="Other - Evaporite")) - setattr(cls, "Other - Glacial", - PermissibleValue(text="Other - Glacial")) - setattr(cls, "Other - Volcanic", - PermissibleValue(text="Other - Volcanic")) - -class ProfilePositionEnum(EnumDefinitionImpl): - - summit = PermissibleValue(text="summit") - shoulder = PermissibleValue(text="shoulder") - backslope = PermissibleValue(text="backslope") - footslope = PermissibleValue(text="footslope") - toeslope = PermissibleValue(text="toeslope") - - _defn = EnumDefinition( - name="ProfilePositionEnum", - ) - -class FurnitureEnum(EnumDefinitionImpl): - - cabinet = PermissibleValue(text="cabinet") - chair = PermissibleValue(text="chair") - desks = PermissibleValue(text="desks") - - _defn = EnumDefinition( - name="FurnitureEnum", - ) - -class DoorTypeEnum(EnumDefinitionImpl): - - composite = PermissibleValue(text="composite") - metal = PermissibleValue(text="metal") - wooden = PermissibleValue(text="wooden") - - _defn = EnumDefinition( - name="DoorTypeEnum", - ) - -class TidalStageEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="TidalStageEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "low tide", - PermissibleValue(text="low tide")) - setattr(cls, "ebb tide", - PermissibleValue(text="ebb tide")) - setattr(cls, "flood tide", - PermissibleValue(text="flood tide")) - setattr(cls, "high tide", - PermissibleValue(text="high tide")) - -class DoorTypeMetalEnum(EnumDefinitionImpl): - - collapsible = PermissibleValue(text="collapsible") - hollow = PermissibleValue(text="hollow") - - _defn = EnumDefinition( - name="DoorTypeMetalEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "corrugated steel", - PermissibleValue(text="corrugated steel")) - setattr(cls, "rolling shutters", - PermissibleValue(text="rolling shutters")) - setattr(cls, "steel plate", - PermissibleValue(text="steel plate")) - -class HandidnessEnum(EnumDefinitionImpl): - - ambidexterity = PermissibleValue(text="ambidexterity") - - _defn = EnumDefinition( - name="HandidnessEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "left handedness", - PermissibleValue(text="left handedness")) - setattr(cls, "mixed-handedness", - PermissibleValue(text="mixed-handedness")) - setattr(cls, "right handedness", - PermissibleValue(text="right handedness")) - -class TillageEnum(EnumDefinitionImpl): - - drill = PermissibleValue(text="drill") - chisel = PermissibleValue(text="chisel") - tined = PermissibleValue(text="tined") - mouldboard = PermissibleValue(text="mouldboard") - - _defn = EnumDefinition( - name="TillageEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "cutting disc", - PermissibleValue(text="cutting disc")) - setattr(cls, "ridge till", - PermissibleValue(text="ridge till")) - setattr(cls, "strip tillage", - PermissibleValue(text="strip tillage")) - setattr(cls, "zonal tillage", - PermissibleValue(text="zonal tillage")) - setattr(cls, "disc plough", - PermissibleValue(text="disc plough")) - -class HcrEnum(EnumDefinitionImpl): - - Coalbed = PermissibleValue(text="Coalbed") - Shale = PermissibleValue(text="Shale") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="HcrEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "Oil Reservoir", - PermissibleValue(text="Oil Reservoir")) - setattr(cls, "Gas Reservoir", - PermissibleValue(text="Gas Reservoir")) - setattr(cls, "Oil Sand", - PermissibleValue(text="Oil Sand")) - setattr(cls, "Tight Oil Reservoir", - PermissibleValue(text="Tight Oil Reservoir")) - setattr(cls, "Tight Gas Reservoir", - PermissibleValue(text="Tight Gas Reservoir")) - -class FreqCleanEnum(EnumDefinitionImpl): - - Daily = PermissibleValue(text="Daily") - Weekly = PermissibleValue(text="Weekly") - Monthly = PermissibleValue(text="Monthly") - Quarterly = PermissibleValue(text="Quarterly") - Annually = PermissibleValue(text="Annually") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="FreqCleanEnum", - ) - -class GrowthHabitEnum(EnumDefinitionImpl): - - erect = PermissibleValue(text="erect") - spreading = PermissibleValue(text="spreading") - prostrate = PermissibleValue(text="prostrate") - - _defn = EnumDefinition( - name="GrowthHabitEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "semi-erect", - PermissibleValue(text="semi-erect")) - -class SeasonUseEnum(EnumDefinitionImpl): - - Spring = PermissibleValue(text="Spring") - Summer = PermissibleValue(text="Summer") - Fall = PermissibleValue(text="Fall") - Winter = PermissibleValue(text="Winter") - - _defn = EnumDefinition( - name="SeasonUseEnum", - ) - -class SrDepEnvEnum(EnumDefinitionImpl): - - Lacustine = PermissibleValue(text="Lacustine") - Fluvioldeltaic = PermissibleValue(text="Fluvioldeltaic") - Fluviomarine = PermissibleValue(text="Fluviomarine") - Marine = PermissibleValue(text="Marine") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SrDepEnvEnum", - ) - -class WaterFeatTypeEnum(EnumDefinitionImpl): - - fountain = PermissibleValue(text="fountain") - pool = PermissibleValue(text="pool") - stream = PermissibleValue(text="stream") - waterfall = PermissibleValue(text="waterfall") - - _defn = EnumDefinition( - name="WaterFeatTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "standing feature", - PermissibleValue(text="standing feature")) - -class SubstructureTypeEnum(EnumDefinitionImpl): - - crawlspace = PermissibleValue(text="crawlspace") - basement = PermissibleValue(text="basement") - - _defn = EnumDefinition( - name="SubstructureTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "slab on grade", - PermissibleValue(text="slab on grade")) - -class IndoorSpaceEnum(EnumDefinitionImpl): - - bedroom = PermissibleValue(text="bedroom") - office = PermissibleValue(text="office") + attic = PermissibleValue(text="attic") bathroom = PermissibleValue(text="bathroom") - foyer = PermissibleValue(text="foyer") - kitchen = PermissibleValue(text="kitchen") - hallway = PermissibleValue(text="hallway") + closet = PermissibleValue(text="closet") elevator = PermissibleValue(text="elevator") + hallway = PermissibleValue(text="hallway") + kitchen = PermissibleValue(text="kitchen") + stairwell = PermissibleValue(text="stairwell") + lobby = PermissibleValue(text="lobby") + vestibule = PermissibleValue(text="vestibule") + laboratory_wet = PermissibleValue(text="laboratory_wet") + laboratory_dry = PermissibleValue(text="laboratory_dry") + gymnasium = PermissibleValue(text="gymnasium") + natatorium = PermissibleValue(text="natatorium") + auditorium = PermissibleValue(text="auditorium") + lockers = PermissibleValue(text="lockers") + cafe = PermissibleValue(text="cafe") + warehouse = PermissibleValue(text="warehouse") _defn = EnumDefinition( - name="IndoorSpaceEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "locker room", - PermissibleValue(text="locker room")) - -class HostSexEnum(EnumDefinitionImpl): - - female = PermissibleValue(text="female") - hermaphrodite = PermissibleValue(text="hermaphrodite") - male = PermissibleValue(text="male") - neuter = PermissibleValue(text="neuter") - - _defn = EnumDefinition( - name="HostSexEnum", - ) - -class WindowTypeEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="WindowTypeEnum", + name="RoomTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "single-hung sash window", - PermissibleValue(text="single-hung sash window")) - setattr(cls, "horizontal sash window", - PermissibleValue(text="horizontal sash window")) - setattr(cls, "fixed window", - PermissibleValue(text="fixed window")) + setattr(cls, "conference room", + PermissibleValue(text="conference room")) + setattr(cls, "examining room", + PermissibleValue(text="examining room")) + setattr(cls, "mail room", + PermissibleValue(text="mail room")) + setattr(cls, "private office", + PermissibleValue(text="private office")) + setattr(cls, "open office", + PermissibleValue(text="open office")) + setattr(cls, ",restroom", + PermissibleValue(text=",restroom")) + setattr(cls, "mechanical or electrical room", + PermissibleValue(text="mechanical or electrical room")) + setattr(cls, "data center", + PermissibleValue(text="data center")) -class SpecificEnum(EnumDefinitionImpl): +class SedimentTypeEnum(EnumDefinitionImpl): - operation = PermissibleValue(text="operation") - construction = PermissibleValue(text="construction") - bid = PermissibleValue(text="bid") - design = PermissibleValue(text="design") - photos = PermissibleValue(text="photos") + biogenous = PermissibleValue(text="biogenous") + cosmogenous = PermissibleValue(text="cosmogenous") + hydrogenous = PermissibleValue(text="hydrogenous") + lithogenous = PermissibleValue(text="lithogenous") _defn = EnumDefinition( - name="SpecificEnum", + name="SedimentTypeEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "as built", - PermissibleValue(text="as built")) - class FaoClassEnum(EnumDefinitionImpl): Acrisols = PermissibleValue(text="Acrisols") @@ -7563,29 +7258,74 @@ class FaoClassEnum(EnumDefinitionImpl): name="FaoClassEnum", ) -class FloorStrucEnum(EnumDefinitionImpl): +class ExtWindowOrientEnum(EnumDefinitionImpl): - balcony = PermissibleValue(text="balcony") - concrete = PermissibleValue(text="concrete") + north = PermissibleValue(text="north") + south = PermissibleValue(text="south") + east = PermissibleValue(text="east") + west = PermissibleValue(text="west") + northeast = PermissibleValue(text="northeast") + southeast = PermissibleValue(text="southeast") + southwest = PermissibleValue(text="southwest") + northwest = PermissibleValue(text="northwest") _defn = EnumDefinition( - name="FloorStrucEnum", + name="ExtWindowOrientEnum", + ) + +class SrGeolAgeEnum(EnumDefinitionImpl): + + Archean = PermissibleValue(text="Archean") + Cambrian = PermissibleValue(text="Cambrian") + Carboniferous = PermissibleValue(text="Carboniferous") + Cenozoic = PermissibleValue(text="Cenozoic") + Cretaceous = PermissibleValue(text="Cretaceous") + Devonian = PermissibleValue(text="Devonian") + Jurassic = PermissibleValue(text="Jurassic") + Mesozoic = PermissibleValue(text="Mesozoic") + Neogene = PermissibleValue(text="Neogene") + Ordovician = PermissibleValue(text="Ordovician") + Paleogene = PermissibleValue(text="Paleogene") + Paleozoic = PermissibleValue(text="Paleozoic") + Permian = PermissibleValue(text="Permian") + Precambrian = PermissibleValue(text="Precambrian") + Proterozoic = PermissibleValue(text="Proterozoic") + Silurian = PermissibleValue(text="Silurian") + Triassic = PermissibleValue(text="Triassic") + other = PermissibleValue(text="other") + + _defn = EnumDefinition( + name="SrGeolAgeEnum", + ) + +class DoorMoveEnum(EnumDefinitionImpl): + + collapsible = PermissibleValue(text="collapsible") + folding = PermissibleValue(text="folding") + revolving = PermissibleValue(text="revolving") + sliding = PermissibleValue(text="sliding") + swinging = PermissibleValue(text="swinging") + + _defn = EnumDefinition( + name="DoorMoveEnum", ) @classmethod def _addvals(cls): - setattr(cls, "floating floor", - PermissibleValue(text="floating floor")) - setattr(cls, "glass floor", - PermissibleValue(text="glass floor")) - setattr(cls, "raised floor", - PermissibleValue(text="raised floor")) - setattr(cls, "sprung floor", - PermissibleValue(text="sprung floor")) - setattr(cls, "wood-framed", - PermissibleValue(text="wood-framed")) + setattr(cls, "rolling shutter", + PermissibleValue(text="rolling shutter")) -class WallTextureEnum(EnumDefinitionImpl): +class DoorDirectEnum(EnumDefinitionImpl): + + inward = PermissibleValue(text="inward") + outward = PermissibleValue(text="outward") + sideways = PermissibleValue(text="sideways") + + _defn = EnumDefinition( + name="DoorDirectEnum", + ) + +class CeilTextureEnum(EnumDefinitionImpl): knockdown = PermissibleValue(text="knockdown") popcorn = PermissibleValue(text="popcorn") @@ -7593,7 +7333,7 @@ class WallTextureEnum(EnumDefinitionImpl): swirl = PermissibleValue(text="swirl") _defn = EnumDefinition( - name="WallTextureEnum", + name="CeilTextureEnum", ) @classmethod @@ -7602,8 +7342,6 @@ def _addvals(cls): PermissibleValue(text="crows feet")) setattr(cls, "crows-foot stomp", PermissibleValue(text="crows-foot stomp")) - setattr(cls, "", - PermissibleValue(text="")) setattr(cls, "double skip", PermissibleValue(text="double skip")) setattr(cls, "hawk and trowel", @@ -7619,124 +7357,274 @@ def _addvals(cls): setattr(cls, "stomp knockdown", PermissibleValue(text="stomp knockdown")) -class TrainStopLocEnum(EnumDefinitionImpl): +class SampMdEnum(EnumDefinitionImpl): - end = PermissibleValue(text="end") - mid = PermissibleValue(text="mid") - downtown = PermissibleValue(text="downtown") + DF = PermissibleValue(text="DF") + RT = PermissibleValue(text="RT") + KB = PermissibleValue(text="KB") + MSL = PermissibleValue(text="MSL") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="TrainStopLocEnum", + name="SampMdEnum", ) -class DrawingsEnum(EnumDefinitionImpl): +class CeilTypeEnum(EnumDefinitionImpl): - operation = PermissibleValue(text="operation") - construction = PermissibleValue(text="construction") - bid = PermissibleValue(text="bid") - design = PermissibleValue(text="design") - diagram = PermissibleValue(text="diagram") - sketch = PermissibleValue(text="sketch") + cathedral = PermissibleValue(text="cathedral") + dropped = PermissibleValue(text="dropped") + concave = PermissibleValue(text="concave") + coffered = PermissibleValue(text="coffered") + cove = PermissibleValue(text="cove") + stretched = PermissibleValue(text="stretched") _defn = EnumDefinition( - name="DrawingsEnum", + name="CeilTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "as built", - PermissibleValue(text="as built")) - setattr(cls, "building navigation map", - PermissibleValue(text="building navigation map")) + setattr(cls, "barrel-shaped", + PermissibleValue(text="barrel-shaped")) -class RoomLocEnum(EnumDefinitionImpl): +class WallLocEnum(EnumDefinitionImpl): + + north = PermissibleValue(text="north") + south = PermissibleValue(text="south") + east = PermissibleValue(text="east") + west = PermissibleValue(text="west") _defn = EnumDefinition( - name="RoomLocEnum", + name="WallLocEnum", + ) + +class DoorTypeMetalEnum(EnumDefinitionImpl): + + collapsible = PermissibleValue(text="collapsible") + hollow = PermissibleValue(text="hollow") + + _defn = EnumDefinition( + name="DoorTypeMetalEnum", ) @classmethod def _addvals(cls): - setattr(cls, "corner room", - PermissibleValue(text="corner room")) - setattr(cls, "interior room", - PermissibleValue(text="interior room")) - setattr(cls, "exterior wall", - PermissibleValue(text="exterior wall")) + setattr(cls, "corrugated steel", + PermissibleValue(text="corrugated steel")) + setattr(cls, "rolling shutters", + PermissibleValue(text="rolling shutters")) + setattr(cls, "steel plate", + PermissibleValue(text="steel plate")) -class LightTypeEnum(EnumDefinitionImpl): +class GenderRestroomEnum(EnumDefinitionImpl): - none = PermissibleValue(text="none") + female = PermissibleValue(text="female") + male = PermissibleValue(text="male") + unisex = PermissibleValue(text="unisex") _defn = EnumDefinition( - name="LightTypeEnum", + name="GenderRestroomEnum", ) @classmethod def _addvals(cls): - setattr(cls, "natural light", - PermissibleValue(text="natural light")) - setattr(cls, "electric light", - PermissibleValue(text="electric light")) - setattr(cls, "desk lamp", - PermissibleValue(text="desk lamp")) - setattr(cls, "flourescent lights", - PermissibleValue(text="flourescent lights")) + setattr(cls, "all gender", + PermissibleValue(text="all gender")) + setattr(cls, "gender neurtral", + PermissibleValue(text="gender neurtral")) + setattr(cls, "male and female", + PermissibleValue(text="male and female")) -class WeekdayEnum(EnumDefinitionImpl): +class VisMediaEnum(EnumDefinitionImpl): - Monday = PermissibleValue(text="Monday") - Tuesday = PermissibleValue(text="Tuesday") - Wednesday = PermissibleValue(text="Wednesday") - Thursday = PermissibleValue(text="Thursday") - Friday = PermissibleValue(text="Friday") - Saturday = PermissibleValue(text="Saturday") - Sunday = PermissibleValue(text="Sunday") + photos = PermissibleValue(text="photos") + videos = PermissibleValue(text="videos") + interiors = PermissibleValue(text="interiors") + equipment = PermissibleValue(text="equipment") + + _defn = EnumDefinition( + name="VisMediaEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "commonly of the building", + PermissibleValue(text="commonly of the building")) + setattr(cls, "site context (adjacent buildings, vegetation, terrain, streets)", + PermissibleValue(text="site context (adjacent buildings, vegetation, terrain, streets)")) + setattr(cls, "3D scans", + PermissibleValue(text="3D scans")) + +class WindowLocEnum(EnumDefinitionImpl): + + north = PermissibleValue(text="north") + south = PermissibleValue(text="south") + east = PermissibleValue(text="east") + west = PermissibleValue(text="west") + + _defn = EnumDefinition( + name="WindowLocEnum", + ) + +class SoilHorizonEnum(EnumDefinitionImpl): + + Permafrost = PermissibleValue(text="Permafrost") + + _defn = EnumDefinition( + name="SoilHorizonEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "O horizon", + PermissibleValue(text="O horizon")) + setattr(cls, "A horizon", + PermissibleValue(text="A horizon")) + setattr(cls, "E horizon", + PermissibleValue(text="E horizon")) + setattr(cls, "B horizon", + PermissibleValue(text="B horizon")) + setattr(cls, "C horizon", + PermissibleValue(text="C horizon")) + setattr(cls, "R layer", + PermissibleValue(text="R layer")) + setattr(cls, "M horizon", + PermissibleValue(text="M horizon")) + +class IndoorSpaceEnum(EnumDefinitionImpl): + + bedroom = PermissibleValue(text="bedroom") + office = PermissibleValue(text="office") + bathroom = PermissibleValue(text="bathroom") + foyer = PermissibleValue(text="foyer") + kitchen = PermissibleValue(text="kitchen") + hallway = PermissibleValue(text="hallway") + elevator = PermissibleValue(text="elevator") + + _defn = EnumDefinition( + name="IndoorSpaceEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "locker room", + PermissibleValue(text="locker room")) + +class DoorTypeEnum(EnumDefinitionImpl): + + composite = PermissibleValue(text="composite") + metal = PermissibleValue(text="metal") + wooden = PermissibleValue(text="wooden") + + _defn = EnumDefinition( + name="DoorTypeEnum", + ) + +class DeposEnvEnum(EnumDefinitionImpl): + + other = PermissibleValue(text="other") + + _defn = EnumDefinition( + name="DeposEnvEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "Continental - Alluvial", + PermissibleValue(text="Continental - Alluvial")) + setattr(cls, "Continental - Aeolian", + PermissibleValue(text="Continental - Aeolian")) + setattr(cls, "Continental - Fluvial", + PermissibleValue(text="Continental - Fluvial")) + setattr(cls, "Continental - Lacustrine", + PermissibleValue(text="Continental - Lacustrine")) + setattr(cls, "Transitional - Deltaic", + PermissibleValue(text="Transitional - Deltaic")) + setattr(cls, "Transitional - Tidal", + PermissibleValue(text="Transitional - Tidal")) + setattr(cls, "Transitional - Lagoonal", + PermissibleValue(text="Transitional - Lagoonal")) + setattr(cls, "Transitional - Beach", + PermissibleValue(text="Transitional - Beach")) + setattr(cls, "Transitional - Lake", + PermissibleValue(text="Transitional - Lake")) + setattr(cls, "Marine - Shallow", + PermissibleValue(text="Marine - Shallow")) + setattr(cls, "Marine - Deep", + PermissibleValue(text="Marine - Deep")) + setattr(cls, "Marine - Reef", + PermissibleValue(text="Marine - Reef")) + setattr(cls, "Other - Evaporite", + PermissibleValue(text="Other - Evaporite")) + setattr(cls, "Other - Glacial", + PermissibleValue(text="Other - Glacial")) + setattr(cls, "Other - Volcanic", + PermissibleValue(text="Other - Volcanic")) + +class SrLithologyEnum(EnumDefinitionImpl): + + Clastic = PermissibleValue(text="Clastic") + Carbonate = PermissibleValue(text="Carbonate") + Coal = PermissibleValue(text="Coal") + Biosilicieous = PermissibleValue(text="Biosilicieous") + other = PermissibleValue(text="other") + + _defn = EnumDefinition( + name="SrLithologyEnum", + ) + +class PlantSexEnum(EnumDefinitionImpl): + + Androdioecious = PermissibleValue(text="Androdioecious") + Androecious = PermissibleValue(text="Androecious") + Androgynous = PermissibleValue(text="Androgynous") + Androgynomonoecious = PermissibleValue(text="Androgynomonoecious") + Andromonoecious = PermissibleValue(text="Andromonoecious") + Bisexual = PermissibleValue(text="Bisexual") + Dichogamous = PermissibleValue(text="Dichogamous") + Diclinous = PermissibleValue(text="Diclinous") + Dioecious = PermissibleValue(text="Dioecious") + Gynodioecious = PermissibleValue(text="Gynodioecious") + Gynoecious = PermissibleValue(text="Gynoecious") + Gynomonoecious = PermissibleValue(text="Gynomonoecious") + Hermaphroditic = PermissibleValue(text="Hermaphroditic") + Imperfect = PermissibleValue(text="Imperfect") + Monoclinous = PermissibleValue(text="Monoclinous") + Monoecious = PermissibleValue(text="Monoecious") + Perfect = PermissibleValue(text="Perfect") + Polygamodioecious = PermissibleValue(text="Polygamodioecious") + Polygamomonoecious = PermissibleValue(text="Polygamomonoecious") + Polygamous = PermissibleValue(text="Polygamous") + Protandrous = PermissibleValue(text="Protandrous") + Protogynous = PermissibleValue(text="Protogynous") + Subandroecious = PermissibleValue(text="Subandroecious") + Subdioecious = PermissibleValue(text="Subdioecious") + Subgynoecious = PermissibleValue(text="Subgynoecious") + Synoecious = PermissibleValue(text="Synoecious") + Trimonoecious = PermissibleValue(text="Trimonoecious") + Trioecious = PermissibleValue(text="Trioecious") + Unisexual = PermissibleValue(text="Unisexual") _defn = EnumDefinition( - name="WeekdayEnum", + name="PlantSexEnum", ) -class ArchStrucEnum(EnumDefinitionImpl): - - building = PermissibleValue(text="building") - shed = PermissibleValue(text="shed") - home = PermissibleValue(text="home") - - _defn = EnumDefinition( - name="ArchStrucEnum", - ) +class SpecificEnum(EnumDefinitionImpl): -class HeatCoolTypeEnum(EnumDefinitionImpl): + operation = PermissibleValue(text="operation") + construction = PermissibleValue(text="construction") + bid = PermissibleValue(text="bid") + design = PermissibleValue(text="design") + photos = PermissibleValue(text="photos") _defn = EnumDefinition( - name="HeatCoolTypeEnum", + name="SpecificEnum", ) @classmethod def _addvals(cls): - setattr(cls, "radiant system", - PermissibleValue(text="radiant system")) - setattr(cls, "heat pump", - PermissibleValue(text="heat pump")) - setattr(cls, "forced air system", - PermissibleValue(text="forced air system")) - setattr(cls, "steam forced heat", - PermissibleValue(text="steam forced heat")) - setattr(cls, "wood stove", - PermissibleValue(text="wood stove")) - -class SampMdEnum(EnumDefinitionImpl): - - DF = PermissibleValue(text="DF") - RT = PermissibleValue(text="RT") - KB = PermissibleValue(text="KB") - MSL = PermissibleValue(text="MSL") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="SampMdEnum", - ) + setattr(cls, "as built", + PermissibleValue(text="as built")) class ExtWallOrientEnum(EnumDefinitionImpl): @@ -7753,203 +7641,224 @@ class ExtWallOrientEnum(EnumDefinitionImpl): name="ExtWallOrientEnum", ) -class MechStrucEnum(EnumDefinitionImpl): - - subway = PermissibleValue(text="subway") - coach = PermissibleValue(text="coach") - carriage = PermissibleValue(text="carriage") - elevator = PermissibleValue(text="elevator") - escalator = PermissibleValue(text="escalator") - boat = PermissibleValue(text="boat") - train = PermissibleValue(text="train") - car = PermissibleValue(text="car") - bus = PermissibleValue(text="bus") - - _defn = EnumDefinition( - name="MechStrucEnum", - ) - -class ExtWindowOrientEnum(EnumDefinitionImpl): +class DoorLocEnum(EnumDefinitionImpl): north = PermissibleValue(text="north") south = PermissibleValue(text="south") east = PermissibleValue(text="east") west = PermissibleValue(text="west") - northeast = PermissibleValue(text="northeast") - southeast = PermissibleValue(text="southeast") - southwest = PermissibleValue(text="southwest") - northwest = PermissibleValue(text="northwest") _defn = EnumDefinition( - name="ExtWindowOrientEnum", + name="DoorLocEnum", ) -class WindowCoverEnum(EnumDefinitionImpl): +class ProfilePositionEnum(EnumDefinitionImpl): - blinds = PermissibleValue(text="blinds") - curtains = PermissibleValue(text="curtains") - none = PermissibleValue(text="none") + summit = PermissibleValue(text="summit") + shoulder = PermissibleValue(text="shoulder") + backslope = PermissibleValue(text="backslope") + footslope = PermissibleValue(text="footslope") + toeslope = PermissibleValue(text="toeslope") _defn = EnumDefinition( - name="WindowCoverEnum", + name="ProfilePositionEnum", ) -class DrainageClassEnum(EnumDefinitionImpl): +class GrowthHabitEnum(EnumDefinitionImpl): - poorly = PermissibleValue(text="poorly") - well = PermissibleValue(text="well") + erect = PermissibleValue(text="erect") + spreading = PermissibleValue(text="spreading") + prostrate = PermissibleValue(text="prostrate") _defn = EnumDefinition( - name="DrainageClassEnum", + name="GrowthHabitEnum", ) @classmethod def _addvals(cls): - setattr(cls, "very poorly", - PermissibleValue(text="very poorly")) - setattr(cls, "somewhat poorly", - PermissibleValue(text="somewhat poorly")) - setattr(cls, "moderately well", - PermissibleValue(text="moderately well")) - setattr(cls, "excessively drained", - PermissibleValue(text="excessively drained")) + setattr(cls, "semi-erect", + PermissibleValue(text="semi-erect")) -class WindowHorizPosEnum(EnumDefinitionImpl): +class SeasonUseEnum(EnumDefinitionImpl): - left = PermissibleValue(text="left") - middle = PermissibleValue(text="middle") - right = PermissibleValue(text="right") + Spring = PermissibleValue(text="Spring") + Summer = PermissibleValue(text="Summer") + Fall = PermissibleValue(text="Fall") + Winter = PermissibleValue(text="Winter") _defn = EnumDefinition( - name="WindowHorizPosEnum", + name="SeasonUseEnum", ) -class SampSubtypeEnum(EnumDefinitionImpl): +class CeilFinishMatEnum(EnumDefinitionImpl): - biofilm = PermissibleValue(text="biofilm") - other = PermissibleValue(text="other") + drywall = PermissibleValue(text="drywall") + tiles = PermissibleValue(text="tiles") + PVC = PermissibleValue(text="PVC") + plasterboard = PermissibleValue(text="plasterboard") + metal = PermissibleValue(text="metal") + fiberglass = PermissibleValue(text="fiberglass") + stucco = PermissibleValue(text="stucco") + wood = PermissibleValue(text="wood") _defn = EnumDefinition( - name="SampSubtypeEnum", + name="CeilFinishMatEnum", ) @classmethod def _addvals(cls): - setattr(cls, "oil phase", - PermissibleValue(text="oil phase")) - setattr(cls, "water phase", - PermissibleValue(text="water phase")) - setattr(cls, "not applicable", - PermissibleValue(text="not applicable")) + setattr(cls, "mineral fibre", + PermissibleValue(text="mineral fibre")) + setattr(cls, "mineral wool/calcium silicate", + PermissibleValue(text="mineral wool/calcium silicate")) -class CeilTextureEnum(EnumDefinitionImpl): +class TillageEnum(EnumDefinitionImpl): - knockdown = PermissibleValue(text="knockdown") - popcorn = PermissibleValue(text="popcorn") - smooth = PermissibleValue(text="smooth") - swirl = PermissibleValue(text="swirl") + drill = PermissibleValue(text="drill") + chisel = PermissibleValue(text="chisel") + tined = PermissibleValue(text="tined") + mouldboard = PermissibleValue(text="mouldboard") _defn = EnumDefinition( - name="CeilTextureEnum", + name="TillageEnum", ) @classmethod def _addvals(cls): - setattr(cls, "crows feet", - PermissibleValue(text="crows feet")) - setattr(cls, "crows-foot stomp", - PermissibleValue(text="crows-foot stomp")) - setattr(cls, "double skip", - PermissibleValue(text="double skip")) - setattr(cls, "hawk and trowel", - PermissibleValue(text="hawk and trowel")) - setattr(cls, "orange peel", - PermissibleValue(text="orange peel")) - setattr(cls, "rosebud stomp", - PermissibleValue(text="rosebud stomp")) - setattr(cls, "Santa-Fe texture", - PermissibleValue(text="Santa-Fe texture")) - setattr(cls, "skip trowel", - PermissibleValue(text="skip trowel")) - setattr(cls, "stomp knockdown", - PermissibleValue(text="stomp knockdown")) + setattr(cls, "cutting disc", + PermissibleValue(text="cutting disc")) + setattr(cls, "ridge till", + PermissibleValue(text="ridge till")) + setattr(cls, "strip tillage", + PermissibleValue(text="strip tillage")) + setattr(cls, "zonal tillage", + PermissibleValue(text="zonal tillage")) + setattr(cls, "disc plough", + PermissibleValue(text="disc plough")) -class RoomSampPosEnum(EnumDefinitionImpl): +class WindowTypeEnum(EnumDefinitionImpl): - center = PermissibleValue(text="center") + _defn = EnumDefinition( + name="WindowTypeEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "single-hung sash window", + PermissibleValue(text="single-hung sash window")) + setattr(cls, "horizontal sash window", + PermissibleValue(text="horizontal sash window")) + setattr(cls, "fixed window", + PermissibleValue(text="fixed window")) + +class CeilCondEnum(EnumDefinitionImpl): + + new = PermissibleValue(text="new") + damaged = PermissibleValue(text="damaged") + rupture = PermissibleValue(text="rupture") _defn = EnumDefinition( - name="RoomSampPosEnum", + name="CeilCondEnum", ) @classmethod def _addvals(cls): - setattr(cls, "north corner", - PermissibleValue(text="north corner")) - setattr(cls, "south corner", - PermissibleValue(text="south corner")) - setattr(cls, "west corner", - PermissibleValue(text="west corner")) - setattr(cls, "east corner", - PermissibleValue(text="east corner")) - setattr(cls, "northeast corner", - PermissibleValue(text="northeast corner")) - setattr(cls, "northwest corner", - PermissibleValue(text="northwest corner")) - setattr(cls, "southeast corner", - PermissibleValue(text="southeast corner")) - setattr(cls, "southwest corner", - PermissibleValue(text="southwest corner")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) -class IndoorSurfEnum(EnumDefinitionImpl): +class HcrGeolAgeEnum(EnumDefinitionImpl): - cabinet = PermissibleValue(text="cabinet") - ceiling = PermissibleValue(text="ceiling") - door = PermissibleValue(text="door") - shelving = PermissibleValue(text="shelving") - window = PermissibleValue(text="window") - wall = PermissibleValue(text="wall") + Archean = PermissibleValue(text="Archean") + Cambrian = PermissibleValue(text="Cambrian") + Carboniferous = PermissibleValue(text="Carboniferous") + Cenozoic = PermissibleValue(text="Cenozoic") + Cretaceous = PermissibleValue(text="Cretaceous") + Devonian = PermissibleValue(text="Devonian") + Jurassic = PermissibleValue(text="Jurassic") + Mesozoic = PermissibleValue(text="Mesozoic") + Neogene = PermissibleValue(text="Neogene") + Ordovician = PermissibleValue(text="Ordovician") + Paleogene = PermissibleValue(text="Paleogene") + Paleozoic = PermissibleValue(text="Paleozoic") + Permian = PermissibleValue(text="Permian") + Precambrian = PermissibleValue(text="Precambrian") + Proterozoic = PermissibleValue(text="Proterozoic") + Silurian = PermissibleValue(text="Silurian") + Triassic = PermissibleValue(text="Triassic") + other = PermissibleValue(text="other") + + _defn = EnumDefinition( + name="HcrGeolAgeEnum", + ) + +class DoorCondEnum(EnumDefinitionImpl): + + damaged = PermissibleValue(text="damaged") + new = PermissibleValue(text="new") + rupture = PermissibleValue(text="rupture") _defn = EnumDefinition( - name="IndoorSurfEnum", + name="DoorCondEnum", ) @classmethod def _addvals(cls): - setattr(cls, "counter top", - PermissibleValue(text="counter top")) - setattr(cls, "vent cover", - PermissibleValue(text="vent cover")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) -class OrganismCountEnum(EnumDefinitionImpl): +class LithologyEnum(EnumDefinitionImpl): - ATP = PermissibleValue(text="ATP") - MPN = PermissibleValue(text="MPN") + Basement = PermissibleValue(text="Basement") + Chalk = PermissibleValue(text="Chalk") + Chert = PermissibleValue(text="Chert") + Coal = PermissibleValue(text="Coal") + Conglomerate = PermissibleValue(text="Conglomerate") + Diatomite = PermissibleValue(text="Diatomite") + Dolomite = PermissibleValue(text="Dolomite") + Limestone = PermissibleValue(text="Limestone") + Sandstone = PermissibleValue(text="Sandstone") + Shale = PermissibleValue(text="Shale") + Siltstone = PermissibleValue(text="Siltstone") + Volcanic = PermissibleValue(text="Volcanic") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="OrganismCountEnum", + name="LithologyEnum", ) -class VisMediaEnum(EnumDefinitionImpl): - - photos = PermissibleValue(text="photos") - videos = PermissibleValue(text="videos") - interiors = PermissibleValue(text="interiors") - equipment = PermissibleValue(text="equipment") +class HeatCoolTypeEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="VisMediaEnum", + name="HeatCoolTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "commonly of the building", - PermissibleValue(text="commonly of the building")) - setattr(cls, "site context (adjacent buildings, vegetation, terrain, streets)", - PermissibleValue(text="site context (adjacent buildings, vegetation, terrain, streets)")) - setattr(cls, "3D scans", - PermissibleValue(text="3D scans")) + setattr(cls, "radiant system", + PermissibleValue(text="radiant system")) + setattr(cls, "heat pump", + PermissibleValue(text="heat pump")) + setattr(cls, "forced air system", + PermissibleValue(text="forced air system")) + setattr(cls, "steam forced heat", + PermissibleValue(text="steam forced heat")) + setattr(cls, "wood stove", + PermissibleValue(text="wood stove")) + +class BuildingSettingEnum(EnumDefinitionImpl): + + urban = PermissibleValue(text="urban") + suburban = PermissibleValue(text="suburban") + exurban = PermissibleValue(text="exurban") + rural = PermissibleValue(text="rural") + + _defn = EnumDefinition( + name="BuildingSettingEnum", + ) class RoomCondtEnum(EnumDefinitionImpl): @@ -7970,46 +7879,40 @@ def _addvals(cls): setattr(cls, "visible signs of mold/mildew", PermissibleValue(text="visible signs of mold/mildew")) -class SampCollectPointEnum(EnumDefinitionImpl): - - well = PermissibleValue(text="well") - wellhead = PermissibleValue(text="wellhead") - separator = PermissibleValue(text="separator") - other = PermissibleValue(text="other") +class RelSampLocEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="SampCollectPointEnum", + name="RelSampLocEnum", ) @classmethod def _addvals(cls): - setattr(cls, "test well", - PermissibleValue(text="test well")) - setattr(cls, "drilling rig", - PermissibleValue(text="drilling rig")) - setattr(cls, "storage tank", - PermissibleValue(text="storage tank")) + setattr(cls, "edge of car", + PermissibleValue(text="edge of car")) + setattr(cls, "center of car", + PermissibleValue(text="center of car")) + setattr(cls, "under a seat", + PermissibleValue(text="under a seat")) -class SampCaptStatusEnum(EnumDefinitionImpl): +class WallSurfTreatmentEnum(EnumDefinitionImpl): - other = PermissibleValue(text="other") + painted = PermissibleValue(text="painted") + paneling = PermissibleValue(text="paneling") + stucco = PermissibleValue(text="stucco") + fabric = PermissibleValue(text="fabric") _defn = EnumDefinition( - name="SampCaptStatusEnum", + name="WallSurfTreatmentEnum", ) @classmethod def _addvals(cls): - setattr(cls, "active surveillance in response to an outbreak", - PermissibleValue(text="active surveillance in response to an outbreak")) - setattr(cls, "active surveillance not initiated by an outbreak", - PermissibleValue(text="active surveillance not initiated by an outbreak")) - setattr(cls, "farm sample", - PermissibleValue(text="farm sample")) - setattr(cls, "market sample", - PermissibleValue(text="market sample")) + setattr(cls, "wall paper", + PermissibleValue(text="wall paper")) + setattr(cls, "no treatment", + PermissibleValue(text="no treatment")) -class RoomTypeEnum(EnumDefinitionImpl): +class RoomConnectedEnum(EnumDefinitionImpl): attic = PermissibleValue(text="attic") bathroom = PermissibleValue(text="bathroom") @@ -8017,20 +7920,11 @@ class RoomTypeEnum(EnumDefinitionImpl): elevator = PermissibleValue(text="elevator") hallway = PermissibleValue(text="hallway") kitchen = PermissibleValue(text="kitchen") + office = PermissibleValue(text="office") stairwell = PermissibleValue(text="stairwell") - lobby = PermissibleValue(text="lobby") - vestibule = PermissibleValue(text="vestibule") - laboratory_wet = PermissibleValue(text="laboratory_wet") - laboratory_dry = PermissibleValue(text="laboratory_dry") - gymnasium = PermissibleValue(text="gymnasium") - natatorium = PermissibleValue(text="natatorium") - auditorium = PermissibleValue(text="auditorium") - lockers = PermissibleValue(text="lockers") - cafe = PermissibleValue(text="cafe") - warehouse = PermissibleValue(text="warehouse") _defn = EnumDefinition( - name="RoomTypeEnum", + name="RoomConnectedEnum", ) @classmethod @@ -8041,71 +7935,128 @@ def _addvals(cls): PermissibleValue(text="examining room")) setattr(cls, "mail room", PermissibleValue(text="mail room")) - setattr(cls, "private office", - PermissibleValue(text="private office")) - setattr(cls, "open office", - PermissibleValue(text="open office")) - setattr(cls, ",restroom", - PermissibleValue(text=",restroom")) - setattr(cls, "mechanical or electrical room", - PermissibleValue(text="mechanical or electrical room")) - setattr(cls, "data center", - PermissibleValue(text="data center")) -class SampDisStageEnum(EnumDefinitionImpl): +class WindowVertPosEnum(EnumDefinitionImpl): - dissemination = PermissibleValue(text="dissemination") - infection = PermissibleValue(text="infection") - inoculation = PermissibleValue(text="inoculation") - penetration = PermissibleValue(text="penetration") - other = PermissibleValue(text="other") + bottom = PermissibleValue(text="bottom") + middle = PermissibleValue(text="middle") + top = PermissibleValue(text="top") + low = PermissibleValue(text="low") + high = PermissibleValue(text="high") _defn = EnumDefinition( - name="SampDisStageEnum", + name="WindowVertPosEnum", + ) + +class WeekdayEnum(EnumDefinitionImpl): + + Monday = PermissibleValue(text="Monday") + Tuesday = PermissibleValue(text="Tuesday") + Wednesday = PermissibleValue(text="Wednesday") + Thursday = PermissibleValue(text="Thursday") + Friday = PermissibleValue(text="Friday") + Saturday = PermissibleValue(text="Saturday") + Sunday = PermissibleValue(text="Sunday") + + _defn = EnumDefinition( + name="WeekdayEnum", + ) + +class RoomSampPosEnum(EnumDefinitionImpl): + + center = PermissibleValue(text="center") + + _defn = EnumDefinition( + name="RoomSampPosEnum", ) @classmethod def _addvals(cls): - setattr(cls, "growth and reproduction", - PermissibleValue(text="growth and reproduction")) + setattr(cls, "north corner", + PermissibleValue(text="north corner")) + setattr(cls, "south corner", + PermissibleValue(text="south corner")) + setattr(cls, "west corner", + PermissibleValue(text="west corner")) + setattr(cls, "east corner", + PermissibleValue(text="east corner")) + setattr(cls, "northeast corner", + PermissibleValue(text="northeast corner")) + setattr(cls, "northwest corner", + PermissibleValue(text="northwest corner")) + setattr(cls, "southeast corner", + PermissibleValue(text="southeast corner")) + setattr(cls, "southwest corner", + PermissibleValue(text="southwest corner")) -class FloorCondEnum(EnumDefinitionImpl): +class DoorMatEnum(EnumDefinitionImpl): - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") + aluminum = PermissibleValue(text="aluminum") + fiberboard = PermissibleValue(text="fiberboard") + fiberglass = PermissibleValue(text="fiberglass") + metal = PermissibleValue(text="metal") + vinyl = PermissibleValue(text="vinyl") + wood = PermissibleValue(text="wood") _defn = EnumDefinition( - name="FloorCondEnum", + name="DoorMatEnum", ) @classmethod def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) + setattr(cls, "cellular PVC", + PermissibleValue(text="cellular PVC")) + setattr(cls, "engineered plastic", + PermissibleValue(text="engineered plastic")) + setattr(cls, "thermoplastic alloy", + PermissibleValue(text="thermoplastic alloy")) + setattr(cls, "wood/plastic composite", + PermissibleValue(text="wood/plastic composite")) -class LithologyEnum(EnumDefinitionImpl): +class BiolStatEnum(EnumDefinitionImpl): - Basement = PermissibleValue(text="Basement") - Chalk = PermissibleValue(text="Chalk") - Chert = PermissibleValue(text="Chert") - Coal = PermissibleValue(text="Coal") - Conglomerate = PermissibleValue(text="Conglomerate") - Diatomite = PermissibleValue(text="Diatomite") - Dolomite = PermissibleValue(text="Dolomite") - Limestone = PermissibleValue(text="Limestone") - Sandstone = PermissibleValue(text="Sandstone") - Shale = PermissibleValue(text="Shale") - Siltstone = PermissibleValue(text="Siltstone") - Volcanic = PermissibleValue(text="Volcanic") - other = PermissibleValue(text="other") + wild = PermissibleValue(text="wild") + natural = PermissibleValue(text="natural") + hybrid = PermissibleValue(text="hybrid") + mutant = PermissibleValue(text="mutant") + + _defn = EnumDefinition( + name="BiolStatEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "semi-natural", + PermissibleValue(text="semi-natural")) + setattr(cls, "inbred line", + PermissibleValue(text="inbred line")) + setattr(cls, "breeder's line", + PermissibleValue(text="breeder's line")) + setattr(cls, "clonal selection", + PermissibleValue(text="clonal selection")) + +class FloorStrucEnum(EnumDefinitionImpl): + + balcony = PermissibleValue(text="balcony") + concrete = PermissibleValue(text="concrete") _defn = EnumDefinition( - name="LithologyEnum", + name="FloorStrucEnum", ) + @classmethod + def _addvals(cls): + setattr(cls, "floating floor", + PermissibleValue(text="floating floor")) + setattr(cls, "glass floor", + PermissibleValue(text="glass floor")) + setattr(cls, "raised floor", + PermissibleValue(text="raised floor")) + setattr(cls, "sprung floor", + PermissibleValue(text="sprung floor")) + setattr(cls, "wood-framed", + PermissibleValue(text="wood-framed")) + class DoorTypeWoodEnum(EnumDefinitionImpl): battened = PermissibleValue(text="battened") @@ -8133,110 +8084,174 @@ def _addvals(cls): setattr(cls, "wire gauged", PermissibleValue(text="wire gauged")) -class WallFinishMatEnum(EnumDefinitionImpl): +class OrganismCountEnum(EnumDefinitionImpl): - plaster = PermissibleValue(text="plaster") - tile = PermissibleValue(text="tile") - terrazzo = PermissibleValue(text="terrazzo") - wood = PermissibleValue(text="wood") - metal = PermissibleValue(text="metal") - masonry = PermissibleValue(text="masonry") + ATP = PermissibleValue(text="ATP") + MPN = PermissibleValue(text="MPN") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="WallFinishMatEnum", + name="OrganismCountEnum", + ) + +class ShadingDeviceCondEnum(EnumDefinitionImpl): + + damaged = PermissibleValue(text="damaged") + new = PermissibleValue(text="new") + rupture = PermissibleValue(text="rupture") + + _defn = EnumDefinition( + name="ShadingDeviceCondEnum", ) @classmethod def _addvals(cls): - setattr(cls, "gypsum plaster", - PermissibleValue(text="gypsum plaster")) - setattr(cls, "veneer plaster", - PermissibleValue(text="veneer plaster")) - setattr(cls, "gypsum board", - PermissibleValue(text="gypsum board")) - setattr(cls, "stone facing", - PermissibleValue(text="stone facing")) - setattr(cls, "acoustical treatment", - PermissibleValue(text="acoustical treatment")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) -class GenderRestroomEnum(EnumDefinitionImpl): +class HcrEnum(EnumDefinitionImpl): - female = PermissibleValue(text="female") - male = PermissibleValue(text="male") - unisex = PermissibleValue(text="unisex") + Coalbed = PermissibleValue(text="Coalbed") + Shale = PermissibleValue(text="Shale") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="GenderRestroomEnum", + name="HcrEnum", ) @classmethod def _addvals(cls): - setattr(cls, "all gender", - PermissibleValue(text="all gender")) - setattr(cls, "gender neurtral", - PermissibleValue(text="gender neurtral")) - setattr(cls, "male and female", - PermissibleValue(text="male and female")) + setattr(cls, "Oil Reservoir", + PermissibleValue(text="Oil Reservoir")) + setattr(cls, "Gas Reservoir", + PermissibleValue(text="Gas Reservoir")) + setattr(cls, "Oil Sand", + PermissibleValue(text="Oil Sand")) + setattr(cls, "Tight Oil Reservoir", + PermissibleValue(text="Tight Oil Reservoir")) + setattr(cls, "Tight Gas Reservoir", + PermissibleValue(text="Tight Gas Reservoir")) -class IntWallCondEnum(EnumDefinitionImpl): +class MechStrucEnum(EnumDefinitionImpl): - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") + subway = PermissibleValue(text="subway") + coach = PermissibleValue(text="coach") + carriage = PermissibleValue(text="carriage") + elevator = PermissibleValue(text="elevator") + escalator = PermissibleValue(text="escalator") + boat = PermissibleValue(text="boat") + train = PermissibleValue(text="train") + car = PermissibleValue(text="car") + bus = PermissibleValue(text="bus") _defn = EnumDefinition( - name="IntWallCondEnum", + name="MechStrucEnum", + ) + +class HcProducedEnum(EnumDefinitionImpl): + + Oil = PermissibleValue(text="Oil") + Gas = PermissibleValue(text="Gas") + Bitumen = PermissibleValue(text="Bitumen") + other = PermissibleValue(text="other") + + _defn = EnumDefinition( + name="HcProducedEnum", ) @classmethod def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) + setattr(cls, "Gas-Condensate", + PermissibleValue(text="Gas-Condensate")) + setattr(cls, "Coalbed Methane", + PermissibleValue(text="Coalbed Methane")) -class FloorWaterMoldEnum(EnumDefinitionImpl): +class ShadingDeviceTypeEnum(EnumDefinitionImpl): - condensation = PermissibleValue(text="condensation") + tree = PermissibleValue(text="tree") + trellis = PermissibleValue(text="trellis") _defn = EnumDefinition( - name="FloorWaterMoldEnum", + name="ShadingDeviceTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "mold odor", - PermissibleValue(text="mold odor")) - setattr(cls, "wet floor", - PermissibleValue(text="wet floor")) - setattr(cls, "water stains", - PermissibleValue(text="water stains")) - setattr(cls, "wall discoloration", - PermissibleValue(text="wall discoloration")) - setattr(cls, "floor discoloration", - PermissibleValue(text="floor discoloration")) - setattr(cls, "ceiling discoloration", - PermissibleValue(text="ceiling discoloration")) - setattr(cls, "peeling paint or wallpaper", - PermissibleValue(text="peeling paint or wallpaper")) - setattr(cls, "bulging walls", - PermissibleValue(text="bulging walls")) + setattr(cls, "bahama shutters", + PermissibleValue(text="bahama shutters")) + setattr(cls, "exterior roll blind", + PermissibleValue(text="exterior roll blind")) + setattr(cls, "gambrel awning", + PermissibleValue(text="gambrel awning")) + setattr(cls, "hood awning", + PermissibleValue(text="hood awning")) + setattr(cls, "porchroller awning", + PermissibleValue(text="porchroller awning")) + setattr(cls, "sarasota shutters", + PermissibleValue(text="sarasota shutters")) + setattr(cls, "slatted aluminum", + PermissibleValue(text="slatted aluminum")) + setattr(cls, "solid aluminum awning", + PermissibleValue(text="solid aluminum awning")) + setattr(cls, "sun screen", + PermissibleValue(text="sun screen")) + setattr(cls, "venetian awning", + PermissibleValue(text="venetian awning")) -class SampFloorEnum(EnumDefinitionImpl): +class QuadPosEnum(EnumDefinitionImpl): - basement = PermissibleValue(text="basement") - lobby = PermissibleValue(text="lobby") + _defn = EnumDefinition( + name="QuadPosEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "North side", + PermissibleValue(text="North side")) + setattr(cls, "West side", + PermissibleValue(text="West side")) + setattr(cls, "South side", + PermissibleValue(text="South side")) + setattr(cls, "East side", + PermissibleValue(text="East side")) + +class SrKerogTypeEnum(EnumDefinitionImpl): + + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="SampFloorEnum", + name="SrKerogTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "1st floor", - PermissibleValue(text="1st floor")) - setattr(cls, "2nd floor", - PermissibleValue(text="2nd floor")) + setattr(cls, "Type I", + PermissibleValue(text="Type I")) + setattr(cls, "Type II", + PermissibleValue(text="Type II")) + setattr(cls, "Type III", + PermissibleValue(text="Type III")) + setattr(cls, "Type IV", + PermissibleValue(text="Type IV")) + +class FloorCondEnum(EnumDefinitionImpl): + + new = PermissibleValue(text="new") + damaged = PermissibleValue(text="damaged") + rupture = PermissibleValue(text="rupture") + + _defn = EnumDefinition( + name="FloorCondEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) class HeatDelivLocEnum(EnumDefinitionImpl): @@ -8249,214 +8264,223 @@ class HeatDelivLocEnum(EnumDefinitionImpl): name="HeatDelivLocEnum", ) -class BiolStatEnum(EnumDefinitionImpl): +class HostSexEnum(EnumDefinitionImpl): - wild = PermissibleValue(text="wild") - natural = PermissibleValue(text="natural") - hybrid = PermissibleValue(text="hybrid") - mutant = PermissibleValue(text="mutant") + female = PermissibleValue(text="female") + hermaphrodite = PermissibleValue(text="hermaphrodite") + male = PermissibleValue(text="male") + neuter = PermissibleValue(text="neuter") _defn = EnumDefinition( - name="BiolStatEnum", + name="HostSexEnum", + ) + +class WindowCondEnum(EnumDefinitionImpl): + + damaged = PermissibleValue(text="damaged") + new = PermissibleValue(text="new") + rupture = PermissibleValue(text="rupture") + + _defn = EnumDefinition( + name="WindowCondEnum", ) @classmethod def _addvals(cls): - setattr(cls, "semi-natural", - PermissibleValue(text="semi-natural")) - setattr(cls, "inbred line", - PermissibleValue(text="inbred line")) - setattr(cls, "breeder's line", - PermissibleValue(text="breeder's line")) - setattr(cls, "clonal selection", - PermissibleValue(text="clonal selection")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) -class ShadingDeviceTypeEnum(EnumDefinitionImpl): +class HandidnessEnum(EnumDefinitionImpl): + + ambidexterity = PermissibleValue(text="ambidexterity") + + _defn = EnumDefinition( + name="HandidnessEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "left handedness", + PermissibleValue(text="left handedness")) + setattr(cls, "mixed-handedness", + PermissibleValue(text="mixed-handedness")) + setattr(cls, "right handedness", + PermissibleValue(text="right handedness")) - tree = PermissibleValue(text="tree") - trellis = PermissibleValue(text="trellis") +class WallConstTypeEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="ShadingDeviceTypeEnum", + name="WallConstTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "bahama shutters", - PermissibleValue(text="bahama shutters")) - setattr(cls, "exterior roll blind", - PermissibleValue(text="exterior roll blind")) - setattr(cls, "gambrel awning", - PermissibleValue(text="gambrel awning")) - setattr(cls, "hood awning", - PermissibleValue(text="hood awning")) - setattr(cls, "porchroller awning", - PermissibleValue(text="porchroller awning")) - setattr(cls, "sarasota shutters", - PermissibleValue(text="sarasota shutters")) - setattr(cls, "slatted aluminum", - PermissibleValue(text="slatted aluminum")) - setattr(cls, "solid aluminum awning", - PermissibleValue(text="solid aluminum awning")) - setattr(cls, "sun screen", - PermissibleValue(text="sun screen")) - setattr(cls, "venetian awning", - PermissibleValue(text="venetian awning")) + setattr(cls, "frame construction", + PermissibleValue(text="frame construction")) + setattr(cls, "joisted masonry", + PermissibleValue(text="joisted masonry")) + setattr(cls, "light noncombustible", + PermissibleValue(text="light noncombustible")) + setattr(cls, "masonry noncombustible", + PermissibleValue(text="masonry noncombustible")) + setattr(cls, "modified fire resistive", + PermissibleValue(text="modified fire resistive")) + setattr(cls, "fire resistive", + PermissibleValue(text="fire resistive")) -class TrainStatLocEnum(EnumDefinitionImpl): +class BuildOccupTypeEnum(EnumDefinitionImpl): - riverside = PermissibleValue(text="riverside") + office = PermissibleValue(text="office") + market = PermissibleValue(text="market") + restaurant = PermissibleValue(text="restaurant") + residence = PermissibleValue(text="residence") + school = PermissibleValue(text="school") + residential = PermissibleValue(text="residential") + commercial = PermissibleValue(text="commercial") + airport = PermissibleValue(text="airport") _defn = EnumDefinition( - name="TrainStatLocEnum", + name="BuildOccupTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "south station above ground", - PermissibleValue(text="south station above ground")) - setattr(cls, "south station underground", - PermissibleValue(text="south station underground")) - setattr(cls, "south station amtrak", - PermissibleValue(text="south station amtrak")) - setattr(cls, "forest hills", - PermissibleValue(text="forest hills")) + setattr(cls, "low rise", + PermissibleValue(text="low rise")) + setattr(cls, "high rise", + PermissibleValue(text="high rise")) + setattr(cls, "wood framed", + PermissibleValue(text="wood framed")) + setattr(cls, "health care", + PermissibleValue(text="health care")) + setattr(cls, "sports complex", + PermissibleValue(text="sports complex")) -class WindowMatEnum(EnumDefinitionImpl): +class OxyStatSampEnum(EnumDefinitionImpl): - clad = PermissibleValue(text="clad") - fiberglass = PermissibleValue(text="fiberglass") - metal = PermissibleValue(text="metal") - vinyl = PermissibleValue(text="vinyl") - wood = PermissibleValue(text="wood") + aerobic = PermissibleValue(text="aerobic") + anaerobic = PermissibleValue(text="anaerobic") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="WindowMatEnum", + name="OxyStatSampEnum", ) -class SampWeatherEnum(EnumDefinitionImpl): +class FilterTypeEnum(EnumDefinitionImpl): - cloudy = PermissibleValue(text="cloudy") - foggy = PermissibleValue(text="foggy") - hail = PermissibleValue(text="hail") - rain = PermissibleValue(text="rain") - snow = PermissibleValue(text="snow") - sleet = PermissibleValue(text="sleet") - sunny = PermissibleValue(text="sunny") - windy = PermissibleValue(text="windy") + HEPA = PermissibleValue(text="HEPA") + electrostatic = PermissibleValue(text="electrostatic") _defn = EnumDefinition( - name="SampWeatherEnum", + name="FilterTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "clear sky", - PermissibleValue(text="clear sky")) + setattr(cls, "particulate air filter", + PermissibleValue(text="particulate air filter")) + setattr(cls, "chemical air filter", + PermissibleValue(text="chemical air filter")) + setattr(cls, "low-MERV pleated media", + PermissibleValue(text="low-MERV pleated media")) + setattr(cls, "gas-phase or ultraviolet air treatments", + PermissibleValue(text="gas-phase or ultraviolet air treatments")) -class BioticRelationshipEnum(EnumDefinitionImpl): +class SampFloorEnum(EnumDefinitionImpl): - parasite = PermissibleValue(text="parasite") - commensal = PermissibleValue(text="commensal") - symbiont = PermissibleValue(text="symbiont") + basement = PermissibleValue(text="basement") + lobby = PermissibleValue(text="lobby") _defn = EnumDefinition( - name="BioticRelationshipEnum", + name="SampFloorEnum", ) @classmethod def _addvals(cls): - setattr(cls, "free living", - PermissibleValue(text="free living")) + setattr(cls, "1st floor", + PermissibleValue(text="1st floor")) + setattr(cls, "2nd floor", + PermissibleValue(text="2nd floor")) -class DoorCondEnum(EnumDefinitionImpl): +class FurnitureEnum(EnumDefinitionImpl): - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") + cabinet = PermissibleValue(text="cabinet") + chair = PermissibleValue(text="chair") + desks = PermissibleValue(text="desks") _defn = EnumDefinition( - name="DoorCondEnum", + name="FurnitureEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - -class TrainLineEnum(EnumDefinitionImpl): +class SampDisStageEnum(EnumDefinitionImpl): - red = PermissibleValue(text="red") - green = PermissibleValue(text="green") - orange = PermissibleValue(text="orange") + dissemination = PermissibleValue(text="dissemination") + infection = PermissibleValue(text="infection") + inoculation = PermissibleValue(text="inoculation") + penetration = PermissibleValue(text="penetration") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="TrainLineEnum", + name="SampDisStageEnum", ) -class BuildDocsEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "growth and reproduction", + PermissibleValue(text="growth and reproduction")) - schedule = PermissibleValue(text="schedule") - sections = PermissibleValue(text="sections") - submittals = PermissibleValue(text="submittals") - windows = PermissibleValue(text="windows") +class SubstructureTypeEnum(EnumDefinitionImpl): + + crawlspace = PermissibleValue(text="crawlspace") + basement = PermissibleValue(text="basement") _defn = EnumDefinition( - name="BuildDocsEnum", + name="SubstructureTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "building information model", - PermissibleValue(text="building information model")) - setattr(cls, "commissioning report", - PermissibleValue(text="commissioning report")) - setattr(cls, "complaint logs", - PermissibleValue(text="complaint logs")) - setattr(cls, "contract administration", - PermissibleValue(text="contract administration")) - setattr(cls, "cost estimate", - PermissibleValue(text="cost estimate")) - setattr(cls, "janitorial schedules or logs", - PermissibleValue(text="janitorial schedules or logs")) - setattr(cls, "maintenance plans", - PermissibleValue(text="maintenance plans")) - setattr(cls, "shop drawings", - PermissibleValue(text="shop drawings")) - setattr(cls, "ventilation system", - PermissibleValue(text="ventilation system")) + setattr(cls, "slab on grade", + PermissibleValue(text="slab on grade")) -class DoorLocEnum(EnumDefinitionImpl): +class DoorCompTypeEnum(EnumDefinitionImpl): - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") + revolving = PermissibleValue(text="revolving") + sliding = PermissibleValue(text="sliding") + telescopic = PermissibleValue(text="telescopic") _defn = EnumDefinition( - name="DoorLocEnum", + name="DoorCompTypeEnum", ) -class SrKerogTypeEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "metal covered", + PermissibleValue(text="metal covered")) - other = PermissibleValue(text="other") +class PlantGrowthMedEnum(EnumDefinitionImpl): + + perlite = PermissibleValue(text="perlite") + pumice = PermissibleValue(text="pumice") + sand = PermissibleValue(text="sand") + soil = PermissibleValue(text="soil") + vermiculite = PermissibleValue(text="vermiculite") + water = PermissibleValue(text="water") _defn = EnumDefinition( - name="SrKerogTypeEnum", + name="PlantGrowthMedEnum", ) @classmethod def _addvals(cls): - setattr(cls, "Type I", - PermissibleValue(text="Type I")) - setattr(cls, "Type II", - PermissibleValue(text="Type II")) - setattr(cls, "Type III", - PermissibleValue(text="Type III")) - setattr(cls, "Type IV", - PermissibleValue(text="Type IV")) + setattr(cls, "other artificial liquid medium", + PermissibleValue(text="other artificial liquid medium")) + setattr(cls, "other artificial solid medium", + PermissibleValue(text="other artificial solid medium")) + setattr(cls, "peat moss", + PermissibleValue(text="peat moss")) # Slots class slots: @@ -11014,29 +11038,29 @@ class slots: slots.xylene = Slot(uri=MIXS['0000156'], name="xylene", curie=MIXS.curie('0000156'), model_uri=NMDC.xylene, domain=None, range=Optional[Union[dict, QuantityValue]]) -slots.investigation_field = Slot(uri=NMDC.investigation_field, name="investigation field", curie=NMDC.curie('investigation_field'), - model_uri=NMDC.investigation_field, domain=None, range=Optional[str]) +slots.has_unit = Slot(uri=NMDC.has_unit, name="has unit", curie=NMDC.curie('has_unit'), + model_uri=NMDC.has_unit, domain=None, range=Optional[str]) -slots.core_field = Slot(uri=NMDC.core_field, name="core field", curie=NMDC.curie('core_field'), - model_uri=NMDC.core_field, domain=None, range=Optional[str]) +slots.sequencing_field = Slot(uri=NMDC.sequencing_field, name="sequencing field", curie=NMDC.curie('sequencing_field'), + model_uri=NMDC.sequencing_field, domain=None, range=Optional[str]) -slots.nucleic_acid_sequence_source_field = Slot(uri=NMDC.nucleic_acid_sequence_source_field, name="nucleic acid sequence source field", curie=NMDC.curie('nucleic_acid_sequence_source_field'), - model_uri=NMDC.nucleic_acid_sequence_source_field, domain=None, range=Optional[str]) +slots.has_raw_value = Slot(uri=NMDC.has_raw_value, name="has raw value", curie=NMDC.curie('has_raw_value'), + model_uri=NMDC.has_raw_value, domain=None, range=Optional[str]) -slots.has_numeric_value = Slot(uri=NMDC.has_numeric_value, name="has numeric value", curie=NMDC.curie('has_numeric_value'), - model_uri=NMDC.has_numeric_value, domain=None, range=Optional[float]) +slots.core_field = Slot(uri=NMDC.core_field, name="core field", curie=NMDC.curie('core_field'), + model_uri=NMDC.core_field, domain=None, range=Optional[str]) slots.environment_field = Slot(uri=NMDC.environment_field, name="environment field", curie=NMDC.curie('environment_field'), model_uri=NMDC.environment_field, domain=None, range=Optional[str]) -slots.has_unit = Slot(uri=NMDC.has_unit, name="has unit", curie=NMDC.curie('has_unit'), - model_uri=NMDC.has_unit, domain=None, range=Optional[str]) +slots.has_numeric_value = Slot(uri=NMDC.has_numeric_value, name="has numeric value", curie=NMDC.curie('has_numeric_value'), + model_uri=NMDC.has_numeric_value, domain=None, range=Optional[float]) -slots.sequencing_field = Slot(uri=NMDC.sequencing_field, name="sequencing field", curie=NMDC.curie('sequencing_field'), - model_uri=NMDC.sequencing_field, domain=None, range=Optional[str]) +slots.nucleic_acid_sequence_source_field = Slot(uri=NMDC.nucleic_acid_sequence_source_field, name="nucleic acid sequence source field", curie=NMDC.curie('nucleic_acid_sequence_source_field'), + model_uri=NMDC.nucleic_acid_sequence_source_field, domain=None, range=Optional[str]) -slots.has_raw_value = Slot(uri=NMDC.has_raw_value, name="has raw value", curie=NMDC.curie('has_raw_value'), - model_uri=NMDC.has_raw_value, domain=None, range=Optional[str]) +slots.investigation_field = Slot(uri=NMDC.investigation_field, name="investigation field", curie=NMDC.curie('investigation_field'), + model_uri=NMDC.investigation_field, domain=None, range=Optional[str]) slots.chemical = Slot(uri=NMDC.chemical, name="chemical", curie=NMDC.curie('chemical'), model_uri=NMDC.chemical, domain=None, range=Optional[Union[str, ChemicalEntityId]]) @@ -11401,7 +11425,7 @@ class slots: pattern=re.compile(r'.*')) slots.MetaproteomicsAnalysisActivity_used = Slot(uri=NMDC.used, name="MetaproteomicsAnalysisActivity_used", curie=NMDC.curie('used'), - model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[Union[str, InstrumentId]], mappings = [PROV.used]) + model_uri=NMDC.MetaproteomicsAnalysisActivity_used, domain=MetaproteomicsAnalysisActivity, range=Optional[str], mappings = [PROV.used]) slots.MetaproteomicsAnalysisActivity_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysisActivity_id", curie=NMDC.curie('id'), model_uri=NMDC.MetaproteomicsAnalysisActivity_id, domain=MetaproteomicsAnalysisActivity, range=Union[str, MetaproteomicsAnalysisActivityId], diff --git a/nmdc_schema/nmdc_schema_accepting_legacy_ids.schema.json b/nmdc_schema/nmdc_schema_accepting_legacy_ids.schema.json index 95c3e7fd54..85e8b72a75 100644 --- a/nmdc_schema/nmdc_schema_accepting_legacy_ids.schema.json +++ b/nmdc_schema/nmdc_schema_accepting_legacy_ids.schema.json @@ -1400,7 +1400,7 @@ }, "lat_lon": { "$ref": "#/$defs/GeolocationValue", - "description": "This is currently a required field but it's not clear if this should be required for human hosts" + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system" }, "lbc_thirty": { "$ref": "#/$defs/QuantityValue", @@ -8152,5 +8152,5 @@ }, "title": "NMDC", "type": "object", - "version": "v8.0.0" + "version": "v8.1.0" } diff --git a/nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml b/nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml index 92ec2e59e3..a5617fb213 100644 --- a/nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml +++ b/nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml @@ -11,7 +11,7 @@ notes: - not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1 id: https://w3id.org/nmdc/nmdc -version: v8.0.0 +version: v8.1.0 license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: CATH: @@ -347,6 +347,10 @@ types: string: name: string description: A character string + notes: + - In RDF serializations, a slot with range of string is treated as a literal or + type xsd:string. If you are authoring schemas in LinkML YAML, the type is + referenced with the lower case "string". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Text @@ -355,6 +359,9 @@ types: integer: name: integer description: An integer + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "integer". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Integer @@ -363,6 +370,9 @@ types: boolean: name: boolean description: A binary (true or false) value + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "boolean". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Boolean @@ -372,6 +382,9 @@ types: float: name: float description: A real number that conforms to the xsd:float specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "float". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Float @@ -380,6 +393,9 @@ types: double: name: double description: A real number that conforms to the xsd:double specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "double". from_schema: https://w3id.org/nmdc/nmdc close_mappings: - schema:Float @@ -389,6 +405,9 @@ types: name: decimal description: A real number with arbitrary precision that conforms to the xsd:decimal specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "decimal". from_schema: https://w3id.org/nmdc/nmdc broad_mappings: - schema:Number @@ -400,17 +419,21 @@ types: particular day notes: - URI is dateTime because OWL reasoners do not work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "time". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Time base: XSDTime - uri: xsd:dateTime + uri: xsd:time repr: str date: name: date description: a date (year, month and day) in an idealized calendar notes: - URI is dateTime because OWL reasoners don't work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Date @@ -420,6 +443,9 @@ types: datetime: name: datetime description: The combination of a date and time + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "datetime". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:DateTime @@ -429,6 +455,9 @@ types: date_or_datetime: name: date_or_datetime description: Either a date or a datetime + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date_or_datetime". from_schema: https://w3id.org/nmdc/nmdc base: str uri: linkml:DateOrDatetime @@ -436,6 +465,9 @@ types: uriorcurie: name: uriorcurie description: a URI or a CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uriorcurie". from_schema: https://w3id.org/nmdc/nmdc base: URIorCURIE uri: xsd:anyURI @@ -444,6 +476,9 @@ types: name: curie conforms_to: https://www.w3.org/TR/curie/ description: a compact URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "curie". comments: - in RDF serializations this MUST be expanded to a URI - in non-RDF serializations MAY be serialized as the compact representation @@ -455,6 +490,9 @@ types: name: uri conforms_to: https://www.ietf.org/rfc/rfc3987.txt description: a complete URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uri". comments: - in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which @@ -468,6 +506,9 @@ types: ncname: name: ncname description: Prefix part of CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "ncname". from_schema: https://w3id.org/nmdc/nmdc base: NCName uri: xsd:string @@ -475,8 +516,11 @@ types: objectidentifier: name: objectidentifier description: A URI or CURIE that represents an object in the model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "objectidentifier". comments: - - Used for inheritence and type checking + - Used for inheritance and type checking from_schema: https://w3id.org/nmdc/nmdc base: ElementIdentifier uri: shex:iri @@ -484,10 +528,52 @@ types: nodeidentifier: name: nodeidentifier description: A URI, CURIE or BNODE that represents a node in a model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "nodeidentifier". from_schema: https://w3id.org/nmdc/nmdc base: NodeIdentifier uri: shex:nonLiteral repr: str + jsonpointer: + name: jsonpointer + conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 + description: A string encoding a JSON Pointer. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to a valid object within the current + instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpointer". + from_schema: https://w3id.org/nmdc/nmdc + base: str + uri: xsd:string + repr: str + jsonpath: + name: jsonpath + conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html + description: A string encoding a JSON Path. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to zero or more valid objects within + the current instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpath". + from_schema: https://w3id.org/nmdc/nmdc + base: str + uri: xsd:string + repr: str + sparqlpath: + name: sparqlpath + conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths + description: A string encoding a SPARQL Property Path. The value of the string + MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects + within the current instance document when encoded as RDF. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "sparqlpath". + from_schema: https://w3id.org/nmdc/nmdc + base: str + uri: xsd:string + repr: str enums: StatusEnum: name: StatusEnum @@ -1190,26 +1276,6 @@ enums: text: soil water_extract_soil: text: water_extract_soil - door_direct_enum: - name: door_direct_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - inward: - text: inward - outward: - text: outward - sideways: - text: sideways - oxy_stat_samp_enum: - name: oxy_stat_samp_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - aerobic: - text: aerobic - anaerobic: - text: anaerobic - other: - text: other surf_air_cont_enum: name: surf_air_cont_enum from_schema: https://w3id.org/nmdc/nmdc @@ -1230,164 +1296,164 @@ enums: text: nutrients biocides: text: biocides - window_vert_pos_enum: - name: window_vert_pos_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - bottom: - text: bottom - middle: - text: middle - top: - text: top - low: - text: low - high: - text: high - filter_type_enum: - name: filter_type_enum + water_feat_type_enum: + name: water_feat_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - particulate air filter: - text: particulate air filter - chemical air filter: - text: chemical air filter - low-MERV pleated media: - text: low-MERV pleated media - HEPA: - text: HEPA - electrostatic: - text: electrostatic - gas-phase or ultraviolet air treatments: - text: gas-phase or ultraviolet air treatments - rel_samp_loc_enum: - name: rel_samp_loc_enum + fountain: + text: fountain + pool: + text: pool + standing feature: + text: standing feature + stream: + text: stream + waterfall: + text: waterfall + samp_collect_point_enum: + name: samp_collect_point_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - edge of car: - text: edge of car - center of car: - text: center of car - under a seat: - text: under a seat - sediment_type_enum: - name: sediment_type_enum + well: + text: well + test well: + text: test well + drilling rig: + text: drilling rig + wellhead: + text: wellhead + separator: + text: separator + storage tank: + text: storage tank + other: + text: other + floor_water_mold_enum: + name: floor_water_mold_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - biogenous: - text: biogenous - cosmogenous: - text: cosmogenous - hydrogenous: - text: hydrogenous - lithogenous: - text: lithogenous - occup_document_enum: - name: occup_document_enum + mold odor: + text: mold odor + wet floor: + text: wet floor + water stains: + text: water stains + wall discoloration: + text: wall discoloration + floor discoloration: + text: floor discoloration + ceiling discoloration: + text: ceiling discoloration + peeling paint or wallpaper: + text: peeling paint or wallpaper + bulging walls: + text: bulging walls + condensation: + text: condensation + wall_texture_enum: + name: wall_texture_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - automated count: - text: automated count - estimate: - text: estimate - manual count: - text: manual count - videos: - text: videos - room_connected_enum: - name: room_connected_enum + crows feet: + text: crows feet + crows-foot stomp: + text: crows-foot stomp + ? '' + : text: '' + double skip: + text: double skip + hawk and trowel: + text: hawk and trowel + knockdown: + text: knockdown + popcorn: + text: popcorn + orange peel: + text: orange peel + rosebud stomp: + text: rosebud stomp + Santa-Fe texture: + text: Santa-Fe texture + skip trowel: + text: skip trowel + smooth: + text: smooth + stomp knockdown: + text: stomp knockdown + swirl: + text: swirl + samp_subtype_enum: + name: samp_subtype_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - attic: - text: attic - bathroom: - text: bathroom - closet: - text: closet - conference room: - text: conference room - elevator: - text: elevator - examining room: - text: examining room - hallway: - text: hallway - kitchen: - text: kitchen - mail room: - text: mail room - office: - text: office - stairwell: - text: stairwell - quad_pos_enum: - name: quad_pos_enum + oil phase: + text: oil phase + water phase: + text: water phase + biofilm: + text: biofilm + not applicable: + text: not applicable + other: + text: other + drainage_class_enum: + name: drainage_class_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - North side: - text: North side - West side: - text: West side - South side: - text: South side - East side: - text: East side - sr_geol_age_enum: - name: sr_geol_age_enum + very poorly: + text: very poorly + poorly: + text: poorly + somewhat poorly: + text: somewhat poorly + moderately well: + text: moderately well + well: + text: well + excessively drained: + text: excessively drained + freq_clean_enum: + name: freq_clean_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Archean: - text: Archean - Cambrian: - text: Cambrian - Carboniferous: - text: Carboniferous - Cenozoic: - text: Cenozoic - Cretaceous: - text: Cretaceous - Devonian: - text: Devonian - Jurassic: - text: Jurassic - Mesozoic: - text: Mesozoic - Neogene: - text: Neogene - Ordovician: - text: Ordovician - Paleogene: - text: Paleogene - Paleozoic: - text: Paleozoic - Permian: - text: Permian - Precambrian: - text: Precambrian - Proterozoic: - text: Proterozoic - Silurian: - text: Silurian - Triassic: - text: Triassic + Daily: + text: Daily + Weekly: + text: Weekly + Monthly: + text: Monthly + Quarterly: + text: Quarterly + Annually: + text: Annually other: text: other - door_move_enum: - name: door_move_enum + biotic_relationship_enum: + name: biotic_relationship_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - collapsible: - text: collapsible - folding: - text: folding - revolving: - text: revolving - rolling shutter: - text: rolling shutter - sliding: - text: sliding - swinging: - text: swinging + free living: + text: free living + parasite: + text: parasite + commensal: + text: commensal + symbiont: + text: symbiont + light_type_enum: + name: light_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + natural light: + text: natural light + electric light: + text: electric light + desk lamp: + text: desk lamp + flourescent lights: + text: flourescent lights + none: + text: none cur_land_use_enum: name: cur_land_use_enum from_schema: https://w3id.org/nmdc/nmdc @@ -1583,142 +1649,146 @@ enums: value: vine crops (grapes) examples: - value: grapes - hcr_geol_age_enum: - name: hcr_geol_age_enum + drawings_enum: + name: drawings_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Archean: - text: Archean - Cambrian: - text: Cambrian - Carboniferous: - text: Carboniferous - Cenozoic: - text: Cenozoic - Cretaceous: - text: Cretaceous - Devonian: - text: Devonian - Jurassic: - text: Jurassic - Mesozoic: - text: Mesozoic - Neogene: - text: Neogene - Ordovician: - text: Ordovician - Paleogene: - text: Paleogene - Paleozoic: - text: Paleozoic - Permian: - text: Permian - Precambrian: - text: Precambrian - Proterozoic: - text: Proterozoic - Silurian: - text: Silurian - Triassic: - text: Triassic + operation: + text: operation + as built: + text: as built + construction: + text: construction + bid: + text: bid + design: + text: design + building navigation map: + text: building navigation map + diagram: + text: diagram + sketch: + text: sketch + indoor_surf_enum: + name: indoor_surf_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + cabinet: + text: cabinet + ceiling: + text: ceiling + counter top: + text: counter top + door: + text: door + shelving: + text: shelving + vent cover: + text: vent cover + window: + text: window + wall: + text: wall + samp_capt_status_enum: + name: samp_capt_status_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + active surveillance in response to an outbreak: + text: active surveillance in response to an outbreak + active surveillance not initiated by an outbreak: + text: active surveillance not initiated by an outbreak + farm sample: + text: farm sample + market sample: + text: market sample other: text: other - wall_const_type_enum: - name: wall_const_type_enum + room_loc_enum: + name: room_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - frame construction: - text: frame construction - joisted masonry: - text: joisted masonry - light noncombustible: - text: light noncombustible - masonry noncombustible: - text: masonry noncombustible - modified fire resistive: - text: modified fire resistive - fire resistive: - text: fire resistive - plant_sex_enum: - name: plant_sex_enum + corner room: + text: corner room + interior room: + text: interior room + exterior wall: + text: exterior wall + occup_document_enum: + name: occup_document_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Androdioecious: - text: Androdioecious - Androecious: - text: Androecious - Androgynous: - text: Androgynous - Androgynomonoecious: - text: Androgynomonoecious - Andromonoecious: - text: Andromonoecious - Bisexual: - text: Bisexual - Dichogamous: - text: Dichogamous - Diclinous: - text: Diclinous - Dioecious: - text: Dioecious - Gynodioecious: - text: Gynodioecious - Gynoecious: - text: Gynoecious - Gynomonoecious: - text: Gynomonoecious - Hermaphroditic: - text: Hermaphroditic - Imperfect: - text: Imperfect - Monoclinous: - text: Monoclinous - Monoecious: - text: Monoecious - Perfect: - text: Perfect - Polygamodioecious: - text: Polygamodioecious - Polygamomonoecious: - text: Polygamomonoecious - Polygamous: - text: Polygamous - Protandrous: - text: Protandrous - Protogynous: - text: Protogynous - Subandroecious: - text: Subandroecious - Subdioecious: - text: Subdioecious - Subgynoecious: - text: Subgynoecious - Synoecious: - text: Synoecious - Trimonoecious: - text: Trimonoecious - Trioecious: - text: Trioecious - Unisexual: - text: Unisexual - ceil_type_enum: - name: ceil_type_enum + automated count: + text: automated count + estimate: + text: estimate + manual count: + text: manual count + videos: + text: videos + arch_struc_enum: + name: arch_struc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - cathedral: - text: cathedral - dropped: - text: dropped - concave: - text: concave - barrel-shaped: - text: barrel-shaped - coffered: - text: coffered - cove: - text: cove - stretched: - text: stretched + building: + text: building + shed: + text: shed + home: + text: home + wall_finish_mat_enum: + name: wall_finish_mat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + plaster: + text: plaster + gypsum plaster: + text: gypsum plaster + veneer plaster: + text: veneer plaster + gypsum board: + text: gypsum board + tile: + text: tile + terrazzo: + text: terrazzo + stone facing: + text: stone facing + acoustical treatment: + text: acoustical treatment + wood: + text: wood + metal: + text: metal + masonry: + text: masonry + window_mat_enum: + name: window_mat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + clad: + text: clad + fiberglass: + text: fiberglass + metal: + text: metal + vinyl: + text: vinyl + wood: + text: wood + int_wall_cond_enum: + name: int_wall_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture floor_finish_mat_enum: name: floor_finish_mat_enum from_schema: https://w3id.org/nmdc/nmdc @@ -1759,584 +1829,240 @@ enums: text: paint none or unfinished: text: none or unfinished - wall_loc_enum: - name: wall_loc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - wall_surf_treatment_enum: - name: wall_surf_treatment_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - painted: - text: painted - wall paper: - text: wall paper - no treatment: - text: no treatment - paneling: - text: paneling - stucco: - text: stucco - fabric: - text: fabric - window_cond_enum: - name: window_cond_enum + build_docs_enum: + name: build_docs_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - door_mat_enum: - name: door_mat_enum + building information model: + text: building information model + commissioning report: + text: commissioning report + complaint logs: + text: complaint logs + contract administration: + text: contract administration + cost estimate: + text: cost estimate + janitorial schedules or logs: + text: janitorial schedules or logs + maintenance plans: + text: maintenance plans + schedule: + text: schedule + sections: + text: sections + shop drawings: + text: shop drawings + submittals: + text: submittals + ventilation system: + text: ventilation system + windows: + text: windows + surf_material_enum: + name: surf_material_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - aluminum: - text: aluminum - cellular PVC: - text: cellular PVC - engineered plastic: - text: engineered plastic - fiberboard: - text: fiberboard - fiberglass: - text: fiberglass + adobe: + text: adobe + carpet: + text: carpet + cinder blocks: + text: cinder blocks + concrete: + text: concrete + hay bales: + text: hay bales + glass: + text: glass metal: text: metal - thermoplastic alloy: - text: thermoplastic alloy + paint: + text: paint + plastic: + text: plastic + stainless steel: + text: stainless steel + stone: + text: stone + stucco: + text: stucco + tile: + text: tile vinyl: text: vinyl wood: text: wood - wood/plastic composite: - text: wood/plastic composite - soil_horizon_enum: - name: soil_horizon_enum + tidal_stage_enum: + name: tidal_stage_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - O horizon: - text: O horizon - A horizon: - text: A horizon - E horizon: - text: E horizon - B horizon: - text: B horizon - C horizon: - text: C horizon - R layer: - text: R layer - Permafrost: - text: Permafrost - M horizon: - text: M horizon - ceil_finish_mat_enum: - name: ceil_finish_mat_enum + low tide: + text: low tide + ebb tide: + text: ebb tide + flood tide: + text: flood tide + high tide: + text: high tide + window_horiz_pos_enum: + name: window_horiz_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - drywall: - text: drywall - mineral fibre: - text: mineral fibre - tiles: - text: tiles - PVC: - text: PVC - plasterboard: - text: plasterboard - metal: - text: metal - fiberglass: - text: fiberglass - stucco: - text: stucco - mineral wool/calcium silicate: - text: mineral wool/calcium silicate - wood: - text: wood - shading_device_cond_enum: - name: shading_device_cond_enum + left: + text: left + middle: + text: middle + right: + text: right + train_stop_loc_enum: + name: train_stop_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - hc_produced_enum: - name: hc_produced_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Oil: - text: Oil - Gas-Condensate: - text: Gas-Condensate - Gas: - text: Gas - Bitumen: - text: Bitumen - Coalbed Methane: - text: Coalbed Methane - other: - text: other - door_comp_type_enum: - name: door_comp_type_enum + end: + text: end + mid: + text: mid + downtown: + text: downtown + train_line_enum: + name: train_line_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - metal covered: - text: metal covered - revolving: - text: revolving - sliding: - text: sliding - telescopic: - text: telescopic - window_loc_enum: - name: window_loc_enum + red: + text: red + green: + text: green + orange: + text: orange + train_stat_loc_enum: + name: train_stat_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - sr_lithology_enum: - name: sr_lithology_enum + south station above ground: + text: south station above ground + south station underground: + text: south station underground + south station amtrak: + text: south station amtrak + forest hills: + text: forest hills + riverside: + text: riverside + sr_dep_env_enum: + name: sr_dep_env_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Clastic: - text: Clastic - Carbonate: - text: Carbonate - Coal: - text: Coal - Biosilicieous: - text: Biosilicieous + Lacustine: + text: Lacustine + Fluvioldeltaic: + text: Fluvioldeltaic + Fluviomarine: + text: Fluviomarine + Marine: + text: Marine other: text: other - plant_growth_med_enum: - name: plant_growth_med_enum + samp_weather_enum: + name: samp_weather_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - other artificial liquid medium: - text: other artificial liquid medium - other artificial solid medium: - text: other artificial solid medium - peat moss: - text: peat moss - perlite: - text: perlite - pumice: - text: pumice - sand: - text: sand - soil: - text: soil - vermiculite: - text: vermiculite - water: - text: water - surf_material_enum: - name: surf_material_enum + clear sky: + text: clear sky + cloudy: + text: cloudy + foggy: + text: foggy + hail: + text: hail + rain: + text: rain + snow: + text: snow + sleet: + text: sleet + sunny: + text: sunny + windy: + text: windy + window_cover_enum: + name: window_cover_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - adobe: - text: adobe - carpet: - text: carpet - cinder blocks: - text: cinder blocks - concrete: - text: concrete - hay bales: - text: hay bales - glass: - text: glass - metal: - text: metal - paint: - text: paint - plastic: - text: plastic - stainless steel: - text: stainless steel - stone: - text: stone - stucco: - text: stucco - tile: - text: tile - vinyl: - text: vinyl - wood: - text: wood - ceil_cond_enum: - name: ceil_cond_enum + blinds: + text: blinds + curtains: + text: curtains + none: + text: none + room_type_enum: + name: room_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - building_setting_enum: - name: building_setting_enum + attic: + text: attic + bathroom: + text: bathroom + closet: + text: closet + conference room: + text: conference room + elevator: + text: elevator + examining room: + text: examining room + hallway: + text: hallway + kitchen: + text: kitchen + mail room: + text: mail room + private office: + text: private office + open office: + text: open office + stairwell: + text: stairwell + ',restroom': + text: ',restroom' + lobby: + text: lobby + vestibule: + text: vestibule + mechanical or electrical room: + text: mechanical or electrical room + data center: + text: data center + laboratory_wet: + text: laboratory_wet + laboratory_dry: + text: laboratory_dry + gymnasium: + text: gymnasium + natatorium: + text: natatorium + auditorium: + text: auditorium + lockers: + text: lockers + cafe: + text: cafe + warehouse: + text: warehouse + sediment_type_enum: + name: sediment_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - urban: - text: urban - suburban: - text: suburban - exurban: - text: exurban - rural: - text: rural - build_occup_type_enum: - name: build_occup_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - office: - text: office - market: - text: market - restaurant: - text: restaurant - residence: - text: residence - school: - text: school - residential: - text: residential - commercial: - text: commercial - low rise: - text: low rise - high rise: - text: high rise - wood framed: - text: wood framed - health care: - text: health care - airport: - text: airport - sports complex: - text: sports complex - depos_env_enum: - name: depos_env_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Continental - Alluvial: - text: Continental - Alluvial - Continental - Aeolian: - text: Continental - Aeolian - Continental - Fluvial: - text: Continental - Fluvial - Continental - Lacustrine: - text: Continental - Lacustrine - Transitional - Deltaic: - text: Transitional - Deltaic - Transitional - Tidal: - text: Transitional - Tidal - Transitional - Lagoonal: - text: Transitional - Lagoonal - Transitional - Beach: - text: Transitional - Beach - Transitional - Lake: - text: Transitional - Lake - Marine - Shallow: - text: Marine - Shallow - Marine - Deep: - text: Marine - Deep - Marine - Reef: - text: Marine - Reef - Other - Evaporite: - text: Other - Evaporite - Other - Glacial: - text: Other - Glacial - Other - Volcanic: - text: Other - Volcanic - other: - text: other - profile_position_enum: - name: profile_position_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - summit: - text: summit - shoulder: - text: shoulder - backslope: - text: backslope - footslope: - text: footslope - toeslope: - text: toeslope - furniture_enum: - name: furniture_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - cabinet: - text: cabinet - chair: - text: chair - desks: - text: desks - door_type_enum: - name: door_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - composite: - text: composite - metal: - text: metal - wooden: - text: wooden - tidal_stage_enum: - name: tidal_stage_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - low tide: - text: low tide - ebb tide: - text: ebb tide - flood tide: - text: flood tide - high tide: - text: high tide - door_type_metal_enum: - name: door_type_metal_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - collapsible: - text: collapsible - corrugated steel: - text: corrugated steel - hollow: - text: hollow - rolling shutters: - text: rolling shutters - steel plate: - text: steel plate - handidness_enum: - name: handidness_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - ambidexterity: - text: ambidexterity - left handedness: - text: left handedness - mixed-handedness: - text: mixed-handedness - right handedness: - text: right handedness - tillage_enum: - name: tillage_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - drill: - text: drill - cutting disc: - text: cutting disc - ridge till: - text: ridge till - strip tillage: - text: strip tillage - zonal tillage: - text: zonal tillage - chisel: - text: chisel - tined: - text: tined - mouldboard: - text: mouldboard - disc plough: - text: disc plough - hcr_enum: - name: hcr_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Oil Reservoir: - text: Oil Reservoir - Gas Reservoir: - text: Gas Reservoir - Oil Sand: - text: Oil Sand - Coalbed: - text: Coalbed - Shale: - text: Shale - Tight Oil Reservoir: - text: Tight Oil Reservoir - Tight Gas Reservoir: - text: Tight Gas Reservoir - other: - text: other - freq_clean_enum: - name: freq_clean_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Daily: - text: Daily - Weekly: - text: Weekly - Monthly: - text: Monthly - Quarterly: - text: Quarterly - Annually: - text: Annually - other: - text: other - growth_habit_enum: - name: growth_habit_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - erect: - text: erect - semi-erect: - text: semi-erect - spreading: - text: spreading - prostrate: - text: prostrate - season_use_enum: - name: season_use_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Spring: - text: Spring - Summer: - text: Summer - Fall: - text: Fall - Winter: - text: Winter - sr_dep_env_enum: - name: sr_dep_env_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Lacustine: - text: Lacustine - Fluvioldeltaic: - text: Fluvioldeltaic - Fluviomarine: - text: Fluviomarine - Marine: - text: Marine - other: - text: other - water_feat_type_enum: - name: water_feat_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - fountain: - text: fountain - pool: - text: pool - standing feature: - text: standing feature - stream: - text: stream - waterfall: - text: waterfall - substructure_type_enum: - name: substructure_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - crawlspace: - text: crawlspace - slab on grade: - text: slab on grade - basement: - text: basement - indoor_space_enum: - name: indoor_space_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - bedroom: - text: bedroom - office: - text: office - bathroom: - text: bathroom - foyer: - text: foyer - kitchen: - text: kitchen - locker room: - text: locker room - hallway: - text: hallway - elevator: - text: elevator - host_sex_enum: - name: host_sex_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - female: - text: female - hermaphrodite: - text: hermaphrodite - male: - text: male - neuter: - text: neuter - window_type_enum: - name: window_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - single-hung sash window: - text: single-hung sash window - horizontal sash window: - text: horizontal sash window - fixed window: - text: fixed window - specific_enum: - name: specific_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - photos: - text: photos - fao_class_enum: - name: fao_class_enum + biogenous: + text: biogenous + cosmogenous: + text: cosmogenous + hydrogenous: + text: hydrogenous + lithogenous: + text: lithogenous + fao_class_enum: + name: fao_class_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: Acrisols: @@ -2391,166 +2117,404 @@ enums: text: Vertisols Yermosols: text: Yermosols - floor_struc_enum: - name: floor_struc_enum + ext_window_orient_enum: + name: ext_window_orient_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - balcony: - text: balcony - floating floor: - text: floating floor - glass floor: - text: glass floor - raised floor: - text: raised floor - sprung floor: - text: sprung floor - wood-framed: - text: wood-framed - concrete: - text: concrete - wall_texture_enum: - name: wall_texture_enum + north: + text: north + south: + text: south + east: + text: east + west: + text: west + northeast: + text: northeast + southeast: + text: southeast + southwest: + text: southwest + northwest: + text: northwest + sr_geol_age_enum: + name: sr_geol_age_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + Archean: + text: Archean + Cambrian: + text: Cambrian + Carboniferous: + text: Carboniferous + Cenozoic: + text: Cenozoic + Cretaceous: + text: Cretaceous + Devonian: + text: Devonian + Jurassic: + text: Jurassic + Mesozoic: + text: Mesozoic + Neogene: + text: Neogene + Ordovician: + text: Ordovician + Paleogene: + text: Paleogene + Paleozoic: + text: Paleozoic + Permian: + text: Permian + Precambrian: + text: Precambrian + Proterozoic: + text: Proterozoic + Silurian: + text: Silurian + Triassic: + text: Triassic + other: + text: other + door_move_enum: + name: door_move_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + collapsible: + text: collapsible + folding: + text: folding + revolving: + text: revolving + rolling shutter: + text: rolling shutter + sliding: + text: sliding + swinging: + text: swinging + door_direct_enum: + name: door_direct_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + inward: + text: inward + outward: + text: outward + sideways: + text: sideways + ceil_texture_enum: + name: ceil_texture_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + crows feet: + text: crows feet + crows-foot stomp: + text: crows-foot stomp + double skip: + text: double skip + hawk and trowel: + text: hawk and trowel + knockdown: + text: knockdown + popcorn: + text: popcorn + orange peel: + text: orange peel + rosebud stomp: + text: rosebud stomp + Santa-Fe texture: + text: Santa-Fe texture + skip trowel: + text: skip trowel + smooth: + text: smooth + stomp knockdown: + text: stomp knockdown + swirl: + text: swirl + samp_md_enum: + name: samp_md_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + DF: + text: DF + RT: + text: RT + KB: + text: KB + MSL: + text: MSL + other: + text: other + ceil_type_enum: + name: ceil_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + cathedral: + text: cathedral + dropped: + text: dropped + concave: + text: concave + barrel-shaped: + text: barrel-shaped + coffered: + text: coffered + cove: + text: cove + stretched: + text: stretched + wall_loc_enum: + name: wall_loc_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + north: + text: north + south: + text: south + east: + text: east + west: + text: west + door_type_metal_enum: + name: door_type_metal_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + collapsible: + text: collapsible + corrugated steel: + text: corrugated steel + hollow: + text: hollow + rolling shutters: + text: rolling shutters + steel plate: + text: steel plate + gender_restroom_enum: + name: gender_restroom_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + all gender: + text: all gender + female: + text: female + gender neurtral: + text: gender neurtral + male: + text: male + male and female: + text: male and female + unisex: + text: unisex + vis_media_enum: + name: vis_media_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - ? '' - : text: '' - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - train_stop_loc_enum: - name: train_stop_loc_enum + photos: + text: photos + videos: + text: videos + commonly of the building: + text: commonly of the building + site context (adjacent buildings, vegetation, terrain, streets): + text: site context (adjacent buildings, vegetation, terrain, streets) + interiors: + text: interiors + equipment: + text: equipment + 3D scans: + text: 3D scans + window_loc_enum: + name: window_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - end: - text: end - mid: - text: mid - downtown: - text: downtown - drawings_enum: - name: drawings_enum + north: + text: north + south: + text: south + east: + text: east + west: + text: west + soil_horizon_enum: + name: soil_horizon_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - building navigation map: - text: building navigation map - diagram: - text: diagram - sketch: - text: sketch - room_loc_enum: - name: room_loc_enum + O horizon: + text: O horizon + A horizon: + text: A horizon + E horizon: + text: E horizon + B horizon: + text: B horizon + C horizon: + text: C horizon + R layer: + text: R layer + Permafrost: + text: Permafrost + M horizon: + text: M horizon + indoor_space_enum: + name: indoor_space_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - corner room: - text: corner room - interior room: - text: interior room - exterior wall: - text: exterior wall - light_type_enum: - name: light_type_enum + bedroom: + text: bedroom + office: + text: office + bathroom: + text: bathroom + foyer: + text: foyer + kitchen: + text: kitchen + locker room: + text: locker room + hallway: + text: hallway + elevator: + text: elevator + door_type_enum: + name: door_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - natural light: - text: natural light - electric light: - text: electric light - desk lamp: - text: desk lamp - flourescent lights: - text: flourescent lights - none: - text: none - weekday_enum: - name: weekday_enum + composite: + text: composite + metal: + text: metal + wooden: + text: wooden + depos_env_enum: + name: depos_env_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Monday: - text: Monday - Tuesday: - text: Tuesday - Wednesday: - text: Wednesday - Thursday: - text: Thursday - Friday: - text: Friday - Saturday: - text: Saturday - Sunday: - text: Sunday - arch_struc_enum: - name: arch_struc_enum + Continental - Alluvial: + text: Continental - Alluvial + Continental - Aeolian: + text: Continental - Aeolian + Continental - Fluvial: + text: Continental - Fluvial + Continental - Lacustrine: + text: Continental - Lacustrine + Transitional - Deltaic: + text: Transitional - Deltaic + Transitional - Tidal: + text: Transitional - Tidal + Transitional - Lagoonal: + text: Transitional - Lagoonal + Transitional - Beach: + text: Transitional - Beach + Transitional - Lake: + text: Transitional - Lake + Marine - Shallow: + text: Marine - Shallow + Marine - Deep: + text: Marine - Deep + Marine - Reef: + text: Marine - Reef + Other - Evaporite: + text: Other - Evaporite + Other - Glacial: + text: Other - Glacial + Other - Volcanic: + text: Other - Volcanic + other: + text: other + sr_lithology_enum: + name: sr_lithology_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - building: - text: building - shed: - text: shed - home: - text: home - heat_cool_type_enum: - name: heat_cool_type_enum + Clastic: + text: Clastic + Carbonate: + text: Carbonate + Coal: + text: Coal + Biosilicieous: + text: Biosilicieous + other: + text: other + plant_sex_enum: + name: plant_sex_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - radiant system: - text: radiant system - heat pump: - text: heat pump - forced air system: - text: forced air system - steam forced heat: - text: steam forced heat - wood stove: - text: wood stove - samp_md_enum: - name: samp_md_enum + Androdioecious: + text: Androdioecious + Androecious: + text: Androecious + Androgynous: + text: Androgynous + Androgynomonoecious: + text: Androgynomonoecious + Andromonoecious: + text: Andromonoecious + Bisexual: + text: Bisexual + Dichogamous: + text: Dichogamous + Diclinous: + text: Diclinous + Dioecious: + text: Dioecious + Gynodioecious: + text: Gynodioecious + Gynoecious: + text: Gynoecious + Gynomonoecious: + text: Gynomonoecious + Hermaphroditic: + text: Hermaphroditic + Imperfect: + text: Imperfect + Monoclinous: + text: Monoclinous + Monoecious: + text: Monoecious + Perfect: + text: Perfect + Polygamodioecious: + text: Polygamodioecious + Polygamomonoecious: + text: Polygamomonoecious + Polygamous: + text: Polygamous + Protandrous: + text: Protandrous + Protogynous: + text: Protogynous + Subandroecious: + text: Subandroecious + Subdioecious: + text: Subdioecious + Subgynoecious: + text: Subgynoecious + Synoecious: + text: Synoecious + Trimonoecious: + text: Trimonoecious + Trioecious: + text: Trioecious + Unisexual: + text: Unisexual + specific_enum: + name: specific_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - DF: - text: DF - RT: - text: RT - KB: - text: KB - MSL: - text: MSL - other: - text: other + operation: + text: operation + as built: + text: as built + construction: + text: construction + bid: + text: bid + design: + text: design + photos: + text: photos ext_wall_orient_enum: name: ext_wall_orient_enum from_schema: https://w3id.org/nmdc/nmdc @@ -2571,30 +2535,8 @@ enums: text: southwest northwest: text: northwest - mech_struc_enum: - name: mech_struc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - subway: - text: subway - coach: - text: coach - carriage: - text: carriage - elevator: - text: elevator - escalator: - text: escalator - boat: - text: boat - train: - text: train - car: - text: car - bus: - text: bus - ext_window_orient_enum: - name: ext_window_orient_enum + door_loc_enum: + name: door_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: north: @@ -2605,164 +2547,224 @@ enums: text: east west: text: west - northeast: - text: northeast - southeast: - text: southeast - southwest: - text: southwest - northwest: - text: northwest - window_cover_enum: - name: window_cover_enum + profile_position_enum: + name: profile_position_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - blinds: - text: blinds - curtains: - text: curtains - none: - text: none - drainage_class_enum: - name: drainage_class_enum + summit: + text: summit + shoulder: + text: shoulder + backslope: + text: backslope + footslope: + text: footslope + toeslope: + text: toeslope + growth_habit_enum: + name: growth_habit_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - very poorly: - text: very poorly - poorly: - text: poorly - somewhat poorly: - text: somewhat poorly - moderately well: - text: moderately well - well: - text: well - excessively drained: - text: excessively drained - window_horiz_pos_enum: - name: window_horiz_pos_enum + erect: + text: erect + semi-erect: + text: semi-erect + spreading: + text: spreading + prostrate: + text: prostrate + season_use_enum: + name: season_use_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - left: - text: left - middle: - text: middle - right: - text: right - samp_subtype_enum: - name: samp_subtype_enum + Spring: + text: Spring + Summer: + text: Summer + Fall: + text: Fall + Winter: + text: Winter + ceil_finish_mat_enum: + name: ceil_finish_mat_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - oil phase: - text: oil phase - water phase: - text: water phase - biofilm: - text: biofilm - not applicable: - text: not applicable - other: - text: other - ceil_texture_enum: - name: ceil_texture_enum + drywall: + text: drywall + mineral fibre: + text: mineral fibre + tiles: + text: tiles + PVC: + text: PVC + plasterboard: + text: plasterboard + metal: + text: metal + fiberglass: + text: fiberglass + stucco: + text: stucco + mineral wool/calcium silicate: + text: mineral wool/calcium silicate + wood: + text: wood + tillage_enum: + name: tillage_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - room_samp_pos_enum: - name: room_samp_pos_enum + drill: + text: drill + cutting disc: + text: cutting disc + ridge till: + text: ridge till + strip tillage: + text: strip tillage + zonal tillage: + text: zonal tillage + chisel: + text: chisel + tined: + text: tined + mouldboard: + text: mouldboard + disc plough: + text: disc plough + window_type_enum: + name: window_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + single-hung sash window: + text: single-hung sash window + horizontal sash window: + text: horizontal sash window + fixed window: + text: fixed window + ceil_cond_enum: + name: ceil_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture + hcr_geol_age_enum: + name: hcr_geol_age_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north corner: - text: north corner - south corner: - text: south corner - west corner: - text: west corner - east corner: - text: east corner - northeast corner: - text: northeast corner - northwest corner: - text: northwest corner - southeast corner: - text: southeast corner - southwest corner: - text: southwest corner - center: - text: center - indoor_surf_enum: - name: indoor_surf_enum + Archean: + text: Archean + Cambrian: + text: Cambrian + Carboniferous: + text: Carboniferous + Cenozoic: + text: Cenozoic + Cretaceous: + text: Cretaceous + Devonian: + text: Devonian + Jurassic: + text: Jurassic + Mesozoic: + text: Mesozoic + Neogene: + text: Neogene + Ordovician: + text: Ordovician + Paleogene: + text: Paleogene + Paleozoic: + text: Paleozoic + Permian: + text: Permian + Precambrian: + text: Precambrian + Proterozoic: + text: Proterozoic + Silurian: + text: Silurian + Triassic: + text: Triassic + other: + text: other + door_cond_enum: + name: door_cond_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - cabinet: - text: cabinet - ceiling: - text: ceiling - counter top: - text: counter top - door: - text: door - shelving: - text: shelving - vent cover: - text: vent cover - window: - text: window - wall: - text: wall - organism_count_enum: - name: organism_count_enum + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + lithology_enum: + name: lithology_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - ATP: - text: ATP - MPN: - text: MPN + Basement: + text: Basement + Chalk: + text: Chalk + Chert: + text: Chert + Coal: + text: Coal + Conglomerate: + text: Conglomerate + Diatomite: + text: Diatomite + Dolomite: + text: Dolomite + Limestone: + text: Limestone + Sandstone: + text: Sandstone + Shale: + text: Shale + Siltstone: + text: Siltstone + Volcanic: + text: Volcanic other: text: other - vis_media_enum: - name: vis_media_enum + heat_cool_type_enum: + name: heat_cool_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - photos: - text: photos - videos: - text: videos - commonly of the building: - text: commonly of the building - site context (adjacent buildings, vegetation, terrain, streets): - text: site context (adjacent buildings, vegetation, terrain, streets) - interiors: - text: interiors - equipment: - text: equipment - 3D scans: - text: 3D scans + radiant system: + text: radiant system + heat pump: + text: heat pump + forced air system: + text: forced air system + steam forced heat: + text: steam forced heat + wood stove: + text: wood stove + building_setting_enum: + name: building_setting_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + urban: + text: urban + suburban: + text: suburban + exurban: + text: exurban + rural: + text: rural room_condt_enum: name: room_condt_enum from_schema: https://w3id.org/nmdc/nmdc @@ -2779,40 +2781,34 @@ enums: text: rupture visible signs of mold/mildew: text: visible signs of mold/mildew - samp_collect_point_enum: - name: samp_collect_point_enum + rel_samp_loc_enum: + name: rel_samp_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - well: - text: well - test well: - text: test well - drilling rig: - text: drilling rig - wellhead: - text: wellhead - separator: - text: separator - storage tank: - text: storage tank - other: - text: other - samp_capt_status_enum: - name: samp_capt_status_enum + edge of car: + text: edge of car + center of car: + text: center of car + under a seat: + text: under a seat + wall_surf_treatment_enum: + name: wall_surf_treatment_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - active surveillance in response to an outbreak: - text: active surveillance in response to an outbreak - active surveillance not initiated by an outbreak: - text: active surveillance not initiated by an outbreak - farm sample: - text: farm sample - market sample: - text: market sample - other: - text: other - room_type_enum: - name: room_type_enum + painted: + text: painted + wall paper: + text: wall paper + no treatment: + text: no treatment + paneling: + text: paneling + stucco: + text: stucco + fabric: + text: fabric + room_connected_enum: + name: room_connected_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: attic: @@ -2829,102 +2825,130 @@ enums: text: examining room hallway: text: hallway - kitchen: - text: kitchen - mail room: - text: mail room - private office: - text: private office - open office: - text: open office - stairwell: - text: stairwell - ',restroom': - text: ',restroom' - lobby: - text: lobby - vestibule: - text: vestibule - mechanical or electrical room: - text: mechanical or electrical room - data center: - text: data center - laboratory_wet: - text: laboratory_wet - laboratory_dry: - text: laboratory_dry - gymnasium: - text: gymnasium - natatorium: - text: natatorium - auditorium: - text: auditorium - lockers: - text: lockers - cafe: - text: cafe - warehouse: - text: warehouse - samp_dis_stage_enum: - name: samp_dis_stage_enum + kitchen: + text: kitchen + mail room: + text: mail room + office: + text: office + stairwell: + text: stairwell + window_vert_pos_enum: + name: window_vert_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - dissemination: - text: dissemination - growth and reproduction: - text: growth and reproduction - infection: - text: infection - inoculation: - text: inoculation - penetration: - text: penetration - other: - text: other - floor_cond_enum: - name: floor_cond_enum + bottom: + text: bottom + middle: + text: middle + top: + text: top + low: + text: low + high: + text: high + weekday_enum: + name: weekday_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - lithology_enum: - name: lithology_enum + Monday: + text: Monday + Tuesday: + text: Tuesday + Wednesday: + text: Wednesday + Thursday: + text: Thursday + Friday: + text: Friday + Saturday: + text: Saturday + Sunday: + text: Sunday + room_samp_pos_enum: + name: room_samp_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Basement: - text: Basement - Chalk: - text: Chalk - Chert: - text: Chert - Coal: - text: Coal - Conglomerate: - text: Conglomerate - Diatomite: - text: Diatomite - Dolomite: - text: Dolomite - Limestone: - text: Limestone - Sandstone: - text: Sandstone - Shale: - text: Shale - Siltstone: - text: Siltstone - Volcanic: - text: Volcanic - other: - text: other + north corner: + text: north corner + south corner: + text: south corner + west corner: + text: west corner + east corner: + text: east corner + northeast corner: + text: northeast corner + northwest corner: + text: northwest corner + southeast corner: + text: southeast corner + southwest corner: + text: southwest corner + center: + text: center + door_mat_enum: + name: door_mat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + aluminum: + text: aluminum + cellular PVC: + text: cellular PVC + engineered plastic: + text: engineered plastic + fiberboard: + text: fiberboard + fiberglass: + text: fiberglass + metal: + text: metal + thermoplastic alloy: + text: thermoplastic alloy + vinyl: + text: vinyl + wood: + text: wood + wood/plastic composite: + text: wood/plastic composite + biol_stat_enum: + name: biol_stat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + wild: + text: wild + natural: + text: natural + semi-natural: + text: semi-natural + inbred line: + text: inbred line + breeder's line: + text: breeder's line + hybrid: + text: hybrid + clonal selection: + text: clonal selection + mutant: + text: mutant + floor_struc_enum: + name: floor_struc_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + balcony: + text: balcony + floating floor: + text: floating floor + glass floor: + text: glass floor + raised floor: + text: raised floor + sprung floor: + text: sprung floor + wood-framed: + text: wood-framed + concrete: + text: concrete door_type_wood_enum: name: door_type_wood_enum from_schema: https://w3id.org/nmdc/nmdc @@ -2949,128 +2973,88 @@ enums: text: louvered wire gauged: text: wire gauged - wall_finish_mat_enum: - name: wall_finish_mat_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - plaster: - text: plaster - gypsum plaster: - text: gypsum plaster - veneer plaster: - text: veneer plaster - gypsum board: - text: gypsum board - tile: - text: tile - terrazzo: - text: terrazzo - stone facing: - text: stone facing - acoustical treatment: - text: acoustical treatment - wood: - text: wood - metal: - text: metal - masonry: - text: masonry - gender_restroom_enum: - name: gender_restroom_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - all gender: - text: all gender - female: - text: female - gender neurtral: - text: gender neurtral - male: - text: male - male and female: - text: male and female - unisex: - text: unisex - int_wall_cond_enum: - name: int_wall_cond_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - floor_water_mold_enum: - name: floor_water_mold_enum + organism_count_enum: + name: organism_count_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - mold odor: - text: mold odor - wet floor: - text: wet floor - water stains: - text: water stains - wall discoloration: - text: wall discoloration - floor discoloration: - text: floor discoloration - ceiling discoloration: - text: ceiling discoloration - peeling paint or wallpaper: - text: peeling paint or wallpaper - bulging walls: - text: bulging walls - condensation: - text: condensation - samp_floor_enum: - name: samp_floor_enum + ATP: + text: ATP + MPN: + text: MPN + other: + text: other + shading_device_cond_enum: + name: shading_device_cond_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - 1st floor: - text: 1st floor - 2nd floor: - text: 2nd floor - basement: - text: basement - lobby: - text: lobby - heat_deliv_loc_enum: - name: heat_deliv_loc_enum + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + hcr_enum: + name: hcr_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - biol_stat_enum: - name: biol_stat_enum + Oil Reservoir: + text: Oil Reservoir + Gas Reservoir: + text: Gas Reservoir + Oil Sand: + text: Oil Sand + Coalbed: + text: Coalbed + Shale: + text: Shale + Tight Oil Reservoir: + text: Tight Oil Reservoir + Tight Gas Reservoir: + text: Tight Gas Reservoir + other: + text: other + mech_struc_enum: + name: mech_struc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - wild: - text: wild - natural: - text: natural - semi-natural: - text: semi-natural - inbred line: - text: inbred line - breeder's line: - text: breeder's line - hybrid: - text: hybrid - clonal selection: - text: clonal selection - mutant: - text: mutant + subway: + text: subway + coach: + text: coach + carriage: + text: carriage + elevator: + text: elevator + escalator: + text: escalator + boat: + text: boat + train: + text: train + car: + text: car + bus: + text: bus + hc_produced_enum: + name: hc_produced_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + Oil: + text: Oil + Gas-Condensate: + text: Gas-Condensate + Gas: + text: Gas + Bitumen: + text: Bitumen + Coalbed Methane: + text: Coalbed Methane + other: + text: other shading_device_type_enum: name: shading_device_type_enum from_schema: https://w3id.org/nmdc/nmdc @@ -3099,148 +3083,250 @@ enums: text: trellis venetian awning: text: venetian awning - train_stat_loc_enum: - name: train_stat_loc_enum + quad_pos_enum: + name: quad_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - south station above ground: - text: south station above ground - south station underground: - text: south station underground - south station amtrak: - text: south station amtrak - forest hills: - text: forest hills - riverside: - text: riverside - window_mat_enum: - name: window_mat_enum + North side: + text: North side + West side: + text: West side + South side: + text: South side + East side: + text: East side + sr_kerog_type_enum: + name: sr_kerog_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - clad: - text: clad - fiberglass: - text: fiberglass - metal: - text: metal - vinyl: - text: vinyl - wood: - text: wood - samp_weather_enum: - name: samp_weather_enum + Type I: + text: Type I + Type II: + text: Type II + Type III: + text: Type III + Type IV: + text: Type IV + other: + text: other + floor_cond_enum: + name: floor_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture + heat_deliv_loc_enum: + name: heat_deliv_loc_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + north: + text: north + south: + text: south + east: + text: east + west: + text: west + host_sex_enum: + name: host_sex_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + female: + text: female + hermaphrodite: + text: hermaphrodite + male: + text: male + neuter: + text: neuter + window_cond_enum: + name: window_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + handidness_enum: + name: handidness_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + ambidexterity: + text: ambidexterity + left handedness: + text: left handedness + mixed-handedness: + text: mixed-handedness + right handedness: + text: right handedness + wall_const_type_enum: + name: wall_const_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + frame construction: + text: frame construction + joisted masonry: + text: joisted masonry + light noncombustible: + text: light noncombustible + masonry noncombustible: + text: masonry noncombustible + modified fire resistive: + text: modified fire resistive + fire resistive: + text: fire resistive + build_occup_type_enum: + name: build_occup_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + office: + text: office + market: + text: market + restaurant: + text: restaurant + residence: + text: residence + school: + text: school + residential: + text: residential + commercial: + text: commercial + low rise: + text: low rise + high rise: + text: high rise + wood framed: + text: wood framed + health care: + text: health care + airport: + text: airport + sports complex: + text: sports complex + oxy_stat_samp_enum: + name: oxy_stat_samp_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - clear sky: - text: clear sky - cloudy: - text: cloudy - foggy: - text: foggy - hail: - text: hail - rain: - text: rain - snow: - text: snow - sleet: - text: sleet - sunny: - text: sunny - windy: - text: windy - biotic_relationship_enum: - name: biotic_relationship_enum + aerobic: + text: aerobic + anaerobic: + text: anaerobic + other: + text: other + filter_type_enum: + name: filter_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - free living: - text: free living - parasite: - text: parasite - commensal: - text: commensal - symbiont: - text: symbiont - door_cond_enum: - name: door_cond_enum + particulate air filter: + text: particulate air filter + chemical air filter: + text: chemical air filter + low-MERV pleated media: + text: low-MERV pleated media + HEPA: + text: HEPA + electrostatic: + text: electrostatic + gas-phase or ultraviolet air treatments: + text: gas-phase or ultraviolet air treatments + samp_floor_enum: + name: samp_floor_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - train_line_enum: - name: train_line_enum + 1st floor: + text: 1st floor + 2nd floor: + text: 2nd floor + basement: + text: basement + lobby: + text: lobby + furniture_enum: + name: furniture_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - red: - text: red - green: - text: green - orange: - text: orange - build_docs_enum: - name: build_docs_enum + cabinet: + text: cabinet + chair: + text: chair + desks: + text: desks + samp_dis_stage_enum: + name: samp_dis_stage_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - building information model: - text: building information model - commissioning report: - text: commissioning report - complaint logs: - text: complaint logs - contract administration: - text: contract administration - cost estimate: - text: cost estimate - janitorial schedules or logs: - text: janitorial schedules or logs - maintenance plans: - text: maintenance plans - schedule: - text: schedule - sections: - text: sections - shop drawings: - text: shop drawings - submittals: - text: submittals - ventilation system: - text: ventilation system - windows: - text: windows - door_loc_enum: - name: door_loc_enum + dissemination: + text: dissemination + growth and reproduction: + text: growth and reproduction + infection: + text: infection + inoculation: + text: inoculation + penetration: + text: penetration + other: + text: other + substructure_type_enum: + name: substructure_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - sr_kerog_type_enum: - name: sr_kerog_type_enum + crawlspace: + text: crawlspace + slab on grade: + text: slab on grade + basement: + text: basement + door_comp_type_enum: + name: door_comp_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Type I: - text: Type I - Type II: - text: Type II - Type III: - text: Type III - Type IV: - text: Type IV - other: - text: other + metal covered: + text: metal covered + revolving: + text: revolving + sliding: + text: sliding + telescopic: + text: telescopic + plant_growth_med_enum: + name: plant_growth_med_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + other artificial liquid medium: + text: other artificial liquid medium + other artificial solid medium: + text: other artificial solid medium + peat moss: + text: peat moss + perlite: + text: perlite + pumice: + text: pumice + sand: + text: sand + soil: + text: soil + vermiculite: + text: vermiculite + water: + text: water slots: metagenome_annotation_id: name: metagenome_annotation_id @@ -5531,8 +5617,6 @@ slots: examples: - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 2 string_serialization: '{date, arbitrary precision}' slot_group: MIxS Inspired @@ -5549,8 +5633,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 1 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -5568,8 +5650,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 3 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -5587,8 +5667,6 @@ slots: examples: - value: 'experimental treatment: value' from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:experimental_factor|additional_info rank: 7 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5603,8 +5681,6 @@ slots: - value: C18 - value: Basix PES, 13-100-106 FisherSci from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:filter_type rank: 6 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5622,8 +5698,6 @@ slots: - value: 13C glucose - value: H218O from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:chem_administration rank: 16 string_serialization: '{termLabel} {[termID]}; {timestamp}' slot_group: MIxS Inspired @@ -5640,8 +5714,6 @@ slots: - value: https://doi.org/10.1016/0038-0717(87)90052-6 - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:micro_biomass_meth rank: 11 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5656,8 +5728,6 @@ slots: - value: https://doi.org/10.1016/0038-0717(87)90052-6 - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:micro_biomass_meth rank: 13 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5672,8 +5742,6 @@ slots: examples: - value: 0.05 ug C/g dry soil from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:microbial_biomass rank: 10 string_serialization: '{float} {unit}' slot_group: MIxS Inspired @@ -5688,8 +5756,6 @@ slots: examples: - value: 0.05 ug N/g dry soil from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:microbial_biomass rank: 12 string_serialization: '{float} {unit}' slot_group: MIxS Inspired @@ -5702,8 +5768,6 @@ slots: examples: - value: insect 0.23 ug; plant 1g from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:biomass|microbial_biomass rank: 8 string_serialization: '{text};{float} {unit}' slot_group: MIxS Inspired @@ -5716,8 +5780,6 @@ slots: examples: - value: https://doi.org/10.1038/s41467-021-26181-3 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:microbial_biomass rank: 9 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5730,8 +5792,6 @@ slots: examples: - value: https://doi.org/10.1016/0038-0717(85)90144-0 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:org_nitro|tot_nitro_cont_meth rank: 14 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5744,8 +5804,6 @@ slots: - This is an open text field to provide any treatments that cannot be captured in the provided slots. from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:additional_info rank: 15 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5763,8 +5821,6 @@ slots: examples: - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 4 string_serialization: '{date, arbitrary precision}' slot_group: MIxS Inspired @@ -5781,8 +5837,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 5 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -17361,19 +17415,28 @@ slots: slot_uri: MIXS:0000156 multivalued: false range: QuantityValue - investigation field: - name: investigation field - description: field describing aspect of the investigation/study to which the sample - belongs + has unit: + name: has unit + description: Example "m" + from_schema: https://w3id.org/nmdc/nmdc + owner: QuantityValue + sequencing field: + name: sequencing field from_schema: https://w3id.org/nmdc/nmdc abstract: true + has raw value: + name: has raw value + from_schema: https://w3id.org/nmdc/nmdc + string_serialization: '{has numeric value} {has unit}' + owner: QuantityValue core field: name: core field description: basic fields from_schema: https://w3id.org/nmdc/nmdc abstract: true - nucleic acid sequence source field: - name: nucleic acid sequence source field + environment field: + name: environment field + description: field describing environmental aspect of a sample from_schema: https://w3id.org/nmdc/nmdc abstract: true has numeric value: @@ -17381,25 +17444,16 @@ slots: from_schema: https://w3id.org/nmdc/nmdc owner: QuantityValue range: double - environment field: - name: environment field - description: field describing environmental aspect of a sample + nucleic acid sequence source field: + name: nucleic acid sequence source field from_schema: https://w3id.org/nmdc/nmdc abstract: true - has unit: - name: has unit - description: Example "m" - from_schema: https://w3id.org/nmdc/nmdc - owner: QuantityValue - sequencing field: - name: sequencing field + investigation field: + name: investigation field + description: field describing aspect of the investigation/study to which the sample + belongs from_schema: https://w3id.org/nmdc/nmdc abstract: true - has raw value: - name: has raw value - from_schema: https://w3id.org/nmdc/nmdc - string_serialization: '{has numeric value} {has unit}' - owner: QuantityValue chemical: name: chemical description: from reaction participant class @@ -18486,10 +18540,9 @@ classes: Matches the entity that has been submitted to NMDC lat_lon: name: lat_lon - description: This is currently a required field but it's not clear if this - should be required for human hosts - notes: - - required where? + todos: + - This is currently a required field but it's not clear if this should be + required for human hosts env_broad_scale: name: env_broad_scale required: true @@ -19438,7 +19491,6 @@ classes: used: name: used description: The instrument used to collect the data used in the analysis - range: Instrument id: name: id required: true diff --git a/nmdc_schema/nmdc_schema_merged.yaml b/nmdc_schema/nmdc_schema_merged.yaml index 0590ebf185..98749183d9 100644 --- a/nmdc_schema/nmdc_schema_merged.yaml +++ b/nmdc_schema/nmdc_schema_merged.yaml @@ -11,7 +11,7 @@ notes: - not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1 id: https://w3id.org/nmdc/nmdc -version: v8.0.0 +version: v8.1.0 license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: CATH: @@ -347,6 +347,10 @@ types: string: name: string description: A character string + notes: + - In RDF serializations, a slot with range of string is treated as a literal or + type xsd:string. If you are authoring schemas in LinkML YAML, the type is + referenced with the lower case "string". from_schema: https://w3id.org/linkml/types exact_mappings: - schema:Text @@ -355,6 +359,9 @@ types: integer: name: integer description: An integer + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "integer". from_schema: https://w3id.org/linkml/types exact_mappings: - schema:Integer @@ -363,6 +370,9 @@ types: boolean: name: boolean description: A binary (true or false) value + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "boolean". from_schema: https://w3id.org/linkml/types exact_mappings: - schema:Boolean @@ -372,6 +382,9 @@ types: float: name: float description: A real number that conforms to the xsd:float specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "float". from_schema: https://w3id.org/linkml/types exact_mappings: - schema:Float @@ -380,6 +393,9 @@ types: double: name: double description: A real number that conforms to the xsd:double specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "double". from_schema: https://w3id.org/linkml/types close_mappings: - schema:Float @@ -389,6 +405,9 @@ types: name: decimal description: A real number with arbitrary precision that conforms to the xsd:decimal specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "decimal". from_schema: https://w3id.org/linkml/types broad_mappings: - schema:Number @@ -400,17 +419,21 @@ types: particular day notes: - URI is dateTime because OWL reasoners do not work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "time". from_schema: https://w3id.org/linkml/types exact_mappings: - schema:Time base: XSDTime - uri: xsd:dateTime + uri: xsd:time repr: str date: name: date description: a date (year, month and day) in an idealized calendar notes: - URI is dateTime because OWL reasoners don't work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date". from_schema: https://w3id.org/linkml/types exact_mappings: - schema:Date @@ -420,6 +443,9 @@ types: datetime: name: datetime description: The combination of a date and time + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "datetime". from_schema: https://w3id.org/linkml/types exact_mappings: - schema:DateTime @@ -429,6 +455,9 @@ types: date_or_datetime: name: date_or_datetime description: Either a date or a datetime + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date_or_datetime". from_schema: https://w3id.org/linkml/types base: str uri: linkml:DateOrDatetime @@ -436,6 +465,9 @@ types: uriorcurie: name: uriorcurie description: a URI or a CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uriorcurie". from_schema: https://w3id.org/linkml/types base: URIorCURIE uri: xsd:anyURI @@ -444,6 +476,9 @@ types: name: curie conforms_to: https://www.w3.org/TR/curie/ description: a compact URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "curie". comments: - in RDF serializations this MUST be expanded to a URI - in non-RDF serializations MAY be serialized as the compact representation @@ -455,6 +490,9 @@ types: name: uri conforms_to: https://www.ietf.org/rfc/rfc3987.txt description: a complete URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uri". comments: - in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which @@ -468,6 +506,9 @@ types: ncname: name: ncname description: Prefix part of CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "ncname". from_schema: https://w3id.org/linkml/types base: NCName uri: xsd:string @@ -475,8 +516,11 @@ types: objectidentifier: name: objectidentifier description: A URI or CURIE that represents an object in the model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "objectidentifier". comments: - - Used for inheritence and type checking + - Used for inheritance and type checking from_schema: https://w3id.org/linkml/types base: ElementIdentifier uri: shex:iri @@ -484,10 +528,52 @@ types: nodeidentifier: name: nodeidentifier description: A URI, CURIE or BNODE that represents a node in a model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "nodeidentifier". from_schema: https://w3id.org/linkml/types base: NodeIdentifier uri: shex:nonLiteral repr: str + jsonpointer: + name: jsonpointer + conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 + description: A string encoding a JSON Pointer. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to a valid object within the current + instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpointer". + from_schema: https://w3id.org/linkml/types + base: str + uri: xsd:string + repr: str + jsonpath: + name: jsonpath + conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html + description: A string encoding a JSON Path. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to zero or more valid objects within + the current instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpath". + from_schema: https://w3id.org/linkml/types + base: str + uri: xsd:string + repr: str + sparqlpath: + name: sparqlpath + conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths + description: A string encoding a SPARQL Property Path. The value of the string + MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects + within the current instance document when encoded as RDF. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "sparqlpath". + from_schema: https://w3id.org/linkml/types + base: str + uri: xsd:string + repr: str enums: StatusEnum: name: StatusEnum @@ -1190,26 +1276,6 @@ enums: text: soil water_extract_soil: text: water_extract_soil - door_direct_enum: - name: door_direct_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - inward: - text: inward - outward: - text: outward - sideways: - text: sideways - oxy_stat_samp_enum: - name: oxy_stat_samp_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - aerobic: - text: aerobic - anaerobic: - text: anaerobic - other: - text: other surf_air_cont_enum: name: surf_air_cont_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml @@ -1230,164 +1296,164 @@ enums: text: nutrients biocides: text: biocides - window_vert_pos_enum: - name: window_vert_pos_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - bottom: - text: bottom - middle: - text: middle - top: - text: top - low: - text: low - high: - text: high - filter_type_enum: - name: filter_type_enum + water_feat_type_enum: + name: water_feat_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - particulate air filter: - text: particulate air filter - chemical air filter: - text: chemical air filter - low-MERV pleated media: - text: low-MERV pleated media - HEPA: - text: HEPA - electrostatic: - text: electrostatic - gas-phase or ultraviolet air treatments: - text: gas-phase or ultraviolet air treatments - rel_samp_loc_enum: - name: rel_samp_loc_enum + fountain: + text: fountain + pool: + text: pool + standing feature: + text: standing feature + stream: + text: stream + waterfall: + text: waterfall + samp_collect_point_enum: + name: samp_collect_point_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - edge of car: - text: edge of car - center of car: - text: center of car - under a seat: - text: under a seat - sediment_type_enum: - name: sediment_type_enum + well: + text: well + test well: + text: test well + drilling rig: + text: drilling rig + wellhead: + text: wellhead + separator: + text: separator + storage tank: + text: storage tank + other: + text: other + floor_water_mold_enum: + name: floor_water_mold_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - biogenous: - text: biogenous - cosmogenous: - text: cosmogenous - hydrogenous: - text: hydrogenous - lithogenous: - text: lithogenous - occup_document_enum: - name: occup_document_enum + mold odor: + text: mold odor + wet floor: + text: wet floor + water stains: + text: water stains + wall discoloration: + text: wall discoloration + floor discoloration: + text: floor discoloration + ceiling discoloration: + text: ceiling discoloration + peeling paint or wallpaper: + text: peeling paint or wallpaper + bulging walls: + text: bulging walls + condensation: + text: condensation + wall_texture_enum: + name: wall_texture_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - automated count: - text: automated count - estimate: - text: estimate - manual count: - text: manual count - videos: - text: videos - room_connected_enum: - name: room_connected_enum + crows feet: + text: crows feet + crows-foot stomp: + text: crows-foot stomp + ? '' + : text: '' + double skip: + text: double skip + hawk and trowel: + text: hawk and trowel + knockdown: + text: knockdown + popcorn: + text: popcorn + orange peel: + text: orange peel + rosebud stomp: + text: rosebud stomp + Santa-Fe texture: + text: Santa-Fe texture + skip trowel: + text: skip trowel + smooth: + text: smooth + stomp knockdown: + text: stomp knockdown + swirl: + text: swirl + samp_subtype_enum: + name: samp_subtype_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - attic: - text: attic - bathroom: - text: bathroom - closet: - text: closet - conference room: - text: conference room - elevator: - text: elevator - examining room: - text: examining room - hallway: - text: hallway - kitchen: - text: kitchen - mail room: - text: mail room - office: - text: office - stairwell: - text: stairwell - quad_pos_enum: - name: quad_pos_enum + oil phase: + text: oil phase + water phase: + text: water phase + biofilm: + text: biofilm + not applicable: + text: not applicable + other: + text: other + drainage_class_enum: + name: drainage_class_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - North side: - text: North side - West side: - text: West side - South side: - text: South side - East side: - text: East side - sr_geol_age_enum: - name: sr_geol_age_enum + very poorly: + text: very poorly + poorly: + text: poorly + somewhat poorly: + text: somewhat poorly + moderately well: + text: moderately well + well: + text: well + excessively drained: + text: excessively drained + freq_clean_enum: + name: freq_clean_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - Archean: - text: Archean - Cambrian: - text: Cambrian - Carboniferous: - text: Carboniferous - Cenozoic: - text: Cenozoic - Cretaceous: - text: Cretaceous - Devonian: - text: Devonian - Jurassic: - text: Jurassic - Mesozoic: - text: Mesozoic - Neogene: - text: Neogene - Ordovician: - text: Ordovician - Paleogene: - text: Paleogene - Paleozoic: - text: Paleozoic - Permian: - text: Permian - Precambrian: - text: Precambrian - Proterozoic: - text: Proterozoic - Silurian: - text: Silurian - Triassic: - text: Triassic + Daily: + text: Daily + Weekly: + text: Weekly + Monthly: + text: Monthly + Quarterly: + text: Quarterly + Annually: + text: Annually other: text: other - door_move_enum: - name: door_move_enum + biotic_relationship_enum: + name: biotic_relationship_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - collapsible: - text: collapsible - folding: - text: folding - revolving: - text: revolving - rolling shutter: - text: rolling shutter - sliding: - text: sliding - swinging: - text: swinging + free living: + text: free living + parasite: + text: parasite + commensal: + text: commensal + symbiont: + text: symbiont + light_type_enum: + name: light_type_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + natural light: + text: natural light + electric light: + text: electric light + desk lamp: + text: desk lamp + flourescent lights: + text: flourescent lights + none: + text: none cur_land_use_enum: name: cur_land_use_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml @@ -1583,142 +1649,146 @@ enums: value: vine crops (grapes) examples: - value: grapes - hcr_geol_age_enum: - name: hcr_geol_age_enum + drawings_enum: + name: drawings_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - Archean: - text: Archean - Cambrian: - text: Cambrian - Carboniferous: - text: Carboniferous - Cenozoic: - text: Cenozoic - Cretaceous: - text: Cretaceous - Devonian: - text: Devonian - Jurassic: - text: Jurassic - Mesozoic: - text: Mesozoic - Neogene: - text: Neogene - Ordovician: - text: Ordovician - Paleogene: - text: Paleogene - Paleozoic: - text: Paleozoic - Permian: - text: Permian - Precambrian: - text: Precambrian - Proterozoic: - text: Proterozoic - Silurian: - text: Silurian - Triassic: - text: Triassic + operation: + text: operation + as built: + text: as built + construction: + text: construction + bid: + text: bid + design: + text: design + building navigation map: + text: building navigation map + diagram: + text: diagram + sketch: + text: sketch + indoor_surf_enum: + name: indoor_surf_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + cabinet: + text: cabinet + ceiling: + text: ceiling + counter top: + text: counter top + door: + text: door + shelving: + text: shelving + vent cover: + text: vent cover + window: + text: window + wall: + text: wall + samp_capt_status_enum: + name: samp_capt_status_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + active surveillance in response to an outbreak: + text: active surveillance in response to an outbreak + active surveillance not initiated by an outbreak: + text: active surveillance not initiated by an outbreak + farm sample: + text: farm sample + market sample: + text: market sample other: text: other - wall_const_type_enum: - name: wall_const_type_enum + room_loc_enum: + name: room_loc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - frame construction: - text: frame construction - joisted masonry: - text: joisted masonry - light noncombustible: - text: light noncombustible - masonry noncombustible: - text: masonry noncombustible - modified fire resistive: - text: modified fire resistive - fire resistive: - text: fire resistive - plant_sex_enum: - name: plant_sex_enum + corner room: + text: corner room + interior room: + text: interior room + exterior wall: + text: exterior wall + occup_document_enum: + name: occup_document_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - Androdioecious: - text: Androdioecious - Androecious: - text: Androecious - Androgynous: - text: Androgynous - Androgynomonoecious: - text: Androgynomonoecious - Andromonoecious: - text: Andromonoecious - Bisexual: - text: Bisexual - Dichogamous: - text: Dichogamous - Diclinous: - text: Diclinous - Dioecious: - text: Dioecious - Gynodioecious: - text: Gynodioecious - Gynoecious: - text: Gynoecious - Gynomonoecious: - text: Gynomonoecious - Hermaphroditic: - text: Hermaphroditic - Imperfect: - text: Imperfect - Monoclinous: - text: Monoclinous - Monoecious: - text: Monoecious - Perfect: - text: Perfect - Polygamodioecious: - text: Polygamodioecious - Polygamomonoecious: - text: Polygamomonoecious - Polygamous: - text: Polygamous - Protandrous: - text: Protandrous - Protogynous: - text: Protogynous - Subandroecious: - text: Subandroecious - Subdioecious: - text: Subdioecious - Subgynoecious: - text: Subgynoecious - Synoecious: - text: Synoecious - Trimonoecious: - text: Trimonoecious - Trioecious: - text: Trioecious - Unisexual: - text: Unisexual - ceil_type_enum: - name: ceil_type_enum + automated count: + text: automated count + estimate: + text: estimate + manual count: + text: manual count + videos: + text: videos + arch_struc_enum: + name: arch_struc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - cathedral: - text: cathedral - dropped: - text: dropped - concave: - text: concave - barrel-shaped: - text: barrel-shaped - coffered: - text: coffered - cove: - text: cove - stretched: - text: stretched + building: + text: building + shed: + text: shed + home: + text: home + wall_finish_mat_enum: + name: wall_finish_mat_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + plaster: + text: plaster + gypsum plaster: + text: gypsum plaster + veneer plaster: + text: veneer plaster + gypsum board: + text: gypsum board + tile: + text: tile + terrazzo: + text: terrazzo + stone facing: + text: stone facing + acoustical treatment: + text: acoustical treatment + wood: + text: wood + metal: + text: metal + masonry: + text: masonry + window_mat_enum: + name: window_mat_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + clad: + text: clad + fiberglass: + text: fiberglass + metal: + text: metal + vinyl: + text: vinyl + wood: + text: wood + int_wall_cond_enum: + name: int_wall_cond_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture floor_finish_mat_enum: name: floor_finish_mat_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml @@ -1759,584 +1829,240 @@ enums: text: paint none or unfinished: text: none or unfinished - wall_loc_enum: - name: wall_loc_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - wall_surf_treatment_enum: - name: wall_surf_treatment_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - painted: - text: painted - wall paper: - text: wall paper - no treatment: - text: no treatment - paneling: - text: paneling - stucco: - text: stucco - fabric: - text: fabric - window_cond_enum: - name: window_cond_enum + build_docs_enum: + name: build_docs_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - door_mat_enum: - name: door_mat_enum + building information model: + text: building information model + commissioning report: + text: commissioning report + complaint logs: + text: complaint logs + contract administration: + text: contract administration + cost estimate: + text: cost estimate + janitorial schedules or logs: + text: janitorial schedules or logs + maintenance plans: + text: maintenance plans + schedule: + text: schedule + sections: + text: sections + shop drawings: + text: shop drawings + submittals: + text: submittals + ventilation system: + text: ventilation system + windows: + text: windows + surf_material_enum: + name: surf_material_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - aluminum: - text: aluminum - cellular PVC: - text: cellular PVC - engineered plastic: - text: engineered plastic - fiberboard: - text: fiberboard - fiberglass: - text: fiberglass + adobe: + text: adobe + carpet: + text: carpet + cinder blocks: + text: cinder blocks + concrete: + text: concrete + hay bales: + text: hay bales + glass: + text: glass metal: text: metal - thermoplastic alloy: - text: thermoplastic alloy + paint: + text: paint + plastic: + text: plastic + stainless steel: + text: stainless steel + stone: + text: stone + stucco: + text: stucco + tile: + text: tile vinyl: text: vinyl wood: text: wood - wood/plastic composite: - text: wood/plastic composite - soil_horizon_enum: - name: soil_horizon_enum + tidal_stage_enum: + name: tidal_stage_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - O horizon: - text: O horizon - A horizon: - text: A horizon - E horizon: - text: E horizon - B horizon: - text: B horizon - C horizon: - text: C horizon - R layer: - text: R layer - Permafrost: - text: Permafrost - M horizon: - text: M horizon - ceil_finish_mat_enum: - name: ceil_finish_mat_enum + low tide: + text: low tide + ebb tide: + text: ebb tide + flood tide: + text: flood tide + high tide: + text: high tide + window_horiz_pos_enum: + name: window_horiz_pos_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - drywall: - text: drywall - mineral fibre: - text: mineral fibre - tiles: - text: tiles - PVC: - text: PVC - plasterboard: - text: plasterboard - metal: - text: metal - fiberglass: - text: fiberglass - stucco: - text: stucco - mineral wool/calcium silicate: - text: mineral wool/calcium silicate - wood: - text: wood - shading_device_cond_enum: - name: shading_device_cond_enum + left: + text: left + middle: + text: middle + right: + text: right + train_stop_loc_enum: + name: train_stop_loc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - hc_produced_enum: - name: hc_produced_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - Oil: - text: Oil - Gas-Condensate: - text: Gas-Condensate - Gas: - text: Gas - Bitumen: - text: Bitumen - Coalbed Methane: - text: Coalbed Methane - other: - text: other - door_comp_type_enum: - name: door_comp_type_enum + end: + text: end + mid: + text: mid + downtown: + text: downtown + train_line_enum: + name: train_line_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - metal covered: - text: metal covered - revolving: - text: revolving - sliding: - text: sliding - telescopic: - text: telescopic - window_loc_enum: - name: window_loc_enum + red: + text: red + green: + text: green + orange: + text: orange + train_stat_loc_enum: + name: train_stat_loc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - sr_lithology_enum: - name: sr_lithology_enum + south station above ground: + text: south station above ground + south station underground: + text: south station underground + south station amtrak: + text: south station amtrak + forest hills: + text: forest hills + riverside: + text: riverside + sr_dep_env_enum: + name: sr_dep_env_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - Clastic: - text: Clastic - Carbonate: - text: Carbonate - Coal: - text: Coal - Biosilicieous: - text: Biosilicieous + Lacustine: + text: Lacustine + Fluvioldeltaic: + text: Fluvioldeltaic + Fluviomarine: + text: Fluviomarine + Marine: + text: Marine other: text: other - plant_growth_med_enum: - name: plant_growth_med_enum + samp_weather_enum: + name: samp_weather_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - other artificial liquid medium: - text: other artificial liquid medium - other artificial solid medium: - text: other artificial solid medium - peat moss: - text: peat moss - perlite: - text: perlite - pumice: - text: pumice - sand: - text: sand - soil: - text: soil - vermiculite: - text: vermiculite - water: - text: water - surf_material_enum: - name: surf_material_enum + clear sky: + text: clear sky + cloudy: + text: cloudy + foggy: + text: foggy + hail: + text: hail + rain: + text: rain + snow: + text: snow + sleet: + text: sleet + sunny: + text: sunny + windy: + text: windy + window_cover_enum: + name: window_cover_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - adobe: - text: adobe - carpet: - text: carpet - cinder blocks: - text: cinder blocks - concrete: - text: concrete - hay bales: - text: hay bales - glass: - text: glass - metal: - text: metal - paint: - text: paint - plastic: - text: plastic - stainless steel: - text: stainless steel - stone: - text: stone - stucco: - text: stucco - tile: - text: tile - vinyl: - text: vinyl - wood: - text: wood - ceil_cond_enum: - name: ceil_cond_enum + blinds: + text: blinds + curtains: + text: curtains + none: + text: none + room_type_enum: + name: room_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - building_setting_enum: - name: building_setting_enum + attic: + text: attic + bathroom: + text: bathroom + closet: + text: closet + conference room: + text: conference room + elevator: + text: elevator + examining room: + text: examining room + hallway: + text: hallway + kitchen: + text: kitchen + mail room: + text: mail room + private office: + text: private office + open office: + text: open office + stairwell: + text: stairwell + ',restroom': + text: ',restroom' + lobby: + text: lobby + vestibule: + text: vestibule + mechanical or electrical room: + text: mechanical or electrical room + data center: + text: data center + laboratory_wet: + text: laboratory_wet + laboratory_dry: + text: laboratory_dry + gymnasium: + text: gymnasium + natatorium: + text: natatorium + auditorium: + text: auditorium + lockers: + text: lockers + cafe: + text: cafe + warehouse: + text: warehouse + sediment_type_enum: + name: sediment_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - urban: - text: urban - suburban: - text: suburban - exurban: - text: exurban - rural: - text: rural - build_occup_type_enum: - name: build_occup_type_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - office: - text: office - market: - text: market - restaurant: - text: restaurant - residence: - text: residence - school: - text: school - residential: - text: residential - commercial: - text: commercial - low rise: - text: low rise - high rise: - text: high rise - wood framed: - text: wood framed - health care: - text: health care - airport: - text: airport - sports complex: - text: sports complex - depos_env_enum: - name: depos_env_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - Continental - Alluvial: - text: Continental - Alluvial - Continental - Aeolian: - text: Continental - Aeolian - Continental - Fluvial: - text: Continental - Fluvial - Continental - Lacustrine: - text: Continental - Lacustrine - Transitional - Deltaic: - text: Transitional - Deltaic - Transitional - Tidal: - text: Transitional - Tidal - Transitional - Lagoonal: - text: Transitional - Lagoonal - Transitional - Beach: - text: Transitional - Beach - Transitional - Lake: - text: Transitional - Lake - Marine - Shallow: - text: Marine - Shallow - Marine - Deep: - text: Marine - Deep - Marine - Reef: - text: Marine - Reef - Other - Evaporite: - text: Other - Evaporite - Other - Glacial: - text: Other - Glacial - Other - Volcanic: - text: Other - Volcanic - other: - text: other - profile_position_enum: - name: profile_position_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - summit: - text: summit - shoulder: - text: shoulder - backslope: - text: backslope - footslope: - text: footslope - toeslope: - text: toeslope - furniture_enum: - name: furniture_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - cabinet: - text: cabinet - chair: - text: chair - desks: - text: desks - door_type_enum: - name: door_type_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - composite: - text: composite - metal: - text: metal - wooden: - text: wooden - tidal_stage_enum: - name: tidal_stage_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - low tide: - text: low tide - ebb tide: - text: ebb tide - flood tide: - text: flood tide - high tide: - text: high tide - door_type_metal_enum: - name: door_type_metal_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - collapsible: - text: collapsible - corrugated steel: - text: corrugated steel - hollow: - text: hollow - rolling shutters: - text: rolling shutters - steel plate: - text: steel plate - handidness_enum: - name: handidness_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - ambidexterity: - text: ambidexterity - left handedness: - text: left handedness - mixed-handedness: - text: mixed-handedness - right handedness: - text: right handedness - tillage_enum: - name: tillage_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - drill: - text: drill - cutting disc: - text: cutting disc - ridge till: - text: ridge till - strip tillage: - text: strip tillage - zonal tillage: - text: zonal tillage - chisel: - text: chisel - tined: - text: tined - mouldboard: - text: mouldboard - disc plough: - text: disc plough - hcr_enum: - name: hcr_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - Oil Reservoir: - text: Oil Reservoir - Gas Reservoir: - text: Gas Reservoir - Oil Sand: - text: Oil Sand - Coalbed: - text: Coalbed - Shale: - text: Shale - Tight Oil Reservoir: - text: Tight Oil Reservoir - Tight Gas Reservoir: - text: Tight Gas Reservoir - other: - text: other - freq_clean_enum: - name: freq_clean_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - Daily: - text: Daily - Weekly: - text: Weekly - Monthly: - text: Monthly - Quarterly: - text: Quarterly - Annually: - text: Annually - other: - text: other - growth_habit_enum: - name: growth_habit_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - erect: - text: erect - semi-erect: - text: semi-erect - spreading: - text: spreading - prostrate: - text: prostrate - season_use_enum: - name: season_use_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - Spring: - text: Spring - Summer: - text: Summer - Fall: - text: Fall - Winter: - text: Winter - sr_dep_env_enum: - name: sr_dep_env_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - Lacustine: - text: Lacustine - Fluvioldeltaic: - text: Fluvioldeltaic - Fluviomarine: - text: Fluviomarine - Marine: - text: Marine - other: - text: other - water_feat_type_enum: - name: water_feat_type_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - fountain: - text: fountain - pool: - text: pool - standing feature: - text: standing feature - stream: - text: stream - waterfall: - text: waterfall - substructure_type_enum: - name: substructure_type_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - crawlspace: - text: crawlspace - slab on grade: - text: slab on grade - basement: - text: basement - indoor_space_enum: - name: indoor_space_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - bedroom: - text: bedroom - office: - text: office - bathroom: - text: bathroom - foyer: - text: foyer - kitchen: - text: kitchen - locker room: - text: locker room - hallway: - text: hallway - elevator: - text: elevator - host_sex_enum: - name: host_sex_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - female: - text: female - hermaphrodite: - text: hermaphrodite - male: - text: male - neuter: - text: neuter - window_type_enum: - name: window_type_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - single-hung sash window: - text: single-hung sash window - horizontal sash window: - text: horizontal sash window - fixed window: - text: fixed window - specific_enum: - name: specific_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - photos: - text: photos - fao_class_enum: - name: fao_class_enum + biogenous: + text: biogenous + cosmogenous: + text: cosmogenous + hydrogenous: + text: hydrogenous + lithogenous: + text: lithogenous + fao_class_enum: + name: fao_class_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: Acrisols: @@ -2391,166 +2117,404 @@ enums: text: Vertisols Yermosols: text: Yermosols - floor_struc_enum: - name: floor_struc_enum + ext_window_orient_enum: + name: ext_window_orient_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - balcony: - text: balcony - floating floor: - text: floating floor - glass floor: - text: glass floor - raised floor: - text: raised floor - sprung floor: - text: sprung floor - wood-framed: - text: wood-framed - concrete: - text: concrete - wall_texture_enum: - name: wall_texture_enum + north: + text: north + south: + text: south + east: + text: east + west: + text: west + northeast: + text: northeast + southeast: + text: southeast + southwest: + text: southwest + northwest: + text: northwest + sr_geol_age_enum: + name: sr_geol_age_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + Archean: + text: Archean + Cambrian: + text: Cambrian + Carboniferous: + text: Carboniferous + Cenozoic: + text: Cenozoic + Cretaceous: + text: Cretaceous + Devonian: + text: Devonian + Jurassic: + text: Jurassic + Mesozoic: + text: Mesozoic + Neogene: + text: Neogene + Ordovician: + text: Ordovician + Paleogene: + text: Paleogene + Paleozoic: + text: Paleozoic + Permian: + text: Permian + Precambrian: + text: Precambrian + Proterozoic: + text: Proterozoic + Silurian: + text: Silurian + Triassic: + text: Triassic + other: + text: other + door_move_enum: + name: door_move_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + collapsible: + text: collapsible + folding: + text: folding + revolving: + text: revolving + rolling shutter: + text: rolling shutter + sliding: + text: sliding + swinging: + text: swinging + door_direct_enum: + name: door_direct_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + inward: + text: inward + outward: + text: outward + sideways: + text: sideways + ceil_texture_enum: + name: ceil_texture_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + crows feet: + text: crows feet + crows-foot stomp: + text: crows-foot stomp + double skip: + text: double skip + hawk and trowel: + text: hawk and trowel + knockdown: + text: knockdown + popcorn: + text: popcorn + orange peel: + text: orange peel + rosebud stomp: + text: rosebud stomp + Santa-Fe texture: + text: Santa-Fe texture + skip trowel: + text: skip trowel + smooth: + text: smooth + stomp knockdown: + text: stomp knockdown + swirl: + text: swirl + samp_md_enum: + name: samp_md_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + DF: + text: DF + RT: + text: RT + KB: + text: KB + MSL: + text: MSL + other: + text: other + ceil_type_enum: + name: ceil_type_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + cathedral: + text: cathedral + dropped: + text: dropped + concave: + text: concave + barrel-shaped: + text: barrel-shaped + coffered: + text: coffered + cove: + text: cove + stretched: + text: stretched + wall_loc_enum: + name: wall_loc_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + north: + text: north + south: + text: south + east: + text: east + west: + text: west + door_type_metal_enum: + name: door_type_metal_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + collapsible: + text: collapsible + corrugated steel: + text: corrugated steel + hollow: + text: hollow + rolling shutters: + text: rolling shutters + steel plate: + text: steel plate + gender_restroom_enum: + name: gender_restroom_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + all gender: + text: all gender + female: + text: female + gender neurtral: + text: gender neurtral + male: + text: male + male and female: + text: male and female + unisex: + text: unisex + vis_media_enum: + name: vis_media_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - ? '' - : text: '' - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - train_stop_loc_enum: - name: train_stop_loc_enum + photos: + text: photos + videos: + text: videos + commonly of the building: + text: commonly of the building + site context (adjacent buildings, vegetation, terrain, streets): + text: site context (adjacent buildings, vegetation, terrain, streets) + interiors: + text: interiors + equipment: + text: equipment + 3D scans: + text: 3D scans + window_loc_enum: + name: window_loc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - end: - text: end - mid: - text: mid - downtown: - text: downtown - drawings_enum: - name: drawings_enum + north: + text: north + south: + text: south + east: + text: east + west: + text: west + soil_horizon_enum: + name: soil_horizon_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - building navigation map: - text: building navigation map - diagram: - text: diagram - sketch: - text: sketch - room_loc_enum: - name: room_loc_enum + O horizon: + text: O horizon + A horizon: + text: A horizon + E horizon: + text: E horizon + B horizon: + text: B horizon + C horizon: + text: C horizon + R layer: + text: R layer + Permafrost: + text: Permafrost + M horizon: + text: M horizon + indoor_space_enum: + name: indoor_space_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - corner room: - text: corner room - interior room: - text: interior room - exterior wall: - text: exterior wall - light_type_enum: - name: light_type_enum + bedroom: + text: bedroom + office: + text: office + bathroom: + text: bathroom + foyer: + text: foyer + kitchen: + text: kitchen + locker room: + text: locker room + hallway: + text: hallway + elevator: + text: elevator + door_type_enum: + name: door_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - natural light: - text: natural light - electric light: - text: electric light - desk lamp: - text: desk lamp - flourescent lights: - text: flourescent lights - none: - text: none - weekday_enum: - name: weekday_enum + composite: + text: composite + metal: + text: metal + wooden: + text: wooden + depos_env_enum: + name: depos_env_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - Monday: - text: Monday - Tuesday: - text: Tuesday - Wednesday: - text: Wednesday - Thursday: - text: Thursday - Friday: - text: Friday - Saturday: - text: Saturday - Sunday: - text: Sunday - arch_struc_enum: - name: arch_struc_enum + Continental - Alluvial: + text: Continental - Alluvial + Continental - Aeolian: + text: Continental - Aeolian + Continental - Fluvial: + text: Continental - Fluvial + Continental - Lacustrine: + text: Continental - Lacustrine + Transitional - Deltaic: + text: Transitional - Deltaic + Transitional - Tidal: + text: Transitional - Tidal + Transitional - Lagoonal: + text: Transitional - Lagoonal + Transitional - Beach: + text: Transitional - Beach + Transitional - Lake: + text: Transitional - Lake + Marine - Shallow: + text: Marine - Shallow + Marine - Deep: + text: Marine - Deep + Marine - Reef: + text: Marine - Reef + Other - Evaporite: + text: Other - Evaporite + Other - Glacial: + text: Other - Glacial + Other - Volcanic: + text: Other - Volcanic + other: + text: other + sr_lithology_enum: + name: sr_lithology_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - building: - text: building - shed: - text: shed - home: - text: home - heat_cool_type_enum: - name: heat_cool_type_enum + Clastic: + text: Clastic + Carbonate: + text: Carbonate + Coal: + text: Coal + Biosilicieous: + text: Biosilicieous + other: + text: other + plant_sex_enum: + name: plant_sex_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - radiant system: - text: radiant system - heat pump: - text: heat pump - forced air system: - text: forced air system - steam forced heat: - text: steam forced heat - wood stove: - text: wood stove - samp_md_enum: - name: samp_md_enum + Androdioecious: + text: Androdioecious + Androecious: + text: Androecious + Androgynous: + text: Androgynous + Androgynomonoecious: + text: Androgynomonoecious + Andromonoecious: + text: Andromonoecious + Bisexual: + text: Bisexual + Dichogamous: + text: Dichogamous + Diclinous: + text: Diclinous + Dioecious: + text: Dioecious + Gynodioecious: + text: Gynodioecious + Gynoecious: + text: Gynoecious + Gynomonoecious: + text: Gynomonoecious + Hermaphroditic: + text: Hermaphroditic + Imperfect: + text: Imperfect + Monoclinous: + text: Monoclinous + Monoecious: + text: Monoecious + Perfect: + text: Perfect + Polygamodioecious: + text: Polygamodioecious + Polygamomonoecious: + text: Polygamomonoecious + Polygamous: + text: Polygamous + Protandrous: + text: Protandrous + Protogynous: + text: Protogynous + Subandroecious: + text: Subandroecious + Subdioecious: + text: Subdioecious + Subgynoecious: + text: Subgynoecious + Synoecious: + text: Synoecious + Trimonoecious: + text: Trimonoecious + Trioecious: + text: Trioecious + Unisexual: + text: Unisexual + specific_enum: + name: specific_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - DF: - text: DF - RT: - text: RT - KB: - text: KB - MSL: - text: MSL - other: - text: other + operation: + text: operation + as built: + text: as built + construction: + text: construction + bid: + text: bid + design: + text: design + photos: + text: photos ext_wall_orient_enum: name: ext_wall_orient_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml @@ -2571,30 +2535,8 @@ enums: text: southwest northwest: text: northwest - mech_struc_enum: - name: mech_struc_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - subway: - text: subway - coach: - text: coach - carriage: - text: carriage - elevator: - text: elevator - escalator: - text: escalator - boat: - text: boat - train: - text: train - car: - text: car - bus: - text: bus - ext_window_orient_enum: - name: ext_window_orient_enum + door_loc_enum: + name: door_loc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: north: @@ -2605,164 +2547,224 @@ enums: text: east west: text: west - northeast: - text: northeast - southeast: - text: southeast - southwest: - text: southwest - northwest: - text: northwest - window_cover_enum: - name: window_cover_enum + profile_position_enum: + name: profile_position_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - blinds: - text: blinds - curtains: - text: curtains - none: - text: none - drainage_class_enum: - name: drainage_class_enum + summit: + text: summit + shoulder: + text: shoulder + backslope: + text: backslope + footslope: + text: footslope + toeslope: + text: toeslope + growth_habit_enum: + name: growth_habit_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - very poorly: - text: very poorly - poorly: - text: poorly - somewhat poorly: - text: somewhat poorly - moderately well: - text: moderately well - well: - text: well - excessively drained: - text: excessively drained - window_horiz_pos_enum: - name: window_horiz_pos_enum + erect: + text: erect + semi-erect: + text: semi-erect + spreading: + text: spreading + prostrate: + text: prostrate + season_use_enum: + name: season_use_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - left: - text: left - middle: - text: middle - right: - text: right - samp_subtype_enum: - name: samp_subtype_enum + Spring: + text: Spring + Summer: + text: Summer + Fall: + text: Fall + Winter: + text: Winter + ceil_finish_mat_enum: + name: ceil_finish_mat_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - oil phase: - text: oil phase - water phase: - text: water phase - biofilm: - text: biofilm - not applicable: - text: not applicable - other: - text: other - ceil_texture_enum: - name: ceil_texture_enum + drywall: + text: drywall + mineral fibre: + text: mineral fibre + tiles: + text: tiles + PVC: + text: PVC + plasterboard: + text: plasterboard + metal: + text: metal + fiberglass: + text: fiberglass + stucco: + text: stucco + mineral wool/calcium silicate: + text: mineral wool/calcium silicate + wood: + text: wood + tillage_enum: + name: tillage_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - room_samp_pos_enum: - name: room_samp_pos_enum + drill: + text: drill + cutting disc: + text: cutting disc + ridge till: + text: ridge till + strip tillage: + text: strip tillage + zonal tillage: + text: zonal tillage + chisel: + text: chisel + tined: + text: tined + mouldboard: + text: mouldboard + disc plough: + text: disc plough + window_type_enum: + name: window_type_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + single-hung sash window: + text: single-hung sash window + horizontal sash window: + text: horizontal sash window + fixed window: + text: fixed window + ceil_cond_enum: + name: ceil_cond_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture + hcr_geol_age_enum: + name: hcr_geol_age_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - north corner: - text: north corner - south corner: - text: south corner - west corner: - text: west corner - east corner: - text: east corner - northeast corner: - text: northeast corner - northwest corner: - text: northwest corner - southeast corner: - text: southeast corner - southwest corner: - text: southwest corner - center: - text: center - indoor_surf_enum: - name: indoor_surf_enum + Archean: + text: Archean + Cambrian: + text: Cambrian + Carboniferous: + text: Carboniferous + Cenozoic: + text: Cenozoic + Cretaceous: + text: Cretaceous + Devonian: + text: Devonian + Jurassic: + text: Jurassic + Mesozoic: + text: Mesozoic + Neogene: + text: Neogene + Ordovician: + text: Ordovician + Paleogene: + text: Paleogene + Paleozoic: + text: Paleozoic + Permian: + text: Permian + Precambrian: + text: Precambrian + Proterozoic: + text: Proterozoic + Silurian: + text: Silurian + Triassic: + text: Triassic + other: + text: other + door_cond_enum: + name: door_cond_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - cabinet: - text: cabinet - ceiling: - text: ceiling - counter top: - text: counter top - door: - text: door - shelving: - text: shelving - vent cover: - text: vent cover - window: - text: window - wall: - text: wall - organism_count_enum: - name: organism_count_enum + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + lithology_enum: + name: lithology_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - ATP: - text: ATP - MPN: - text: MPN + Basement: + text: Basement + Chalk: + text: Chalk + Chert: + text: Chert + Coal: + text: Coal + Conglomerate: + text: Conglomerate + Diatomite: + text: Diatomite + Dolomite: + text: Dolomite + Limestone: + text: Limestone + Sandstone: + text: Sandstone + Shale: + text: Shale + Siltstone: + text: Siltstone + Volcanic: + text: Volcanic other: text: other - vis_media_enum: - name: vis_media_enum + heat_cool_type_enum: + name: heat_cool_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - photos: - text: photos - videos: - text: videos - commonly of the building: - text: commonly of the building - site context (adjacent buildings, vegetation, terrain, streets): - text: site context (adjacent buildings, vegetation, terrain, streets) - interiors: - text: interiors - equipment: - text: equipment - 3D scans: - text: 3D scans + radiant system: + text: radiant system + heat pump: + text: heat pump + forced air system: + text: forced air system + steam forced heat: + text: steam forced heat + wood stove: + text: wood stove + building_setting_enum: + name: building_setting_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + urban: + text: urban + suburban: + text: suburban + exurban: + text: exurban + rural: + text: rural room_condt_enum: name: room_condt_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml @@ -2779,40 +2781,34 @@ enums: text: rupture visible signs of mold/mildew: text: visible signs of mold/mildew - samp_collect_point_enum: - name: samp_collect_point_enum + rel_samp_loc_enum: + name: rel_samp_loc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - well: - text: well - test well: - text: test well - drilling rig: - text: drilling rig - wellhead: - text: wellhead - separator: - text: separator - storage tank: - text: storage tank - other: - text: other - samp_capt_status_enum: - name: samp_capt_status_enum + edge of car: + text: edge of car + center of car: + text: center of car + under a seat: + text: under a seat + wall_surf_treatment_enum: + name: wall_surf_treatment_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - active surveillance in response to an outbreak: - text: active surveillance in response to an outbreak - active surveillance not initiated by an outbreak: - text: active surveillance not initiated by an outbreak - farm sample: - text: farm sample - market sample: - text: market sample - other: - text: other - room_type_enum: - name: room_type_enum + painted: + text: painted + wall paper: + text: wall paper + no treatment: + text: no treatment + paneling: + text: paneling + stucco: + text: stucco + fabric: + text: fabric + room_connected_enum: + name: room_connected_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: attic: @@ -2829,102 +2825,130 @@ enums: text: examining room hallway: text: hallway - kitchen: - text: kitchen - mail room: - text: mail room - private office: - text: private office - open office: - text: open office - stairwell: - text: stairwell - ',restroom': - text: ',restroom' - lobby: - text: lobby - vestibule: - text: vestibule - mechanical or electrical room: - text: mechanical or electrical room - data center: - text: data center - laboratory_wet: - text: laboratory_wet - laboratory_dry: - text: laboratory_dry - gymnasium: - text: gymnasium - natatorium: - text: natatorium - auditorium: - text: auditorium - lockers: - text: lockers - cafe: - text: cafe - warehouse: - text: warehouse - samp_dis_stage_enum: - name: samp_dis_stage_enum + kitchen: + text: kitchen + mail room: + text: mail room + office: + text: office + stairwell: + text: stairwell + window_vert_pos_enum: + name: window_vert_pos_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - dissemination: - text: dissemination - growth and reproduction: - text: growth and reproduction - infection: - text: infection - inoculation: - text: inoculation - penetration: - text: penetration - other: - text: other - floor_cond_enum: - name: floor_cond_enum + bottom: + text: bottom + middle: + text: middle + top: + text: top + low: + text: low + high: + text: high + weekday_enum: + name: weekday_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - lithology_enum: - name: lithology_enum + Monday: + text: Monday + Tuesday: + text: Tuesday + Wednesday: + text: Wednesday + Thursday: + text: Thursday + Friday: + text: Friday + Saturday: + text: Saturday + Sunday: + text: Sunday + room_samp_pos_enum: + name: room_samp_pos_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - Basement: - text: Basement - Chalk: - text: Chalk - Chert: - text: Chert - Coal: - text: Coal - Conglomerate: - text: Conglomerate - Diatomite: - text: Diatomite - Dolomite: - text: Dolomite - Limestone: - text: Limestone - Sandstone: - text: Sandstone - Shale: - text: Shale - Siltstone: - text: Siltstone - Volcanic: - text: Volcanic - other: - text: other + north corner: + text: north corner + south corner: + text: south corner + west corner: + text: west corner + east corner: + text: east corner + northeast corner: + text: northeast corner + northwest corner: + text: northwest corner + southeast corner: + text: southeast corner + southwest corner: + text: southwest corner + center: + text: center + door_mat_enum: + name: door_mat_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + aluminum: + text: aluminum + cellular PVC: + text: cellular PVC + engineered plastic: + text: engineered plastic + fiberboard: + text: fiberboard + fiberglass: + text: fiberglass + metal: + text: metal + thermoplastic alloy: + text: thermoplastic alloy + vinyl: + text: vinyl + wood: + text: wood + wood/plastic composite: + text: wood/plastic composite + biol_stat_enum: + name: biol_stat_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + wild: + text: wild + natural: + text: natural + semi-natural: + text: semi-natural + inbred line: + text: inbred line + breeder's line: + text: breeder's line + hybrid: + text: hybrid + clonal selection: + text: clonal selection + mutant: + text: mutant + floor_struc_enum: + name: floor_struc_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + balcony: + text: balcony + floating floor: + text: floating floor + glass floor: + text: glass floor + raised floor: + text: raised floor + sprung floor: + text: sprung floor + wood-framed: + text: wood-framed + concrete: + text: concrete door_type_wood_enum: name: door_type_wood_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml @@ -2949,128 +2973,88 @@ enums: text: louvered wire gauged: text: wire gauged - wall_finish_mat_enum: - name: wall_finish_mat_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - plaster: - text: plaster - gypsum plaster: - text: gypsum plaster - veneer plaster: - text: veneer plaster - gypsum board: - text: gypsum board - tile: - text: tile - terrazzo: - text: terrazzo - stone facing: - text: stone facing - acoustical treatment: - text: acoustical treatment - wood: - text: wood - metal: - text: metal - masonry: - text: masonry - gender_restroom_enum: - name: gender_restroom_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - all gender: - text: all gender - female: - text: female - gender neurtral: - text: gender neurtral - male: - text: male - male and female: - text: male and female - unisex: - text: unisex - int_wall_cond_enum: - name: int_wall_cond_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - floor_water_mold_enum: - name: floor_water_mold_enum + organism_count_enum: + name: organism_count_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - mold odor: - text: mold odor - wet floor: - text: wet floor - water stains: - text: water stains - wall discoloration: - text: wall discoloration - floor discoloration: - text: floor discoloration - ceiling discoloration: - text: ceiling discoloration - peeling paint or wallpaper: - text: peeling paint or wallpaper - bulging walls: - text: bulging walls - condensation: - text: condensation - samp_floor_enum: - name: samp_floor_enum + ATP: + text: ATP + MPN: + text: MPN + other: + text: other + shading_device_cond_enum: + name: shading_device_cond_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - 1st floor: - text: 1st floor - 2nd floor: - text: 2nd floor - basement: - text: basement - lobby: - text: lobby - heat_deliv_loc_enum: - name: heat_deliv_loc_enum + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + hcr_enum: + name: hcr_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - biol_stat_enum: - name: biol_stat_enum + Oil Reservoir: + text: Oil Reservoir + Gas Reservoir: + text: Gas Reservoir + Oil Sand: + text: Oil Sand + Coalbed: + text: Coalbed + Shale: + text: Shale + Tight Oil Reservoir: + text: Tight Oil Reservoir + Tight Gas Reservoir: + text: Tight Gas Reservoir + other: + text: other + mech_struc_enum: + name: mech_struc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - wild: - text: wild - natural: - text: natural - semi-natural: - text: semi-natural - inbred line: - text: inbred line - breeder's line: - text: breeder's line - hybrid: - text: hybrid - clonal selection: - text: clonal selection - mutant: - text: mutant + subway: + text: subway + coach: + text: coach + carriage: + text: carriage + elevator: + text: elevator + escalator: + text: escalator + boat: + text: boat + train: + text: train + car: + text: car + bus: + text: bus + hc_produced_enum: + name: hc_produced_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + Oil: + text: Oil + Gas-Condensate: + text: Gas-Condensate + Gas: + text: Gas + Bitumen: + text: Bitumen + Coalbed Methane: + text: Coalbed Methane + other: + text: other shading_device_type_enum: name: shading_device_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml @@ -3099,148 +3083,250 @@ enums: text: trellis venetian awning: text: venetian awning - train_stat_loc_enum: - name: train_stat_loc_enum + quad_pos_enum: + name: quad_pos_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - south station above ground: - text: south station above ground - south station underground: - text: south station underground - south station amtrak: - text: south station amtrak - forest hills: - text: forest hills - riverside: - text: riverside - window_mat_enum: - name: window_mat_enum + North side: + text: North side + West side: + text: West side + South side: + text: South side + East side: + text: East side + sr_kerog_type_enum: + name: sr_kerog_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - clad: - text: clad - fiberglass: - text: fiberglass - metal: - text: metal - vinyl: - text: vinyl - wood: - text: wood - samp_weather_enum: - name: samp_weather_enum + Type I: + text: Type I + Type II: + text: Type II + Type III: + text: Type III + Type IV: + text: Type IV + other: + text: other + floor_cond_enum: + name: floor_cond_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture + heat_deliv_loc_enum: + name: heat_deliv_loc_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + north: + text: north + south: + text: south + east: + text: east + west: + text: west + host_sex_enum: + name: host_sex_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + female: + text: female + hermaphrodite: + text: hermaphrodite + male: + text: male + neuter: + text: neuter + window_cond_enum: + name: window_cond_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + handidness_enum: + name: handidness_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + ambidexterity: + text: ambidexterity + left handedness: + text: left handedness + mixed-handedness: + text: mixed-handedness + right handedness: + text: right handedness + wall_const_type_enum: + name: wall_const_type_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + frame construction: + text: frame construction + joisted masonry: + text: joisted masonry + light noncombustible: + text: light noncombustible + masonry noncombustible: + text: masonry noncombustible + modified fire resistive: + text: modified fire resistive + fire resistive: + text: fire resistive + build_occup_type_enum: + name: build_occup_type_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + office: + text: office + market: + text: market + restaurant: + text: restaurant + residence: + text: residence + school: + text: school + residential: + text: residential + commercial: + text: commercial + low rise: + text: low rise + high rise: + text: high rise + wood framed: + text: wood framed + health care: + text: health care + airport: + text: airport + sports complex: + text: sports complex + oxy_stat_samp_enum: + name: oxy_stat_samp_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - clear sky: - text: clear sky - cloudy: - text: cloudy - foggy: - text: foggy - hail: - text: hail - rain: - text: rain - snow: - text: snow - sleet: - text: sleet - sunny: - text: sunny - windy: - text: windy - biotic_relationship_enum: - name: biotic_relationship_enum + aerobic: + text: aerobic + anaerobic: + text: anaerobic + other: + text: other + filter_type_enum: + name: filter_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - free living: - text: free living - parasite: - text: parasite - commensal: - text: commensal - symbiont: - text: symbiont - door_cond_enum: - name: door_cond_enum + particulate air filter: + text: particulate air filter + chemical air filter: + text: chemical air filter + low-MERV pleated media: + text: low-MERV pleated media + HEPA: + text: HEPA + electrostatic: + text: electrostatic + gas-phase or ultraviolet air treatments: + text: gas-phase or ultraviolet air treatments + samp_floor_enum: + name: samp_floor_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - train_line_enum: - name: train_line_enum + 1st floor: + text: 1st floor + 2nd floor: + text: 2nd floor + basement: + text: basement + lobby: + text: lobby + furniture_enum: + name: furniture_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - red: - text: red - green: - text: green - orange: - text: orange - build_docs_enum: - name: build_docs_enum + cabinet: + text: cabinet + chair: + text: chair + desks: + text: desks + samp_dis_stage_enum: + name: samp_dis_stage_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - building information model: - text: building information model - commissioning report: - text: commissioning report - complaint logs: - text: complaint logs - contract administration: - text: contract administration - cost estimate: - text: cost estimate - janitorial schedules or logs: - text: janitorial schedules or logs - maintenance plans: - text: maintenance plans - schedule: - text: schedule - sections: - text: sections - shop drawings: - text: shop drawings - submittals: - text: submittals - ventilation system: - text: ventilation system - windows: - text: windows - door_loc_enum: - name: door_loc_enum + dissemination: + text: dissemination + growth and reproduction: + text: growth and reproduction + infection: + text: infection + inoculation: + text: inoculation + penetration: + text: penetration + other: + text: other + substructure_type_enum: + name: substructure_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - sr_kerog_type_enum: - name: sr_kerog_type_enum + crawlspace: + text: crawlspace + slab on grade: + text: slab on grade + basement: + text: basement + door_comp_type_enum: + name: door_comp_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - Type I: - text: Type I - Type II: - text: Type II - Type III: - text: Type III - Type IV: - text: Type IV - other: - text: other + metal covered: + text: metal covered + revolving: + text: revolving + sliding: + text: sliding + telescopic: + text: telescopic + plant_growth_med_enum: + name: plant_growth_med_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + other artificial liquid medium: + text: other artificial liquid medium + other artificial solid medium: + text: other artificial solid medium + peat moss: + text: peat moss + perlite: + text: perlite + pumice: + text: pumice + sand: + text: sand + soil: + text: soil + vermiculite: + text: vermiculite + water: + text: water slots: metagenome_annotation_id: name: metagenome_annotation_id @@ -5531,8 +5617,6 @@ slots: examples: - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:collection_date rank: 2 string_serialization: '{date, arbitrary precision}' slot_group: MIxS Inspired @@ -5549,8 +5633,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:collection_date rank: 1 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -5568,8 +5650,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:collection_date rank: 3 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -5587,8 +5667,6 @@ slots: examples: - value: 'experimental treatment: value' from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:experimental_factor|additional_info rank: 7 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5603,8 +5681,6 @@ slots: - value: C18 - value: Basix PES, 13-100-106 FisherSci from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:filter_type rank: 6 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5622,8 +5698,6 @@ slots: - value: 13C glucose - value: H218O from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:chem_administration rank: 16 string_serialization: '{termLabel} {[termID]}; {timestamp}' slot_group: MIxS Inspired @@ -5640,8 +5714,6 @@ slots: - value: https://doi.org/10.1016/0038-0717(87)90052-6 - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:micro_biomass_meth rank: 11 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5656,8 +5728,6 @@ slots: - value: https://doi.org/10.1016/0038-0717(87)90052-6 - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:micro_biomass_meth rank: 13 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5672,8 +5742,6 @@ slots: examples: - value: 0.05 ug C/g dry soil from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:microbial_biomass rank: 10 string_serialization: '{float} {unit}' slot_group: MIxS Inspired @@ -5688,8 +5756,6 @@ slots: examples: - value: 0.05 ug N/g dry soil from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:microbial_biomass rank: 12 string_serialization: '{float} {unit}' slot_group: MIxS Inspired @@ -5702,8 +5768,6 @@ slots: examples: - value: insect 0.23 ug; plant 1g from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:biomass|microbial_biomass rank: 8 string_serialization: '{text};{float} {unit}' slot_group: MIxS Inspired @@ -5716,8 +5780,6 @@ slots: examples: - value: https://doi.org/10.1038/s41467-021-26181-3 from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:microbial_biomass rank: 9 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5730,8 +5792,6 @@ slots: examples: - value: https://doi.org/10.1016/0038-0717(85)90144-0 from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:org_nitro|tot_nitro_cont_meth rank: 14 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5744,8 +5804,6 @@ slots: - This is an open text field to provide any treatments that cannot be captured in the provided slots. from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:additional_info rank: 15 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5763,8 +5821,6 @@ slots: examples: - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:collection_date rank: 4 string_serialization: '{date, arbitrary precision}' slot_group: MIxS Inspired @@ -5781,8 +5837,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:collection_date rank: 5 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -17361,19 +17415,28 @@ slots: slot_uri: MIXS:0000156 multivalued: false range: QuantityValue - investigation field: - name: investigation field - description: field describing aspect of the investigation/study to which the sample - belongs + has unit: + name: has unit + description: Example "m" + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + owner: QuantityValue + sequencing field: + name: sequencing field from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml abstract: true + has raw value: + name: has raw value + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + string_serialization: '{has numeric value} {has unit}' + owner: QuantityValue core field: name: core field description: basic fields from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml abstract: true - nucleic acid sequence source field: - name: nucleic acid sequence source field + environment field: + name: environment field + description: field describing environmental aspect of a sample from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml abstract: true has numeric value: @@ -17381,25 +17444,16 @@ slots: from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml owner: QuantityValue range: double - environment field: - name: environment field - description: field describing environmental aspect of a sample + nucleic acid sequence source field: + name: nucleic acid sequence source field from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml abstract: true - has unit: - name: has unit - description: Example "m" - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - owner: QuantityValue - sequencing field: - name: sequencing field + investigation field: + name: investigation field + description: field describing aspect of the investigation/study to which the sample + belongs from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml abstract: true - has raw value: - name: has raw value - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - string_serialization: '{has numeric value} {has unit}' - owner: QuantityValue chemical: name: chemical description: from reaction participant class @@ -18479,10 +18533,9 @@ classes: Matches the entity that has been submitted to NMDC lat_lon: name: lat_lon - description: This is currently a required field but it's not clear if this - should be required for human hosts - notes: - - required where? + todos: + - This is currently a required field but it's not clear if this should be + required for human hosts env_broad_scale: name: env_broad_scale required: true @@ -19417,7 +19470,6 @@ classes: used: name: used description: The instrument used to collect the data used in the analysis - range: Instrument id: name: id required: true diff --git a/project.Makefile b/project.Makefile index afa639abcf..46349142ed 100644 --- a/project.Makefile +++ b/project.Makefile @@ -407,29 +407,37 @@ nmdc_schema/nmdc_schema_accepting_legacy_ids.py: nmdc_schema/nmdc_schema_accepti # ---- # recommended setup: -# 1. . ~/sshproxy.sh -u +# 1. . ~/sshproxy.sh -u {YOUR_NERSC_USERNAME} # 2. ssh -i ~/.ssh/nersc -L27777:mongo-loadbalancer.nmdc.production.svc.spin.nersc.org:27017 -o ServerAliveInterval=60 {YOUR_NERSC_USERNAME}@dtn01.nersc.gov # todo mongodb collection stats vs Database slots report # todo convert to json # todo compress large files -# todo: allow different api base addresses # todo: switch to API method for getting collection names and stats: https://api.microbiomedata.org/nmdcschema/collection_stats # partially implemented -# todo: add start time reporting make-rdf: rdf-clean local/mongo_as_nmdc_database_validation.log local/mongo_as_nmdc_database_cuire_repaired.ttl temp: -# --selected-collections functional_annotation_agg \ # huge, no publically avaiaible reference data (kegg) +# --selected-collections functional_annotation_agg \ # huge, no publicly available reference data (kegg) # --selected-collections metaproteomics_analysis_activity_set \ # next slowest +# when connecting to the dev MongoDB, also use --client-base-url https://api-dev.microbiomedata.org +# make pre-composed prod and dev makefile tasks! since they require the user to provide a matching mongo port and api url + local/mongo_as_unvalidated_nmdc_database.yaml: date # 276.50 seconds on 2023-08-30 without functional_annotation_agg or metaproteomics_analysis_activity_set time $(RUN) pure-export \ + --client-base-url https://api.microbiomedata.org \ + --endpoint-prefix nmdcschema \ + --env-file local/.env \ --max-docs-per-coll 10000000 \ + --mongo-db-name nmdc \ + --mongo-host localhost \ + --mongo-port 27777 \ --output-yaml $@ \ --page-size 10000 \ + --schema-file src/schema/nmdc.yaml \ --selected-collections biosample_set \ --selected-collections data_object_set \ --selected-collections extraction_set \ @@ -463,12 +471,14 @@ local/mongo_as_nmdc_database_validation.log: nmdc_schema/nmdc_schema_accepting_l date # 5m57.559s without functional_annotation_agg or metaproteomics_analysis_activity_set time $(RUN) linkml-validate --schema $^ > $@ +# from riot: +# WARNING: java.io.tmpdir directory does not exist + local/mongo_as_nmdc_database.ttl: nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml local/mongo_as_nmdc_database_rdf_safe.yaml date # 681.99 seconds on 2023-08-30 without functional_annotation_agg or metaproteomics_analysis_activity_set time $(RUN) linkml-convert --output $@ --schema $^ export _JAVA_OPTIONS=-Djava.io.tmpdir=local - $(RIOT) --validate $@ # < 1 minute - # WARNING: java.io.tmpdir directory does not exist # todo: still getting anyurl typed string statement objects in RDF. I added a workarround in anyuri-strings-to-iris @@ -479,7 +489,8 @@ local/mongo_as_nmdc_database_cuire_repaired.ttl: local/mongo_as_nmdc_database.tt --jsonld-context-jsons project/jsonld/nmdc.context.jsonld \ --emsl-biosample-uuid-replacement emsl_biosample_uuid_like \ --output-ttl $@ - -# $(RIOT) --validate # < 1 minute + export _JAVA_OPTIONS=-Djava.io.tmpdir=local + - $(RIOT) --validate $@ # < 1 minute date # ---- diff --git a/project/jsonld/nmdc.context.jsonld b/project/jsonld/nmdc.context.jsonld index c46cb918cf..880e8e2107 100644 --- a/project/jsonld/nmdc.context.jsonld +++ b/project/jsonld/nmdc.context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-09-21T12:49:06", + "generation_date": "2023-10-03T12:25:37", "source": "nmdc.yaml" }, "@context": { diff --git a/project/jsonschema/nmdc.schema.json b/project/jsonschema/nmdc.schema.json index b3d909ce11..9fc084fa4f 100644 --- a/project/jsonschema/nmdc.schema.json +++ b/project/jsonschema/nmdc.schema.json @@ -1400,7 +1400,7 @@ }, "lat_lon": { "$ref": "#/$defs/GeolocationValue", - "description": "This is currently a required field but it's not clear if this should be required for human hosts" + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system" }, "lbc_thirty": { "$ref": "#/$defs/QuantityValue", @@ -8152,5 +8152,5 @@ }, "title": "NMDC", "type": "object", - "version": "v8.0.0" + "version": "v8.1.0" } \ No newline at end of file diff --git a/project/nmdc_materialized_patterns.schema.json b/project/nmdc_materialized_patterns.schema.json index e9eb9b8fc2..e9e80fa399 100644 --- a/project/nmdc_materialized_patterns.schema.json +++ b/project/nmdc_materialized_patterns.schema.json @@ -1400,7 +1400,7 @@ }, "lat_lon": { "$ref": "#/$defs/GeolocationValue", - "description": "This is currently a required field but it's not clear if this should be required for human hosts" + "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system" }, "lbc_thirty": { "$ref": "#/$defs/QuantityValue", @@ -8152,5 +8152,5 @@ }, "title": "NMDC", "type": "object", - "version": "v8.0.0" + "version": "v8.1.0" } diff --git a/project/nmdc_materialized_patterns.yaml b/project/nmdc_materialized_patterns.yaml index 2f26913595..0c1b992946 100644 --- a/project/nmdc_materialized_patterns.yaml +++ b/project/nmdc_materialized_patterns.yaml @@ -11,7 +11,7 @@ notes: - not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1 id: https://w3id.org/nmdc/nmdc -version: v8.0.0 +version: v8.1.0 license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: CATH: @@ -347,6 +347,10 @@ types: string: name: string description: A character string + notes: + - In RDF serializations, a slot with range of string is treated as a literal or + type xsd:string. If you are authoring schemas in LinkML YAML, the type is + referenced with the lower case "string". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Text @@ -355,6 +359,9 @@ types: integer: name: integer description: An integer + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "integer". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Integer @@ -363,6 +370,9 @@ types: boolean: name: boolean description: A binary (true or false) value + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "boolean". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Boolean @@ -372,6 +382,9 @@ types: float: name: float description: A real number that conforms to the xsd:float specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "float". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Float @@ -380,6 +393,9 @@ types: double: name: double description: A real number that conforms to the xsd:double specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "double". from_schema: https://w3id.org/nmdc/nmdc close_mappings: - schema:Float @@ -389,6 +405,9 @@ types: name: decimal description: A real number with arbitrary precision that conforms to the xsd:decimal specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "decimal". from_schema: https://w3id.org/nmdc/nmdc broad_mappings: - schema:Number @@ -400,17 +419,21 @@ types: particular day notes: - URI is dateTime because OWL reasoners do not work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "time". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Time base: XSDTime - uri: xsd:dateTime + uri: xsd:time repr: str date: name: date description: a date (year, month and day) in an idealized calendar notes: - URI is dateTime because OWL reasoners don't work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Date @@ -420,6 +443,9 @@ types: datetime: name: datetime description: The combination of a date and time + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "datetime". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:DateTime @@ -429,6 +455,9 @@ types: date_or_datetime: name: date_or_datetime description: Either a date or a datetime + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date_or_datetime". from_schema: https://w3id.org/nmdc/nmdc base: str uri: linkml:DateOrDatetime @@ -436,6 +465,9 @@ types: uriorcurie: name: uriorcurie description: a URI or a CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uriorcurie". from_schema: https://w3id.org/nmdc/nmdc base: URIorCURIE uri: xsd:anyURI @@ -444,6 +476,9 @@ types: name: curie conforms_to: https://www.w3.org/TR/curie/ description: a compact URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "curie". comments: - in RDF serializations this MUST be expanded to a URI - in non-RDF serializations MAY be serialized as the compact representation @@ -455,6 +490,9 @@ types: name: uri conforms_to: https://www.ietf.org/rfc/rfc3987.txt description: a complete URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uri". comments: - in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which @@ -468,6 +506,9 @@ types: ncname: name: ncname description: Prefix part of CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "ncname". from_schema: https://w3id.org/nmdc/nmdc base: NCName uri: xsd:string @@ -475,8 +516,11 @@ types: objectidentifier: name: objectidentifier description: A URI or CURIE that represents an object in the model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "objectidentifier". comments: - - Used for inheritence and type checking + - Used for inheritance and type checking from_schema: https://w3id.org/nmdc/nmdc base: ElementIdentifier uri: shex:iri @@ -484,10 +528,52 @@ types: nodeidentifier: name: nodeidentifier description: A URI, CURIE or BNODE that represents a node in a model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "nodeidentifier". from_schema: https://w3id.org/nmdc/nmdc base: NodeIdentifier uri: shex:nonLiteral repr: str + jsonpointer: + name: jsonpointer + conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 + description: A string encoding a JSON Pointer. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to a valid object within the current + instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpointer". + from_schema: https://w3id.org/nmdc/nmdc + base: str + uri: xsd:string + repr: str + jsonpath: + name: jsonpath + conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html + description: A string encoding a JSON Path. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to zero or more valid objects within + the current instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpath". + from_schema: https://w3id.org/nmdc/nmdc + base: str + uri: xsd:string + repr: str + sparqlpath: + name: sparqlpath + conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths + description: A string encoding a SPARQL Property Path. The value of the string + MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects + within the current instance document when encoded as RDF. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "sparqlpath". + from_schema: https://w3id.org/nmdc/nmdc + base: str + uri: xsd:string + repr: str enums: StatusEnum: name: StatusEnum @@ -1190,26 +1276,6 @@ enums: text: soil water_extract_soil: text: water_extract_soil - door_direct_enum: - name: door_direct_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - inward: - text: inward - outward: - text: outward - sideways: - text: sideways - oxy_stat_samp_enum: - name: oxy_stat_samp_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - aerobic: - text: aerobic - anaerobic: - text: anaerobic - other: - text: other surf_air_cont_enum: name: surf_air_cont_enum from_schema: https://w3id.org/nmdc/nmdc @@ -1230,164 +1296,164 @@ enums: text: nutrients biocides: text: biocides - window_vert_pos_enum: - name: window_vert_pos_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - bottom: - text: bottom - middle: - text: middle - top: - text: top - low: - text: low - high: - text: high - filter_type_enum: - name: filter_type_enum + water_feat_type_enum: + name: water_feat_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - particulate air filter: - text: particulate air filter - chemical air filter: - text: chemical air filter - low-MERV pleated media: - text: low-MERV pleated media - HEPA: - text: HEPA - electrostatic: - text: electrostatic - gas-phase or ultraviolet air treatments: - text: gas-phase or ultraviolet air treatments - rel_samp_loc_enum: - name: rel_samp_loc_enum + fountain: + text: fountain + pool: + text: pool + standing feature: + text: standing feature + stream: + text: stream + waterfall: + text: waterfall + samp_collect_point_enum: + name: samp_collect_point_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - edge of car: - text: edge of car - center of car: - text: center of car - under a seat: - text: under a seat - sediment_type_enum: - name: sediment_type_enum + well: + text: well + test well: + text: test well + drilling rig: + text: drilling rig + wellhead: + text: wellhead + separator: + text: separator + storage tank: + text: storage tank + other: + text: other + floor_water_mold_enum: + name: floor_water_mold_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - biogenous: - text: biogenous - cosmogenous: - text: cosmogenous - hydrogenous: - text: hydrogenous - lithogenous: - text: lithogenous - occup_document_enum: - name: occup_document_enum + mold odor: + text: mold odor + wet floor: + text: wet floor + water stains: + text: water stains + wall discoloration: + text: wall discoloration + floor discoloration: + text: floor discoloration + ceiling discoloration: + text: ceiling discoloration + peeling paint or wallpaper: + text: peeling paint or wallpaper + bulging walls: + text: bulging walls + condensation: + text: condensation + wall_texture_enum: + name: wall_texture_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - automated count: - text: automated count - estimate: - text: estimate - manual count: - text: manual count - videos: - text: videos - room_connected_enum: - name: room_connected_enum + crows feet: + text: crows feet + crows-foot stomp: + text: crows-foot stomp + ? '' + : text: '' + double skip: + text: double skip + hawk and trowel: + text: hawk and trowel + knockdown: + text: knockdown + popcorn: + text: popcorn + orange peel: + text: orange peel + rosebud stomp: + text: rosebud stomp + Santa-Fe texture: + text: Santa-Fe texture + skip trowel: + text: skip trowel + smooth: + text: smooth + stomp knockdown: + text: stomp knockdown + swirl: + text: swirl + samp_subtype_enum: + name: samp_subtype_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - attic: - text: attic - bathroom: - text: bathroom - closet: - text: closet - conference room: - text: conference room - elevator: - text: elevator - examining room: - text: examining room - hallway: - text: hallway - kitchen: - text: kitchen - mail room: - text: mail room - office: - text: office - stairwell: - text: stairwell - quad_pos_enum: - name: quad_pos_enum + oil phase: + text: oil phase + water phase: + text: water phase + biofilm: + text: biofilm + not applicable: + text: not applicable + other: + text: other + drainage_class_enum: + name: drainage_class_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - North side: - text: North side - West side: - text: West side - South side: - text: South side - East side: - text: East side - sr_geol_age_enum: - name: sr_geol_age_enum + very poorly: + text: very poorly + poorly: + text: poorly + somewhat poorly: + text: somewhat poorly + moderately well: + text: moderately well + well: + text: well + excessively drained: + text: excessively drained + freq_clean_enum: + name: freq_clean_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Archean: - text: Archean - Cambrian: - text: Cambrian - Carboniferous: - text: Carboniferous - Cenozoic: - text: Cenozoic - Cretaceous: - text: Cretaceous - Devonian: - text: Devonian - Jurassic: - text: Jurassic - Mesozoic: - text: Mesozoic - Neogene: - text: Neogene - Ordovician: - text: Ordovician - Paleogene: - text: Paleogene - Paleozoic: - text: Paleozoic - Permian: - text: Permian - Precambrian: - text: Precambrian - Proterozoic: - text: Proterozoic - Silurian: - text: Silurian - Triassic: - text: Triassic + Daily: + text: Daily + Weekly: + text: Weekly + Monthly: + text: Monthly + Quarterly: + text: Quarterly + Annually: + text: Annually other: text: other - door_move_enum: - name: door_move_enum + biotic_relationship_enum: + name: biotic_relationship_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - collapsible: - text: collapsible - folding: - text: folding - revolving: - text: revolving - rolling shutter: - text: rolling shutter - sliding: - text: sliding - swinging: - text: swinging + free living: + text: free living + parasite: + text: parasite + commensal: + text: commensal + symbiont: + text: symbiont + light_type_enum: + name: light_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + natural light: + text: natural light + electric light: + text: electric light + desk lamp: + text: desk lamp + flourescent lights: + text: flourescent lights + none: + text: none cur_land_use_enum: name: cur_land_use_enum from_schema: https://w3id.org/nmdc/nmdc @@ -1583,142 +1649,146 @@ enums: value: vine crops (grapes) examples: - value: grapes - hcr_geol_age_enum: - name: hcr_geol_age_enum + drawings_enum: + name: drawings_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Archean: - text: Archean - Cambrian: - text: Cambrian - Carboniferous: - text: Carboniferous - Cenozoic: - text: Cenozoic - Cretaceous: - text: Cretaceous - Devonian: - text: Devonian - Jurassic: - text: Jurassic - Mesozoic: - text: Mesozoic - Neogene: - text: Neogene - Ordovician: - text: Ordovician - Paleogene: - text: Paleogene - Paleozoic: - text: Paleozoic - Permian: - text: Permian - Precambrian: - text: Precambrian - Proterozoic: - text: Proterozoic - Silurian: - text: Silurian - Triassic: - text: Triassic + operation: + text: operation + as built: + text: as built + construction: + text: construction + bid: + text: bid + design: + text: design + building navigation map: + text: building navigation map + diagram: + text: diagram + sketch: + text: sketch + indoor_surf_enum: + name: indoor_surf_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + cabinet: + text: cabinet + ceiling: + text: ceiling + counter top: + text: counter top + door: + text: door + shelving: + text: shelving + vent cover: + text: vent cover + window: + text: window + wall: + text: wall + samp_capt_status_enum: + name: samp_capt_status_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + active surveillance in response to an outbreak: + text: active surveillance in response to an outbreak + active surveillance not initiated by an outbreak: + text: active surveillance not initiated by an outbreak + farm sample: + text: farm sample + market sample: + text: market sample other: text: other - wall_const_type_enum: - name: wall_const_type_enum + room_loc_enum: + name: room_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - frame construction: - text: frame construction - joisted masonry: - text: joisted masonry - light noncombustible: - text: light noncombustible - masonry noncombustible: - text: masonry noncombustible - modified fire resistive: - text: modified fire resistive - fire resistive: - text: fire resistive - plant_sex_enum: - name: plant_sex_enum + corner room: + text: corner room + interior room: + text: interior room + exterior wall: + text: exterior wall + occup_document_enum: + name: occup_document_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Androdioecious: - text: Androdioecious - Androecious: - text: Androecious - Androgynous: - text: Androgynous - Androgynomonoecious: - text: Androgynomonoecious - Andromonoecious: - text: Andromonoecious - Bisexual: - text: Bisexual - Dichogamous: - text: Dichogamous - Diclinous: - text: Diclinous - Dioecious: - text: Dioecious - Gynodioecious: - text: Gynodioecious - Gynoecious: - text: Gynoecious - Gynomonoecious: - text: Gynomonoecious - Hermaphroditic: - text: Hermaphroditic - Imperfect: - text: Imperfect - Monoclinous: - text: Monoclinous - Monoecious: - text: Monoecious - Perfect: - text: Perfect - Polygamodioecious: - text: Polygamodioecious - Polygamomonoecious: - text: Polygamomonoecious - Polygamous: - text: Polygamous - Protandrous: - text: Protandrous - Protogynous: - text: Protogynous - Subandroecious: - text: Subandroecious - Subdioecious: - text: Subdioecious - Subgynoecious: - text: Subgynoecious - Synoecious: - text: Synoecious - Trimonoecious: - text: Trimonoecious - Trioecious: - text: Trioecious - Unisexual: - text: Unisexual - ceil_type_enum: - name: ceil_type_enum + automated count: + text: automated count + estimate: + text: estimate + manual count: + text: manual count + videos: + text: videos + arch_struc_enum: + name: arch_struc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - cathedral: - text: cathedral - dropped: - text: dropped - concave: - text: concave - barrel-shaped: - text: barrel-shaped - coffered: - text: coffered - cove: - text: cove - stretched: - text: stretched + building: + text: building + shed: + text: shed + home: + text: home + wall_finish_mat_enum: + name: wall_finish_mat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + plaster: + text: plaster + gypsum plaster: + text: gypsum plaster + veneer plaster: + text: veneer plaster + gypsum board: + text: gypsum board + tile: + text: tile + terrazzo: + text: terrazzo + stone facing: + text: stone facing + acoustical treatment: + text: acoustical treatment + wood: + text: wood + metal: + text: metal + masonry: + text: masonry + window_mat_enum: + name: window_mat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + clad: + text: clad + fiberglass: + text: fiberglass + metal: + text: metal + vinyl: + text: vinyl + wood: + text: wood + int_wall_cond_enum: + name: int_wall_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture floor_finish_mat_enum: name: floor_finish_mat_enum from_schema: https://w3id.org/nmdc/nmdc @@ -1759,584 +1829,240 @@ enums: text: paint none or unfinished: text: none or unfinished - wall_loc_enum: - name: wall_loc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - wall_surf_treatment_enum: - name: wall_surf_treatment_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - painted: - text: painted - wall paper: - text: wall paper - no treatment: - text: no treatment - paneling: - text: paneling - stucco: - text: stucco - fabric: - text: fabric - window_cond_enum: - name: window_cond_enum + build_docs_enum: + name: build_docs_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - door_mat_enum: - name: door_mat_enum + building information model: + text: building information model + commissioning report: + text: commissioning report + complaint logs: + text: complaint logs + contract administration: + text: contract administration + cost estimate: + text: cost estimate + janitorial schedules or logs: + text: janitorial schedules or logs + maintenance plans: + text: maintenance plans + schedule: + text: schedule + sections: + text: sections + shop drawings: + text: shop drawings + submittals: + text: submittals + ventilation system: + text: ventilation system + windows: + text: windows + surf_material_enum: + name: surf_material_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - aluminum: - text: aluminum - cellular PVC: - text: cellular PVC - engineered plastic: - text: engineered plastic - fiberboard: - text: fiberboard - fiberglass: - text: fiberglass + adobe: + text: adobe + carpet: + text: carpet + cinder blocks: + text: cinder blocks + concrete: + text: concrete + hay bales: + text: hay bales + glass: + text: glass metal: text: metal - thermoplastic alloy: - text: thermoplastic alloy + paint: + text: paint + plastic: + text: plastic + stainless steel: + text: stainless steel + stone: + text: stone + stucco: + text: stucco + tile: + text: tile vinyl: text: vinyl wood: text: wood - wood/plastic composite: - text: wood/plastic composite - soil_horizon_enum: - name: soil_horizon_enum + tidal_stage_enum: + name: tidal_stage_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - O horizon: - text: O horizon - A horizon: - text: A horizon - E horizon: - text: E horizon - B horizon: - text: B horizon - C horizon: - text: C horizon - R layer: - text: R layer - Permafrost: - text: Permafrost - M horizon: - text: M horizon - ceil_finish_mat_enum: - name: ceil_finish_mat_enum + low tide: + text: low tide + ebb tide: + text: ebb tide + flood tide: + text: flood tide + high tide: + text: high tide + window_horiz_pos_enum: + name: window_horiz_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - drywall: - text: drywall - mineral fibre: - text: mineral fibre - tiles: - text: tiles - PVC: - text: PVC - plasterboard: - text: plasterboard - metal: - text: metal - fiberglass: - text: fiberglass - stucco: - text: stucco - mineral wool/calcium silicate: - text: mineral wool/calcium silicate - wood: - text: wood - shading_device_cond_enum: - name: shading_device_cond_enum + left: + text: left + middle: + text: middle + right: + text: right + train_stop_loc_enum: + name: train_stop_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - hc_produced_enum: - name: hc_produced_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Oil: - text: Oil - Gas-Condensate: - text: Gas-Condensate - Gas: - text: Gas - Bitumen: - text: Bitumen - Coalbed Methane: - text: Coalbed Methane - other: - text: other - door_comp_type_enum: - name: door_comp_type_enum + end: + text: end + mid: + text: mid + downtown: + text: downtown + train_line_enum: + name: train_line_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - metal covered: - text: metal covered - revolving: - text: revolving - sliding: - text: sliding - telescopic: - text: telescopic - window_loc_enum: - name: window_loc_enum + red: + text: red + green: + text: green + orange: + text: orange + train_stat_loc_enum: + name: train_stat_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - sr_lithology_enum: - name: sr_lithology_enum + south station above ground: + text: south station above ground + south station underground: + text: south station underground + south station amtrak: + text: south station amtrak + forest hills: + text: forest hills + riverside: + text: riverside + sr_dep_env_enum: + name: sr_dep_env_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Clastic: - text: Clastic - Carbonate: - text: Carbonate - Coal: - text: Coal - Biosilicieous: - text: Biosilicieous + Lacustine: + text: Lacustine + Fluvioldeltaic: + text: Fluvioldeltaic + Fluviomarine: + text: Fluviomarine + Marine: + text: Marine other: text: other - plant_growth_med_enum: - name: plant_growth_med_enum + samp_weather_enum: + name: samp_weather_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - other artificial liquid medium: - text: other artificial liquid medium - other artificial solid medium: - text: other artificial solid medium - peat moss: - text: peat moss - perlite: - text: perlite - pumice: - text: pumice - sand: - text: sand - soil: - text: soil - vermiculite: - text: vermiculite - water: - text: water - surf_material_enum: - name: surf_material_enum + clear sky: + text: clear sky + cloudy: + text: cloudy + foggy: + text: foggy + hail: + text: hail + rain: + text: rain + snow: + text: snow + sleet: + text: sleet + sunny: + text: sunny + windy: + text: windy + window_cover_enum: + name: window_cover_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - adobe: - text: adobe - carpet: - text: carpet - cinder blocks: - text: cinder blocks - concrete: - text: concrete - hay bales: - text: hay bales - glass: - text: glass - metal: - text: metal - paint: - text: paint - plastic: - text: plastic - stainless steel: - text: stainless steel - stone: - text: stone - stucco: - text: stucco - tile: - text: tile - vinyl: - text: vinyl - wood: - text: wood - ceil_cond_enum: - name: ceil_cond_enum + blinds: + text: blinds + curtains: + text: curtains + none: + text: none + room_type_enum: + name: room_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - building_setting_enum: - name: building_setting_enum + attic: + text: attic + bathroom: + text: bathroom + closet: + text: closet + conference room: + text: conference room + elevator: + text: elevator + examining room: + text: examining room + hallway: + text: hallway + kitchen: + text: kitchen + mail room: + text: mail room + private office: + text: private office + open office: + text: open office + stairwell: + text: stairwell + ',restroom': + text: ',restroom' + lobby: + text: lobby + vestibule: + text: vestibule + mechanical or electrical room: + text: mechanical or electrical room + data center: + text: data center + laboratory_wet: + text: laboratory_wet + laboratory_dry: + text: laboratory_dry + gymnasium: + text: gymnasium + natatorium: + text: natatorium + auditorium: + text: auditorium + lockers: + text: lockers + cafe: + text: cafe + warehouse: + text: warehouse + sediment_type_enum: + name: sediment_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - urban: - text: urban - suburban: - text: suburban - exurban: - text: exurban - rural: - text: rural - build_occup_type_enum: - name: build_occup_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - office: - text: office - market: - text: market - restaurant: - text: restaurant - residence: - text: residence - school: - text: school - residential: - text: residential - commercial: - text: commercial - low rise: - text: low rise - high rise: - text: high rise - wood framed: - text: wood framed - health care: - text: health care - airport: - text: airport - sports complex: - text: sports complex - depos_env_enum: - name: depos_env_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Continental - Alluvial: - text: Continental - Alluvial - Continental - Aeolian: - text: Continental - Aeolian - Continental - Fluvial: - text: Continental - Fluvial - Continental - Lacustrine: - text: Continental - Lacustrine - Transitional - Deltaic: - text: Transitional - Deltaic - Transitional - Tidal: - text: Transitional - Tidal - Transitional - Lagoonal: - text: Transitional - Lagoonal - Transitional - Beach: - text: Transitional - Beach - Transitional - Lake: - text: Transitional - Lake - Marine - Shallow: - text: Marine - Shallow - Marine - Deep: - text: Marine - Deep - Marine - Reef: - text: Marine - Reef - Other - Evaporite: - text: Other - Evaporite - Other - Glacial: - text: Other - Glacial - Other - Volcanic: - text: Other - Volcanic - other: - text: other - profile_position_enum: - name: profile_position_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - summit: - text: summit - shoulder: - text: shoulder - backslope: - text: backslope - footslope: - text: footslope - toeslope: - text: toeslope - furniture_enum: - name: furniture_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - cabinet: - text: cabinet - chair: - text: chair - desks: - text: desks - door_type_enum: - name: door_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - composite: - text: composite - metal: - text: metal - wooden: - text: wooden - tidal_stage_enum: - name: tidal_stage_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - low tide: - text: low tide - ebb tide: - text: ebb tide - flood tide: - text: flood tide - high tide: - text: high tide - door_type_metal_enum: - name: door_type_metal_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - collapsible: - text: collapsible - corrugated steel: - text: corrugated steel - hollow: - text: hollow - rolling shutters: - text: rolling shutters - steel plate: - text: steel plate - handidness_enum: - name: handidness_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - ambidexterity: - text: ambidexterity - left handedness: - text: left handedness - mixed-handedness: - text: mixed-handedness - right handedness: - text: right handedness - tillage_enum: - name: tillage_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - drill: - text: drill - cutting disc: - text: cutting disc - ridge till: - text: ridge till - strip tillage: - text: strip tillage - zonal tillage: - text: zonal tillage - chisel: - text: chisel - tined: - text: tined - mouldboard: - text: mouldboard - disc plough: - text: disc plough - hcr_enum: - name: hcr_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Oil Reservoir: - text: Oil Reservoir - Gas Reservoir: - text: Gas Reservoir - Oil Sand: - text: Oil Sand - Coalbed: - text: Coalbed - Shale: - text: Shale - Tight Oil Reservoir: - text: Tight Oil Reservoir - Tight Gas Reservoir: - text: Tight Gas Reservoir - other: - text: other - freq_clean_enum: - name: freq_clean_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Daily: - text: Daily - Weekly: - text: Weekly - Monthly: - text: Monthly - Quarterly: - text: Quarterly - Annually: - text: Annually - other: - text: other - growth_habit_enum: - name: growth_habit_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - erect: - text: erect - semi-erect: - text: semi-erect - spreading: - text: spreading - prostrate: - text: prostrate - season_use_enum: - name: season_use_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Spring: - text: Spring - Summer: - text: Summer - Fall: - text: Fall - Winter: - text: Winter - sr_dep_env_enum: - name: sr_dep_env_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Lacustine: - text: Lacustine - Fluvioldeltaic: - text: Fluvioldeltaic - Fluviomarine: - text: Fluviomarine - Marine: - text: Marine - other: - text: other - water_feat_type_enum: - name: water_feat_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - fountain: - text: fountain - pool: - text: pool - standing feature: - text: standing feature - stream: - text: stream - waterfall: - text: waterfall - substructure_type_enum: - name: substructure_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - crawlspace: - text: crawlspace - slab on grade: - text: slab on grade - basement: - text: basement - indoor_space_enum: - name: indoor_space_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - bedroom: - text: bedroom - office: - text: office - bathroom: - text: bathroom - foyer: - text: foyer - kitchen: - text: kitchen - locker room: - text: locker room - hallway: - text: hallway - elevator: - text: elevator - host_sex_enum: - name: host_sex_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - female: - text: female - hermaphrodite: - text: hermaphrodite - male: - text: male - neuter: - text: neuter - window_type_enum: - name: window_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - single-hung sash window: - text: single-hung sash window - horizontal sash window: - text: horizontal sash window - fixed window: - text: fixed window - specific_enum: - name: specific_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - photos: - text: photos - fao_class_enum: - name: fao_class_enum + biogenous: + text: biogenous + cosmogenous: + text: cosmogenous + hydrogenous: + text: hydrogenous + lithogenous: + text: lithogenous + fao_class_enum: + name: fao_class_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: Acrisols: @@ -2391,166 +2117,404 @@ enums: text: Vertisols Yermosols: text: Yermosols - floor_struc_enum: - name: floor_struc_enum + ext_window_orient_enum: + name: ext_window_orient_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - balcony: - text: balcony - floating floor: - text: floating floor - glass floor: - text: glass floor - raised floor: - text: raised floor - sprung floor: - text: sprung floor - wood-framed: - text: wood-framed - concrete: - text: concrete - wall_texture_enum: - name: wall_texture_enum + north: + text: north + south: + text: south + east: + text: east + west: + text: west + northeast: + text: northeast + southeast: + text: southeast + southwest: + text: southwest + northwest: + text: northwest + sr_geol_age_enum: + name: sr_geol_age_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + Archean: + text: Archean + Cambrian: + text: Cambrian + Carboniferous: + text: Carboniferous + Cenozoic: + text: Cenozoic + Cretaceous: + text: Cretaceous + Devonian: + text: Devonian + Jurassic: + text: Jurassic + Mesozoic: + text: Mesozoic + Neogene: + text: Neogene + Ordovician: + text: Ordovician + Paleogene: + text: Paleogene + Paleozoic: + text: Paleozoic + Permian: + text: Permian + Precambrian: + text: Precambrian + Proterozoic: + text: Proterozoic + Silurian: + text: Silurian + Triassic: + text: Triassic + other: + text: other + door_move_enum: + name: door_move_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + collapsible: + text: collapsible + folding: + text: folding + revolving: + text: revolving + rolling shutter: + text: rolling shutter + sliding: + text: sliding + swinging: + text: swinging + door_direct_enum: + name: door_direct_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + inward: + text: inward + outward: + text: outward + sideways: + text: sideways + ceil_texture_enum: + name: ceil_texture_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + crows feet: + text: crows feet + crows-foot stomp: + text: crows-foot stomp + double skip: + text: double skip + hawk and trowel: + text: hawk and trowel + knockdown: + text: knockdown + popcorn: + text: popcorn + orange peel: + text: orange peel + rosebud stomp: + text: rosebud stomp + Santa-Fe texture: + text: Santa-Fe texture + skip trowel: + text: skip trowel + smooth: + text: smooth + stomp knockdown: + text: stomp knockdown + swirl: + text: swirl + samp_md_enum: + name: samp_md_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + DF: + text: DF + RT: + text: RT + KB: + text: KB + MSL: + text: MSL + other: + text: other + ceil_type_enum: + name: ceil_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + cathedral: + text: cathedral + dropped: + text: dropped + concave: + text: concave + barrel-shaped: + text: barrel-shaped + coffered: + text: coffered + cove: + text: cove + stretched: + text: stretched + wall_loc_enum: + name: wall_loc_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + north: + text: north + south: + text: south + east: + text: east + west: + text: west + door_type_metal_enum: + name: door_type_metal_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + collapsible: + text: collapsible + corrugated steel: + text: corrugated steel + hollow: + text: hollow + rolling shutters: + text: rolling shutters + steel plate: + text: steel plate + gender_restroom_enum: + name: gender_restroom_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + all gender: + text: all gender + female: + text: female + gender neurtral: + text: gender neurtral + male: + text: male + male and female: + text: male and female + unisex: + text: unisex + vis_media_enum: + name: vis_media_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - ? '' - : text: '' - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - train_stop_loc_enum: - name: train_stop_loc_enum + photos: + text: photos + videos: + text: videos + commonly of the building: + text: commonly of the building + site context (adjacent buildings, vegetation, terrain, streets): + text: site context (adjacent buildings, vegetation, terrain, streets) + interiors: + text: interiors + equipment: + text: equipment + 3D scans: + text: 3D scans + window_loc_enum: + name: window_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - end: - text: end - mid: - text: mid - downtown: - text: downtown - drawings_enum: - name: drawings_enum + north: + text: north + south: + text: south + east: + text: east + west: + text: west + soil_horizon_enum: + name: soil_horizon_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - building navigation map: - text: building navigation map - diagram: - text: diagram - sketch: - text: sketch - room_loc_enum: - name: room_loc_enum + O horizon: + text: O horizon + A horizon: + text: A horizon + E horizon: + text: E horizon + B horizon: + text: B horizon + C horizon: + text: C horizon + R layer: + text: R layer + Permafrost: + text: Permafrost + M horizon: + text: M horizon + indoor_space_enum: + name: indoor_space_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - corner room: - text: corner room - interior room: - text: interior room - exterior wall: - text: exterior wall - light_type_enum: - name: light_type_enum + bedroom: + text: bedroom + office: + text: office + bathroom: + text: bathroom + foyer: + text: foyer + kitchen: + text: kitchen + locker room: + text: locker room + hallway: + text: hallway + elevator: + text: elevator + door_type_enum: + name: door_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - natural light: - text: natural light - electric light: - text: electric light - desk lamp: - text: desk lamp - flourescent lights: - text: flourescent lights - none: - text: none - weekday_enum: - name: weekday_enum + composite: + text: composite + metal: + text: metal + wooden: + text: wooden + depos_env_enum: + name: depos_env_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Monday: - text: Monday - Tuesday: - text: Tuesday - Wednesday: - text: Wednesday - Thursday: - text: Thursday - Friday: - text: Friday - Saturday: - text: Saturday - Sunday: - text: Sunday - arch_struc_enum: - name: arch_struc_enum + Continental - Alluvial: + text: Continental - Alluvial + Continental - Aeolian: + text: Continental - Aeolian + Continental - Fluvial: + text: Continental - Fluvial + Continental - Lacustrine: + text: Continental - Lacustrine + Transitional - Deltaic: + text: Transitional - Deltaic + Transitional - Tidal: + text: Transitional - Tidal + Transitional - Lagoonal: + text: Transitional - Lagoonal + Transitional - Beach: + text: Transitional - Beach + Transitional - Lake: + text: Transitional - Lake + Marine - Shallow: + text: Marine - Shallow + Marine - Deep: + text: Marine - Deep + Marine - Reef: + text: Marine - Reef + Other - Evaporite: + text: Other - Evaporite + Other - Glacial: + text: Other - Glacial + Other - Volcanic: + text: Other - Volcanic + other: + text: other + sr_lithology_enum: + name: sr_lithology_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - building: - text: building - shed: - text: shed - home: - text: home - heat_cool_type_enum: - name: heat_cool_type_enum + Clastic: + text: Clastic + Carbonate: + text: Carbonate + Coal: + text: Coal + Biosilicieous: + text: Biosilicieous + other: + text: other + plant_sex_enum: + name: plant_sex_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - radiant system: - text: radiant system - heat pump: - text: heat pump - forced air system: - text: forced air system - steam forced heat: - text: steam forced heat - wood stove: - text: wood stove - samp_md_enum: - name: samp_md_enum + Androdioecious: + text: Androdioecious + Androecious: + text: Androecious + Androgynous: + text: Androgynous + Androgynomonoecious: + text: Androgynomonoecious + Andromonoecious: + text: Andromonoecious + Bisexual: + text: Bisexual + Dichogamous: + text: Dichogamous + Diclinous: + text: Diclinous + Dioecious: + text: Dioecious + Gynodioecious: + text: Gynodioecious + Gynoecious: + text: Gynoecious + Gynomonoecious: + text: Gynomonoecious + Hermaphroditic: + text: Hermaphroditic + Imperfect: + text: Imperfect + Monoclinous: + text: Monoclinous + Monoecious: + text: Monoecious + Perfect: + text: Perfect + Polygamodioecious: + text: Polygamodioecious + Polygamomonoecious: + text: Polygamomonoecious + Polygamous: + text: Polygamous + Protandrous: + text: Protandrous + Protogynous: + text: Protogynous + Subandroecious: + text: Subandroecious + Subdioecious: + text: Subdioecious + Subgynoecious: + text: Subgynoecious + Synoecious: + text: Synoecious + Trimonoecious: + text: Trimonoecious + Trioecious: + text: Trioecious + Unisexual: + text: Unisexual + specific_enum: + name: specific_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - DF: - text: DF - RT: - text: RT - KB: - text: KB - MSL: - text: MSL - other: - text: other + operation: + text: operation + as built: + text: as built + construction: + text: construction + bid: + text: bid + design: + text: design + photos: + text: photos ext_wall_orient_enum: name: ext_wall_orient_enum from_schema: https://w3id.org/nmdc/nmdc @@ -2571,30 +2535,8 @@ enums: text: southwest northwest: text: northwest - mech_struc_enum: - name: mech_struc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - subway: - text: subway - coach: - text: coach - carriage: - text: carriage - elevator: - text: elevator - escalator: - text: escalator - boat: - text: boat - train: - text: train - car: - text: car - bus: - text: bus - ext_window_orient_enum: - name: ext_window_orient_enum + door_loc_enum: + name: door_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: north: @@ -2605,164 +2547,224 @@ enums: text: east west: text: west - northeast: - text: northeast - southeast: - text: southeast - southwest: - text: southwest - northwest: - text: northwest - window_cover_enum: - name: window_cover_enum + profile_position_enum: + name: profile_position_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - blinds: - text: blinds - curtains: - text: curtains - none: - text: none - drainage_class_enum: - name: drainage_class_enum + summit: + text: summit + shoulder: + text: shoulder + backslope: + text: backslope + footslope: + text: footslope + toeslope: + text: toeslope + growth_habit_enum: + name: growth_habit_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - very poorly: - text: very poorly - poorly: - text: poorly - somewhat poorly: - text: somewhat poorly - moderately well: - text: moderately well - well: - text: well - excessively drained: - text: excessively drained - window_horiz_pos_enum: - name: window_horiz_pos_enum + erect: + text: erect + semi-erect: + text: semi-erect + spreading: + text: spreading + prostrate: + text: prostrate + season_use_enum: + name: season_use_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - left: - text: left - middle: - text: middle - right: - text: right - samp_subtype_enum: - name: samp_subtype_enum + Spring: + text: Spring + Summer: + text: Summer + Fall: + text: Fall + Winter: + text: Winter + ceil_finish_mat_enum: + name: ceil_finish_mat_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - oil phase: - text: oil phase - water phase: - text: water phase - biofilm: - text: biofilm - not applicable: - text: not applicable - other: - text: other - ceil_texture_enum: - name: ceil_texture_enum + drywall: + text: drywall + mineral fibre: + text: mineral fibre + tiles: + text: tiles + PVC: + text: PVC + plasterboard: + text: plasterboard + metal: + text: metal + fiberglass: + text: fiberglass + stucco: + text: stucco + mineral wool/calcium silicate: + text: mineral wool/calcium silicate + wood: + text: wood + tillage_enum: + name: tillage_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - room_samp_pos_enum: - name: room_samp_pos_enum + drill: + text: drill + cutting disc: + text: cutting disc + ridge till: + text: ridge till + strip tillage: + text: strip tillage + zonal tillage: + text: zonal tillage + chisel: + text: chisel + tined: + text: tined + mouldboard: + text: mouldboard + disc plough: + text: disc plough + window_type_enum: + name: window_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + single-hung sash window: + text: single-hung sash window + horizontal sash window: + text: horizontal sash window + fixed window: + text: fixed window + ceil_cond_enum: + name: ceil_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture + hcr_geol_age_enum: + name: hcr_geol_age_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north corner: - text: north corner - south corner: - text: south corner - west corner: - text: west corner - east corner: - text: east corner - northeast corner: - text: northeast corner - northwest corner: - text: northwest corner - southeast corner: - text: southeast corner - southwest corner: - text: southwest corner - center: - text: center - indoor_surf_enum: - name: indoor_surf_enum + Archean: + text: Archean + Cambrian: + text: Cambrian + Carboniferous: + text: Carboniferous + Cenozoic: + text: Cenozoic + Cretaceous: + text: Cretaceous + Devonian: + text: Devonian + Jurassic: + text: Jurassic + Mesozoic: + text: Mesozoic + Neogene: + text: Neogene + Ordovician: + text: Ordovician + Paleogene: + text: Paleogene + Paleozoic: + text: Paleozoic + Permian: + text: Permian + Precambrian: + text: Precambrian + Proterozoic: + text: Proterozoic + Silurian: + text: Silurian + Triassic: + text: Triassic + other: + text: other + door_cond_enum: + name: door_cond_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - cabinet: - text: cabinet - ceiling: - text: ceiling - counter top: - text: counter top - door: - text: door - shelving: - text: shelving - vent cover: - text: vent cover - window: - text: window - wall: - text: wall - organism_count_enum: - name: organism_count_enum + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + lithology_enum: + name: lithology_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - ATP: - text: ATP - MPN: - text: MPN + Basement: + text: Basement + Chalk: + text: Chalk + Chert: + text: Chert + Coal: + text: Coal + Conglomerate: + text: Conglomerate + Diatomite: + text: Diatomite + Dolomite: + text: Dolomite + Limestone: + text: Limestone + Sandstone: + text: Sandstone + Shale: + text: Shale + Siltstone: + text: Siltstone + Volcanic: + text: Volcanic other: text: other - vis_media_enum: - name: vis_media_enum + heat_cool_type_enum: + name: heat_cool_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - photos: - text: photos - videos: - text: videos - commonly of the building: - text: commonly of the building - site context (adjacent buildings, vegetation, terrain, streets): - text: site context (adjacent buildings, vegetation, terrain, streets) - interiors: - text: interiors - equipment: - text: equipment - 3D scans: - text: 3D scans + radiant system: + text: radiant system + heat pump: + text: heat pump + forced air system: + text: forced air system + steam forced heat: + text: steam forced heat + wood stove: + text: wood stove + building_setting_enum: + name: building_setting_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + urban: + text: urban + suburban: + text: suburban + exurban: + text: exurban + rural: + text: rural room_condt_enum: name: room_condt_enum from_schema: https://w3id.org/nmdc/nmdc @@ -2779,40 +2781,34 @@ enums: text: rupture visible signs of mold/mildew: text: visible signs of mold/mildew - samp_collect_point_enum: - name: samp_collect_point_enum + rel_samp_loc_enum: + name: rel_samp_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - well: - text: well - test well: - text: test well - drilling rig: - text: drilling rig - wellhead: - text: wellhead - separator: - text: separator - storage tank: - text: storage tank - other: - text: other - samp_capt_status_enum: - name: samp_capt_status_enum + edge of car: + text: edge of car + center of car: + text: center of car + under a seat: + text: under a seat + wall_surf_treatment_enum: + name: wall_surf_treatment_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - active surveillance in response to an outbreak: - text: active surveillance in response to an outbreak - active surveillance not initiated by an outbreak: - text: active surveillance not initiated by an outbreak - farm sample: - text: farm sample - market sample: - text: market sample - other: - text: other - room_type_enum: - name: room_type_enum + painted: + text: painted + wall paper: + text: wall paper + no treatment: + text: no treatment + paneling: + text: paneling + stucco: + text: stucco + fabric: + text: fabric + room_connected_enum: + name: room_connected_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: attic: @@ -2829,102 +2825,130 @@ enums: text: examining room hallway: text: hallway - kitchen: - text: kitchen - mail room: - text: mail room - private office: - text: private office - open office: - text: open office - stairwell: - text: stairwell - ',restroom': - text: ',restroom' - lobby: - text: lobby - vestibule: - text: vestibule - mechanical or electrical room: - text: mechanical or electrical room - data center: - text: data center - laboratory_wet: - text: laboratory_wet - laboratory_dry: - text: laboratory_dry - gymnasium: - text: gymnasium - natatorium: - text: natatorium - auditorium: - text: auditorium - lockers: - text: lockers - cafe: - text: cafe - warehouse: - text: warehouse - samp_dis_stage_enum: - name: samp_dis_stage_enum + kitchen: + text: kitchen + mail room: + text: mail room + office: + text: office + stairwell: + text: stairwell + window_vert_pos_enum: + name: window_vert_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - dissemination: - text: dissemination - growth and reproduction: - text: growth and reproduction - infection: - text: infection - inoculation: - text: inoculation - penetration: - text: penetration - other: - text: other - floor_cond_enum: - name: floor_cond_enum + bottom: + text: bottom + middle: + text: middle + top: + text: top + low: + text: low + high: + text: high + weekday_enum: + name: weekday_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - lithology_enum: - name: lithology_enum + Monday: + text: Monday + Tuesday: + text: Tuesday + Wednesday: + text: Wednesday + Thursday: + text: Thursday + Friday: + text: Friday + Saturday: + text: Saturday + Sunday: + text: Sunday + room_samp_pos_enum: + name: room_samp_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Basement: - text: Basement - Chalk: - text: Chalk - Chert: - text: Chert - Coal: - text: Coal - Conglomerate: - text: Conglomerate - Diatomite: - text: Diatomite - Dolomite: - text: Dolomite - Limestone: - text: Limestone - Sandstone: - text: Sandstone - Shale: - text: Shale - Siltstone: - text: Siltstone - Volcanic: - text: Volcanic - other: - text: other + north corner: + text: north corner + south corner: + text: south corner + west corner: + text: west corner + east corner: + text: east corner + northeast corner: + text: northeast corner + northwest corner: + text: northwest corner + southeast corner: + text: southeast corner + southwest corner: + text: southwest corner + center: + text: center + door_mat_enum: + name: door_mat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + aluminum: + text: aluminum + cellular PVC: + text: cellular PVC + engineered plastic: + text: engineered plastic + fiberboard: + text: fiberboard + fiberglass: + text: fiberglass + metal: + text: metal + thermoplastic alloy: + text: thermoplastic alloy + vinyl: + text: vinyl + wood: + text: wood + wood/plastic composite: + text: wood/plastic composite + biol_stat_enum: + name: biol_stat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + wild: + text: wild + natural: + text: natural + semi-natural: + text: semi-natural + inbred line: + text: inbred line + breeder's line: + text: breeder's line + hybrid: + text: hybrid + clonal selection: + text: clonal selection + mutant: + text: mutant + floor_struc_enum: + name: floor_struc_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + balcony: + text: balcony + floating floor: + text: floating floor + glass floor: + text: glass floor + raised floor: + text: raised floor + sprung floor: + text: sprung floor + wood-framed: + text: wood-framed + concrete: + text: concrete door_type_wood_enum: name: door_type_wood_enum from_schema: https://w3id.org/nmdc/nmdc @@ -2949,128 +2973,88 @@ enums: text: louvered wire gauged: text: wire gauged - wall_finish_mat_enum: - name: wall_finish_mat_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - plaster: - text: plaster - gypsum plaster: - text: gypsum plaster - veneer plaster: - text: veneer plaster - gypsum board: - text: gypsum board - tile: - text: tile - terrazzo: - text: terrazzo - stone facing: - text: stone facing - acoustical treatment: - text: acoustical treatment - wood: - text: wood - metal: - text: metal - masonry: - text: masonry - gender_restroom_enum: - name: gender_restroom_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - all gender: - text: all gender - female: - text: female - gender neurtral: - text: gender neurtral - male: - text: male - male and female: - text: male and female - unisex: - text: unisex - int_wall_cond_enum: - name: int_wall_cond_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - floor_water_mold_enum: - name: floor_water_mold_enum + organism_count_enum: + name: organism_count_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - mold odor: - text: mold odor - wet floor: - text: wet floor - water stains: - text: water stains - wall discoloration: - text: wall discoloration - floor discoloration: - text: floor discoloration - ceiling discoloration: - text: ceiling discoloration - peeling paint or wallpaper: - text: peeling paint or wallpaper - bulging walls: - text: bulging walls - condensation: - text: condensation - samp_floor_enum: - name: samp_floor_enum + ATP: + text: ATP + MPN: + text: MPN + other: + text: other + shading_device_cond_enum: + name: shading_device_cond_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - 1st floor: - text: 1st floor - 2nd floor: - text: 2nd floor - basement: - text: basement - lobby: - text: lobby - heat_deliv_loc_enum: - name: heat_deliv_loc_enum + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + hcr_enum: + name: hcr_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - biol_stat_enum: - name: biol_stat_enum + Oil Reservoir: + text: Oil Reservoir + Gas Reservoir: + text: Gas Reservoir + Oil Sand: + text: Oil Sand + Coalbed: + text: Coalbed + Shale: + text: Shale + Tight Oil Reservoir: + text: Tight Oil Reservoir + Tight Gas Reservoir: + text: Tight Gas Reservoir + other: + text: other + mech_struc_enum: + name: mech_struc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - wild: - text: wild - natural: - text: natural - semi-natural: - text: semi-natural - inbred line: - text: inbred line - breeder's line: - text: breeder's line - hybrid: - text: hybrid - clonal selection: - text: clonal selection - mutant: - text: mutant + subway: + text: subway + coach: + text: coach + carriage: + text: carriage + elevator: + text: elevator + escalator: + text: escalator + boat: + text: boat + train: + text: train + car: + text: car + bus: + text: bus + hc_produced_enum: + name: hc_produced_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + Oil: + text: Oil + Gas-Condensate: + text: Gas-Condensate + Gas: + text: Gas + Bitumen: + text: Bitumen + Coalbed Methane: + text: Coalbed Methane + other: + text: other shading_device_type_enum: name: shading_device_type_enum from_schema: https://w3id.org/nmdc/nmdc @@ -3099,148 +3083,250 @@ enums: text: trellis venetian awning: text: venetian awning - train_stat_loc_enum: - name: train_stat_loc_enum + quad_pos_enum: + name: quad_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - south station above ground: - text: south station above ground - south station underground: - text: south station underground - south station amtrak: - text: south station amtrak - forest hills: - text: forest hills - riverside: - text: riverside - window_mat_enum: - name: window_mat_enum + North side: + text: North side + West side: + text: West side + South side: + text: South side + East side: + text: East side + sr_kerog_type_enum: + name: sr_kerog_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - clad: - text: clad - fiberglass: - text: fiberglass - metal: - text: metal - vinyl: - text: vinyl - wood: - text: wood - samp_weather_enum: - name: samp_weather_enum + Type I: + text: Type I + Type II: + text: Type II + Type III: + text: Type III + Type IV: + text: Type IV + other: + text: other + floor_cond_enum: + name: floor_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture + heat_deliv_loc_enum: + name: heat_deliv_loc_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + north: + text: north + south: + text: south + east: + text: east + west: + text: west + host_sex_enum: + name: host_sex_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + female: + text: female + hermaphrodite: + text: hermaphrodite + male: + text: male + neuter: + text: neuter + window_cond_enum: + name: window_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + handidness_enum: + name: handidness_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + ambidexterity: + text: ambidexterity + left handedness: + text: left handedness + mixed-handedness: + text: mixed-handedness + right handedness: + text: right handedness + wall_const_type_enum: + name: wall_const_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + frame construction: + text: frame construction + joisted masonry: + text: joisted masonry + light noncombustible: + text: light noncombustible + masonry noncombustible: + text: masonry noncombustible + modified fire resistive: + text: modified fire resistive + fire resistive: + text: fire resistive + build_occup_type_enum: + name: build_occup_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + office: + text: office + market: + text: market + restaurant: + text: restaurant + residence: + text: residence + school: + text: school + residential: + text: residential + commercial: + text: commercial + low rise: + text: low rise + high rise: + text: high rise + wood framed: + text: wood framed + health care: + text: health care + airport: + text: airport + sports complex: + text: sports complex + oxy_stat_samp_enum: + name: oxy_stat_samp_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - clear sky: - text: clear sky - cloudy: - text: cloudy - foggy: - text: foggy - hail: - text: hail - rain: - text: rain - snow: - text: snow - sleet: - text: sleet - sunny: - text: sunny - windy: - text: windy - biotic_relationship_enum: - name: biotic_relationship_enum + aerobic: + text: aerobic + anaerobic: + text: anaerobic + other: + text: other + filter_type_enum: + name: filter_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - free living: - text: free living - parasite: - text: parasite - commensal: - text: commensal - symbiont: - text: symbiont - door_cond_enum: - name: door_cond_enum + particulate air filter: + text: particulate air filter + chemical air filter: + text: chemical air filter + low-MERV pleated media: + text: low-MERV pleated media + HEPA: + text: HEPA + electrostatic: + text: electrostatic + gas-phase or ultraviolet air treatments: + text: gas-phase or ultraviolet air treatments + samp_floor_enum: + name: samp_floor_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - train_line_enum: - name: train_line_enum + 1st floor: + text: 1st floor + 2nd floor: + text: 2nd floor + basement: + text: basement + lobby: + text: lobby + furniture_enum: + name: furniture_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - red: - text: red - green: - text: green - orange: - text: orange - build_docs_enum: - name: build_docs_enum + cabinet: + text: cabinet + chair: + text: chair + desks: + text: desks + samp_dis_stage_enum: + name: samp_dis_stage_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - building information model: - text: building information model - commissioning report: - text: commissioning report - complaint logs: - text: complaint logs - contract administration: - text: contract administration - cost estimate: - text: cost estimate - janitorial schedules or logs: - text: janitorial schedules or logs - maintenance plans: - text: maintenance plans - schedule: - text: schedule - sections: - text: sections - shop drawings: - text: shop drawings - submittals: - text: submittals - ventilation system: - text: ventilation system - windows: - text: windows - door_loc_enum: - name: door_loc_enum + dissemination: + text: dissemination + growth and reproduction: + text: growth and reproduction + infection: + text: infection + inoculation: + text: inoculation + penetration: + text: penetration + other: + text: other + substructure_type_enum: + name: substructure_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - sr_kerog_type_enum: - name: sr_kerog_type_enum + crawlspace: + text: crawlspace + slab on grade: + text: slab on grade + basement: + text: basement + door_comp_type_enum: + name: door_comp_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Type I: - text: Type I - Type II: - text: Type II - Type III: - text: Type III - Type IV: - text: Type IV - other: - text: other + metal covered: + text: metal covered + revolving: + text: revolving + sliding: + text: sliding + telescopic: + text: telescopic + plant_growth_med_enum: + name: plant_growth_med_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + other artificial liquid medium: + text: other artificial liquid medium + other artificial solid medium: + text: other artificial solid medium + peat moss: + text: peat moss + perlite: + text: perlite + pumice: + text: pumice + sand: + text: sand + soil: + text: soil + vermiculite: + text: vermiculite + water: + text: water slots: metagenome_annotation_id: name: metagenome_annotation_id @@ -5531,8 +5617,6 @@ slots: examples: - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 2 string_serialization: '{date, arbitrary precision}' slot_group: MIxS Inspired @@ -5549,8 +5633,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 1 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -5568,8 +5650,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 3 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -5587,8 +5667,6 @@ slots: examples: - value: 'experimental treatment: value' from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:experimental_factor|additional_info rank: 7 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5603,8 +5681,6 @@ slots: - value: C18 - value: Basix PES, 13-100-106 FisherSci from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:filter_type rank: 6 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5622,8 +5698,6 @@ slots: - value: 13C glucose - value: H218O from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:chem_administration rank: 16 string_serialization: '{termLabel} {[termID]}; {timestamp}' slot_group: MIxS Inspired @@ -5640,8 +5714,6 @@ slots: - value: https://doi.org/10.1016/0038-0717(87)90052-6 - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:micro_biomass_meth rank: 11 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5656,8 +5728,6 @@ slots: - value: https://doi.org/10.1016/0038-0717(87)90052-6 - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:micro_biomass_meth rank: 13 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5672,8 +5742,6 @@ slots: examples: - value: 0.05 ug C/g dry soil from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:microbial_biomass rank: 10 string_serialization: '{float} {unit}' slot_group: MIxS Inspired @@ -5688,8 +5756,6 @@ slots: examples: - value: 0.05 ug N/g dry soil from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:microbial_biomass rank: 12 string_serialization: '{float} {unit}' slot_group: MIxS Inspired @@ -5702,8 +5768,6 @@ slots: examples: - value: insect 0.23 ug; plant 1g from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:biomass|microbial_biomass rank: 8 string_serialization: '{text};{float} {unit}' slot_group: MIxS Inspired @@ -5716,8 +5780,6 @@ slots: examples: - value: https://doi.org/10.1038/s41467-021-26181-3 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:microbial_biomass rank: 9 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5730,8 +5792,6 @@ slots: examples: - value: https://doi.org/10.1016/0038-0717(85)90144-0 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:org_nitro|tot_nitro_cont_meth rank: 14 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5744,8 +5804,6 @@ slots: - This is an open text field to provide any treatments that cannot be captured in the provided slots. from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:additional_info rank: 15 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5763,8 +5821,6 @@ slots: examples: - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 4 string_serialization: '{date, arbitrary precision}' slot_group: MIxS Inspired @@ -5781,8 +5837,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 5 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -17361,19 +17415,28 @@ slots: slot_uri: MIXS:0000156 multivalued: false range: QuantityValue - investigation field: - name: investigation field - description: field describing aspect of the investigation/study to which the sample - belongs + has unit: + name: has unit + description: Example "m" + from_schema: https://w3id.org/nmdc/nmdc + owner: QuantityValue + sequencing field: + name: sequencing field from_schema: https://w3id.org/nmdc/nmdc abstract: true + has raw value: + name: has raw value + from_schema: https://w3id.org/nmdc/nmdc + string_serialization: '{has numeric value} {has unit}' + owner: QuantityValue core field: name: core field description: basic fields from_schema: https://w3id.org/nmdc/nmdc abstract: true - nucleic acid sequence source field: - name: nucleic acid sequence source field + environment field: + name: environment field + description: field describing environmental aspect of a sample from_schema: https://w3id.org/nmdc/nmdc abstract: true has numeric value: @@ -17381,25 +17444,16 @@ slots: from_schema: https://w3id.org/nmdc/nmdc owner: QuantityValue range: double - environment field: - name: environment field - description: field describing environmental aspect of a sample + nucleic acid sequence source field: + name: nucleic acid sequence source field from_schema: https://w3id.org/nmdc/nmdc abstract: true - has unit: - name: has unit - description: Example "m" - from_schema: https://w3id.org/nmdc/nmdc - owner: QuantityValue - sequencing field: - name: sequencing field + investigation field: + name: investigation field + description: field describing aspect of the investigation/study to which the sample + belongs from_schema: https://w3id.org/nmdc/nmdc abstract: true - has raw value: - name: has raw value - from_schema: https://w3id.org/nmdc/nmdc - string_serialization: '{has numeric value} {has unit}' - owner: QuantityValue chemical: name: chemical description: from reaction participant class @@ -18486,10 +18540,9 @@ classes: Matches the entity that has been submitted to NMDC lat_lon: name: lat_lon - description: This is currently a required field but it's not clear if this - should be required for human hosts - notes: - - required where? + todos: + - This is currently a required field but it's not clear if this should be + required for human hosts env_broad_scale: name: env_broad_scale required: true @@ -19438,7 +19491,6 @@ classes: used: name: used description: The instrument used to collect the data used in the analysis - range: Instrument id: name: id required: true diff --git a/project/nmdc_schema_generated.yaml b/project/nmdc_schema_generated.yaml index 2f26913595..0c1b992946 100644 --- a/project/nmdc_schema_generated.yaml +++ b/project/nmdc_schema_generated.yaml @@ -11,7 +11,7 @@ notes: - not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1 id: https://w3id.org/nmdc/nmdc -version: v8.0.0 +version: v8.1.0 license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: CATH: @@ -347,6 +347,10 @@ types: string: name: string description: A character string + notes: + - In RDF serializations, a slot with range of string is treated as a literal or + type xsd:string. If you are authoring schemas in LinkML YAML, the type is + referenced with the lower case "string". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Text @@ -355,6 +359,9 @@ types: integer: name: integer description: An integer + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "integer". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Integer @@ -363,6 +370,9 @@ types: boolean: name: boolean description: A binary (true or false) value + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "boolean". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Boolean @@ -372,6 +382,9 @@ types: float: name: float description: A real number that conforms to the xsd:float specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "float". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Float @@ -380,6 +393,9 @@ types: double: name: double description: A real number that conforms to the xsd:double specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "double". from_schema: https://w3id.org/nmdc/nmdc close_mappings: - schema:Float @@ -389,6 +405,9 @@ types: name: decimal description: A real number with arbitrary precision that conforms to the xsd:decimal specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "decimal". from_schema: https://w3id.org/nmdc/nmdc broad_mappings: - schema:Number @@ -400,17 +419,21 @@ types: particular day notes: - URI is dateTime because OWL reasoners do not work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "time". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Time base: XSDTime - uri: xsd:dateTime + uri: xsd:time repr: str date: name: date description: a date (year, month and day) in an idealized calendar notes: - URI is dateTime because OWL reasoners don't work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Date @@ -420,6 +443,9 @@ types: datetime: name: datetime description: The combination of a date and time + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "datetime". from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:DateTime @@ -429,6 +455,9 @@ types: date_or_datetime: name: date_or_datetime description: Either a date or a datetime + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date_or_datetime". from_schema: https://w3id.org/nmdc/nmdc base: str uri: linkml:DateOrDatetime @@ -436,6 +465,9 @@ types: uriorcurie: name: uriorcurie description: a URI or a CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uriorcurie". from_schema: https://w3id.org/nmdc/nmdc base: URIorCURIE uri: xsd:anyURI @@ -444,6 +476,9 @@ types: name: curie conforms_to: https://www.w3.org/TR/curie/ description: a compact URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "curie". comments: - in RDF serializations this MUST be expanded to a URI - in non-RDF serializations MAY be serialized as the compact representation @@ -455,6 +490,9 @@ types: name: uri conforms_to: https://www.ietf.org/rfc/rfc3987.txt description: a complete URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uri". comments: - in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which @@ -468,6 +506,9 @@ types: ncname: name: ncname description: Prefix part of CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "ncname". from_schema: https://w3id.org/nmdc/nmdc base: NCName uri: xsd:string @@ -475,8 +516,11 @@ types: objectidentifier: name: objectidentifier description: A URI or CURIE that represents an object in the model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "objectidentifier". comments: - - Used for inheritence and type checking + - Used for inheritance and type checking from_schema: https://w3id.org/nmdc/nmdc base: ElementIdentifier uri: shex:iri @@ -484,10 +528,52 @@ types: nodeidentifier: name: nodeidentifier description: A URI, CURIE or BNODE that represents a node in a model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "nodeidentifier". from_schema: https://w3id.org/nmdc/nmdc base: NodeIdentifier uri: shex:nonLiteral repr: str + jsonpointer: + name: jsonpointer + conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 + description: A string encoding a JSON Pointer. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to a valid object within the current + instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpointer". + from_schema: https://w3id.org/nmdc/nmdc + base: str + uri: xsd:string + repr: str + jsonpath: + name: jsonpath + conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html + description: A string encoding a JSON Path. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to zero or more valid objects within + the current instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpath". + from_schema: https://w3id.org/nmdc/nmdc + base: str + uri: xsd:string + repr: str + sparqlpath: + name: sparqlpath + conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths + description: A string encoding a SPARQL Property Path. The value of the string + MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects + within the current instance document when encoded as RDF. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "sparqlpath". + from_schema: https://w3id.org/nmdc/nmdc + base: str + uri: xsd:string + repr: str enums: StatusEnum: name: StatusEnum @@ -1190,26 +1276,6 @@ enums: text: soil water_extract_soil: text: water_extract_soil - door_direct_enum: - name: door_direct_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - inward: - text: inward - outward: - text: outward - sideways: - text: sideways - oxy_stat_samp_enum: - name: oxy_stat_samp_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - aerobic: - text: aerobic - anaerobic: - text: anaerobic - other: - text: other surf_air_cont_enum: name: surf_air_cont_enum from_schema: https://w3id.org/nmdc/nmdc @@ -1230,164 +1296,164 @@ enums: text: nutrients biocides: text: biocides - window_vert_pos_enum: - name: window_vert_pos_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - bottom: - text: bottom - middle: - text: middle - top: - text: top - low: - text: low - high: - text: high - filter_type_enum: - name: filter_type_enum + water_feat_type_enum: + name: water_feat_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - particulate air filter: - text: particulate air filter - chemical air filter: - text: chemical air filter - low-MERV pleated media: - text: low-MERV pleated media - HEPA: - text: HEPA - electrostatic: - text: electrostatic - gas-phase or ultraviolet air treatments: - text: gas-phase or ultraviolet air treatments - rel_samp_loc_enum: - name: rel_samp_loc_enum + fountain: + text: fountain + pool: + text: pool + standing feature: + text: standing feature + stream: + text: stream + waterfall: + text: waterfall + samp_collect_point_enum: + name: samp_collect_point_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - edge of car: - text: edge of car - center of car: - text: center of car - under a seat: - text: under a seat - sediment_type_enum: - name: sediment_type_enum + well: + text: well + test well: + text: test well + drilling rig: + text: drilling rig + wellhead: + text: wellhead + separator: + text: separator + storage tank: + text: storage tank + other: + text: other + floor_water_mold_enum: + name: floor_water_mold_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - biogenous: - text: biogenous - cosmogenous: - text: cosmogenous - hydrogenous: - text: hydrogenous - lithogenous: - text: lithogenous - occup_document_enum: - name: occup_document_enum + mold odor: + text: mold odor + wet floor: + text: wet floor + water stains: + text: water stains + wall discoloration: + text: wall discoloration + floor discoloration: + text: floor discoloration + ceiling discoloration: + text: ceiling discoloration + peeling paint or wallpaper: + text: peeling paint or wallpaper + bulging walls: + text: bulging walls + condensation: + text: condensation + wall_texture_enum: + name: wall_texture_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - automated count: - text: automated count - estimate: - text: estimate - manual count: - text: manual count - videos: - text: videos - room_connected_enum: - name: room_connected_enum + crows feet: + text: crows feet + crows-foot stomp: + text: crows-foot stomp + ? '' + : text: '' + double skip: + text: double skip + hawk and trowel: + text: hawk and trowel + knockdown: + text: knockdown + popcorn: + text: popcorn + orange peel: + text: orange peel + rosebud stomp: + text: rosebud stomp + Santa-Fe texture: + text: Santa-Fe texture + skip trowel: + text: skip trowel + smooth: + text: smooth + stomp knockdown: + text: stomp knockdown + swirl: + text: swirl + samp_subtype_enum: + name: samp_subtype_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - attic: - text: attic - bathroom: - text: bathroom - closet: - text: closet - conference room: - text: conference room - elevator: - text: elevator - examining room: - text: examining room - hallway: - text: hallway - kitchen: - text: kitchen - mail room: - text: mail room - office: - text: office - stairwell: - text: stairwell - quad_pos_enum: - name: quad_pos_enum + oil phase: + text: oil phase + water phase: + text: water phase + biofilm: + text: biofilm + not applicable: + text: not applicable + other: + text: other + drainage_class_enum: + name: drainage_class_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - North side: - text: North side - West side: - text: West side - South side: - text: South side - East side: - text: East side - sr_geol_age_enum: - name: sr_geol_age_enum + very poorly: + text: very poorly + poorly: + text: poorly + somewhat poorly: + text: somewhat poorly + moderately well: + text: moderately well + well: + text: well + excessively drained: + text: excessively drained + freq_clean_enum: + name: freq_clean_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Archean: - text: Archean - Cambrian: - text: Cambrian - Carboniferous: - text: Carboniferous - Cenozoic: - text: Cenozoic - Cretaceous: - text: Cretaceous - Devonian: - text: Devonian - Jurassic: - text: Jurassic - Mesozoic: - text: Mesozoic - Neogene: - text: Neogene - Ordovician: - text: Ordovician - Paleogene: - text: Paleogene - Paleozoic: - text: Paleozoic - Permian: - text: Permian - Precambrian: - text: Precambrian - Proterozoic: - text: Proterozoic - Silurian: - text: Silurian - Triassic: - text: Triassic + Daily: + text: Daily + Weekly: + text: Weekly + Monthly: + text: Monthly + Quarterly: + text: Quarterly + Annually: + text: Annually other: text: other - door_move_enum: - name: door_move_enum + biotic_relationship_enum: + name: biotic_relationship_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - collapsible: - text: collapsible - folding: - text: folding - revolving: - text: revolving - rolling shutter: - text: rolling shutter - sliding: - text: sliding - swinging: - text: swinging + free living: + text: free living + parasite: + text: parasite + commensal: + text: commensal + symbiont: + text: symbiont + light_type_enum: + name: light_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + natural light: + text: natural light + electric light: + text: electric light + desk lamp: + text: desk lamp + flourescent lights: + text: flourescent lights + none: + text: none cur_land_use_enum: name: cur_land_use_enum from_schema: https://w3id.org/nmdc/nmdc @@ -1583,142 +1649,146 @@ enums: value: vine crops (grapes) examples: - value: grapes - hcr_geol_age_enum: - name: hcr_geol_age_enum + drawings_enum: + name: drawings_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Archean: - text: Archean - Cambrian: - text: Cambrian - Carboniferous: - text: Carboniferous - Cenozoic: - text: Cenozoic - Cretaceous: - text: Cretaceous - Devonian: - text: Devonian - Jurassic: - text: Jurassic - Mesozoic: - text: Mesozoic - Neogene: - text: Neogene - Ordovician: - text: Ordovician - Paleogene: - text: Paleogene - Paleozoic: - text: Paleozoic - Permian: - text: Permian - Precambrian: - text: Precambrian - Proterozoic: - text: Proterozoic - Silurian: - text: Silurian - Triassic: - text: Triassic + operation: + text: operation + as built: + text: as built + construction: + text: construction + bid: + text: bid + design: + text: design + building navigation map: + text: building navigation map + diagram: + text: diagram + sketch: + text: sketch + indoor_surf_enum: + name: indoor_surf_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + cabinet: + text: cabinet + ceiling: + text: ceiling + counter top: + text: counter top + door: + text: door + shelving: + text: shelving + vent cover: + text: vent cover + window: + text: window + wall: + text: wall + samp_capt_status_enum: + name: samp_capt_status_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + active surveillance in response to an outbreak: + text: active surveillance in response to an outbreak + active surveillance not initiated by an outbreak: + text: active surveillance not initiated by an outbreak + farm sample: + text: farm sample + market sample: + text: market sample other: text: other - wall_const_type_enum: - name: wall_const_type_enum + room_loc_enum: + name: room_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - frame construction: - text: frame construction - joisted masonry: - text: joisted masonry - light noncombustible: - text: light noncombustible - masonry noncombustible: - text: masonry noncombustible - modified fire resistive: - text: modified fire resistive - fire resistive: - text: fire resistive - plant_sex_enum: - name: plant_sex_enum + corner room: + text: corner room + interior room: + text: interior room + exterior wall: + text: exterior wall + occup_document_enum: + name: occup_document_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Androdioecious: - text: Androdioecious - Androecious: - text: Androecious - Androgynous: - text: Androgynous - Androgynomonoecious: - text: Androgynomonoecious - Andromonoecious: - text: Andromonoecious - Bisexual: - text: Bisexual - Dichogamous: - text: Dichogamous - Diclinous: - text: Diclinous - Dioecious: - text: Dioecious - Gynodioecious: - text: Gynodioecious - Gynoecious: - text: Gynoecious - Gynomonoecious: - text: Gynomonoecious - Hermaphroditic: - text: Hermaphroditic - Imperfect: - text: Imperfect - Monoclinous: - text: Monoclinous - Monoecious: - text: Monoecious - Perfect: - text: Perfect - Polygamodioecious: - text: Polygamodioecious - Polygamomonoecious: - text: Polygamomonoecious - Polygamous: - text: Polygamous - Protandrous: - text: Protandrous - Protogynous: - text: Protogynous - Subandroecious: - text: Subandroecious - Subdioecious: - text: Subdioecious - Subgynoecious: - text: Subgynoecious - Synoecious: - text: Synoecious - Trimonoecious: - text: Trimonoecious - Trioecious: - text: Trioecious - Unisexual: - text: Unisexual - ceil_type_enum: - name: ceil_type_enum + automated count: + text: automated count + estimate: + text: estimate + manual count: + text: manual count + videos: + text: videos + arch_struc_enum: + name: arch_struc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - cathedral: - text: cathedral - dropped: - text: dropped - concave: - text: concave - barrel-shaped: - text: barrel-shaped - coffered: - text: coffered - cove: - text: cove - stretched: - text: stretched + building: + text: building + shed: + text: shed + home: + text: home + wall_finish_mat_enum: + name: wall_finish_mat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + plaster: + text: plaster + gypsum plaster: + text: gypsum plaster + veneer plaster: + text: veneer plaster + gypsum board: + text: gypsum board + tile: + text: tile + terrazzo: + text: terrazzo + stone facing: + text: stone facing + acoustical treatment: + text: acoustical treatment + wood: + text: wood + metal: + text: metal + masonry: + text: masonry + window_mat_enum: + name: window_mat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + clad: + text: clad + fiberglass: + text: fiberglass + metal: + text: metal + vinyl: + text: vinyl + wood: + text: wood + int_wall_cond_enum: + name: int_wall_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture floor_finish_mat_enum: name: floor_finish_mat_enum from_schema: https://w3id.org/nmdc/nmdc @@ -1759,584 +1829,240 @@ enums: text: paint none or unfinished: text: none or unfinished - wall_loc_enum: - name: wall_loc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - wall_surf_treatment_enum: - name: wall_surf_treatment_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - painted: - text: painted - wall paper: - text: wall paper - no treatment: - text: no treatment - paneling: - text: paneling - stucco: - text: stucco - fabric: - text: fabric - window_cond_enum: - name: window_cond_enum + build_docs_enum: + name: build_docs_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - door_mat_enum: - name: door_mat_enum + building information model: + text: building information model + commissioning report: + text: commissioning report + complaint logs: + text: complaint logs + contract administration: + text: contract administration + cost estimate: + text: cost estimate + janitorial schedules or logs: + text: janitorial schedules or logs + maintenance plans: + text: maintenance plans + schedule: + text: schedule + sections: + text: sections + shop drawings: + text: shop drawings + submittals: + text: submittals + ventilation system: + text: ventilation system + windows: + text: windows + surf_material_enum: + name: surf_material_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - aluminum: - text: aluminum - cellular PVC: - text: cellular PVC - engineered plastic: - text: engineered plastic - fiberboard: - text: fiberboard - fiberglass: - text: fiberglass + adobe: + text: adobe + carpet: + text: carpet + cinder blocks: + text: cinder blocks + concrete: + text: concrete + hay bales: + text: hay bales + glass: + text: glass metal: text: metal - thermoplastic alloy: - text: thermoplastic alloy + paint: + text: paint + plastic: + text: plastic + stainless steel: + text: stainless steel + stone: + text: stone + stucco: + text: stucco + tile: + text: tile vinyl: text: vinyl wood: text: wood - wood/plastic composite: - text: wood/plastic composite - soil_horizon_enum: - name: soil_horizon_enum + tidal_stage_enum: + name: tidal_stage_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - O horizon: - text: O horizon - A horizon: - text: A horizon - E horizon: - text: E horizon - B horizon: - text: B horizon - C horizon: - text: C horizon - R layer: - text: R layer - Permafrost: - text: Permafrost - M horizon: - text: M horizon - ceil_finish_mat_enum: - name: ceil_finish_mat_enum + low tide: + text: low tide + ebb tide: + text: ebb tide + flood tide: + text: flood tide + high tide: + text: high tide + window_horiz_pos_enum: + name: window_horiz_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - drywall: - text: drywall - mineral fibre: - text: mineral fibre - tiles: - text: tiles - PVC: - text: PVC - plasterboard: - text: plasterboard - metal: - text: metal - fiberglass: - text: fiberglass - stucco: - text: stucco - mineral wool/calcium silicate: - text: mineral wool/calcium silicate - wood: - text: wood - shading_device_cond_enum: - name: shading_device_cond_enum + left: + text: left + middle: + text: middle + right: + text: right + train_stop_loc_enum: + name: train_stop_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - hc_produced_enum: - name: hc_produced_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Oil: - text: Oil - Gas-Condensate: - text: Gas-Condensate - Gas: - text: Gas - Bitumen: - text: Bitumen - Coalbed Methane: - text: Coalbed Methane - other: - text: other - door_comp_type_enum: - name: door_comp_type_enum + end: + text: end + mid: + text: mid + downtown: + text: downtown + train_line_enum: + name: train_line_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - metal covered: - text: metal covered - revolving: - text: revolving - sliding: - text: sliding - telescopic: - text: telescopic - window_loc_enum: - name: window_loc_enum + red: + text: red + green: + text: green + orange: + text: orange + train_stat_loc_enum: + name: train_stat_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - sr_lithology_enum: - name: sr_lithology_enum + south station above ground: + text: south station above ground + south station underground: + text: south station underground + south station amtrak: + text: south station amtrak + forest hills: + text: forest hills + riverside: + text: riverside + sr_dep_env_enum: + name: sr_dep_env_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Clastic: - text: Clastic - Carbonate: - text: Carbonate - Coal: - text: Coal - Biosilicieous: - text: Biosilicieous + Lacustine: + text: Lacustine + Fluvioldeltaic: + text: Fluvioldeltaic + Fluviomarine: + text: Fluviomarine + Marine: + text: Marine other: text: other - plant_growth_med_enum: - name: plant_growth_med_enum + samp_weather_enum: + name: samp_weather_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - other artificial liquid medium: - text: other artificial liquid medium - other artificial solid medium: - text: other artificial solid medium - peat moss: - text: peat moss - perlite: - text: perlite - pumice: - text: pumice - sand: - text: sand - soil: - text: soil - vermiculite: - text: vermiculite - water: - text: water - surf_material_enum: - name: surf_material_enum + clear sky: + text: clear sky + cloudy: + text: cloudy + foggy: + text: foggy + hail: + text: hail + rain: + text: rain + snow: + text: snow + sleet: + text: sleet + sunny: + text: sunny + windy: + text: windy + window_cover_enum: + name: window_cover_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - adobe: - text: adobe - carpet: - text: carpet - cinder blocks: - text: cinder blocks - concrete: - text: concrete - hay bales: - text: hay bales - glass: - text: glass - metal: - text: metal - paint: - text: paint - plastic: - text: plastic - stainless steel: - text: stainless steel - stone: - text: stone - stucco: - text: stucco - tile: - text: tile - vinyl: - text: vinyl - wood: - text: wood - ceil_cond_enum: - name: ceil_cond_enum + blinds: + text: blinds + curtains: + text: curtains + none: + text: none + room_type_enum: + name: room_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - building_setting_enum: - name: building_setting_enum + attic: + text: attic + bathroom: + text: bathroom + closet: + text: closet + conference room: + text: conference room + elevator: + text: elevator + examining room: + text: examining room + hallway: + text: hallway + kitchen: + text: kitchen + mail room: + text: mail room + private office: + text: private office + open office: + text: open office + stairwell: + text: stairwell + ',restroom': + text: ',restroom' + lobby: + text: lobby + vestibule: + text: vestibule + mechanical or electrical room: + text: mechanical or electrical room + data center: + text: data center + laboratory_wet: + text: laboratory_wet + laboratory_dry: + text: laboratory_dry + gymnasium: + text: gymnasium + natatorium: + text: natatorium + auditorium: + text: auditorium + lockers: + text: lockers + cafe: + text: cafe + warehouse: + text: warehouse + sediment_type_enum: + name: sediment_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - urban: - text: urban - suburban: - text: suburban - exurban: - text: exurban - rural: - text: rural - build_occup_type_enum: - name: build_occup_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - office: - text: office - market: - text: market - restaurant: - text: restaurant - residence: - text: residence - school: - text: school - residential: - text: residential - commercial: - text: commercial - low rise: - text: low rise - high rise: - text: high rise - wood framed: - text: wood framed - health care: - text: health care - airport: - text: airport - sports complex: - text: sports complex - depos_env_enum: - name: depos_env_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Continental - Alluvial: - text: Continental - Alluvial - Continental - Aeolian: - text: Continental - Aeolian - Continental - Fluvial: - text: Continental - Fluvial - Continental - Lacustrine: - text: Continental - Lacustrine - Transitional - Deltaic: - text: Transitional - Deltaic - Transitional - Tidal: - text: Transitional - Tidal - Transitional - Lagoonal: - text: Transitional - Lagoonal - Transitional - Beach: - text: Transitional - Beach - Transitional - Lake: - text: Transitional - Lake - Marine - Shallow: - text: Marine - Shallow - Marine - Deep: - text: Marine - Deep - Marine - Reef: - text: Marine - Reef - Other - Evaporite: - text: Other - Evaporite - Other - Glacial: - text: Other - Glacial - Other - Volcanic: - text: Other - Volcanic - other: - text: other - profile_position_enum: - name: profile_position_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - summit: - text: summit - shoulder: - text: shoulder - backslope: - text: backslope - footslope: - text: footslope - toeslope: - text: toeslope - furniture_enum: - name: furniture_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - cabinet: - text: cabinet - chair: - text: chair - desks: - text: desks - door_type_enum: - name: door_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - composite: - text: composite - metal: - text: metal - wooden: - text: wooden - tidal_stage_enum: - name: tidal_stage_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - low tide: - text: low tide - ebb tide: - text: ebb tide - flood tide: - text: flood tide - high tide: - text: high tide - door_type_metal_enum: - name: door_type_metal_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - collapsible: - text: collapsible - corrugated steel: - text: corrugated steel - hollow: - text: hollow - rolling shutters: - text: rolling shutters - steel plate: - text: steel plate - handidness_enum: - name: handidness_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - ambidexterity: - text: ambidexterity - left handedness: - text: left handedness - mixed-handedness: - text: mixed-handedness - right handedness: - text: right handedness - tillage_enum: - name: tillage_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - drill: - text: drill - cutting disc: - text: cutting disc - ridge till: - text: ridge till - strip tillage: - text: strip tillage - zonal tillage: - text: zonal tillage - chisel: - text: chisel - tined: - text: tined - mouldboard: - text: mouldboard - disc plough: - text: disc plough - hcr_enum: - name: hcr_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Oil Reservoir: - text: Oil Reservoir - Gas Reservoir: - text: Gas Reservoir - Oil Sand: - text: Oil Sand - Coalbed: - text: Coalbed - Shale: - text: Shale - Tight Oil Reservoir: - text: Tight Oil Reservoir - Tight Gas Reservoir: - text: Tight Gas Reservoir - other: - text: other - freq_clean_enum: - name: freq_clean_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Daily: - text: Daily - Weekly: - text: Weekly - Monthly: - text: Monthly - Quarterly: - text: Quarterly - Annually: - text: Annually - other: - text: other - growth_habit_enum: - name: growth_habit_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - erect: - text: erect - semi-erect: - text: semi-erect - spreading: - text: spreading - prostrate: - text: prostrate - season_use_enum: - name: season_use_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Spring: - text: Spring - Summer: - text: Summer - Fall: - text: Fall - Winter: - text: Winter - sr_dep_env_enum: - name: sr_dep_env_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - Lacustine: - text: Lacustine - Fluvioldeltaic: - text: Fluvioldeltaic - Fluviomarine: - text: Fluviomarine - Marine: - text: Marine - other: - text: other - water_feat_type_enum: - name: water_feat_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - fountain: - text: fountain - pool: - text: pool - standing feature: - text: standing feature - stream: - text: stream - waterfall: - text: waterfall - substructure_type_enum: - name: substructure_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - crawlspace: - text: crawlspace - slab on grade: - text: slab on grade - basement: - text: basement - indoor_space_enum: - name: indoor_space_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - bedroom: - text: bedroom - office: - text: office - bathroom: - text: bathroom - foyer: - text: foyer - kitchen: - text: kitchen - locker room: - text: locker room - hallway: - text: hallway - elevator: - text: elevator - host_sex_enum: - name: host_sex_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - female: - text: female - hermaphrodite: - text: hermaphrodite - male: - text: male - neuter: - text: neuter - window_type_enum: - name: window_type_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - single-hung sash window: - text: single-hung sash window - horizontal sash window: - text: horizontal sash window - fixed window: - text: fixed window - specific_enum: - name: specific_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - photos: - text: photos - fao_class_enum: - name: fao_class_enum + biogenous: + text: biogenous + cosmogenous: + text: cosmogenous + hydrogenous: + text: hydrogenous + lithogenous: + text: lithogenous + fao_class_enum: + name: fao_class_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: Acrisols: @@ -2391,166 +2117,404 @@ enums: text: Vertisols Yermosols: text: Yermosols - floor_struc_enum: - name: floor_struc_enum + ext_window_orient_enum: + name: ext_window_orient_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - balcony: - text: balcony - floating floor: - text: floating floor - glass floor: - text: glass floor - raised floor: - text: raised floor - sprung floor: - text: sprung floor - wood-framed: - text: wood-framed - concrete: - text: concrete - wall_texture_enum: - name: wall_texture_enum + north: + text: north + south: + text: south + east: + text: east + west: + text: west + northeast: + text: northeast + southeast: + text: southeast + southwest: + text: southwest + northwest: + text: northwest + sr_geol_age_enum: + name: sr_geol_age_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + Archean: + text: Archean + Cambrian: + text: Cambrian + Carboniferous: + text: Carboniferous + Cenozoic: + text: Cenozoic + Cretaceous: + text: Cretaceous + Devonian: + text: Devonian + Jurassic: + text: Jurassic + Mesozoic: + text: Mesozoic + Neogene: + text: Neogene + Ordovician: + text: Ordovician + Paleogene: + text: Paleogene + Paleozoic: + text: Paleozoic + Permian: + text: Permian + Precambrian: + text: Precambrian + Proterozoic: + text: Proterozoic + Silurian: + text: Silurian + Triassic: + text: Triassic + other: + text: other + door_move_enum: + name: door_move_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + collapsible: + text: collapsible + folding: + text: folding + revolving: + text: revolving + rolling shutter: + text: rolling shutter + sliding: + text: sliding + swinging: + text: swinging + door_direct_enum: + name: door_direct_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + inward: + text: inward + outward: + text: outward + sideways: + text: sideways + ceil_texture_enum: + name: ceil_texture_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + crows feet: + text: crows feet + crows-foot stomp: + text: crows-foot stomp + double skip: + text: double skip + hawk and trowel: + text: hawk and trowel + knockdown: + text: knockdown + popcorn: + text: popcorn + orange peel: + text: orange peel + rosebud stomp: + text: rosebud stomp + Santa-Fe texture: + text: Santa-Fe texture + skip trowel: + text: skip trowel + smooth: + text: smooth + stomp knockdown: + text: stomp knockdown + swirl: + text: swirl + samp_md_enum: + name: samp_md_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + DF: + text: DF + RT: + text: RT + KB: + text: KB + MSL: + text: MSL + other: + text: other + ceil_type_enum: + name: ceil_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + cathedral: + text: cathedral + dropped: + text: dropped + concave: + text: concave + barrel-shaped: + text: barrel-shaped + coffered: + text: coffered + cove: + text: cove + stretched: + text: stretched + wall_loc_enum: + name: wall_loc_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + north: + text: north + south: + text: south + east: + text: east + west: + text: west + door_type_metal_enum: + name: door_type_metal_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + collapsible: + text: collapsible + corrugated steel: + text: corrugated steel + hollow: + text: hollow + rolling shutters: + text: rolling shutters + steel plate: + text: steel plate + gender_restroom_enum: + name: gender_restroom_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + all gender: + text: all gender + female: + text: female + gender neurtral: + text: gender neurtral + male: + text: male + male and female: + text: male and female + unisex: + text: unisex + vis_media_enum: + name: vis_media_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - ? '' - : text: '' - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - train_stop_loc_enum: - name: train_stop_loc_enum + photos: + text: photos + videos: + text: videos + commonly of the building: + text: commonly of the building + site context (adjacent buildings, vegetation, terrain, streets): + text: site context (adjacent buildings, vegetation, terrain, streets) + interiors: + text: interiors + equipment: + text: equipment + 3D scans: + text: 3D scans + window_loc_enum: + name: window_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - end: - text: end - mid: - text: mid - downtown: - text: downtown - drawings_enum: - name: drawings_enum + north: + text: north + south: + text: south + east: + text: east + west: + text: west + soil_horizon_enum: + name: soil_horizon_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - building navigation map: - text: building navigation map - diagram: - text: diagram - sketch: - text: sketch - room_loc_enum: - name: room_loc_enum + O horizon: + text: O horizon + A horizon: + text: A horizon + E horizon: + text: E horizon + B horizon: + text: B horizon + C horizon: + text: C horizon + R layer: + text: R layer + Permafrost: + text: Permafrost + M horizon: + text: M horizon + indoor_space_enum: + name: indoor_space_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - corner room: - text: corner room - interior room: - text: interior room - exterior wall: - text: exterior wall - light_type_enum: - name: light_type_enum + bedroom: + text: bedroom + office: + text: office + bathroom: + text: bathroom + foyer: + text: foyer + kitchen: + text: kitchen + locker room: + text: locker room + hallway: + text: hallway + elevator: + text: elevator + door_type_enum: + name: door_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - natural light: - text: natural light - electric light: - text: electric light - desk lamp: - text: desk lamp - flourescent lights: - text: flourescent lights - none: - text: none - weekday_enum: - name: weekday_enum + composite: + text: composite + metal: + text: metal + wooden: + text: wooden + depos_env_enum: + name: depos_env_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Monday: - text: Monday - Tuesday: - text: Tuesday - Wednesday: - text: Wednesday - Thursday: - text: Thursday - Friday: - text: Friday - Saturday: - text: Saturday - Sunday: - text: Sunday - arch_struc_enum: - name: arch_struc_enum + Continental - Alluvial: + text: Continental - Alluvial + Continental - Aeolian: + text: Continental - Aeolian + Continental - Fluvial: + text: Continental - Fluvial + Continental - Lacustrine: + text: Continental - Lacustrine + Transitional - Deltaic: + text: Transitional - Deltaic + Transitional - Tidal: + text: Transitional - Tidal + Transitional - Lagoonal: + text: Transitional - Lagoonal + Transitional - Beach: + text: Transitional - Beach + Transitional - Lake: + text: Transitional - Lake + Marine - Shallow: + text: Marine - Shallow + Marine - Deep: + text: Marine - Deep + Marine - Reef: + text: Marine - Reef + Other - Evaporite: + text: Other - Evaporite + Other - Glacial: + text: Other - Glacial + Other - Volcanic: + text: Other - Volcanic + other: + text: other + sr_lithology_enum: + name: sr_lithology_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - building: - text: building - shed: - text: shed - home: - text: home - heat_cool_type_enum: - name: heat_cool_type_enum + Clastic: + text: Clastic + Carbonate: + text: Carbonate + Coal: + text: Coal + Biosilicieous: + text: Biosilicieous + other: + text: other + plant_sex_enum: + name: plant_sex_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - radiant system: - text: radiant system - heat pump: - text: heat pump - forced air system: - text: forced air system - steam forced heat: - text: steam forced heat - wood stove: - text: wood stove - samp_md_enum: - name: samp_md_enum + Androdioecious: + text: Androdioecious + Androecious: + text: Androecious + Androgynous: + text: Androgynous + Androgynomonoecious: + text: Androgynomonoecious + Andromonoecious: + text: Andromonoecious + Bisexual: + text: Bisexual + Dichogamous: + text: Dichogamous + Diclinous: + text: Diclinous + Dioecious: + text: Dioecious + Gynodioecious: + text: Gynodioecious + Gynoecious: + text: Gynoecious + Gynomonoecious: + text: Gynomonoecious + Hermaphroditic: + text: Hermaphroditic + Imperfect: + text: Imperfect + Monoclinous: + text: Monoclinous + Monoecious: + text: Monoecious + Perfect: + text: Perfect + Polygamodioecious: + text: Polygamodioecious + Polygamomonoecious: + text: Polygamomonoecious + Polygamous: + text: Polygamous + Protandrous: + text: Protandrous + Protogynous: + text: Protogynous + Subandroecious: + text: Subandroecious + Subdioecious: + text: Subdioecious + Subgynoecious: + text: Subgynoecious + Synoecious: + text: Synoecious + Trimonoecious: + text: Trimonoecious + Trioecious: + text: Trioecious + Unisexual: + text: Unisexual + specific_enum: + name: specific_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - DF: - text: DF - RT: - text: RT - KB: - text: KB - MSL: - text: MSL - other: - text: other + operation: + text: operation + as built: + text: as built + construction: + text: construction + bid: + text: bid + design: + text: design + photos: + text: photos ext_wall_orient_enum: name: ext_wall_orient_enum from_schema: https://w3id.org/nmdc/nmdc @@ -2571,30 +2535,8 @@ enums: text: southwest northwest: text: northwest - mech_struc_enum: - name: mech_struc_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - subway: - text: subway - coach: - text: coach - carriage: - text: carriage - elevator: - text: elevator - escalator: - text: escalator - boat: - text: boat - train: - text: train - car: - text: car - bus: - text: bus - ext_window_orient_enum: - name: ext_window_orient_enum + door_loc_enum: + name: door_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: north: @@ -2605,164 +2547,224 @@ enums: text: east west: text: west - northeast: - text: northeast - southeast: - text: southeast - southwest: - text: southwest - northwest: - text: northwest - window_cover_enum: - name: window_cover_enum + profile_position_enum: + name: profile_position_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - blinds: - text: blinds - curtains: - text: curtains - none: - text: none - drainage_class_enum: - name: drainage_class_enum + summit: + text: summit + shoulder: + text: shoulder + backslope: + text: backslope + footslope: + text: footslope + toeslope: + text: toeslope + growth_habit_enum: + name: growth_habit_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - very poorly: - text: very poorly - poorly: - text: poorly - somewhat poorly: - text: somewhat poorly - moderately well: - text: moderately well - well: - text: well - excessively drained: - text: excessively drained - window_horiz_pos_enum: - name: window_horiz_pos_enum + erect: + text: erect + semi-erect: + text: semi-erect + spreading: + text: spreading + prostrate: + text: prostrate + season_use_enum: + name: season_use_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - left: - text: left - middle: - text: middle - right: - text: right - samp_subtype_enum: - name: samp_subtype_enum + Spring: + text: Spring + Summer: + text: Summer + Fall: + text: Fall + Winter: + text: Winter + ceil_finish_mat_enum: + name: ceil_finish_mat_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - oil phase: - text: oil phase - water phase: - text: water phase - biofilm: - text: biofilm - not applicable: - text: not applicable - other: - text: other - ceil_texture_enum: - name: ceil_texture_enum + drywall: + text: drywall + mineral fibre: + text: mineral fibre + tiles: + text: tiles + PVC: + text: PVC + plasterboard: + text: plasterboard + metal: + text: metal + fiberglass: + text: fiberglass + stucco: + text: stucco + mineral wool/calcium silicate: + text: mineral wool/calcium silicate + wood: + text: wood + tillage_enum: + name: tillage_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - room_samp_pos_enum: - name: room_samp_pos_enum + drill: + text: drill + cutting disc: + text: cutting disc + ridge till: + text: ridge till + strip tillage: + text: strip tillage + zonal tillage: + text: zonal tillage + chisel: + text: chisel + tined: + text: tined + mouldboard: + text: mouldboard + disc plough: + text: disc plough + window_type_enum: + name: window_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + single-hung sash window: + text: single-hung sash window + horizontal sash window: + text: horizontal sash window + fixed window: + text: fixed window + ceil_cond_enum: + name: ceil_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture + hcr_geol_age_enum: + name: hcr_geol_age_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north corner: - text: north corner - south corner: - text: south corner - west corner: - text: west corner - east corner: - text: east corner - northeast corner: - text: northeast corner - northwest corner: - text: northwest corner - southeast corner: - text: southeast corner - southwest corner: - text: southwest corner - center: - text: center - indoor_surf_enum: - name: indoor_surf_enum + Archean: + text: Archean + Cambrian: + text: Cambrian + Carboniferous: + text: Carboniferous + Cenozoic: + text: Cenozoic + Cretaceous: + text: Cretaceous + Devonian: + text: Devonian + Jurassic: + text: Jurassic + Mesozoic: + text: Mesozoic + Neogene: + text: Neogene + Ordovician: + text: Ordovician + Paleogene: + text: Paleogene + Paleozoic: + text: Paleozoic + Permian: + text: Permian + Precambrian: + text: Precambrian + Proterozoic: + text: Proterozoic + Silurian: + text: Silurian + Triassic: + text: Triassic + other: + text: other + door_cond_enum: + name: door_cond_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - cabinet: - text: cabinet - ceiling: - text: ceiling - counter top: - text: counter top - door: - text: door - shelving: - text: shelving - vent cover: - text: vent cover - window: - text: window - wall: - text: wall - organism_count_enum: - name: organism_count_enum + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + lithology_enum: + name: lithology_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - ATP: - text: ATP - MPN: - text: MPN + Basement: + text: Basement + Chalk: + text: Chalk + Chert: + text: Chert + Coal: + text: Coal + Conglomerate: + text: Conglomerate + Diatomite: + text: Diatomite + Dolomite: + text: Dolomite + Limestone: + text: Limestone + Sandstone: + text: Sandstone + Shale: + text: Shale + Siltstone: + text: Siltstone + Volcanic: + text: Volcanic other: text: other - vis_media_enum: - name: vis_media_enum + heat_cool_type_enum: + name: heat_cool_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - photos: - text: photos - videos: - text: videos - commonly of the building: - text: commonly of the building - site context (adjacent buildings, vegetation, terrain, streets): - text: site context (adjacent buildings, vegetation, terrain, streets) - interiors: - text: interiors - equipment: - text: equipment - 3D scans: - text: 3D scans + radiant system: + text: radiant system + heat pump: + text: heat pump + forced air system: + text: forced air system + steam forced heat: + text: steam forced heat + wood stove: + text: wood stove + building_setting_enum: + name: building_setting_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + urban: + text: urban + suburban: + text: suburban + exurban: + text: exurban + rural: + text: rural room_condt_enum: name: room_condt_enum from_schema: https://w3id.org/nmdc/nmdc @@ -2779,40 +2781,34 @@ enums: text: rupture visible signs of mold/mildew: text: visible signs of mold/mildew - samp_collect_point_enum: - name: samp_collect_point_enum + rel_samp_loc_enum: + name: rel_samp_loc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - well: - text: well - test well: - text: test well - drilling rig: - text: drilling rig - wellhead: - text: wellhead - separator: - text: separator - storage tank: - text: storage tank - other: - text: other - samp_capt_status_enum: - name: samp_capt_status_enum + edge of car: + text: edge of car + center of car: + text: center of car + under a seat: + text: under a seat + wall_surf_treatment_enum: + name: wall_surf_treatment_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - active surveillance in response to an outbreak: - text: active surveillance in response to an outbreak - active surveillance not initiated by an outbreak: - text: active surveillance not initiated by an outbreak - farm sample: - text: farm sample - market sample: - text: market sample - other: - text: other - room_type_enum: - name: room_type_enum + painted: + text: painted + wall paper: + text: wall paper + no treatment: + text: no treatment + paneling: + text: paneling + stucco: + text: stucco + fabric: + text: fabric + room_connected_enum: + name: room_connected_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: attic: @@ -2829,102 +2825,130 @@ enums: text: examining room hallway: text: hallway - kitchen: - text: kitchen - mail room: - text: mail room - private office: - text: private office - open office: - text: open office - stairwell: - text: stairwell - ',restroom': - text: ',restroom' - lobby: - text: lobby - vestibule: - text: vestibule - mechanical or electrical room: - text: mechanical or electrical room - data center: - text: data center - laboratory_wet: - text: laboratory_wet - laboratory_dry: - text: laboratory_dry - gymnasium: - text: gymnasium - natatorium: - text: natatorium - auditorium: - text: auditorium - lockers: - text: lockers - cafe: - text: cafe - warehouse: - text: warehouse - samp_dis_stage_enum: - name: samp_dis_stage_enum + kitchen: + text: kitchen + mail room: + text: mail room + office: + text: office + stairwell: + text: stairwell + window_vert_pos_enum: + name: window_vert_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - dissemination: - text: dissemination - growth and reproduction: - text: growth and reproduction - infection: - text: infection - inoculation: - text: inoculation - penetration: - text: penetration - other: - text: other - floor_cond_enum: - name: floor_cond_enum + bottom: + text: bottom + middle: + text: middle + top: + text: top + low: + text: low + high: + text: high + weekday_enum: + name: weekday_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - lithology_enum: - name: lithology_enum + Monday: + text: Monday + Tuesday: + text: Tuesday + Wednesday: + text: Wednesday + Thursday: + text: Thursday + Friday: + text: Friday + Saturday: + text: Saturday + Sunday: + text: Sunday + room_samp_pos_enum: + name: room_samp_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Basement: - text: Basement - Chalk: - text: Chalk - Chert: - text: Chert - Coal: - text: Coal - Conglomerate: - text: Conglomerate - Diatomite: - text: Diatomite - Dolomite: - text: Dolomite - Limestone: - text: Limestone - Sandstone: - text: Sandstone - Shale: - text: Shale - Siltstone: - text: Siltstone - Volcanic: - text: Volcanic - other: - text: other + north corner: + text: north corner + south corner: + text: south corner + west corner: + text: west corner + east corner: + text: east corner + northeast corner: + text: northeast corner + northwest corner: + text: northwest corner + southeast corner: + text: southeast corner + southwest corner: + text: southwest corner + center: + text: center + door_mat_enum: + name: door_mat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + aluminum: + text: aluminum + cellular PVC: + text: cellular PVC + engineered plastic: + text: engineered plastic + fiberboard: + text: fiberboard + fiberglass: + text: fiberglass + metal: + text: metal + thermoplastic alloy: + text: thermoplastic alloy + vinyl: + text: vinyl + wood: + text: wood + wood/plastic composite: + text: wood/plastic composite + biol_stat_enum: + name: biol_stat_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + wild: + text: wild + natural: + text: natural + semi-natural: + text: semi-natural + inbred line: + text: inbred line + breeder's line: + text: breeder's line + hybrid: + text: hybrid + clonal selection: + text: clonal selection + mutant: + text: mutant + floor_struc_enum: + name: floor_struc_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + balcony: + text: balcony + floating floor: + text: floating floor + glass floor: + text: glass floor + raised floor: + text: raised floor + sprung floor: + text: sprung floor + wood-framed: + text: wood-framed + concrete: + text: concrete door_type_wood_enum: name: door_type_wood_enum from_schema: https://w3id.org/nmdc/nmdc @@ -2949,128 +2973,88 @@ enums: text: louvered wire gauged: text: wire gauged - wall_finish_mat_enum: - name: wall_finish_mat_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - plaster: - text: plaster - gypsum plaster: - text: gypsum plaster - veneer plaster: - text: veneer plaster - gypsum board: - text: gypsum board - tile: - text: tile - terrazzo: - text: terrazzo - stone facing: - text: stone facing - acoustical treatment: - text: acoustical treatment - wood: - text: wood - metal: - text: metal - masonry: - text: masonry - gender_restroom_enum: - name: gender_restroom_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - all gender: - text: all gender - female: - text: female - gender neurtral: - text: gender neurtral - male: - text: male - male and female: - text: male and female - unisex: - text: unisex - int_wall_cond_enum: - name: int_wall_cond_enum - from_schema: https://w3id.org/nmdc/nmdc - permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - floor_water_mold_enum: - name: floor_water_mold_enum + organism_count_enum: + name: organism_count_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - mold odor: - text: mold odor - wet floor: - text: wet floor - water stains: - text: water stains - wall discoloration: - text: wall discoloration - floor discoloration: - text: floor discoloration - ceiling discoloration: - text: ceiling discoloration - peeling paint or wallpaper: - text: peeling paint or wallpaper - bulging walls: - text: bulging walls - condensation: - text: condensation - samp_floor_enum: - name: samp_floor_enum + ATP: + text: ATP + MPN: + text: MPN + other: + text: other + shading_device_cond_enum: + name: shading_device_cond_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - 1st floor: - text: 1st floor - 2nd floor: - text: 2nd floor - basement: - text: basement - lobby: - text: lobby - heat_deliv_loc_enum: - name: heat_deliv_loc_enum + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + hcr_enum: + name: hcr_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - biol_stat_enum: - name: biol_stat_enum + Oil Reservoir: + text: Oil Reservoir + Gas Reservoir: + text: Gas Reservoir + Oil Sand: + text: Oil Sand + Coalbed: + text: Coalbed + Shale: + text: Shale + Tight Oil Reservoir: + text: Tight Oil Reservoir + Tight Gas Reservoir: + text: Tight Gas Reservoir + other: + text: other + mech_struc_enum: + name: mech_struc_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - wild: - text: wild - natural: - text: natural - semi-natural: - text: semi-natural - inbred line: - text: inbred line - breeder's line: - text: breeder's line - hybrid: - text: hybrid - clonal selection: - text: clonal selection - mutant: - text: mutant + subway: + text: subway + coach: + text: coach + carriage: + text: carriage + elevator: + text: elevator + escalator: + text: escalator + boat: + text: boat + train: + text: train + car: + text: car + bus: + text: bus + hc_produced_enum: + name: hc_produced_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + Oil: + text: Oil + Gas-Condensate: + text: Gas-Condensate + Gas: + text: Gas + Bitumen: + text: Bitumen + Coalbed Methane: + text: Coalbed Methane + other: + text: other shading_device_type_enum: name: shading_device_type_enum from_schema: https://w3id.org/nmdc/nmdc @@ -3099,148 +3083,250 @@ enums: text: trellis venetian awning: text: venetian awning - train_stat_loc_enum: - name: train_stat_loc_enum + quad_pos_enum: + name: quad_pos_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - south station above ground: - text: south station above ground - south station underground: - text: south station underground - south station amtrak: - text: south station amtrak - forest hills: - text: forest hills - riverside: - text: riverside - window_mat_enum: - name: window_mat_enum + North side: + text: North side + West side: + text: West side + South side: + text: South side + East side: + text: East side + sr_kerog_type_enum: + name: sr_kerog_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - clad: - text: clad - fiberglass: - text: fiberglass - metal: - text: metal - vinyl: - text: vinyl - wood: - text: wood - samp_weather_enum: - name: samp_weather_enum + Type I: + text: Type I + Type II: + text: Type II + Type III: + text: Type III + Type IV: + text: Type IV + other: + text: other + floor_cond_enum: + name: floor_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture + heat_deliv_loc_enum: + name: heat_deliv_loc_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + north: + text: north + south: + text: south + east: + text: east + west: + text: west + host_sex_enum: + name: host_sex_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + female: + text: female + hermaphrodite: + text: hermaphrodite + male: + text: male + neuter: + text: neuter + window_cond_enum: + name: window_cond_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + handidness_enum: + name: handidness_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + ambidexterity: + text: ambidexterity + left handedness: + text: left handedness + mixed-handedness: + text: mixed-handedness + right handedness: + text: right handedness + wall_const_type_enum: + name: wall_const_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + frame construction: + text: frame construction + joisted masonry: + text: joisted masonry + light noncombustible: + text: light noncombustible + masonry noncombustible: + text: masonry noncombustible + modified fire resistive: + text: modified fire resistive + fire resistive: + text: fire resistive + build_occup_type_enum: + name: build_occup_type_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + office: + text: office + market: + text: market + restaurant: + text: restaurant + residence: + text: residence + school: + text: school + residential: + text: residential + commercial: + text: commercial + low rise: + text: low rise + high rise: + text: high rise + wood framed: + text: wood framed + health care: + text: health care + airport: + text: airport + sports complex: + text: sports complex + oxy_stat_samp_enum: + name: oxy_stat_samp_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - clear sky: - text: clear sky - cloudy: - text: cloudy - foggy: - text: foggy - hail: - text: hail - rain: - text: rain - snow: - text: snow - sleet: - text: sleet - sunny: - text: sunny - windy: - text: windy - biotic_relationship_enum: - name: biotic_relationship_enum + aerobic: + text: aerobic + anaerobic: + text: anaerobic + other: + text: other + filter_type_enum: + name: filter_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - free living: - text: free living - parasite: - text: parasite - commensal: - text: commensal - symbiont: - text: symbiont - door_cond_enum: - name: door_cond_enum + particulate air filter: + text: particulate air filter + chemical air filter: + text: chemical air filter + low-MERV pleated media: + text: low-MERV pleated media + HEPA: + text: HEPA + electrostatic: + text: electrostatic + gas-phase or ultraviolet air treatments: + text: gas-phase or ultraviolet air treatments + samp_floor_enum: + name: samp_floor_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - train_line_enum: - name: train_line_enum + 1st floor: + text: 1st floor + 2nd floor: + text: 2nd floor + basement: + text: basement + lobby: + text: lobby + furniture_enum: + name: furniture_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - red: - text: red - green: - text: green - orange: - text: orange - build_docs_enum: - name: build_docs_enum + cabinet: + text: cabinet + chair: + text: chair + desks: + text: desks + samp_dis_stage_enum: + name: samp_dis_stage_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - building information model: - text: building information model - commissioning report: - text: commissioning report - complaint logs: - text: complaint logs - contract administration: - text: contract administration - cost estimate: - text: cost estimate - janitorial schedules or logs: - text: janitorial schedules or logs - maintenance plans: - text: maintenance plans - schedule: - text: schedule - sections: - text: sections - shop drawings: - text: shop drawings - submittals: - text: submittals - ventilation system: - text: ventilation system - windows: - text: windows - door_loc_enum: - name: door_loc_enum + dissemination: + text: dissemination + growth and reproduction: + text: growth and reproduction + infection: + text: infection + inoculation: + text: inoculation + penetration: + text: penetration + other: + text: other + substructure_type_enum: + name: substructure_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - sr_kerog_type_enum: - name: sr_kerog_type_enum + crawlspace: + text: crawlspace + slab on grade: + text: slab on grade + basement: + text: basement + door_comp_type_enum: + name: door_comp_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: - Type I: - text: Type I - Type II: - text: Type II - Type III: - text: Type III - Type IV: - text: Type IV - other: - text: other + metal covered: + text: metal covered + revolving: + text: revolving + sliding: + text: sliding + telescopic: + text: telescopic + plant_growth_med_enum: + name: plant_growth_med_enum + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + other artificial liquid medium: + text: other artificial liquid medium + other artificial solid medium: + text: other artificial solid medium + peat moss: + text: peat moss + perlite: + text: perlite + pumice: + text: pumice + sand: + text: sand + soil: + text: soil + vermiculite: + text: vermiculite + water: + text: water slots: metagenome_annotation_id: name: metagenome_annotation_id @@ -5531,8 +5617,6 @@ slots: examples: - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 2 string_serialization: '{date, arbitrary precision}' slot_group: MIxS Inspired @@ -5549,8 +5633,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 1 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -5568,8 +5650,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 3 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -5587,8 +5667,6 @@ slots: examples: - value: 'experimental treatment: value' from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:experimental_factor|additional_info rank: 7 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5603,8 +5681,6 @@ slots: - value: C18 - value: Basix PES, 13-100-106 FisherSci from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:filter_type rank: 6 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5622,8 +5698,6 @@ slots: - value: 13C glucose - value: H218O from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:chem_administration rank: 16 string_serialization: '{termLabel} {[termID]}; {timestamp}' slot_group: MIxS Inspired @@ -5640,8 +5714,6 @@ slots: - value: https://doi.org/10.1016/0038-0717(87)90052-6 - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:micro_biomass_meth rank: 11 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5656,8 +5728,6 @@ slots: - value: https://doi.org/10.1016/0038-0717(87)90052-6 - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:micro_biomass_meth rank: 13 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5672,8 +5742,6 @@ slots: examples: - value: 0.05 ug C/g dry soil from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:microbial_biomass rank: 10 string_serialization: '{float} {unit}' slot_group: MIxS Inspired @@ -5688,8 +5756,6 @@ slots: examples: - value: 0.05 ug N/g dry soil from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:microbial_biomass rank: 12 string_serialization: '{float} {unit}' slot_group: MIxS Inspired @@ -5702,8 +5768,6 @@ slots: examples: - value: insect 0.23 ug; plant 1g from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:biomass|microbial_biomass rank: 8 string_serialization: '{text};{float} {unit}' slot_group: MIxS Inspired @@ -5716,8 +5780,6 @@ slots: examples: - value: https://doi.org/10.1038/s41467-021-26181-3 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:microbial_biomass rank: 9 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5730,8 +5792,6 @@ slots: examples: - value: https://doi.org/10.1016/0038-0717(85)90144-0 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:org_nitro|tot_nitro_cont_meth rank: 14 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5744,8 +5804,6 @@ slots: - This is an open text field to provide any treatments that cannot be captured in the provided slots. from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:additional_info rank: 15 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5763,8 +5821,6 @@ slots: examples: - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 4 string_serialization: '{date, arbitrary precision}' slot_group: MIxS Inspired @@ -5781,8 +5837,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc - see_also: - - MIxS:collection_date rank: 5 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -17361,19 +17415,28 @@ slots: slot_uri: MIXS:0000156 multivalued: false range: QuantityValue - investigation field: - name: investigation field - description: field describing aspect of the investigation/study to which the sample - belongs + has unit: + name: has unit + description: Example "m" + from_schema: https://w3id.org/nmdc/nmdc + owner: QuantityValue + sequencing field: + name: sequencing field from_schema: https://w3id.org/nmdc/nmdc abstract: true + has raw value: + name: has raw value + from_schema: https://w3id.org/nmdc/nmdc + string_serialization: '{has numeric value} {has unit}' + owner: QuantityValue core field: name: core field description: basic fields from_schema: https://w3id.org/nmdc/nmdc abstract: true - nucleic acid sequence source field: - name: nucleic acid sequence source field + environment field: + name: environment field + description: field describing environmental aspect of a sample from_schema: https://w3id.org/nmdc/nmdc abstract: true has numeric value: @@ -17381,25 +17444,16 @@ slots: from_schema: https://w3id.org/nmdc/nmdc owner: QuantityValue range: double - environment field: - name: environment field - description: field describing environmental aspect of a sample + nucleic acid sequence source field: + name: nucleic acid sequence source field from_schema: https://w3id.org/nmdc/nmdc abstract: true - has unit: - name: has unit - description: Example "m" - from_schema: https://w3id.org/nmdc/nmdc - owner: QuantityValue - sequencing field: - name: sequencing field + investigation field: + name: investigation field + description: field describing aspect of the investigation/study to which the sample + belongs from_schema: https://w3id.org/nmdc/nmdc abstract: true - has raw value: - name: has raw value - from_schema: https://w3id.org/nmdc/nmdc - string_serialization: '{has numeric value} {has unit}' - owner: QuantityValue chemical: name: chemical description: from reaction participant class @@ -18486,10 +18540,9 @@ classes: Matches the entity that has been submitted to NMDC lat_lon: name: lat_lon - description: This is currently a required field but it's not clear if this - should be required for human hosts - notes: - - required where? + todos: + - This is currently a required field but it's not clear if this should be + required for human hosts env_broad_scale: name: env_broad_scale required: true @@ -19438,7 +19491,6 @@ classes: used: name: used description: The instrument used to collect the data used in the analysis - range: Instrument id: name: id required: true diff --git a/project/nmdc_schema_merged.yaml b/project/nmdc_schema_merged.yaml index 0590ebf185..98749183d9 100644 --- a/project/nmdc_schema_merged.yaml +++ b/project/nmdc_schema_merged.yaml @@ -11,7 +11,7 @@ notes: - not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1 id: https://w3id.org/nmdc/nmdc -version: v8.0.0 +version: v8.1.0 license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: CATH: @@ -347,6 +347,10 @@ types: string: name: string description: A character string + notes: + - In RDF serializations, a slot with range of string is treated as a literal or + type xsd:string. If you are authoring schemas in LinkML YAML, the type is + referenced with the lower case "string". from_schema: https://w3id.org/linkml/types exact_mappings: - schema:Text @@ -355,6 +359,9 @@ types: integer: name: integer description: An integer + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "integer". from_schema: https://w3id.org/linkml/types exact_mappings: - schema:Integer @@ -363,6 +370,9 @@ types: boolean: name: boolean description: A binary (true or false) value + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "boolean". from_schema: https://w3id.org/linkml/types exact_mappings: - schema:Boolean @@ -372,6 +382,9 @@ types: float: name: float description: A real number that conforms to the xsd:float specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "float". from_schema: https://w3id.org/linkml/types exact_mappings: - schema:Float @@ -380,6 +393,9 @@ types: double: name: double description: A real number that conforms to the xsd:double specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "double". from_schema: https://w3id.org/linkml/types close_mappings: - schema:Float @@ -389,6 +405,9 @@ types: name: decimal description: A real number with arbitrary precision that conforms to the xsd:decimal specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "decimal". from_schema: https://w3id.org/linkml/types broad_mappings: - schema:Number @@ -400,17 +419,21 @@ types: particular day notes: - URI is dateTime because OWL reasoners do not work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "time". from_schema: https://w3id.org/linkml/types exact_mappings: - schema:Time base: XSDTime - uri: xsd:dateTime + uri: xsd:time repr: str date: name: date description: a date (year, month and day) in an idealized calendar notes: - URI is dateTime because OWL reasoners don't work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date". from_schema: https://w3id.org/linkml/types exact_mappings: - schema:Date @@ -420,6 +443,9 @@ types: datetime: name: datetime description: The combination of a date and time + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "datetime". from_schema: https://w3id.org/linkml/types exact_mappings: - schema:DateTime @@ -429,6 +455,9 @@ types: date_or_datetime: name: date_or_datetime description: Either a date or a datetime + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date_or_datetime". from_schema: https://w3id.org/linkml/types base: str uri: linkml:DateOrDatetime @@ -436,6 +465,9 @@ types: uriorcurie: name: uriorcurie description: a URI or a CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uriorcurie". from_schema: https://w3id.org/linkml/types base: URIorCURIE uri: xsd:anyURI @@ -444,6 +476,9 @@ types: name: curie conforms_to: https://www.w3.org/TR/curie/ description: a compact URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "curie". comments: - in RDF serializations this MUST be expanded to a URI - in non-RDF serializations MAY be serialized as the compact representation @@ -455,6 +490,9 @@ types: name: uri conforms_to: https://www.ietf.org/rfc/rfc3987.txt description: a complete URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uri". comments: - in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which @@ -468,6 +506,9 @@ types: ncname: name: ncname description: Prefix part of CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "ncname". from_schema: https://w3id.org/linkml/types base: NCName uri: xsd:string @@ -475,8 +516,11 @@ types: objectidentifier: name: objectidentifier description: A URI or CURIE that represents an object in the model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "objectidentifier". comments: - - Used for inheritence and type checking + - Used for inheritance and type checking from_schema: https://w3id.org/linkml/types base: ElementIdentifier uri: shex:iri @@ -484,10 +528,52 @@ types: nodeidentifier: name: nodeidentifier description: A URI, CURIE or BNODE that represents a node in a model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "nodeidentifier". from_schema: https://w3id.org/linkml/types base: NodeIdentifier uri: shex:nonLiteral repr: str + jsonpointer: + name: jsonpointer + conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 + description: A string encoding a JSON Pointer. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to a valid object within the current + instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpointer". + from_schema: https://w3id.org/linkml/types + base: str + uri: xsd:string + repr: str + jsonpath: + name: jsonpath + conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html + description: A string encoding a JSON Path. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to zero or more valid objects within + the current instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpath". + from_schema: https://w3id.org/linkml/types + base: str + uri: xsd:string + repr: str + sparqlpath: + name: sparqlpath + conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths + description: A string encoding a SPARQL Property Path. The value of the string + MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects + within the current instance document when encoded as RDF. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "sparqlpath". + from_schema: https://w3id.org/linkml/types + base: str + uri: xsd:string + repr: str enums: StatusEnum: name: StatusEnum @@ -1190,26 +1276,6 @@ enums: text: soil water_extract_soil: text: water_extract_soil - door_direct_enum: - name: door_direct_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - inward: - text: inward - outward: - text: outward - sideways: - text: sideways - oxy_stat_samp_enum: - name: oxy_stat_samp_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - aerobic: - text: aerobic - anaerobic: - text: anaerobic - other: - text: other surf_air_cont_enum: name: surf_air_cont_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml @@ -1230,164 +1296,164 @@ enums: text: nutrients biocides: text: biocides - window_vert_pos_enum: - name: window_vert_pos_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - bottom: - text: bottom - middle: - text: middle - top: - text: top - low: - text: low - high: - text: high - filter_type_enum: - name: filter_type_enum + water_feat_type_enum: + name: water_feat_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - particulate air filter: - text: particulate air filter - chemical air filter: - text: chemical air filter - low-MERV pleated media: - text: low-MERV pleated media - HEPA: - text: HEPA - electrostatic: - text: electrostatic - gas-phase or ultraviolet air treatments: - text: gas-phase or ultraviolet air treatments - rel_samp_loc_enum: - name: rel_samp_loc_enum + fountain: + text: fountain + pool: + text: pool + standing feature: + text: standing feature + stream: + text: stream + waterfall: + text: waterfall + samp_collect_point_enum: + name: samp_collect_point_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - edge of car: - text: edge of car - center of car: - text: center of car - under a seat: - text: under a seat - sediment_type_enum: - name: sediment_type_enum + well: + text: well + test well: + text: test well + drilling rig: + text: drilling rig + wellhead: + text: wellhead + separator: + text: separator + storage tank: + text: storage tank + other: + text: other + floor_water_mold_enum: + name: floor_water_mold_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - biogenous: - text: biogenous - cosmogenous: - text: cosmogenous - hydrogenous: - text: hydrogenous - lithogenous: - text: lithogenous - occup_document_enum: - name: occup_document_enum + mold odor: + text: mold odor + wet floor: + text: wet floor + water stains: + text: water stains + wall discoloration: + text: wall discoloration + floor discoloration: + text: floor discoloration + ceiling discoloration: + text: ceiling discoloration + peeling paint or wallpaper: + text: peeling paint or wallpaper + bulging walls: + text: bulging walls + condensation: + text: condensation + wall_texture_enum: + name: wall_texture_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - automated count: - text: automated count - estimate: - text: estimate - manual count: - text: manual count - videos: - text: videos - room_connected_enum: - name: room_connected_enum + crows feet: + text: crows feet + crows-foot stomp: + text: crows-foot stomp + ? '' + : text: '' + double skip: + text: double skip + hawk and trowel: + text: hawk and trowel + knockdown: + text: knockdown + popcorn: + text: popcorn + orange peel: + text: orange peel + rosebud stomp: + text: rosebud stomp + Santa-Fe texture: + text: Santa-Fe texture + skip trowel: + text: skip trowel + smooth: + text: smooth + stomp knockdown: + text: stomp knockdown + swirl: + text: swirl + samp_subtype_enum: + name: samp_subtype_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - attic: - text: attic - bathroom: - text: bathroom - closet: - text: closet - conference room: - text: conference room - elevator: - text: elevator - examining room: - text: examining room - hallway: - text: hallway - kitchen: - text: kitchen - mail room: - text: mail room - office: - text: office - stairwell: - text: stairwell - quad_pos_enum: - name: quad_pos_enum + oil phase: + text: oil phase + water phase: + text: water phase + biofilm: + text: biofilm + not applicable: + text: not applicable + other: + text: other + drainage_class_enum: + name: drainage_class_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - North side: - text: North side - West side: - text: West side - South side: - text: South side - East side: - text: East side - sr_geol_age_enum: - name: sr_geol_age_enum + very poorly: + text: very poorly + poorly: + text: poorly + somewhat poorly: + text: somewhat poorly + moderately well: + text: moderately well + well: + text: well + excessively drained: + text: excessively drained + freq_clean_enum: + name: freq_clean_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - Archean: - text: Archean - Cambrian: - text: Cambrian - Carboniferous: - text: Carboniferous - Cenozoic: - text: Cenozoic - Cretaceous: - text: Cretaceous - Devonian: - text: Devonian - Jurassic: - text: Jurassic - Mesozoic: - text: Mesozoic - Neogene: - text: Neogene - Ordovician: - text: Ordovician - Paleogene: - text: Paleogene - Paleozoic: - text: Paleozoic - Permian: - text: Permian - Precambrian: - text: Precambrian - Proterozoic: - text: Proterozoic - Silurian: - text: Silurian - Triassic: - text: Triassic + Daily: + text: Daily + Weekly: + text: Weekly + Monthly: + text: Monthly + Quarterly: + text: Quarterly + Annually: + text: Annually other: text: other - door_move_enum: - name: door_move_enum + biotic_relationship_enum: + name: biotic_relationship_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - collapsible: - text: collapsible - folding: - text: folding - revolving: - text: revolving - rolling shutter: - text: rolling shutter - sliding: - text: sliding - swinging: - text: swinging + free living: + text: free living + parasite: + text: parasite + commensal: + text: commensal + symbiont: + text: symbiont + light_type_enum: + name: light_type_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + natural light: + text: natural light + electric light: + text: electric light + desk lamp: + text: desk lamp + flourescent lights: + text: flourescent lights + none: + text: none cur_land_use_enum: name: cur_land_use_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml @@ -1583,142 +1649,146 @@ enums: value: vine crops (grapes) examples: - value: grapes - hcr_geol_age_enum: - name: hcr_geol_age_enum + drawings_enum: + name: drawings_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - Archean: - text: Archean - Cambrian: - text: Cambrian - Carboniferous: - text: Carboniferous - Cenozoic: - text: Cenozoic - Cretaceous: - text: Cretaceous - Devonian: - text: Devonian - Jurassic: - text: Jurassic - Mesozoic: - text: Mesozoic - Neogene: - text: Neogene - Ordovician: - text: Ordovician - Paleogene: - text: Paleogene - Paleozoic: - text: Paleozoic - Permian: - text: Permian - Precambrian: - text: Precambrian - Proterozoic: - text: Proterozoic - Silurian: - text: Silurian - Triassic: - text: Triassic + operation: + text: operation + as built: + text: as built + construction: + text: construction + bid: + text: bid + design: + text: design + building navigation map: + text: building navigation map + diagram: + text: diagram + sketch: + text: sketch + indoor_surf_enum: + name: indoor_surf_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + cabinet: + text: cabinet + ceiling: + text: ceiling + counter top: + text: counter top + door: + text: door + shelving: + text: shelving + vent cover: + text: vent cover + window: + text: window + wall: + text: wall + samp_capt_status_enum: + name: samp_capt_status_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + active surveillance in response to an outbreak: + text: active surveillance in response to an outbreak + active surveillance not initiated by an outbreak: + text: active surveillance not initiated by an outbreak + farm sample: + text: farm sample + market sample: + text: market sample other: text: other - wall_const_type_enum: - name: wall_const_type_enum + room_loc_enum: + name: room_loc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - frame construction: - text: frame construction - joisted masonry: - text: joisted masonry - light noncombustible: - text: light noncombustible - masonry noncombustible: - text: masonry noncombustible - modified fire resistive: - text: modified fire resistive - fire resistive: - text: fire resistive - plant_sex_enum: - name: plant_sex_enum + corner room: + text: corner room + interior room: + text: interior room + exterior wall: + text: exterior wall + occup_document_enum: + name: occup_document_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - Androdioecious: - text: Androdioecious - Androecious: - text: Androecious - Androgynous: - text: Androgynous - Androgynomonoecious: - text: Androgynomonoecious - Andromonoecious: - text: Andromonoecious - Bisexual: - text: Bisexual - Dichogamous: - text: Dichogamous - Diclinous: - text: Diclinous - Dioecious: - text: Dioecious - Gynodioecious: - text: Gynodioecious - Gynoecious: - text: Gynoecious - Gynomonoecious: - text: Gynomonoecious - Hermaphroditic: - text: Hermaphroditic - Imperfect: - text: Imperfect - Monoclinous: - text: Monoclinous - Monoecious: - text: Monoecious - Perfect: - text: Perfect - Polygamodioecious: - text: Polygamodioecious - Polygamomonoecious: - text: Polygamomonoecious - Polygamous: - text: Polygamous - Protandrous: - text: Protandrous - Protogynous: - text: Protogynous - Subandroecious: - text: Subandroecious - Subdioecious: - text: Subdioecious - Subgynoecious: - text: Subgynoecious - Synoecious: - text: Synoecious - Trimonoecious: - text: Trimonoecious - Trioecious: - text: Trioecious - Unisexual: - text: Unisexual - ceil_type_enum: - name: ceil_type_enum + automated count: + text: automated count + estimate: + text: estimate + manual count: + text: manual count + videos: + text: videos + arch_struc_enum: + name: arch_struc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - cathedral: - text: cathedral - dropped: - text: dropped - concave: - text: concave - barrel-shaped: - text: barrel-shaped - coffered: - text: coffered - cove: - text: cove - stretched: - text: stretched + building: + text: building + shed: + text: shed + home: + text: home + wall_finish_mat_enum: + name: wall_finish_mat_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + plaster: + text: plaster + gypsum plaster: + text: gypsum plaster + veneer plaster: + text: veneer plaster + gypsum board: + text: gypsum board + tile: + text: tile + terrazzo: + text: terrazzo + stone facing: + text: stone facing + acoustical treatment: + text: acoustical treatment + wood: + text: wood + metal: + text: metal + masonry: + text: masonry + window_mat_enum: + name: window_mat_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + clad: + text: clad + fiberglass: + text: fiberglass + metal: + text: metal + vinyl: + text: vinyl + wood: + text: wood + int_wall_cond_enum: + name: int_wall_cond_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture floor_finish_mat_enum: name: floor_finish_mat_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml @@ -1759,584 +1829,240 @@ enums: text: paint none or unfinished: text: none or unfinished - wall_loc_enum: - name: wall_loc_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - wall_surf_treatment_enum: - name: wall_surf_treatment_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - painted: - text: painted - wall paper: - text: wall paper - no treatment: - text: no treatment - paneling: - text: paneling - stucco: - text: stucco - fabric: - text: fabric - window_cond_enum: - name: window_cond_enum + build_docs_enum: + name: build_docs_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - door_mat_enum: - name: door_mat_enum + building information model: + text: building information model + commissioning report: + text: commissioning report + complaint logs: + text: complaint logs + contract administration: + text: contract administration + cost estimate: + text: cost estimate + janitorial schedules or logs: + text: janitorial schedules or logs + maintenance plans: + text: maintenance plans + schedule: + text: schedule + sections: + text: sections + shop drawings: + text: shop drawings + submittals: + text: submittals + ventilation system: + text: ventilation system + windows: + text: windows + surf_material_enum: + name: surf_material_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - aluminum: - text: aluminum - cellular PVC: - text: cellular PVC - engineered plastic: - text: engineered plastic - fiberboard: - text: fiberboard - fiberglass: - text: fiberglass + adobe: + text: adobe + carpet: + text: carpet + cinder blocks: + text: cinder blocks + concrete: + text: concrete + hay bales: + text: hay bales + glass: + text: glass metal: text: metal - thermoplastic alloy: - text: thermoplastic alloy + paint: + text: paint + plastic: + text: plastic + stainless steel: + text: stainless steel + stone: + text: stone + stucco: + text: stucco + tile: + text: tile vinyl: text: vinyl wood: text: wood - wood/plastic composite: - text: wood/plastic composite - soil_horizon_enum: - name: soil_horizon_enum + tidal_stage_enum: + name: tidal_stage_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - O horizon: - text: O horizon - A horizon: - text: A horizon - E horizon: - text: E horizon - B horizon: - text: B horizon - C horizon: - text: C horizon - R layer: - text: R layer - Permafrost: - text: Permafrost - M horizon: - text: M horizon - ceil_finish_mat_enum: - name: ceil_finish_mat_enum + low tide: + text: low tide + ebb tide: + text: ebb tide + flood tide: + text: flood tide + high tide: + text: high tide + window_horiz_pos_enum: + name: window_horiz_pos_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - drywall: - text: drywall - mineral fibre: - text: mineral fibre - tiles: - text: tiles - PVC: - text: PVC - plasterboard: - text: plasterboard - metal: - text: metal - fiberglass: - text: fiberglass - stucco: - text: stucco - mineral wool/calcium silicate: - text: mineral wool/calcium silicate - wood: - text: wood - shading_device_cond_enum: - name: shading_device_cond_enum + left: + text: left + middle: + text: middle + right: + text: right + train_stop_loc_enum: + name: train_stop_loc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - hc_produced_enum: - name: hc_produced_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - Oil: - text: Oil - Gas-Condensate: - text: Gas-Condensate - Gas: - text: Gas - Bitumen: - text: Bitumen - Coalbed Methane: - text: Coalbed Methane - other: - text: other - door_comp_type_enum: - name: door_comp_type_enum + end: + text: end + mid: + text: mid + downtown: + text: downtown + train_line_enum: + name: train_line_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - metal covered: - text: metal covered - revolving: - text: revolving - sliding: - text: sliding - telescopic: - text: telescopic - window_loc_enum: - name: window_loc_enum + red: + text: red + green: + text: green + orange: + text: orange + train_stat_loc_enum: + name: train_stat_loc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - sr_lithology_enum: - name: sr_lithology_enum + south station above ground: + text: south station above ground + south station underground: + text: south station underground + south station amtrak: + text: south station amtrak + forest hills: + text: forest hills + riverside: + text: riverside + sr_dep_env_enum: + name: sr_dep_env_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - Clastic: - text: Clastic - Carbonate: - text: Carbonate - Coal: - text: Coal - Biosilicieous: - text: Biosilicieous + Lacustine: + text: Lacustine + Fluvioldeltaic: + text: Fluvioldeltaic + Fluviomarine: + text: Fluviomarine + Marine: + text: Marine other: text: other - plant_growth_med_enum: - name: plant_growth_med_enum + samp_weather_enum: + name: samp_weather_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - other artificial liquid medium: - text: other artificial liquid medium - other artificial solid medium: - text: other artificial solid medium - peat moss: - text: peat moss - perlite: - text: perlite - pumice: - text: pumice - sand: - text: sand - soil: - text: soil - vermiculite: - text: vermiculite - water: - text: water - surf_material_enum: - name: surf_material_enum + clear sky: + text: clear sky + cloudy: + text: cloudy + foggy: + text: foggy + hail: + text: hail + rain: + text: rain + snow: + text: snow + sleet: + text: sleet + sunny: + text: sunny + windy: + text: windy + window_cover_enum: + name: window_cover_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - adobe: - text: adobe - carpet: - text: carpet - cinder blocks: - text: cinder blocks - concrete: - text: concrete - hay bales: - text: hay bales - glass: - text: glass - metal: - text: metal - paint: - text: paint - plastic: - text: plastic - stainless steel: - text: stainless steel - stone: - text: stone - stucco: - text: stucco - tile: - text: tile - vinyl: - text: vinyl - wood: - text: wood - ceil_cond_enum: - name: ceil_cond_enum + blinds: + text: blinds + curtains: + text: curtains + none: + text: none + room_type_enum: + name: room_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - building_setting_enum: - name: building_setting_enum + attic: + text: attic + bathroom: + text: bathroom + closet: + text: closet + conference room: + text: conference room + elevator: + text: elevator + examining room: + text: examining room + hallway: + text: hallway + kitchen: + text: kitchen + mail room: + text: mail room + private office: + text: private office + open office: + text: open office + stairwell: + text: stairwell + ',restroom': + text: ',restroom' + lobby: + text: lobby + vestibule: + text: vestibule + mechanical or electrical room: + text: mechanical or electrical room + data center: + text: data center + laboratory_wet: + text: laboratory_wet + laboratory_dry: + text: laboratory_dry + gymnasium: + text: gymnasium + natatorium: + text: natatorium + auditorium: + text: auditorium + lockers: + text: lockers + cafe: + text: cafe + warehouse: + text: warehouse + sediment_type_enum: + name: sediment_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - urban: - text: urban - suburban: - text: suburban - exurban: - text: exurban - rural: - text: rural - build_occup_type_enum: - name: build_occup_type_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - office: - text: office - market: - text: market - restaurant: - text: restaurant - residence: - text: residence - school: - text: school - residential: - text: residential - commercial: - text: commercial - low rise: - text: low rise - high rise: - text: high rise - wood framed: - text: wood framed - health care: - text: health care - airport: - text: airport - sports complex: - text: sports complex - depos_env_enum: - name: depos_env_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - Continental - Alluvial: - text: Continental - Alluvial - Continental - Aeolian: - text: Continental - Aeolian - Continental - Fluvial: - text: Continental - Fluvial - Continental - Lacustrine: - text: Continental - Lacustrine - Transitional - Deltaic: - text: Transitional - Deltaic - Transitional - Tidal: - text: Transitional - Tidal - Transitional - Lagoonal: - text: Transitional - Lagoonal - Transitional - Beach: - text: Transitional - Beach - Transitional - Lake: - text: Transitional - Lake - Marine - Shallow: - text: Marine - Shallow - Marine - Deep: - text: Marine - Deep - Marine - Reef: - text: Marine - Reef - Other - Evaporite: - text: Other - Evaporite - Other - Glacial: - text: Other - Glacial - Other - Volcanic: - text: Other - Volcanic - other: - text: other - profile_position_enum: - name: profile_position_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - summit: - text: summit - shoulder: - text: shoulder - backslope: - text: backslope - footslope: - text: footslope - toeslope: - text: toeslope - furniture_enum: - name: furniture_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - cabinet: - text: cabinet - chair: - text: chair - desks: - text: desks - door_type_enum: - name: door_type_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - composite: - text: composite - metal: - text: metal - wooden: - text: wooden - tidal_stage_enum: - name: tidal_stage_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - low tide: - text: low tide - ebb tide: - text: ebb tide - flood tide: - text: flood tide - high tide: - text: high tide - door_type_metal_enum: - name: door_type_metal_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - collapsible: - text: collapsible - corrugated steel: - text: corrugated steel - hollow: - text: hollow - rolling shutters: - text: rolling shutters - steel plate: - text: steel plate - handidness_enum: - name: handidness_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - ambidexterity: - text: ambidexterity - left handedness: - text: left handedness - mixed-handedness: - text: mixed-handedness - right handedness: - text: right handedness - tillage_enum: - name: tillage_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - drill: - text: drill - cutting disc: - text: cutting disc - ridge till: - text: ridge till - strip tillage: - text: strip tillage - zonal tillage: - text: zonal tillage - chisel: - text: chisel - tined: - text: tined - mouldboard: - text: mouldboard - disc plough: - text: disc plough - hcr_enum: - name: hcr_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - Oil Reservoir: - text: Oil Reservoir - Gas Reservoir: - text: Gas Reservoir - Oil Sand: - text: Oil Sand - Coalbed: - text: Coalbed - Shale: - text: Shale - Tight Oil Reservoir: - text: Tight Oil Reservoir - Tight Gas Reservoir: - text: Tight Gas Reservoir - other: - text: other - freq_clean_enum: - name: freq_clean_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - Daily: - text: Daily - Weekly: - text: Weekly - Monthly: - text: Monthly - Quarterly: - text: Quarterly - Annually: - text: Annually - other: - text: other - growth_habit_enum: - name: growth_habit_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - erect: - text: erect - semi-erect: - text: semi-erect - spreading: - text: spreading - prostrate: - text: prostrate - season_use_enum: - name: season_use_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - Spring: - text: Spring - Summer: - text: Summer - Fall: - text: Fall - Winter: - text: Winter - sr_dep_env_enum: - name: sr_dep_env_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - Lacustine: - text: Lacustine - Fluvioldeltaic: - text: Fluvioldeltaic - Fluviomarine: - text: Fluviomarine - Marine: - text: Marine - other: - text: other - water_feat_type_enum: - name: water_feat_type_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - fountain: - text: fountain - pool: - text: pool - standing feature: - text: standing feature - stream: - text: stream - waterfall: - text: waterfall - substructure_type_enum: - name: substructure_type_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - crawlspace: - text: crawlspace - slab on grade: - text: slab on grade - basement: - text: basement - indoor_space_enum: - name: indoor_space_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - bedroom: - text: bedroom - office: - text: office - bathroom: - text: bathroom - foyer: - text: foyer - kitchen: - text: kitchen - locker room: - text: locker room - hallway: - text: hallway - elevator: - text: elevator - host_sex_enum: - name: host_sex_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - female: - text: female - hermaphrodite: - text: hermaphrodite - male: - text: male - neuter: - text: neuter - window_type_enum: - name: window_type_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - single-hung sash window: - text: single-hung sash window - horizontal sash window: - text: horizontal sash window - fixed window: - text: fixed window - specific_enum: - name: specific_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - photos: - text: photos - fao_class_enum: - name: fao_class_enum + biogenous: + text: biogenous + cosmogenous: + text: cosmogenous + hydrogenous: + text: hydrogenous + lithogenous: + text: lithogenous + fao_class_enum: + name: fao_class_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: Acrisols: @@ -2391,166 +2117,404 @@ enums: text: Vertisols Yermosols: text: Yermosols - floor_struc_enum: - name: floor_struc_enum + ext_window_orient_enum: + name: ext_window_orient_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - balcony: - text: balcony - floating floor: - text: floating floor - glass floor: - text: glass floor - raised floor: - text: raised floor - sprung floor: - text: sprung floor - wood-framed: - text: wood-framed - concrete: - text: concrete - wall_texture_enum: - name: wall_texture_enum + north: + text: north + south: + text: south + east: + text: east + west: + text: west + northeast: + text: northeast + southeast: + text: southeast + southwest: + text: southwest + northwest: + text: northwest + sr_geol_age_enum: + name: sr_geol_age_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + Archean: + text: Archean + Cambrian: + text: Cambrian + Carboniferous: + text: Carboniferous + Cenozoic: + text: Cenozoic + Cretaceous: + text: Cretaceous + Devonian: + text: Devonian + Jurassic: + text: Jurassic + Mesozoic: + text: Mesozoic + Neogene: + text: Neogene + Ordovician: + text: Ordovician + Paleogene: + text: Paleogene + Paleozoic: + text: Paleozoic + Permian: + text: Permian + Precambrian: + text: Precambrian + Proterozoic: + text: Proterozoic + Silurian: + text: Silurian + Triassic: + text: Triassic + other: + text: other + door_move_enum: + name: door_move_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + collapsible: + text: collapsible + folding: + text: folding + revolving: + text: revolving + rolling shutter: + text: rolling shutter + sliding: + text: sliding + swinging: + text: swinging + door_direct_enum: + name: door_direct_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + inward: + text: inward + outward: + text: outward + sideways: + text: sideways + ceil_texture_enum: + name: ceil_texture_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + crows feet: + text: crows feet + crows-foot stomp: + text: crows-foot stomp + double skip: + text: double skip + hawk and trowel: + text: hawk and trowel + knockdown: + text: knockdown + popcorn: + text: popcorn + orange peel: + text: orange peel + rosebud stomp: + text: rosebud stomp + Santa-Fe texture: + text: Santa-Fe texture + skip trowel: + text: skip trowel + smooth: + text: smooth + stomp knockdown: + text: stomp knockdown + swirl: + text: swirl + samp_md_enum: + name: samp_md_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + DF: + text: DF + RT: + text: RT + KB: + text: KB + MSL: + text: MSL + other: + text: other + ceil_type_enum: + name: ceil_type_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + cathedral: + text: cathedral + dropped: + text: dropped + concave: + text: concave + barrel-shaped: + text: barrel-shaped + coffered: + text: coffered + cove: + text: cove + stretched: + text: stretched + wall_loc_enum: + name: wall_loc_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + north: + text: north + south: + text: south + east: + text: east + west: + text: west + door_type_metal_enum: + name: door_type_metal_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + collapsible: + text: collapsible + corrugated steel: + text: corrugated steel + hollow: + text: hollow + rolling shutters: + text: rolling shutters + steel plate: + text: steel plate + gender_restroom_enum: + name: gender_restroom_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + all gender: + text: all gender + female: + text: female + gender neurtral: + text: gender neurtral + male: + text: male + male and female: + text: male and female + unisex: + text: unisex + vis_media_enum: + name: vis_media_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - ? '' - : text: '' - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - train_stop_loc_enum: - name: train_stop_loc_enum + photos: + text: photos + videos: + text: videos + commonly of the building: + text: commonly of the building + site context (adjacent buildings, vegetation, terrain, streets): + text: site context (adjacent buildings, vegetation, terrain, streets) + interiors: + text: interiors + equipment: + text: equipment + 3D scans: + text: 3D scans + window_loc_enum: + name: window_loc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - end: - text: end - mid: - text: mid - downtown: - text: downtown - drawings_enum: - name: drawings_enum + north: + text: north + south: + text: south + east: + text: east + west: + text: west + soil_horizon_enum: + name: soil_horizon_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - building navigation map: - text: building navigation map - diagram: - text: diagram - sketch: - text: sketch - room_loc_enum: - name: room_loc_enum + O horizon: + text: O horizon + A horizon: + text: A horizon + E horizon: + text: E horizon + B horizon: + text: B horizon + C horizon: + text: C horizon + R layer: + text: R layer + Permafrost: + text: Permafrost + M horizon: + text: M horizon + indoor_space_enum: + name: indoor_space_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - corner room: - text: corner room - interior room: - text: interior room - exterior wall: - text: exterior wall - light_type_enum: - name: light_type_enum + bedroom: + text: bedroom + office: + text: office + bathroom: + text: bathroom + foyer: + text: foyer + kitchen: + text: kitchen + locker room: + text: locker room + hallway: + text: hallway + elevator: + text: elevator + door_type_enum: + name: door_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - natural light: - text: natural light - electric light: - text: electric light - desk lamp: - text: desk lamp - flourescent lights: - text: flourescent lights - none: - text: none - weekday_enum: - name: weekday_enum + composite: + text: composite + metal: + text: metal + wooden: + text: wooden + depos_env_enum: + name: depos_env_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - Monday: - text: Monday - Tuesday: - text: Tuesday - Wednesday: - text: Wednesday - Thursday: - text: Thursday - Friday: - text: Friday - Saturday: - text: Saturday - Sunday: - text: Sunday - arch_struc_enum: - name: arch_struc_enum + Continental - Alluvial: + text: Continental - Alluvial + Continental - Aeolian: + text: Continental - Aeolian + Continental - Fluvial: + text: Continental - Fluvial + Continental - Lacustrine: + text: Continental - Lacustrine + Transitional - Deltaic: + text: Transitional - Deltaic + Transitional - Tidal: + text: Transitional - Tidal + Transitional - Lagoonal: + text: Transitional - Lagoonal + Transitional - Beach: + text: Transitional - Beach + Transitional - Lake: + text: Transitional - Lake + Marine - Shallow: + text: Marine - Shallow + Marine - Deep: + text: Marine - Deep + Marine - Reef: + text: Marine - Reef + Other - Evaporite: + text: Other - Evaporite + Other - Glacial: + text: Other - Glacial + Other - Volcanic: + text: Other - Volcanic + other: + text: other + sr_lithology_enum: + name: sr_lithology_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - building: - text: building - shed: - text: shed - home: - text: home - heat_cool_type_enum: - name: heat_cool_type_enum + Clastic: + text: Clastic + Carbonate: + text: Carbonate + Coal: + text: Coal + Biosilicieous: + text: Biosilicieous + other: + text: other + plant_sex_enum: + name: plant_sex_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - radiant system: - text: radiant system - heat pump: - text: heat pump - forced air system: - text: forced air system - steam forced heat: - text: steam forced heat - wood stove: - text: wood stove - samp_md_enum: - name: samp_md_enum + Androdioecious: + text: Androdioecious + Androecious: + text: Androecious + Androgynous: + text: Androgynous + Androgynomonoecious: + text: Androgynomonoecious + Andromonoecious: + text: Andromonoecious + Bisexual: + text: Bisexual + Dichogamous: + text: Dichogamous + Diclinous: + text: Diclinous + Dioecious: + text: Dioecious + Gynodioecious: + text: Gynodioecious + Gynoecious: + text: Gynoecious + Gynomonoecious: + text: Gynomonoecious + Hermaphroditic: + text: Hermaphroditic + Imperfect: + text: Imperfect + Monoclinous: + text: Monoclinous + Monoecious: + text: Monoecious + Perfect: + text: Perfect + Polygamodioecious: + text: Polygamodioecious + Polygamomonoecious: + text: Polygamomonoecious + Polygamous: + text: Polygamous + Protandrous: + text: Protandrous + Protogynous: + text: Protogynous + Subandroecious: + text: Subandroecious + Subdioecious: + text: Subdioecious + Subgynoecious: + text: Subgynoecious + Synoecious: + text: Synoecious + Trimonoecious: + text: Trimonoecious + Trioecious: + text: Trioecious + Unisexual: + text: Unisexual + specific_enum: + name: specific_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - DF: - text: DF - RT: - text: RT - KB: - text: KB - MSL: - text: MSL - other: - text: other + operation: + text: operation + as built: + text: as built + construction: + text: construction + bid: + text: bid + design: + text: design + photos: + text: photos ext_wall_orient_enum: name: ext_wall_orient_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml @@ -2571,30 +2535,8 @@ enums: text: southwest northwest: text: northwest - mech_struc_enum: - name: mech_struc_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - subway: - text: subway - coach: - text: coach - carriage: - text: carriage - elevator: - text: elevator - escalator: - text: escalator - boat: - text: boat - train: - text: train - car: - text: car - bus: - text: bus - ext_window_orient_enum: - name: ext_window_orient_enum + door_loc_enum: + name: door_loc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: north: @@ -2605,164 +2547,224 @@ enums: text: east west: text: west - northeast: - text: northeast - southeast: - text: southeast - southwest: - text: southwest - northwest: - text: northwest - window_cover_enum: - name: window_cover_enum + profile_position_enum: + name: profile_position_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - blinds: - text: blinds - curtains: - text: curtains - none: - text: none - drainage_class_enum: - name: drainage_class_enum + summit: + text: summit + shoulder: + text: shoulder + backslope: + text: backslope + footslope: + text: footslope + toeslope: + text: toeslope + growth_habit_enum: + name: growth_habit_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - very poorly: - text: very poorly - poorly: - text: poorly - somewhat poorly: - text: somewhat poorly - moderately well: - text: moderately well - well: - text: well - excessively drained: - text: excessively drained - window_horiz_pos_enum: - name: window_horiz_pos_enum + erect: + text: erect + semi-erect: + text: semi-erect + spreading: + text: spreading + prostrate: + text: prostrate + season_use_enum: + name: season_use_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - left: - text: left - middle: - text: middle - right: - text: right - samp_subtype_enum: - name: samp_subtype_enum + Spring: + text: Spring + Summer: + text: Summer + Fall: + text: Fall + Winter: + text: Winter + ceil_finish_mat_enum: + name: ceil_finish_mat_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - oil phase: - text: oil phase - water phase: - text: water phase - biofilm: - text: biofilm - not applicable: - text: not applicable - other: - text: other - ceil_texture_enum: - name: ceil_texture_enum + drywall: + text: drywall + mineral fibre: + text: mineral fibre + tiles: + text: tiles + PVC: + text: PVC + plasterboard: + text: plasterboard + metal: + text: metal + fiberglass: + text: fiberglass + stucco: + text: stucco + mineral wool/calcium silicate: + text: mineral wool/calcium silicate + wood: + text: wood + tillage_enum: + name: tillage_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - room_samp_pos_enum: - name: room_samp_pos_enum + drill: + text: drill + cutting disc: + text: cutting disc + ridge till: + text: ridge till + strip tillage: + text: strip tillage + zonal tillage: + text: zonal tillage + chisel: + text: chisel + tined: + text: tined + mouldboard: + text: mouldboard + disc plough: + text: disc plough + window_type_enum: + name: window_type_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + single-hung sash window: + text: single-hung sash window + horizontal sash window: + text: horizontal sash window + fixed window: + text: fixed window + ceil_cond_enum: + name: ceil_cond_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture + hcr_geol_age_enum: + name: hcr_geol_age_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - north corner: - text: north corner - south corner: - text: south corner - west corner: - text: west corner - east corner: - text: east corner - northeast corner: - text: northeast corner - northwest corner: - text: northwest corner - southeast corner: - text: southeast corner - southwest corner: - text: southwest corner - center: - text: center - indoor_surf_enum: - name: indoor_surf_enum + Archean: + text: Archean + Cambrian: + text: Cambrian + Carboniferous: + text: Carboniferous + Cenozoic: + text: Cenozoic + Cretaceous: + text: Cretaceous + Devonian: + text: Devonian + Jurassic: + text: Jurassic + Mesozoic: + text: Mesozoic + Neogene: + text: Neogene + Ordovician: + text: Ordovician + Paleogene: + text: Paleogene + Paleozoic: + text: Paleozoic + Permian: + text: Permian + Precambrian: + text: Precambrian + Proterozoic: + text: Proterozoic + Silurian: + text: Silurian + Triassic: + text: Triassic + other: + text: other + door_cond_enum: + name: door_cond_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - cabinet: - text: cabinet - ceiling: - text: ceiling - counter top: - text: counter top - door: - text: door - shelving: - text: shelving - vent cover: - text: vent cover - window: - text: window - wall: - text: wall - organism_count_enum: - name: organism_count_enum + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + lithology_enum: + name: lithology_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - ATP: - text: ATP - MPN: - text: MPN + Basement: + text: Basement + Chalk: + text: Chalk + Chert: + text: Chert + Coal: + text: Coal + Conglomerate: + text: Conglomerate + Diatomite: + text: Diatomite + Dolomite: + text: Dolomite + Limestone: + text: Limestone + Sandstone: + text: Sandstone + Shale: + text: Shale + Siltstone: + text: Siltstone + Volcanic: + text: Volcanic other: text: other - vis_media_enum: - name: vis_media_enum + heat_cool_type_enum: + name: heat_cool_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - photos: - text: photos - videos: - text: videos - commonly of the building: - text: commonly of the building - site context (adjacent buildings, vegetation, terrain, streets): - text: site context (adjacent buildings, vegetation, terrain, streets) - interiors: - text: interiors - equipment: - text: equipment - 3D scans: - text: 3D scans + radiant system: + text: radiant system + heat pump: + text: heat pump + forced air system: + text: forced air system + steam forced heat: + text: steam forced heat + wood stove: + text: wood stove + building_setting_enum: + name: building_setting_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + urban: + text: urban + suburban: + text: suburban + exurban: + text: exurban + rural: + text: rural room_condt_enum: name: room_condt_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml @@ -2779,40 +2781,34 @@ enums: text: rupture visible signs of mold/mildew: text: visible signs of mold/mildew - samp_collect_point_enum: - name: samp_collect_point_enum + rel_samp_loc_enum: + name: rel_samp_loc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - well: - text: well - test well: - text: test well - drilling rig: - text: drilling rig - wellhead: - text: wellhead - separator: - text: separator - storage tank: - text: storage tank - other: - text: other - samp_capt_status_enum: - name: samp_capt_status_enum + edge of car: + text: edge of car + center of car: + text: center of car + under a seat: + text: under a seat + wall_surf_treatment_enum: + name: wall_surf_treatment_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - active surveillance in response to an outbreak: - text: active surveillance in response to an outbreak - active surveillance not initiated by an outbreak: - text: active surveillance not initiated by an outbreak - farm sample: - text: farm sample - market sample: - text: market sample - other: - text: other - room_type_enum: - name: room_type_enum + painted: + text: painted + wall paper: + text: wall paper + no treatment: + text: no treatment + paneling: + text: paneling + stucco: + text: stucco + fabric: + text: fabric + room_connected_enum: + name: room_connected_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: attic: @@ -2829,102 +2825,130 @@ enums: text: examining room hallway: text: hallway - kitchen: - text: kitchen - mail room: - text: mail room - private office: - text: private office - open office: - text: open office - stairwell: - text: stairwell - ',restroom': - text: ',restroom' - lobby: - text: lobby - vestibule: - text: vestibule - mechanical or electrical room: - text: mechanical or electrical room - data center: - text: data center - laboratory_wet: - text: laboratory_wet - laboratory_dry: - text: laboratory_dry - gymnasium: - text: gymnasium - natatorium: - text: natatorium - auditorium: - text: auditorium - lockers: - text: lockers - cafe: - text: cafe - warehouse: - text: warehouse - samp_dis_stage_enum: - name: samp_dis_stage_enum + kitchen: + text: kitchen + mail room: + text: mail room + office: + text: office + stairwell: + text: stairwell + window_vert_pos_enum: + name: window_vert_pos_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - dissemination: - text: dissemination - growth and reproduction: - text: growth and reproduction - infection: - text: infection - inoculation: - text: inoculation - penetration: - text: penetration - other: - text: other - floor_cond_enum: - name: floor_cond_enum + bottom: + text: bottom + middle: + text: middle + top: + text: top + low: + text: low + high: + text: high + weekday_enum: + name: weekday_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - lithology_enum: - name: lithology_enum + Monday: + text: Monday + Tuesday: + text: Tuesday + Wednesday: + text: Wednesday + Thursday: + text: Thursday + Friday: + text: Friday + Saturday: + text: Saturday + Sunday: + text: Sunday + room_samp_pos_enum: + name: room_samp_pos_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - Basement: - text: Basement - Chalk: - text: Chalk - Chert: - text: Chert - Coal: - text: Coal - Conglomerate: - text: Conglomerate - Diatomite: - text: Diatomite - Dolomite: - text: Dolomite - Limestone: - text: Limestone - Sandstone: - text: Sandstone - Shale: - text: Shale - Siltstone: - text: Siltstone - Volcanic: - text: Volcanic - other: - text: other + north corner: + text: north corner + south corner: + text: south corner + west corner: + text: west corner + east corner: + text: east corner + northeast corner: + text: northeast corner + northwest corner: + text: northwest corner + southeast corner: + text: southeast corner + southwest corner: + text: southwest corner + center: + text: center + door_mat_enum: + name: door_mat_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + aluminum: + text: aluminum + cellular PVC: + text: cellular PVC + engineered plastic: + text: engineered plastic + fiberboard: + text: fiberboard + fiberglass: + text: fiberglass + metal: + text: metal + thermoplastic alloy: + text: thermoplastic alloy + vinyl: + text: vinyl + wood: + text: wood + wood/plastic composite: + text: wood/plastic composite + biol_stat_enum: + name: biol_stat_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + wild: + text: wild + natural: + text: natural + semi-natural: + text: semi-natural + inbred line: + text: inbred line + breeder's line: + text: breeder's line + hybrid: + text: hybrid + clonal selection: + text: clonal selection + mutant: + text: mutant + floor_struc_enum: + name: floor_struc_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + balcony: + text: balcony + floating floor: + text: floating floor + glass floor: + text: glass floor + raised floor: + text: raised floor + sprung floor: + text: sprung floor + wood-framed: + text: wood-framed + concrete: + text: concrete door_type_wood_enum: name: door_type_wood_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml @@ -2949,128 +2973,88 @@ enums: text: louvered wire gauged: text: wire gauged - wall_finish_mat_enum: - name: wall_finish_mat_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - plaster: - text: plaster - gypsum plaster: - text: gypsum plaster - veneer plaster: - text: veneer plaster - gypsum board: - text: gypsum board - tile: - text: tile - terrazzo: - text: terrazzo - stone facing: - text: stone facing - acoustical treatment: - text: acoustical treatment - wood: - text: wood - metal: - text: metal - masonry: - text: masonry - gender_restroom_enum: - name: gender_restroom_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - all gender: - text: all gender - female: - text: female - gender neurtral: - text: gender neurtral - male: - text: male - male and female: - text: male and female - unisex: - text: unisex - int_wall_cond_enum: - name: int_wall_cond_enum - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - floor_water_mold_enum: - name: floor_water_mold_enum + organism_count_enum: + name: organism_count_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - mold odor: - text: mold odor - wet floor: - text: wet floor - water stains: - text: water stains - wall discoloration: - text: wall discoloration - floor discoloration: - text: floor discoloration - ceiling discoloration: - text: ceiling discoloration - peeling paint or wallpaper: - text: peeling paint or wallpaper - bulging walls: - text: bulging walls - condensation: - text: condensation - samp_floor_enum: - name: samp_floor_enum + ATP: + text: ATP + MPN: + text: MPN + other: + text: other + shading_device_cond_enum: + name: shading_device_cond_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - 1st floor: - text: 1st floor - 2nd floor: - text: 2nd floor - basement: - text: basement - lobby: - text: lobby - heat_deliv_loc_enum: - name: heat_deliv_loc_enum + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + hcr_enum: + name: hcr_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - biol_stat_enum: - name: biol_stat_enum + Oil Reservoir: + text: Oil Reservoir + Gas Reservoir: + text: Gas Reservoir + Oil Sand: + text: Oil Sand + Coalbed: + text: Coalbed + Shale: + text: Shale + Tight Oil Reservoir: + text: Tight Oil Reservoir + Tight Gas Reservoir: + text: Tight Gas Reservoir + other: + text: other + mech_struc_enum: + name: mech_struc_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - wild: - text: wild - natural: - text: natural - semi-natural: - text: semi-natural - inbred line: - text: inbred line - breeder's line: - text: breeder's line - hybrid: - text: hybrid - clonal selection: - text: clonal selection - mutant: - text: mutant + subway: + text: subway + coach: + text: coach + carriage: + text: carriage + elevator: + text: elevator + escalator: + text: escalator + boat: + text: boat + train: + text: train + car: + text: car + bus: + text: bus + hc_produced_enum: + name: hc_produced_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + Oil: + text: Oil + Gas-Condensate: + text: Gas-Condensate + Gas: + text: Gas + Bitumen: + text: Bitumen + Coalbed Methane: + text: Coalbed Methane + other: + text: other shading_device_type_enum: name: shading_device_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml @@ -3099,148 +3083,250 @@ enums: text: trellis venetian awning: text: venetian awning - train_stat_loc_enum: - name: train_stat_loc_enum + quad_pos_enum: + name: quad_pos_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - south station above ground: - text: south station above ground - south station underground: - text: south station underground - south station amtrak: - text: south station amtrak - forest hills: - text: forest hills - riverside: - text: riverside - window_mat_enum: - name: window_mat_enum + North side: + text: North side + West side: + text: West side + South side: + text: South side + East side: + text: East side + sr_kerog_type_enum: + name: sr_kerog_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - clad: - text: clad - fiberglass: - text: fiberglass - metal: - text: metal - vinyl: - text: vinyl - wood: - text: wood - samp_weather_enum: - name: samp_weather_enum + Type I: + text: Type I + Type II: + text: Type II + Type III: + text: Type III + Type IV: + text: Type IV + other: + text: other + floor_cond_enum: + name: floor_cond_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture + heat_deliv_loc_enum: + name: heat_deliv_loc_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + north: + text: north + south: + text: south + east: + text: east + west: + text: west + host_sex_enum: + name: host_sex_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + female: + text: female + hermaphrodite: + text: hermaphrodite + male: + text: male + neuter: + text: neuter + window_cond_enum: + name: window_cond_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + handidness_enum: + name: handidness_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + ambidexterity: + text: ambidexterity + left handedness: + text: left handedness + mixed-handedness: + text: mixed-handedness + right handedness: + text: right handedness + wall_const_type_enum: + name: wall_const_type_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + frame construction: + text: frame construction + joisted masonry: + text: joisted masonry + light noncombustible: + text: light noncombustible + masonry noncombustible: + text: masonry noncombustible + modified fire resistive: + text: modified fire resistive + fire resistive: + text: fire resistive + build_occup_type_enum: + name: build_occup_type_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + office: + text: office + market: + text: market + restaurant: + text: restaurant + residence: + text: residence + school: + text: school + residential: + text: residential + commercial: + text: commercial + low rise: + text: low rise + high rise: + text: high rise + wood framed: + text: wood framed + health care: + text: health care + airport: + text: airport + sports complex: + text: sports complex + oxy_stat_samp_enum: + name: oxy_stat_samp_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - clear sky: - text: clear sky - cloudy: - text: cloudy - foggy: - text: foggy - hail: - text: hail - rain: - text: rain - snow: - text: snow - sleet: - text: sleet - sunny: - text: sunny - windy: - text: windy - biotic_relationship_enum: - name: biotic_relationship_enum + aerobic: + text: aerobic + anaerobic: + text: anaerobic + other: + text: other + filter_type_enum: + name: filter_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - free living: - text: free living - parasite: - text: parasite - commensal: - text: commensal - symbiont: - text: symbiont - door_cond_enum: - name: door_cond_enum + particulate air filter: + text: particulate air filter + chemical air filter: + text: chemical air filter + low-MERV pleated media: + text: low-MERV pleated media + HEPA: + text: HEPA + electrostatic: + text: electrostatic + gas-phase or ultraviolet air treatments: + text: gas-phase or ultraviolet air treatments + samp_floor_enum: + name: samp_floor_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear - train_line_enum: - name: train_line_enum + 1st floor: + text: 1st floor + 2nd floor: + text: 2nd floor + basement: + text: basement + lobby: + text: lobby + furniture_enum: + name: furniture_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - red: - text: red - green: - text: green - orange: - text: orange - build_docs_enum: - name: build_docs_enum + cabinet: + text: cabinet + chair: + text: chair + desks: + text: desks + samp_dis_stage_enum: + name: samp_dis_stage_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - building information model: - text: building information model - commissioning report: - text: commissioning report - complaint logs: - text: complaint logs - contract administration: - text: contract administration - cost estimate: - text: cost estimate - janitorial schedules or logs: - text: janitorial schedules or logs - maintenance plans: - text: maintenance plans - schedule: - text: schedule - sections: - text: sections - shop drawings: - text: shop drawings - submittals: - text: submittals - ventilation system: - text: ventilation system - windows: - text: windows - door_loc_enum: - name: door_loc_enum + dissemination: + text: dissemination + growth and reproduction: + text: growth and reproduction + infection: + text: infection + inoculation: + text: inoculation + penetration: + text: penetration + other: + text: other + substructure_type_enum: + name: substructure_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - sr_kerog_type_enum: - name: sr_kerog_type_enum + crawlspace: + text: crawlspace + slab on grade: + text: slab on grade + basement: + text: basement + door_comp_type_enum: + name: door_comp_type_enum from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml permissible_values: - Type I: - text: Type I - Type II: - text: Type II - Type III: - text: Type III - Type IV: - text: Type IV - other: - text: other + metal covered: + text: metal covered + revolving: + text: revolving + sliding: + text: sliding + telescopic: + text: telescopic + plant_growth_med_enum: + name: plant_growth_med_enum + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + permissible_values: + other artificial liquid medium: + text: other artificial liquid medium + other artificial solid medium: + text: other artificial solid medium + peat moss: + text: peat moss + perlite: + text: perlite + pumice: + text: pumice + sand: + text: sand + soil: + text: soil + vermiculite: + text: vermiculite + water: + text: water slots: metagenome_annotation_id: name: metagenome_annotation_id @@ -5531,8 +5617,6 @@ slots: examples: - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:collection_date rank: 2 string_serialization: '{date, arbitrary precision}' slot_group: MIxS Inspired @@ -5549,8 +5633,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:collection_date rank: 1 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -5568,8 +5650,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:collection_date rank: 3 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -5587,8 +5667,6 @@ slots: examples: - value: 'experimental treatment: value' from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:experimental_factor|additional_info rank: 7 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5603,8 +5681,6 @@ slots: - value: C18 - value: Basix PES, 13-100-106 FisherSci from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:filter_type rank: 6 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5622,8 +5698,6 @@ slots: - value: 13C glucose - value: H218O from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:chem_administration rank: 16 string_serialization: '{termLabel} {[termID]}; {timestamp}' slot_group: MIxS Inspired @@ -5640,8 +5714,6 @@ slots: - value: https://doi.org/10.1016/0038-0717(87)90052-6 - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:micro_biomass_meth rank: 11 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5656,8 +5728,6 @@ slots: - value: https://doi.org/10.1016/0038-0717(87)90052-6 - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:micro_biomass_meth rank: 13 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5672,8 +5742,6 @@ slots: examples: - value: 0.05 ug C/g dry soil from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:microbial_biomass rank: 10 string_serialization: '{float} {unit}' slot_group: MIxS Inspired @@ -5688,8 +5756,6 @@ slots: examples: - value: 0.05 ug N/g dry soil from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:microbial_biomass rank: 12 string_serialization: '{float} {unit}' slot_group: MIxS Inspired @@ -5702,8 +5768,6 @@ slots: examples: - value: insect 0.23 ug; plant 1g from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:biomass|microbial_biomass rank: 8 string_serialization: '{text};{float} {unit}' slot_group: MIxS Inspired @@ -5716,8 +5780,6 @@ slots: examples: - value: https://doi.org/10.1038/s41467-021-26181-3 from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:microbial_biomass rank: 9 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5730,8 +5792,6 @@ slots: examples: - value: https://doi.org/10.1016/0038-0717(85)90144-0 from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:org_nitro|tot_nitro_cont_meth rank: 14 string_serialization: '{PMID}|{DOI}|{URL}' slot_group: MIxS Inspired @@ -5744,8 +5804,6 @@ slots: - This is an open text field to provide any treatments that cannot be captured in the provided slots. from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:additional_info rank: 15 string_serialization: '{text}' slot_group: MIxS Inspired @@ -5763,8 +5821,6 @@ slots: examples: - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:collection_date rank: 4 string_serialization: '{date, arbitrary precision}' slot_group: MIxS Inspired @@ -5781,8 +5837,6 @@ slots: examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/portal/mixs_inspired - see_also: - - MIxS:collection_date rank: 5 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired @@ -17361,19 +17415,28 @@ slots: slot_uri: MIXS:0000156 multivalued: false range: QuantityValue - investigation field: - name: investigation field - description: field describing aspect of the investigation/study to which the sample - belongs + has unit: + name: has unit + description: Example "m" + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + owner: QuantityValue + sequencing field: + name: sequencing field from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml abstract: true + has raw value: + name: has raw value + from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml + string_serialization: '{has numeric value} {has unit}' + owner: QuantityValue core field: name: core field description: basic fields from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml abstract: true - nucleic acid sequence source field: - name: nucleic acid sequence source field + environment field: + name: environment field + description: field describing environmental aspect of a sample from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml abstract: true has numeric value: @@ -17381,25 +17444,16 @@ slots: from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml owner: QuantityValue range: double - environment field: - name: environment field - description: field describing environmental aspect of a sample + nucleic acid sequence source field: + name: nucleic acid sequence source field from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml abstract: true - has unit: - name: has unit - description: Example "m" - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - owner: QuantityValue - sequencing field: - name: sequencing field + investigation field: + name: investigation field + description: field describing aspect of the investigation/study to which the sample + belongs from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml abstract: true - has raw value: - name: has raw value - from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml - string_serialization: '{has numeric value} {has unit}' - owner: QuantityValue chemical: name: chemical description: from reaction participant class @@ -18479,10 +18533,9 @@ classes: Matches the entity that has been submitted to NMDC lat_lon: name: lat_lon - description: This is currently a required field but it's not clear if this - should be required for human hosts - notes: - - required where? + todos: + - This is currently a required field but it's not clear if this should be + required for human hosts env_broad_scale: name: env_broad_scale required: true @@ -19417,7 +19470,6 @@ classes: used: name: used description: The instrument used to collect the data used in the analysis - range: Instrument id: name: id required: true diff --git a/project/owl/nmdc.owl.ttl b/project/owl/nmdc.owl.ttl index 132cae8421..29eb20dc66 100644 --- a/project/owl/nmdc.owl.ttl +++ b/project/owl/nmdc.owl.ttl @@ -1,7 +1,6 @@ @prefix CHEBI: . @prefix EFO: . @prefix FBcv: . -@prefix IAO: . @prefix ISA: . @prefix MS: . @prefix NCIT: . @@ -10,13033 +9,13173 @@ @prefix linkml: . @prefix nmdc: . @prefix owl: . +@prefix pav: . @prefix prov: . @prefix rdf: . @prefix rdfs: . +@prefix sh: . @prefix skos: . @prefix xsd: . -linkml:SubsetDefinition a owl:Class . - -nmdc:AnalyticalSample a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnalyticalSample" ; - dcterms:title "Analytical Sample" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - nmdc:MaterialEntity . - -nmdc:BooleanValue a owl:Class, - linkml:ClassDefinition ; - rdfs:label "BooleanValue" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty nmdc:has_boolean_value ], - nmdc:AttributeValue ; - skos:definition "A value that is a boolean" . - -nmdc:EnvironmentalMaterialTerm a owl:Class, - linkml:ClassDefinition ; - rdfs:label "EnvironmentalMaterialTerm" ; - rdfs:subClassOf nmdc:OntologyClass . - -nmdc:IntegerValue a owl:Class, - linkml:ClassDefinition ; - rdfs:label "IntegerValue" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:has_numeric_value ], - nmdc:AttributeValue ; - skos:definition "A value that is an integer" . - -nmdc:MetatranscriptomeAnnotationActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MetatranscriptomeAnnotationActivity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; - owl:onProperty nmdc:gold_analysis_project_identifiers ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - nmdc:WorkflowExecutionActivity . - -nmdc:MetatranscriptomeAssembly a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MetatranscriptomeAssembly" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:ctg_n90 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:gc_std ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:gc_avg ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:ctg_max ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:ctg_n50 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_n_gt50k ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:ctg_logsum ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_logsum ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaffolds ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_l90 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:asm_score ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_n50 ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:contig_bp ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:gap_pct ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:num_input_reads ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:insdc_assembly_identifiers ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:contigs ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:num_aligned_reads ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_max ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:ctg_powsum ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_powsum ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_bp ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:ctg_l90 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_l50 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_pct_gt50k ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:ctg_l50 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_l_gt50k ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_n90 ], - nmdc:WorkflowExecutionActivity . - -nmdc:OrthologyGroup a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OrthologyGroup" ; - rdfs:subClassOf nmdc:FunctionalAnnotationTerm ; - skos:definition "A set of genes or gene products in which all members are orthologous" ; - skos:exactMatch . - -nmdc:Pathway a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Pathway" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:Reaction ; - owl:onProperty nmdc:has_part ], - nmdc:FunctionalAnnotationTerm ; - skos:altLabel "biological process", - "metabolic pathway", - "signaling pathway" ; - skos:definition "A pathway is a sequence of steps/reactions carried out by an organism or community of organisms" ; - skos:exactMatch . - -nmdc:UrlValue a owl:Class, - linkml:ClassDefinition ; - rdfs:label "UrlValue" ; - rdfs:subClassOf nmdc:AttributeValue ; - skos:definition "A value that is a string that conforms to URL syntax" . - -nmdc:alternate_emails a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "alternate_emails" ; - rdfs:range linkml:String ; - skos:definition "One or more other email addresses for an entity." . - -nmdc:biogas_retention_time a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "biogas_retention_time" ; - rdfs:range linkml:String . + rdfs:label "abs_air_humidity" ; + dcterms:title "absolute air humidity" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "absolute air humidity" ; + skos:definition "Actual mass of water vapor - mh20 - present in the air water vapor mixture" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "gram per gram, kilogram per kilogram, kilogram, pound" . -nmdc:biogas_temperature a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "biogas_temperature" ; - rdfs:range linkml:String . + rdfs:label "add_recov_method" ; + dcterms:title "secondary and tertiary recovery methods and start date" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "secondary and tertiary recovery methods and start date" ; + skos:definition "Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field" ; + skos:inScheme ; + nmdc:expected_value "enumeration;timestamp" ; + nmdc:occurrence "1" . -nmdc:canary a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "canary" ; - rdfs:range linkml:String ; - skos:definition "a slot that can be added and removed as evidence that schema changes have propagated to other systems" . + rdfs:label "additional_info" ; + dcterms:title "additional info" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "additional info" ; + skos:definition "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary" ; + skos:inScheme ; + nmdc:expected_value "text" ; + nmdc:occurrence "1" . -nmdc:completion_date a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "completion_date" ; - rdfs:range linkml:String . + rdfs:label "address" ; + dcterms:title "address" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "address" ; + skos:definition "The street name and building number where the sampling occurred." ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" . -nmdc:ecosystem_path_id a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ecosystem_path_id" ; - rdfs:range linkml:String ; - skos:definition "A unique id representing the GOLD classifiers associated with a sample." . + rdfs:label "adj_room" ; + dcterms:title "adjacent rooms" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "adjacent rooms" ; + skos:definition "List of rooms (room number, room name) immediately adjacent to the sampling room" ; + skos:inScheme ; + nmdc:expected_value "room name;room number" ; + nmdc:occurrence "1" . -nmdc:emsl_store_temp a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "emsl_store_temp" ; - dcterms:title "EMSL sample storage temperature, deg. C" ; - rdfs:range linkml:String ; - skos:definition "The temperature at which the sample should be stored upon delivery to EMSL" . + rdfs:label "aero_struc" ; + dcterms:title "aerospace structure" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "aerospace structure" ; + skos:definition "Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:insdc_analysis_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "insdc_analysis_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:analysis_identifiers, - nmdc:insdc_identifiers . + rdfs:label "agrochem_addition" ; + dcterms:title "history/agrochemical additions" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "history/agrochemical additions" ; + skos:definition "Addition of fertilizers, pesticides, etc. - amount and time of applications" ; + skos:inScheme ; + nmdc:expected_value "agrochemical name;agrochemical amount;timestamp" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram, mole per liter, milligram per liter" . -nmdc:insdc_secondary_sample_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "insdc_secondary_sample_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:biosample_identifiers, - nmdc:insdc_identifiers ; - skos:definition "secondary identifiers for corresponding sample in INSDC" . + rdfs:label "air_PM_concen" ; + dcterms:title "air particulate matter concentration" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "air particulate matter concentration" ; + skos:definition "Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM" ; + skos:inScheme ; + nmdc:expected_value "particulate matter name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "micrograms per cubic meter" . -nmdc:insdc_sra_ena_study_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "insdc_sra_ena_study_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:insdc_identifiers, - nmdc:study_identifiers ; - skos:altLabel "DDBJ SRA identifiers", - "EBI ENA study identifiers", - "NCBI SRA identifiers" ; - skos:definition "identifiers for corresponding project in INSDC SRA / ENA" . + rdfs:label "air_temp" ; + dcterms:title "air temperature" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "air temperature" ; + skos:definition "Temperature of the air at the time of sampling" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "degree Celsius" . -nmdc:keywords a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "keywords" ; - rdfs:range linkml:String ; - skos:definition "A list of keywords that used to associate the entity. Keywords SHOULD come from controlled vocabularies, including MESH, ENVO." ; - skos:exactMatch dcterms:subject . + 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" . -nmdc:mgnify_analysis_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "mgnify_analysis_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:analysis_identifiers, - nmdc:mgnify_identifiers . + 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" . -nmdc:neon_deims_sdr_link a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "neon_deims_sdr_link" ; - rdfs:range linkml:String . + 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" . -nmdc:neon_eco_type a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "neon_eco_type" ; - rdfs:range linkml:String . + rdfs:label "alkalinity" ; + dcterms:title "alkalinity" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "alkalinity" ; + skos:definition "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milliequivalent per liter, milligram per liter" . -nmdc:neon_soil_type a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "neon_soil_type" ; - rdfs:range linkml:String . - -nmdc:nmdc a owl:Ontology ; - rdfs:label "NMDC" ; - IAO:0000700 nmdc:Activity, - nmdc:AttributeValue, - nmdc:CreditAssociation, - nmdc:Database, - nmdc:DissolvingActivity, - nmdc:FunctionalAnnotation, - nmdc:FunctionalAnnotationAggMember, - nmdc:GenomeFeature, - nmdc:LabDevice, - nmdc:MagBin, - nmdc:MaterialContainer, - nmdc:MaterialSamplingActivity, - nmdc:MetaboliteQuantification, - nmdc:NamedThing, - nmdc:PeptideQuantification, - nmdc:ProteinQuantification, - nmdc:Protocol, - nmdc:QualityControlReport, - nmdc:ReactionActivity, - nmdc:ReactionParticipant ; - linkml:id "https://w3id.org/nmdc/nmdc" ; - linkml:imports "annotation", - "basic_slots", - "core", - "external_identifiers", - "linkml:types", - "mixs", - "portal/emsl", - "portal/jgi_metagenomics", - "portal/jgi_metatranscriptomics", - "portal/mixs_inspired", - "portal/sample_id", - "prov", - "sample_prep", - "workflow_execution_activity" . + rdfs:label "alkalinity_method" ; + dcterms:title "alkalinity method" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "alkalinity method" ; + skos:definition "Method used for alkalinity measurement" ; + skos:inScheme ; + nmdc:expected_value "description of method" ; + nmdc:occurrence "1" . -nmdc:sample_collection_day a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sample_collection_day" ; - rdfs:range linkml:Integer . + rdfs:label "alkyl_diethers" ; + dcterms:title "alkyl diethers" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "alkyl diethers" ; + skos:definition "Concentration of alkyl diethers" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "mole per liter" . -nmdc:sample_collection_hour a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sample_collection_hour" ; - rdfs:range linkml:Integer . + rdfs:label "alt" ; + dcterms:title "altitude" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "altitude" ; + skos:definition "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air" ; + skos:inScheme ; + nmdc:expected_value "measurement value" . -nmdc:sample_collection_minute a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sample_collection_minute" ; - rdfs:range linkml:Integer . + rdfs:label "aminopept_act" ; + dcterms:title "aminopeptidase activity" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "aminopeptidase activity" ; + skos:definition "Measurement of aminopeptidase activity" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "mole per liter per hour" . -nmdc:sample_collection_month a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sample_collection_month" ; - rdfs:range linkml:String . + rdfs:label "ammonium" ; + dcterms:title "ammonium" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "ammonium" ; + skos:definition "Concentration of ammonium in the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . -nmdc:sample_collection_year a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sample_collection_year" ; - rdfs:range linkml:Integer . + rdfs:label "amount_light" ; + dcterms:title "amount of light" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "amount of light" ; + skos:definition "The unit of illuminance and luminous emittance, measuring luminous flux per unit area" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "lux, lumens per square meter" . -nmdc:soil_annual_season_temp a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "soil_annual_season_temp" ; - rdfs:range linkml:String . + rdfs:label "ances_data" ; + 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:inScheme ; + nmdc:expected_value "free text" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "has numeric value" ; - rdfs:range linkml:Double . + 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, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "has raw value" ; - rdfs:range linkml:String . + rdfs:label "annual_temp" ; + dcterms:title "mean annual temperature" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "mean annual temperature" ; + skos:definition "Mean annual temperature" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "degree Celsius" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "has unit" ; - rdfs:range linkml:String ; - skos:definition "Example \"m\"" . + rdfs:label "antibiotic_regm" ; + dcterms:title "antibiotic regimen" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "antibiotic regimen" ; + skos:definition "Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens" ; + skos:inScheme ; + nmdc:expected_value "antibiotic name;antibiotic amount;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "milligram" . -nmdc:Instrument a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Instrument" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - nmdc:NamedThing ; - skos:altLabel "device" ; - skos:definition "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI]." ; - skos:exactMatch . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "api" ; + dcterms:title "API gravity" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "API gravity" ; + skos:definition "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API)" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "degrees API" . -nmdc:ProteinQuantification a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ProteinQuantification" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:protein_sum_masic_abundance ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:GeneProduct ; - owl:onProperty nmdc:best_protein ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:peptide_sequence_count ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:GeneProduct ; - owl:onProperty nmdc:all_proteins ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:protein_spectral_count ] ; - skos:definition "This is used to link a metaproteomics analysis workflow to a specific protein" . + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "arch_struc" ; + dcterms:title "architectural structure" ; + rdfs:range nmdc:ArchStrucEnum ; + rdfs:subPropertyOf ; + skos:altLabel "architectural structure" ; + skos:definition "An architectural structure is a human-made, free-standing, immobile outdoor construction" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:activity_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "activity_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:WorkflowExecutionActivity ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of workflow activities." . + rdfs:label "aromatics_pc" ; + dcterms:title "aromatics wt%" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "aromatics wt%" ; + skos:definition "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" ; + skos:inScheme ; + nmdc:expected_value "name;measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "percent" . -nmdc:activity_speed a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "activity_speed" ; - dcterms:title "activity speed" ; - rdfs:range nmdc:QuantityValue ; - skos:altLabel "shake_speed" . + rdfs:label "asphaltenes_pc" ; + dcterms:title "asphaltenes wt%" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "asphaltenes wt%" ; + skos:definition "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" ; + skos:inScheme ; + nmdc:expected_value "name;measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "percent" . -nmdc:activity_temperature a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "activity_temperature" ; - rdfs:range nmdc:QuantityValue . + rdfs:label "atmospheric_data" ; + dcterms:title "atmospheric data" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "atmospheric data" ; + skos:definition "Measurement of atmospheric data; can include multiple data" ; + skos:inScheme ; + nmdc:expected_value "atmospheric data name;measurement value" ; + nmdc:occurrence "m" . -nmdc:activity_time a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "activity_time" ; - dcterms:title "activity time" ; + rdfs:label "avg_dew_point" ; + dcterms:title "average dew point" ; rdfs:range nmdc:QuantityValue ; - skos:altLabel "shake_time" . + rdfs:subPropertyOf ; + skos:altLabel "average dew point" ; + skos:definition "The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "degree Celsius" . -nmdc:alternative_descriptions a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "alternative_descriptions" ; - rdfs:range linkml:String ; - skos:definition "A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific." . + rdfs:label "avg_occup" ; + dcterms:title "average daily occupancy" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "average daily occupancy" ; + skos:definition "Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room." ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" . -nmdc:alternative_names a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "alternative_names" ; - rdfs:range linkml:String ; - skos:definition "A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific." ; - skos:exactMatch dcterms:alternative, - skos:altLabel . + rdfs:label "avg_temp" ; + dcterms:title "average temperature" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "average temperature" ; + skos:definition "The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "degree Celsius" . -nmdc:alternative_titles a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "alternative_titles" ; - rdfs:range linkml:String ; - skos:definition "A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific." ; - skos:exactMatch dcterms:alternative . + rdfs:label "bac_prod" ; + dcterms:title "bacterial production" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "bacterial production" ; + skos:definition "Bacterial production in the water column measured by isotope uptake" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per cubic meter per day" . -nmdc:ammonium_nitrogen a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ammonium_nitrogen" ; - dcterms:title "ammonium nitrogen" ; + rdfs:label "bac_resp" ; + dcterms:title "bacterial respiration" ; rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf nmdc:attribute ; - skos:altLabel "NH4-N", - "ammonium_nitrogen" ; - skos:definition "Concentration of ammonium nitrogen in the sample" ; + rdfs:subPropertyOf ; + skos:altLabel "bacterial respiration" ; + skos:definition "Measurement of bacterial respiration in the water column" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "mg/kg" . + nmdc:preferred_unit "milligram per cubic meter per day, micromole oxygen per liter per hour" . -nmdc:amount_collected a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "amount_collected" ; - dcterms:title "amount collected" ; - rdfs:range nmdc:QuantityValue . + rdfs:label "bacteria_carb_prod" ; + dcterms:title "bacterial carbon production" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "bacterial carbon production" ; + skos:definition "Measurement of bacterial carbon production" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "nanogram per hour" . -nmdc:analysis_type a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "analysis_type" ; - dcterms:title "analysis/data type" ; - rdfs:range nmdc:AnalysisTypeEnum ; - skos:definition "Select all the data types associated or available for this biosample" . + rdfs:label "barometric_press" ; + dcterms:title "barometric pressure" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "barometric pressure" ; + skos:definition "Force per unit area exerted against a surface by the weight of air above that surface" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "millibar" . -nmdc:applies_to_person a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "applies_to_person" ; - rdfs:domain nmdc:CreditAssociation ; - rdfs:range nmdc:PersonValue . + rdfs:label "basin" ; + dcterms:title "basin name" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "basin name" ; + skos:definition "Name of the basin (e.g. Campos)" ; + skos:inScheme ; + nmdc:expected_value "name" ; + nmdc:occurrence "1" . -nmdc:assembly_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "assembly_identifiers" ; - rdfs:range linkml:String . + rdfs:label "bathroom_count" ; + dcterms:title "bathroom count" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "bathroom count" ; + skos:definition "The number of bathrooms in the building" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" . -nmdc:award_dois a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "award_dois" ; - rdfs:range linkml:Uriorcurie ; - rdfs:subPropertyOf nmdc:dois ; - skos:definition "One or more DOIs that links a study, or similar entiry, to information about the funding authority." . + rdfs:label "bedroom_count" ; + dcterms:title "bedroom count" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "bedroom count" ; + skos:definition "The number of bedrooms in the building" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" . -nmdc:bin_name a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "bin_name" ; - rdfs:range linkml:String . + rdfs:label "benzene" ; + dcterms:title "benzene" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "benzene" ; + skos:definition "Concentration of benzene in the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter, parts per million" . -nmdc:bin_quality a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "bin_quality" ; - rdfs:range linkml:String . + rdfs:label "biochem_oxygen_dem" ; + dcterms:title "biochemical oxygen demand" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "biochemical oxygen demand" ; + skos:definition "Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter" . -nmdc:binned_contig_num a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "binned_contig_num" ; - rdfs:range linkml:Integer . + rdfs:label "biocide" ; + dcterms:title "biocide administration" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "biocide administration" ; + skos:definition "List of biocides (commercial name of product and supplier) and date of administration" ; + skos:inScheme ; + nmdc:expected_value "name;name;timestamp" ; + nmdc:occurrence "1" . -nmdc:biosample_categories a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "biosample_categories" ; - dcterms:title "Categories the biosample belongs to" ; - rdfs:range nmdc:BiosampleCategoryEnum . + rdfs:label "biocide_admin_method" ; + dcterms:title "biocide administration method" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "biocide administration method" ; + skos:definition "Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)" ; + skos:inScheme ; + nmdc:expected_value "measurement value;frequency;duration;duration" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter" . -nmdc:biosample_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "biosample_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:Biosample ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of samples within it." . + rdfs:label "biol_stat" ; + dcterms:title "biological status" ; + rdfs:range nmdc:BiolStatEnum ; + rdfs:subPropertyOf ; + skos:altLabel "biological status" ; + skos:definition "The level of genome modification." ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:chemical a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "chemical" ; - rdfs:range nmdc:ChemicalEntity ; - skos:definition "from reaction participant class" . + rdfs:label "biomass" ; + dcterms:title "biomass" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "biomass" ; + skos:definition "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements" ; + skos:inScheme ; + nmdc:expected_value "biomass type;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "ton, kilogram, gram" . -nmdc:chemical_formula a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "chemical_formula" ; - rdfs:range linkml:String ; - skos:definition "A generic grouping for molecular formulae and empirical formulae" . + 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" . -nmdc:collected_from a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "collected_from" ; - rdfs:domain nmdc:Biosample ; - rdfs:range nmdc:FieldResearchSite ; - skos:definition "The Site from which a Biosample was collected" . + 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" . -nmdc:collected_into a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "collected_into" ; - dcterms:title "collected into" ; - rdfs:range nmdc:MaterialContainer . + rdfs:label "bishomohopanol" ; + dcterms:title "bishomohopanol" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "bishomohopanol" ; + skos:definition "Concentration of bishomohopanol" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "microgram per liter, microgram per gram" . -nmdc:collecting_biosamples_from_site_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "collecting_biosamples_from_site_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:CollectingBiosamplesFromSite . + rdfs:label "blood_press_diast" ; + dcterms:title "host blood pressure diastolic" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "host blood pressure diastolic" ; + skos:definition "Resting diastolic blood pressure, measured as mm mercury" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "millimeter mercury" . -nmdc:collection_date_inc a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "collection_date_inc" ; - dcterms:title "incubation collection date" ; - rdfs:range linkml:String ; - skos:definition "Date the incubation was harvested/collected/ended. Only relevant for incubation samples." . + rdfs:label "blood_press_syst" ; + dcterms:title "host blood pressure systolic" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "host blood pressure systolic" ; + skos:definition "Resting systolic blood pressure, measured as mm mercury" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "millimeter mercury" . -nmdc:collection_time a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "collection_time" ; - dcterms:title "collection time, GMT" ; - rdfs:range linkml:String ; - skos:definition "The time of sampling, either as an instance (single point) or interval." . + rdfs:label "bromide" ; + dcterms:title "bromide" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "bromide" ; + skos:definition "Concentration of bromide" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "parts per million" . -nmdc:collection_time_inc a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "collection_time_inc" ; - dcterms:title "incubation collection time, GMT" ; - rdfs:range linkml:String ; - skos:definition "Time the incubation was harvested/collected/ended. Only relevant for incubation samples." . + rdfs:label "build_docs" ; + dcterms:title "design, construction, and operation documents" ; + rdfs:range nmdc:BuildDocsEnum ; + rdfs:subPropertyOf ; + skos:altLabel "design, construction, and operation documents" ; + skos:definition "The building design, construction and operation documents" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:community a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "community" ; - rdfs:range linkml:String . + rdfs:label "build_occup_type" ; + dcterms:title "building occupancy type" ; + rdfs:range nmdc:BuildOccupTypeEnum ; + rdfs:subPropertyOf ; + skos:altLabel "building occupancy type" ; + skos:definition "The primary function for which a building or discrete part of a building is intended to be used" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "m" . -nmdc:completeness a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "completeness" ; - rdfs:range linkml:Float . + rdfs:label "building_setting" ; + dcterms:title "building setting" ; + rdfs:range nmdc:BuildingSettingEnum ; + rdfs:subPropertyOf ; + skos:altLabel "building setting" ; + skos:definition "A location (geography) where a building is set" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:compression_type a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "compression_type" ; - rdfs:range linkml:String ; - skos:definition "If provided, specifies the compression type" . + rdfs:label "built_struc_age" ; + dcterms:title "built structure age" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "built structure age" ; + skos:definition "The age of the built structure since construction" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "year" . -nmdc:container_size a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "container_size" ; - dcterms:title "container size" ; - rdfs:range nmdc:QuantityValue . + rdfs:label "built_struc_set" ; + dcterms:title "built structure setting" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "built structure setting" ; + skos:definition "The characterization of the location of the built structure as high or low human density" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:container_type a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "container_type" ; - dcterms:title "container type" ; - rdfs:range nmdc:ContainerTypeEnum . + rdfs:label "built_struc_type" ; + dcterms:title "built structure type" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "built structure type" ; + skos:definition "A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads" ; + skos:inScheme ; + nmdc:expected_value "free text" ; + nmdc:occurrence "1" . -nmdc:contamination a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "contamination" ; - rdfs:range linkml:Float . + rdfs:label "calcium" ; + dcterms:title "calcium" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "calcium" ; + skos:definition "Concentration of calcium in the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter, micromole per liter, parts per million" . -nmdc:count a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "count" ; - rdfs:range linkml:Integer . + rdfs:label "carb_dioxide" ; + dcterms:title "carbon dioxide" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "carbon dioxide" ; + skos:definition "Carbon dioxide (gas) amount or concentration at the time of sampling" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter, parts per million" . -nmdc:data_object_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "data_object_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:DataObject ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of data objects within it." . + rdfs:label "carb_monoxide" ; + dcterms:title "carbon monoxide" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "carbon monoxide" ; + skos:definition "Carbon monoxide (gas) amount or concentration at the time of sampling" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter, parts per million" . -nmdc:data_object_type a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "data_object_type" ; - rdfs:range nmdc:FileTypeEnum ; - skos:definition "The type of file represented by the data object." . + rdfs:label "carb_nitro_ratio" ; + dcterms:title "carbon/nitrogen ratio" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "carbon/nitrogen ratio" ; + skos:definition "Ratio of amount or concentrations of carbon to nitrogen" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" . -nmdc:dataset_dois a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dataset_dois" ; - rdfs:range linkml:Uriorcurie ; - rdfs:subPropertyOf nmdc:dois ; - skos:definition "One or more DOIs that links a study, or similar entity, to the generated data." . + rdfs:label "ceil_area" ; + dcterms:title "ceiling area" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "ceiling area" ; + skos:definition "The area of the ceiling space within the room" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "square meter" . -nmdc:date_created a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "date_created" ; - rdfs:range linkml:String ; - skos:definition "from database class" . + rdfs:label "ceil_cond" ; + dcterms:title "ceiling condition" ; + rdfs:range nmdc:CeilCondEnum ; + rdfs:subPropertyOf ; + skos:altLabel "ceiling condition" ; + skos:definition "The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:device_type a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "device_type" ; - dcterms:title "device type" ; - rdfs:range nmdc:DeviceTypeEnum ; - skos:altLabel "shaker type" . + rdfs:label "ceil_finish_mat" ; + dcterms:title "ceiling finish material" ; + rdfs:range nmdc:CeilFinishMatEnum ; + rdfs:subPropertyOf ; + skos:altLabel "ceiling finish material" ; + skos:definition "The type of material used to finish a ceiling" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:direction a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "direction" ; - rdfs:range linkml:String ; - skos:definition "One of l->r, r->l, bidirectional, neutral" . + rdfs:label "ceil_struc" ; + dcterms:title "ceiling structure" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "ceiling structure" ; + skos:definition "The construction format of the ceiling" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:display_order a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "display_order" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf nmdc:attribute ; - skos:definition "When rendering information, this attribute to specify the order in which the information should be rendered." . + rdfs:label "ceil_texture" ; + dcterms:title "ceiling texture" ; + rdfs:range nmdc:CeilTextureEnum ; + rdfs:subPropertyOf ; + skos:altLabel "ceiling texture" ; + skos:definition "The feel, appearance, or consistency of a ceiling surface" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:dissolution_aided_by a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dissolution_aided_by" ; - dcterms:title "dissolution aided by" ; - rdfs:range nmdc:LabDevice ; - skos:altLabel "shaker" . + rdfs:label "ceil_thermal_mass" ; + dcterms:title "ceiling thermal mass" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "ceiling thermal mass" ; + skos:definition "The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "joule per degree Celsius" . -nmdc:dissolution_reagent a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dissolution_reagent" ; - dcterms:title "dissolution reagent" ; - rdfs:range nmdc:SolventEnum ; - skos:altLabel "solvent" . + rdfs:label "ceil_type" ; + dcterms:title "ceiling type" ; + rdfs:range nmdc:CeilTypeEnum ; + rdfs:subPropertyOf ; + skos:altLabel "ceiling type" ; + skos:definition "The type of ceiling according to the ceiling's appearance or construction" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:dissolution_volume a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dissolution_volume" ; - dcterms:title "dissolution volume" ; - rdfs:range nmdc:QuantityValue ; - skos:altLabel "volume" . + rdfs:label "ceil_water_mold" ; + dcterms:title "ceiling signs of water/mold" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "ceiling signs of water/mold" ; + skos:definition "Signs of the presence of mold or mildew on the ceiling" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:dissolved_in a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dissolved_in" ; - dcterms:title "dissolved in" ; - rdfs:range nmdc:MaterialContainer ; - skos:altLabel "container" . + rdfs:label "chem_administration" ; + dcterms:title "chemical administration" ; + rdfs:range nmdc:ControlledTermValue ; + rdfs:subPropertyOf ; + skos:altLabel "chemical administration" ; + skos:definition "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi" ; + skos:inScheme ; + nmdc:expected_value "CHEBI;timestamp" ; + nmdc:occurrence "m" . -nmdc:dissolving_activity_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dissolving_activity_set" ; - dcterms:title "dissolving activity set" ; - rdfs:range nmdc:DissolvingActivity . + rdfs:label "chem_mutagen" ; + dcterms:title "chemical mutagen" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "chemical mutagen" ; + skos:definition "Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens" ; + skos:inScheme ; + nmdc:expected_value "mutagen name;mutagen amount;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "milligram per liter" . -nmdc:dna_absorb2 a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dna_absorb2" ; - dcterms:title "DNA absorbance 260/230" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:biomaterial_purity ; - skos:definition "260/230 measurement of DNA sample purity" . + rdfs:label "chem_oxygen_dem" ; + dcterms:title "chemical oxygen demand" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "chemical oxygen demand" ; + skos:definition "A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter" . -nmdc:dna_collect_site a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dna_collect_site" ; - dcterms:title "DNA collection site" ; + rdfs:label "chem_treat_method" ; + dcterms:title "chemical treatment method" ; rdfs:range linkml:String ; - skos:definition "Provide information on the site your DNA sample was collected from" . - -nmdc:dna_cont_type a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "dna_cont_type" ; - dcterms:title "DNA container type" ; - rdfs:range nmdc:JgiContTypeEnum ; - skos:definition "Tube or plate (96-well)" . + rdfs:subPropertyOf ; + skos:altLabel "chemical treatment method" ; + skos:definition "Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)" ; + skos:inScheme ; + nmdc:expected_value "measurement value;frequency;duration;duration" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter" . -nmdc:dna_cont_well a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dna_cont_well" ; - dcterms:title "DNA plate position" ; - rdfs:range linkml:String . + rdfs:label "chem_treatment" ; + dcterms:title "chemical treatment" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "chemical treatment" ; + skos:definition "List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included" ; + skos:inScheme ; + nmdc:expected_value "name;name;timestamp" ; + nmdc:occurrence "1" . -nmdc:dna_container_id a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dna_container_id" ; - dcterms:title "DNA container label" ; - rdfs:range linkml:String . + rdfs:label "chimera_check" ; + dcterms:title "chimera check software" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "chimera check software" ; + skos:definition "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences." ; + skos:inScheme ; + nmdc:expected_value "name and version of software, parameters used" . -nmdc:dna_dnase a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dna_dnase" ; - dcterms:title "DNase treatment DNA" ; - rdfs:range nmdc:YesNoEnum . + rdfs:label "chloride" ; + dcterms:title "chloride" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "chloride" ; + skos:definition "Concentration of chloride in the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter, parts per million" . -nmdc:dna_isolate_meth a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dna_isolate_meth" ; - dcterms:title "DNA isolation method" ; - rdfs:range linkml:String ; - skos:definition "Describe the method/protocol/kit used to extract DNA/RNA." . + rdfs:label "chlorophyll" ; + dcterms:title "chlorophyll" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "chlorophyll" ; + skos:definition "Concentration of chlorophyll" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per cubic meter, microgram per liter" . -nmdc:dna_organisms a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dna_organisms" ; - dcterms:title "DNA expected organisms" ; - rdfs:range linkml:String ; - skos:definition "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture." . + 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" . -nmdc:dna_project_contact a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dna_project_contact" ; - dcterms:title "DNA seq project contact" ; - rdfs:range linkml:String . + rdfs:label "collection_date" ; + dcterms:title "collection date" ; + rdfs:range nmdc:TimestampValue ; + rdfs:subPropertyOf ; + skos:altLabel "collection date" ; + skos:definition "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant" ; + skos:inScheme ; + nmdc:expected_value "date and time" . -nmdc:dna_samp_id a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dna_samp_id" ; - dcterms:title "DNA sample ID" ; - rdfs:range linkml:String . + rdfs:label "conduc" ; + dcterms:title "conductivity" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "conductivity" ; + skos:definition "Electrical conductivity of water" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milliSiemens per centimeter" . -nmdc:dna_sample_format a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dna_sample_format" ; - dcterms:title "DNA sample format" ; - rdfs:range nmdc:DnaSampleFormatEnum ; - skos:definition "Solution in which the DNA sample has been suspended" . - -nmdc:dna_sample_name a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "dna_sample_name" ; - dcterms:title "DNA sample name" ; - rdfs:range linkml:String ; - skos:definition "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only." . - -nmdc:dna_seq_project a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "dna_seq_project" ; - dcterms:title "DNA seq project ID" ; - rdfs:range linkml:String . + rdfs:label "cool_syst_id" ; + dcterms:title "cooling system identifier" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "cooling system identifier" ; + skos:definition "The cooling system identifier" ; + skos:inScheme ; + nmdc:expected_value "unique identifier" ; + nmdc:occurrence "1" . -nmdc:dna_seq_project_name a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dna_seq_project_name" ; - dcterms:title "DNA seq project name" ; - rdfs:range linkml:String . + rdfs:label "crop_rotation" ; + dcterms:title "history/crop rotation" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "history/crop rotation" ; + skos:definition "Whether or not crop is rotated, and if yes, rotation schedule" ; + skos:inScheme ; + nmdc:expected_value "crop rotation status;schedule" ; + nmdc:occurrence "1" . -nmdc:dna_seq_project_pi a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dna_seq_project_pi" ; - dcterms:title "DNA seq project PI" ; - rdfs:range linkml:String . + rdfs:label "cult_root_med" ; + dcterms:title "culture rooting medium" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "culture rooting medium" ; + skos:definition "Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors." ; + skos:inScheme ; + nmdc:expected_value "name, PMID,DOI or url" ; + nmdc:occurrence "1" . -nmdc:dna_volume a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dna_volume" ; - dcterms:title "DNA volume in ul" ; - rdfs:range linkml:Float . + rdfs:label "cur_land_use" ; + dcterms:title "current land use" ; + rdfs:range nmdc:CurLandUseEnum ; + rdfs:subPropertyOf ; + skos:altLabel "current land use" ; + skos:definition "Present state of sample site" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:dnase_rna a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dnase_rna" ; - dcterms:title "DNase treated" ; - rdfs:range nmdc:YesNoEnum . + 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" . -nmdc:embargoed a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "embargoed" ; - rdfs:range linkml:Boolean ; - skos:definition "If true, the data are embargoed and not available for public access." . + 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" . -nmdc:emsl_biosample_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "emsl_biosample_identifiers" ; - dcterms:title "EMSL Biosample Identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:biosample_identifiers, - nmdc:emsl_identifiers ; - skos:definition "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database." . + rdfs:label "date_last_rain" ; + dcterms:title "date last rain" ; + rdfs:range nmdc:TimestampValue ; + rdfs:subPropertyOf ; + skos:altLabel "date last rain" ; + skos:definition "The date of the last time it rained" ; + skos:inScheme ; + nmdc:expected_value "timestamp" ; + nmdc:occurrence "1" . -nmdc:emsl_project_dois a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "emsl_project_dois" ; - dcterms:title "EMSL Project DOI" ; - rdfs:range linkml:Uriorcurie ; - rdfs:subPropertyOf nmdc:dois, - nmdc:emsl_identifiers ; - skos:definition "One or more DOIs that links to an EMSL Research Campaign page." . + rdfs:label "density" ; + dcterms:title "density" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "density" ; + skos:definition "Density of the sample, which is its mass per unit volume (aka volumetric mass density)" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "gram per cubic meter, gram per cubic centimeter" . -nmdc:encodes a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "encodes" ; - rdfs:range nmdc:GeneProduct ; - skos:definition "The gene product encoded by this feature. Typically this is used for a CDS feature or gene feature which will encode a protein. It can also be used by a nc transcript ot gene feature that encoded a ncRNA" . + rdfs:label "depos_env" ; + dcterms:title "depositional environment" ; + rdfs:range nmdc:DeposEnvEnum ; + rdfs:subPropertyOf ; + skos:altLabel "depositional environment" ; + skos:definition "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:end a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "end" ; - rdfs:range linkml:Integer ; - rdfs:subPropertyOf nmdc:gff_coordinate ; - skos:closeMatch ; - skos:definition "The end of the feature in positive 1-based integer coordinates" . + rdfs:label "depth" ; + dcterms:title "depth" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "depth" ; + skos:definition "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples." ; + skos:inScheme ; + nmdc:expected_value "measurement value" . -nmdc:end_date a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "end_date" ; - rdfs:range linkml:String ; - skos:definition "The date on which any process or activity was ended" . + rdfs:label "dew_point" ; + dcterms:title "dew point" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "dew point" ; + skos:definition "The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water." ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "degree Celsius" . -nmdc:env_package a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "env_package" ; + rdfs:label "diether_lipids" ; + dcterms:title "diether lipids" ; rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf nmdc:attribute ; - skos:altLabel "environmental package" ; - skos:definition "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported" . + rdfs:subPropertyOf ; + skos:altLabel "diether lipids" ; + skos:definition "Concentration of diether lipids; can include multiple types of diether lipids" ; + skos:inScheme ; + nmdc:expected_value "diether lipid name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "nanogram per liter" . -nmdc:ess_dive_datasets a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ess_dive_datasets" ; - rdfs:range linkml:String ; - skos:definition "List of ESS-DIVE dataset DOIs" . + rdfs:label "diss_carb_dioxide" ; + dcterms:title "dissolved carbon dioxide" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "dissolved carbon dioxide" ; + skos:definition "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter, milligram per liter" . -nmdc:etl_software_version a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "etl_software_version" ; - rdfs:range linkml:String ; - skos:definition "from database class" . + rdfs:label "diss_hydrogen" ; + dcterms:title "dissolved hydrogen" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "dissolved hydrogen" ; + skos:definition "Concentration of dissolved hydrogen" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter" . -nmdc:execution_resource a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "execution_resource" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf nmdc:attribute . + rdfs:label "diss_inorg_carb" ; + dcterms:title "dissolved inorganic carbon" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "dissolved inorganic carbon" ; + skos:definition "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "microgram per liter, milligram per liter, parts per million" . -nmdc:experimental_factor_other a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "experimental_factor_other" ; - dcterms:title "experimental factor- other" ; - rdfs:range linkml:String ; - skos:definition "Other details about your sample that you feel can't be accurately represented in the available columns." . + rdfs:label "diss_inorg_nitro" ; + dcterms:title "dissolved inorganic nitrogen" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "dissolved inorganic nitrogen" ; + skos:definition "Concentration of dissolved inorganic nitrogen" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "microgram per liter, micromole per liter" . -nmdc:extraction_method a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "extraction_method" ; - rdfs:range linkml:String . + rdfs:label "diss_inorg_phosp" ; + dcterms:title "dissolved inorganic phosphorus" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "dissolved inorganic phosphorus" ; + skos:definition "Concentration of dissolved inorganic phosphorus in the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "microgram per liter, milligram per liter, parts per million" . -nmdc:extraction_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "extraction_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:Extraction ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of extractions within it." . + rdfs:label "diss_iron" ; + dcterms:title "dissolved iron" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "dissolved iron" ; + skos:definition "Concentration of dissolved iron in the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter" . -nmdc:extraction_target a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "extraction_target" ; - rdfs:range nmdc:ExtractionTargetEnum . + rdfs:label "diss_org_carb" ; + dcterms:title "dissolved organic carbon" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "dissolved organic carbon" ; + skos:definition "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter, milligram per liter" . -nmdc:feature_type a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "feature_type" ; - rdfs:range linkml:String ; - skos:definition "TODO: Yuri to write" . + rdfs:label "diss_org_nitro" ; + dcterms:title "dissolved organic nitrogen" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "dissolved organic nitrogen" ; + skos:definition "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "microgram per liter, milligram per liter" . -nmdc:field_research_site_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "field_research_site_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:FieldResearchSite . + rdfs:label "diss_oxygen" ; + dcterms:title "dissolved oxygen" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "dissolved oxygen" ; + skos:definition "Concentration of dissolved oxygen" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per kilogram, milligram per liter" . -nmdc:file_size_bytes a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "file_size_bytes" ; - rdfs:range nmdc:Bytes ; - rdfs:subPropertyOf nmdc:attribute ; - skos:definition "Size of the file in bytes" . + rdfs:label "diss_oxygen_fluid" ; + dcterms:title "dissolved oxygen in fluids" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "dissolved oxygen in fluids" ; + skos:definition "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic)." ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per kilogram, milligram per liter" . -nmdc:filter_method a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "filter_method" ; - dcterms:title "filter method" ; - rdfs:range linkml:String ; - skos:definition "Type of filter used or how the sample was filtered" . + rdfs:label "door_comp_type" ; + dcterms:title "door type, composite" ; + rdfs:range nmdc:DoorCompTypeEnum ; + rdfs:subPropertyOf ; + skos:altLabel "door type, composite" ; + skos:definition "The composite type of the door" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:functional_annotation_agg a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "functional_annotation_agg" ; - rdfs:range nmdc:FunctionalAnnotationAggMember . + rdfs:label "door_cond" ; + dcterms:title "door condition" ; + rdfs:range nmdc:DoorCondEnum ; + rdfs:subPropertyOf ; + skos:altLabel "door condition" ; + skos:definition "The phsical condition of the door" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:functional_annotation_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "functional_annotation_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:FunctionalAnnotation ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of all functional annotations" . + rdfs:label "door_direct" ; + dcterms:title "door direction of opening" ; + rdfs:range nmdc:DoorDirectEnum ; + rdfs:subPropertyOf ; + skos:altLabel "door direction of opening" ; + skos:definition "The direction the door opens" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:funding_sources a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "funding_sources" ; - rdfs:range linkml:String ; - skos:closeMatch NCIT:C39409 ; - skos:definition "A list of organizations, along with the award numbers, that underwrite financial support for projects of a particular type. Typically, they process applications and award funds to the chosen qualified applicants." . + rdfs:label "door_loc" ; + dcterms:title "door location" ; + rdfs:range nmdc:DoorLocEnum ; + rdfs:subPropertyOf ; + skos:altLabel "door location" ; + skos:definition "The relative location of the door in the room" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:gene_count a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gene_count" ; - rdfs:range linkml:Integer . + rdfs:label "door_mat" ; + dcterms:title "door material" ; + rdfs:range nmdc:DoorMatEnum ; + rdfs:subPropertyOf ; + skos:altLabel "door material" ; + skos:definition "The material the door is composed of" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:gene_function_id a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gene_function_id" ; - rdfs:range linkml:Uriorcurie . + rdfs:label "door_move" ; + dcterms:title "door movement" ; + rdfs:range nmdc:DoorMoveEnum ; + rdfs:subPropertyOf ; + skos:altLabel "door movement" ; + skos:definition "The type of movement of the door" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:genome_feature_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "genome_feature_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:GenomeFeature ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of all features" . + rdfs:label "door_size" ; + dcterms:title "door area or size" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "door area or size" ; + skos:definition "The size of the door" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "square meter" . -nmdc:git_url a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "git_url" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf nmdc:attribute . + rdfs:label "door_type" ; + dcterms:title "door type" ; + rdfs:range nmdc:DoorTypeEnum ; + rdfs:subPropertyOf ; + skos:altLabel "door type" ; + skos:definition "The type of door material" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:gnps_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gnps_identifiers" ; - rdfs:range linkml:String . + rdfs:label "door_type_metal" ; + dcterms:title "door type, metal" ; + rdfs:range nmdc:DoorTypeMetalEnum ; + rdfs:subPropertyOf ; + skos:altLabel "door type, metal" ; + skos:definition "The type of metal door" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:gnps_task_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gnps_task_identifiers" ; - dcterms:title "GNPS task identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:gnps_identifiers, - nmdc:study_identifiers ; - skos:definition "identifiers that link a NMDC study to a web-based report about metabolomics analysis progress and results" . + rdfs:label "door_type_wood" ; + dcterms:title "door type, wood" ; + rdfs:range nmdc:DoorTypeWoodEnum ; + rdfs:subPropertyOf ; + skos:altLabel "door type, wood" ; + skos:definition "The type of wood door" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:gold_biosample_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gold_biosample_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:biosample_identifiers, - nmdc:gold_identifiers ; - skos:definition "identifiers for corresponding sample in GOLD" . + rdfs:label "door_water_mold" ; + dcterms:title "door signs of water/mold" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "door signs of water/mold" ; + skos:definition "Signs of the presence of mold or mildew on a door" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:gold_sequencing_project_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gold_sequencing_project_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:gold_identifiers, - nmdc:omics_processing_identifiers ; - skos:definition "identifiers for corresponding sequencing project in GOLD" . + rdfs:label "down_par" ; + dcterms:title "downward PAR" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "downward PAR" ; + skos:definition "Visible waveband radiance and irradiance measurements in the water column" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "microEinstein per square meter per second, microEinstein per square centimeter per second" . -nmdc:gold_study_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gold_study_identifiers" ; - dcterms:title "GOLD Study Identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:gold_identifiers, - nmdc:study_identifiers ; - skos:definition "identifiers for corresponding project(s) in GOLD" . + rdfs:label "drainage_class" ; + dcterms:title "drainage classification" ; + rdfs:range nmdc:DrainageClassEnum ; + rdfs:subPropertyOf ; + skos:altLabel "drainage classification" ; + skos:definition "Drainage classification from a standard system such as the USDA system" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:gtdbtk_class a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gtdbtk_class" ; - rdfs:range linkml:String . + rdfs:label "drawings" ; + dcterms:title "drawings" ; + rdfs:range nmdc:DrawingsEnum ; + rdfs:subPropertyOf ; + skos:altLabel "drawings" ; + skos:definition "The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:gtdbtk_domain a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gtdbtk_domain" ; - rdfs:range linkml:String . + rdfs:label "efficiency_percent" ; + dcterms:title "efficiency percent" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "efficiency percent" ; + skos:definition "Percentage of volatile solids removed from the anaerobic digestor" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter" . -nmdc:gtdbtk_family a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gtdbtk_family" ; - rdfs:range linkml:String . + 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" . -nmdc:gtdbtk_genus a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gtdbtk_genus" ; - rdfs:range linkml:String . + rdfs:label "elevator" ; + dcterms:title "elevator count" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "elevator count" ; + skos:definition "The number of elevators within the built structure" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" . -nmdc:gtdbtk_order a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gtdbtk_order" ; - rdfs:range linkml:String . + rdfs:label "emulsions" ; + dcterms:title "emulsions" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "emulsions" ; + skos:definition "Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types" ; + skos:inScheme ; + nmdc:expected_value "emulsion name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram per liter" . -nmdc:gtdbtk_phylum a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gtdbtk_phylum" ; - rdfs:range linkml:String . + 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." . -nmdc:gtdbtk_species a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gtdbtk_species" ; - rdfs:range linkml:String . + 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." . -nmdc:has_boolean_value a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "has_boolean_value" ; - rdfs:range linkml:Boolean ; - skos:definition "Links a quantity value to a boolean" . + 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]." . -nmdc:has_function a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "has_function" ; - rdfs:range linkml:String . + rdfs:label "escalator" ; + dcterms:title "escalator count" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "escalator count" ; + skos:definition "The number of escalators within the built structure" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" . -nmdc:has_maximum_numeric_value a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "has_maximum_numeric_value" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:has_numeric_value ; - skos:definition "The maximum value part, expressed as number, of the quantity value when the value covers a range." . + rdfs:label "ethylbenzene" ; + dcterms:title "ethylbenzene" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "ethylbenzene" ; + skos:definition "Concentration of ethylbenzene in the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter, parts per million" . -nmdc:has_metabolite_quantifications a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "has_metabolite_quantifications" ; - rdfs:range nmdc:MetaboliteQuantification . + rdfs:label "exp_duct" ; + dcterms:title "exposed ductwork" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "exposed ductwork" ; + skos:definition "The amount of exposed ductwork in the room" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "square meter" . -nmdc:has_minimum_numeric_value a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "has_minimum_numeric_value" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:has_numeric_value ; - skos:definition "The minimum value part, expressed as number, of the quantity value when the value covers a range." . + rdfs:label "exp_pipe" ; + dcterms:title "exposed pipes" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "exposed pipes" ; + skos:definition "The number of exposed pipes in the room" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" . -nmdc:has_part a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "has_part" ; - rdfs:range nmdc:Reaction ; - skos:definition "A pathway can be broken down to a series of reaction step" . + 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" . -nmdc:has_peptide_quantifications a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "has_peptide_quantifications" ; - rdfs:range nmdc:PeptideQuantification . + rdfs:label "ext_door" ; + dcterms:title "exterior door count" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "exterior door count" ; + skos:definition "The number of exterior doors in the built structure" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" . -nmdc:highest_similarity_score a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "highest_similarity_score" ; - rdfs:range linkml:Float . + rdfs:label "ext_wall_orient" ; + dcterms:title "orientations of exterior wall" ; + rdfs:range nmdc:ExtWallOrientEnum ; + rdfs:subPropertyOf ; + skos:altLabel "orientations of exterior wall" ; + skos:definition "The orientation of the exterior wall" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:host_name a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_name" ; - rdfs:range linkml:String . + rdfs:label "ext_window_orient" ; + dcterms:title "orientations of exterior window" ; + rdfs:range nmdc:ExtWindowOrientEnum ; + rdfs:subPropertyOf ; + skos:altLabel "orientations of exterior window" ; + skos:definition "The compass direction the exterior window of the room is facing" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:igsn_biosample_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "igsn_biosample_identifiers" ; - dcterms:title "IGSN Biosample Identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:biosample_identifiers, - nmdc:igsn_identifiers ; - skos:definition "A list of identifiers for the biosample from the IGSN database." . + 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" . -nmdc:igsn_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "igsn_identifiers" ; - rdfs:range linkml:String . + rdfs:label "fao_class" ; + dcterms:title "soil_taxonomic/FAO classification" ; + rdfs:range nmdc:FaoClassEnum ; + rdfs:subPropertyOf ; + skos:altLabel "soil_taxonomic/FAO classification" ; + skos:definition "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:img_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "img_identifiers" ; - dcterms:title "IMG Identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:external_database_identifiers ; - skos:definition "A list of identifiers that relate the biosample to records in the IMG database." . + rdfs:label "fertilizer_regm" ; + dcterms:title "fertilizer regimen" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "fertilizer regimen" ; + skos:definition "Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens" ; + skos:inScheme ; + nmdc:expected_value "fertilizer name;fertilizer amount;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram, mole per liter, milligram per liter" . -nmdc:inchi a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "inchi" ; - rdfs:range linkml:String . + rdfs:label "field" ; + dcterms:title "field name" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "field name" ; + skos:definition "Name of the hydrocarbon field (e.g. Albacora)" ; + skos:inScheme ; + nmdc:expected_value "name" ; + nmdc:occurrence "1" . -nmdc:inchi_key a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "inchi_key" ; - rdfs:range linkml:String . + rdfs:label "filter_type" ; + dcterms:title "filter type" ; + rdfs:range nmdc:FilterTypeEnum ; + rdfs:subPropertyOf ; + skos:altLabel "filter type" ; + skos:definition "A device which removes solid particulates or airborne molecular contaminants" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "m" . -nmdc:input_base_count a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "input_base_count" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:read_qc_analysis_statistic ; - skos:definition "The nucleotide base count number of input reads for QC analysis." . + 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" . -nmdc:input_contig_num a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "input_contig_num" ; - rdfs:range linkml:Integer . + rdfs:label "fireplace_type" ; + dcterms:title "fireplace type" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "fireplace type" ; + skos:definition "A firebox with chimney" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:input_mass a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "input_mass" ; - dcterms:title "sample mass used" ; - rdfs:range nmdc:QuantityValue ; - skos:altLabel "sample mass", - "sample weight" ; - skos:definition "Total mass of sample used in activity." ; - skos:exactMatch MS:1000004 . + 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" . -nmdc:input_read_bases a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "input_read_bases" ; - rdfs:range linkml:Float ; - skos:definition "TODO " . + rdfs:label "floor_age" ; + dcterms:title "floor age" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "floor age" ; + skos:definition "The time period since installment of the carpet or flooring" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "years, weeks, days" . -nmdc:input_read_count a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "input_read_count" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:read_qc_analysis_statistic ; - skos:definition "The sequence count number of input reads for QC analysis." . + rdfs:label "floor_area" ; + dcterms:title "floor area" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "floor area" ; + skos:definition "The area of the floor space within the room" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "square meter" . -nmdc:insdc_bioproject_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "insdc_bioproject_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:insdc_identifiers, - nmdc:study_identifiers ; - skos:altLabel "DDBJ bioproject identifiers", - "NCBI bioproject identifiers" ; - skos:definition "identifiers for corresponding project in INSDC Bioproject" . + rdfs:label "floor_cond" ; + dcterms:title "floor condition" ; + rdfs:range nmdc:FloorCondEnum ; + rdfs:subPropertyOf ; + skos:altLabel "floor condition" ; + skos:definition "The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:insdc_biosample_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "insdc_biosample_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:biosample_identifiers, - nmdc:insdc_identifiers ; - skos:altLabel "DDBJ biosample identifiers", - "EBI biosample identifiers", - "NCBI biosample identifiers" ; - skos:definition "identifiers for corresponding sample in INSDC" . + rdfs:label "floor_count" ; + dcterms:title "floor count" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "floor count" ; + skos:definition "The number of floors in the building, including basements and mechanical penthouse" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" . -nmdc:insdc_experiment_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "insdc_experiment_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:external_database_identifiers, - nmdc:insdc_identifiers . + rdfs:label "floor_finish_mat" ; + dcterms:title "floor finish material" ; + rdfs:range nmdc:FloorFinishMatEnum ; + rdfs:subPropertyOf ; + skos:altLabel "floor finish material" ; + skos:definition "The floor covering type; the finished surface that is walked on" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:is_balanced a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "is_balanced" ; - rdfs:range linkml:Boolean . + rdfs:label "floor_struc" ; + dcterms:title "floor structure" ; + rdfs:range nmdc:FloorStrucEnum ; + rdfs:subPropertyOf ; + skos:altLabel "floor structure" ; + skos:definition "Refers to the structural elements and subfloor upon which the finish flooring is installed" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:is_diastereoselective a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "is_diastereoselective" ; - rdfs:range linkml:Boolean . + rdfs:label "floor_thermal_mass" ; + dcterms:title "floor thermal mass" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "floor thermal mass" ; + skos:definition "The ability of the floor to provide inertia against temperature fluctuations" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "joule per degree Celsius" . -nmdc:is_fully_characterized a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "is_fully_characterized" ; - rdfs:range linkml:Boolean ; - skos:definition "False if includes R-groups" . + rdfs:label "floor_water_mold" ; + dcterms:title "floor signs of water/mold" ; + rdfs:range nmdc:FloorWaterMoldEnum ; + rdfs:subPropertyOf ; + skos:altLabel "floor signs of water/mold" ; + skos:definition "Signs of the presence of mold or mildew in a room" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:is_stereo a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "is_stereo" ; - rdfs:range linkml:Boolean . + rdfs:label "fluor" ; + dcterms:title "fluorescence" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "fluorescence" ; + skos:definition "Raw or converted fluorescence of water" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram chlorophyll a per cubic meter, volts" . -nmdc:is_transport a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "is_transport" ; - rdfs:range linkml:Boolean . - -nmdc:isotope_exposure a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "isotope_exposure" ; - dcterms:title "isotope exposure/addition" ; - rdfs:range linkml:String ; - skos:definition "List isotope exposure or addition applied to your sample." . - -nmdc:jgi_portal_identifiers a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "jgi_portal_identifiers" ; - rdfs:range linkml:String ; - skos:definition "identifiers for entities according to JGI Portal" . - -nmdc:jgi_portal_study_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "jgi_portal_study_identifiers" ; - dcterms:title "JGI Portal Study identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:jgi_portal_identifiers, - nmdc:study_identifiers ; - skos:definition "Identifiers that link a NMDC study to a website hosting raw and analyzed data for a JGI proposal. The suffix of the curie can used to query the GOLD API and is interoperable with an award DOI from OSTI and a GOLD study identifier." . - -nmdc:language a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "language" ; - rdfs:range nmdc:LanguageCode ; - skos:definition "Should use ISO 639-1 code e.g. \"en\", \"fr\"" . - -nmdc:lbc_thirty a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "lbc_thirty" ; - dcterms:title "lime buffer capacity (at 30 minutes)" ; + rdfs:label "freq_clean" ; + dcterms:title "frequency of cleaning" ; rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf nmdc:attribute ; - skos:altLabel "lbc30", - "lbc_thirty", - "lime buffer capacity (at 30 minutes)" ; - skos:definition "lime buffer capacity, determined after 30 minute incubation" ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "ppm CaCO3/pH" . + rdfs:subPropertyOf ; + skos:altLabel "frequency of cleaning" ; + skos:definition "The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually." ; + skos:inScheme ; + nmdc:expected_value "enumeration or {text}" ; + nmdc:occurrence "1" . -nmdc:lbceq a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "lbceq" ; - dcterms:title "lime buffer capacity (after 5 day incubation)" ; + rdfs:label "freq_cook" ; + dcterms:title "frequency of cooking" ; rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf nmdc:attribute ; - skos:altLabel "lbceq", - "lime buffer capacity (at 5-day equilibrium)" ; - skos:definition "lime buffer capacity, determined at equilibrium after 5 day incubation" ; + rdfs:subPropertyOf ; + skos:altLabel "frequency of cooking" ; + skos:definition "The number of times a meal is cooked per week" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "ppm CaCO3/pH" . - -nmdc:left_participants a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "left_participants" ; - rdfs:range nmdc:ReactionParticipant ; - rdfs:subPropertyOf nmdc:has_participants . + nmdc:occurrence "1" . -nmdc:library_preparation_kit a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "library_preparation_kit" ; - rdfs:range linkml:String . + rdfs:label "fungicide_regm" ; + dcterms:title "fungicide regimen" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "fungicide regimen" ; + skos:definition "Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens" ; + skos:inScheme ; + nmdc:expected_value "fungicide name;fungicide amount;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram, mole per liter, milligram per liter" . -nmdc:library_preparation_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "library_preparation_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:LibraryPreparation ; - rdfs:subPropertyOf nmdc:object_set ; - skos:altLabel "library_construction_set" ; - skos:definition "This property links a database object to the set of DNA extractions within it." . + rdfs:label "furniture" ; + dcterms:title "furniture" ; + rdfs:range nmdc:FurnitureEnum ; + rdfs:subPropertyOf ; + skos:altLabel "furniture" ; + skos:definition "The types of furniture present in the sampled room" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:library_type a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "library_type" ; - dcterms:title "library type" ; - rdfs:range nmdc:LibraryTypeEnum . + 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" . -nmdc:location a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "location" ; - rdfs:range linkml:String . + rdfs:label "gaseous_substances" ; + dcterms:title "gaseous substances" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "gaseous substances" ; + skos:definition "Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances" ; + skos:inScheme ; + nmdc:expected_value "gaseous substance name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "micromole per liter" . -nmdc:low_depth_contig_num a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "low_depth_contig_num" ; - rdfs:range linkml:Integer . + rdfs:label "gender_restroom" ; + dcterms:title "gender of restroom" ; + rdfs:range nmdc:GenderRestroomEnum ; + rdfs:subPropertyOf ; + skos:altLabel "gender of restroom" ; + skos:definition "The gender type of the restroom" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:mags_activity_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "mags_activity_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:MagsAnalysisActivity ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of MAGs analysis activities." . + rdfs:label "genetic_mod" ; + dcterms:title "genetic modification" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "genetic modification" ; + skos:definition "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI,url or free text" ; + nmdc:occurrence "1" . -nmdc:mags_list a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "mags_list" ; - rdfs:range nmdc:MagBin . + rdfs:label "geo_loc_name" ; + dcterms:title "geographic location (country and/or sea,region)" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "geographic location (country and/or sea,region)" ; + skos:definition "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)" ; + skos:inScheme ; + nmdc:expected_value "country or sea name (INSDC or GAZ): region(GAZ), specific location name" . -nmdc:manganese a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "manganese" ; - dcterms:title "manganese" ; + rdfs:label "glucosidase_act" ; + dcterms:title "glucosidase activity" ; rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf nmdc:attribute ; - skos:altLabel "manganese" ; - skos:definition "Concentration of manganese in the sample" ; + rdfs:subPropertyOf ; + skos:altLabel "glucosidase activity" ; + skos:definition "Measurement of glucosidase activity" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "mg/kg (ppm)" . + nmdc:preferred_unit "mol per liter per hour" . -nmdc:massive_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "massive_identifiers" ; - rdfs:range linkml:String ; - skos:definition "identifiers for entities according to MASSIVE" . + rdfs:label "gravidity" ; + dcterms:title "gravidity" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "gravidity" ; + skos:definition "Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used" ; + skos:inScheme ; + nmdc:expected_value "gravidity status;timestamp" ; + nmdc:occurrence "1" . -nmdc:massive_study_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "massive_study_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:massive_identifiers, - nmdc:study_identifiers ; - skos:definition "identifiers for corresponding study in MASSIVE" . + rdfs:label "gravity" ; + dcterms:title "gravity" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "gravity" ; + skos:definition "Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments" ; + skos:inScheme ; + nmdc:expected_value "gravity factor value;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "meter per square second, g" . -nmdc:material_sample_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "material_sample_set" ; - dcterms:title "material sample set" ; - rdfs:range nmdc:MaterialSample . + 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" . -nmdc:material_sampling_activity_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "material_sampling_activity_set" ; - dcterms:title "material sampling activity set" ; - rdfs:range nmdc:MaterialSamplingActivity . + rdfs:label "growth_habit" ; + dcterms:title "growth habit" ; + rdfs:range nmdc:GrowthHabitEnum ; + rdfs:subPropertyOf ; + skos:altLabel "growth habit" ; + skos:definition "Characteristic shape, appearance or growth form of a plant species" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:md5_checksum a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "md5_checksum" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf nmdc:attribute ; - skos:definition "MD5 checksum of file (pre-compressed)" . + rdfs:label "growth_hormone_regm" ; + dcterms:title "growth hormone regimen" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "growth hormone regimen" ; + skos:definition "Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens" ; + skos:inScheme ; + nmdc:expected_value "growth hormone name;growth hormone amount;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram, mole per liter, milligram per liter" . -nmdc:members_id a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "members_id" ; - rdfs:range linkml:String . + rdfs:label "hall_count" ; + dcterms:title "hallway/corridor count" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "hallway/corridor count" ; + skos:definition "The total count of hallways and cooridors in the built structure" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" . -nmdc:metabolite_quantified a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "metabolite_quantified" ; - rdfs:range nmdc:ChemicalEntity ; - skos:definition "the specific metabolite identifier" . + rdfs:label "handidness" ; + dcterms:title "handidness" ; + rdfs:range nmdc:HandidnessEnum ; + rdfs:subPropertyOf ; + skos:altLabel "handidness" ; + skos:definition "The handidness of the individual sampled" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:metabolomics_analysis_activity_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "metabolomics_analysis_activity_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:MetabolomicsAnalysisActivity ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of metabolomics analysis activities." . + rdfs:label "has numeric value" ; + rdfs:range linkml:Double ; + skos:inScheme . -nmdc:metagenome_annotation_activity_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "metagenome_annotation_activity_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:MetagenomeAnnotationActivity ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of metagenome annotation activities." . + rdfs:label "has raw value" ; + skos:inScheme . -nmdc:metagenome_annotation_id a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "metagenome_annotation_id" ; - rdfs:range nmdc:WorkflowExecutionActivity . + rdfs:label "has unit" ; + skos:definition "Example \"m\"" ; + skos:inScheme . -nmdc:metagenome_assembly_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "metagenome_assembly_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:MetagenomeAssembly ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of metagenome assembly activities." . + rdfs:label "hc_produced" ; + dcterms:title "hydrocarbon type produced" ; + rdfs:range nmdc:HcProducedEnum ; + rdfs:subPropertyOf ; + skos:altLabel "hydrocarbon type produced" ; + skos:definition "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:metagenome_sequencing_activity_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "metagenome_sequencing_activity_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:MetagenomeSequencingActivity ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of metagenome sequencing activities." . + rdfs:label "hcr" ; + dcterms:title "hydrocarbon resource type" ; + rdfs:range nmdc:HcrEnum ; + rdfs:subPropertyOf ; + skos:altLabel "hydrocarbon resource type" ; + skos:definition "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:metaproteomics_analysis_activity_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "metaproteomics_analysis_activity_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:MetaproteomicsAnalysisActivity ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of metaproteomics analysis activities." . + rdfs:label "hcr_fw_salinity" ; + dcterms:title "formation water salinity" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "formation water salinity" ; + skos:definition "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter" . -nmdc:metatranscriptome_activity_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "metatranscriptome_activity_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:MetatranscriptomeActivity ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of metatranscriptome analysis activities." . + rdfs:label "hcr_geol_age" ; + dcterms:title "hydrocarbon resource geological age" ; + rdfs:range nmdc:HcrGeolAgeEnum ; + rdfs:subPropertyOf ; + skos:altLabel "hydrocarbon resource geological age" ; + skos:definition "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:mgnify_project_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "mgnify_project_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:mgnify_identifiers, - nmdc:study_identifiers ; - skos:definition "identifiers for corresponding project in MGnify" . + rdfs:label "hcr_pressure" ; + dcterms:title "hydrocarbon resource original pressure" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "hydrocarbon resource original pressure" ; + skos:definition "Original pressure of the hydrocarbon resource" ; + skos:inScheme ; + nmdc:expected_value "measurement value range" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "atmosphere, kilopascal" . -nmdc:micro_biomass_c_meth a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "micro_biomass_c_meth" ; - dcterms:title "microbial biomass carbon method" ; - rdfs:range linkml:String ; - skos:definition "Reference or method used in determining microbial biomass carbon" . + rdfs:label "hcr_temp" ; + dcterms:title "hydrocarbon resource original temperature" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "hydrocarbon resource original temperature" ; + skos:definition "Original temperature of the hydrocarbon resource" ; + skos:inScheme ; + nmdc:expected_value "measurement value range" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "degree Celsius" . -nmdc:micro_biomass_n_meth a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "micro_biomass_n_meth" ; - dcterms:title "microbial biomass nitrogen method" ; - rdfs:range linkml:String ; - skos:definition "Reference or method used in determining microbial biomass nitrogen" . + rdfs:label "heat_cool_type" ; + dcterms:title "heating and cooling system type" ; + rdfs:range nmdc:HeatCoolTypeEnum ; + rdfs:subPropertyOf ; + skos:altLabel "heating and cooling system type" ; + skos:definition "Methods of conditioning or heating a room or building" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "m" . -nmdc:microbial_biomass_c a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "microbial_biomass_c" ; - dcterms:title "microbial biomass carbon" ; - rdfs:range linkml:String ; - skos:definition "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer." . + rdfs:label "heat_deliv_loc" ; + dcterms:title "heating delivery locations" ; + rdfs:range nmdc:HeatDelivLocEnum ; + rdfs:subPropertyOf ; + skos:altLabel "heating delivery locations" ; + skos:definition "The location of heat delivery within the room" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:microbial_biomass_n a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "microbial_biomass_n" ; - dcterms:title "microbial biomass nitrogen" ; + rdfs:label "heat_sys_deliv_meth" ; + dcterms:title "heating system delivery method" ; rdfs:range linkml:String ; - skos:definition "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer." . + rdfs:subPropertyOf ; + skos:altLabel "heating system delivery method" ; + skos:definition "The method by which the heat is delivered through the system" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:min_q_value a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "min_q_value" ; - rdfs:range linkml:Float ; - skos:definition "smallest Q-Value associated with the peptide sequence as provided by MSGFPlus tool" . + rdfs:label "heat_system_id" ; + dcterms:title "heating system identifier" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "heating system identifier" ; + skos:definition "The heating system identifier" ; + skos:inScheme ; + nmdc:expected_value "unique identifier" ; + nmdc:occurrence "1" . -nmdc:ncbi_project_name a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ncbi_project_name" ; - rdfs:range linkml:String . + 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" . -nmdc:ncbi_taxonomy_name a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ncbi_taxonomy_name" ; - rdfs:range linkml:String . + 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" . -nmdc:neon_biosample_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "neon_biosample_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:biosample_identifiers, - nmdc:neon_identifiers . + rdfs:label "height_carper_fiber" ; + dcterms:title "height carpet fiber mat" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "height carpet fiber mat" ; + skos:definition "The average carpet fiber height in the indoor environment" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "centimeter" . -nmdc:neon_study_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "neon_study_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:neon_identifiers, - nmdc:study_identifiers . + rdfs:label "herbicide_regm" ; + dcterms:title "herbicide regimen" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "herbicide regimen" ; + skos:definition "Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens" ; + skos:inScheme ; + nmdc:expected_value "herbicide name;herbicide amount;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram, mole per liter, milligram per liter" . -nmdc:nitrate_nitrogen a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "nitrate_nitrogen" ; - dcterms:title "nitrate_nitrogen" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf nmdc:attribute ; - skos:altLabel "NO3-N", - "nitrate_nitrogen" ; - skos:definition "Concentration of nitrate nitrogen in the sample" ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "mg/kg" . + rdfs:label "horizon_meth" ; + dcterms:title "soil horizon method" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "soil horizon method" ; + skos:definition "Reference or method used in determining the horizon" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . -nmdc:nitrite_nitrogen a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "nitrite_nitrogen" ; - dcterms:title "nitrite_nitrogen" ; + rdfs:label "host_age" ; + dcterms:title "host age" ; rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf nmdc:attribute ; - skos:altLabel "NO2-N", - "nitrite_nitrogen" ; - skos:definition "Concentration of nitrite nitrogen in the sample" ; - nmdc:expected_value "measurement value" ; + rdfs:subPropertyOf ; + skos:altLabel "host age" ; + skos:definition "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees" ; + skos:inScheme ; + nmdc:expected_value "value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "mg/kg" . + nmdc:preferred_unit "year, day, hour" . -nmdc:nom_analysis_activity_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "nom_analysis_activity_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:NomAnalysisActivity ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of natural organic matter (NOM) analysis activities." . + rdfs:label "host_body_habitat" ; + dcterms:title "host body habitat" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "host body habitat" ; + skos:definition "Original body habitat where the sample was obtained from" ; + skos:inScheme ; + nmdc:expected_value "free text" ; + nmdc:occurrence "1" . -nmdc:non_microb_biomass a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "non_microb_biomass" ; - dcterms:title "non-microbial biomass" ; - rdfs:range linkml:String ; - skos:definition "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;" . + rdfs:label "host_body_product" ; + dcterms:title "host body product" ; + rdfs:range nmdc:ControlledTermValue ; + rdfs:subPropertyOf ; + skos:altLabel "host body product" ; + skos:definition "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon" ; + skos:inScheme ; + nmdc:expected_value "FMA or UBERON" ; + nmdc:occurrence "1" . -nmdc:non_microb_biomass_method a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "non_microb_biomass_method" ; - dcterms:title "non-microbial biomass method" ; - rdfs:range linkml:String ; - skos:definition "Reference or method used in determining biomass" . + rdfs:label "host_body_site" ; + dcterms:title "host body site" ; + rdfs:range nmdc:ControlledTermValue ; + rdfs:subPropertyOf ; + skos:altLabel "host body site" ; + skos:definition "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON" ; + skos:inScheme ; + nmdc:expected_value "FMA or UBERON" ; + nmdc:occurrence "1" . -nmdc:notes a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "notes" ; - rdfs:range linkml:String ; - skos:definition "from study class" . + rdfs:label "host_body_temp" ; + dcterms:title "host body temperature" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "host body temperature" ; + skos:definition "Core body temperature of the host when sample was collected" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "degree Celsius" . -nmdc:nucleic_acid_concentration a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "nucleic_acid_concentration" ; - rdfs:range nmdc:InstrumentValue . + rdfs:label "host_color" ; + dcterms:title "host color" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "host color" ; + skos:definition "The color of host" ; + skos:inScheme ; + nmdc:expected_value "color" ; + nmdc:occurrence "1" . -nmdc:num_16s a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "num_16s" ; - rdfs:range linkml:Integer . + rdfs:label "host_common_name" ; + dcterms:title "host common name" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "host common name" ; + skos:definition "Common name of the host." ; + skos:inScheme ; + nmdc:expected_value "common name" ; + nmdc:occurrence "1" . -nmdc:num_23s a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "num_23s" ; - rdfs:range linkml:Integer . + rdfs:label "host_diet" ; + dcterms:title "host diet" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "host diet" ; + skos:definition "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types" ; + skos:inScheme ; + nmdc:expected_value "diet type" ; + nmdc:occurrence "m" . -nmdc:num_5s a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "num_5s" ; - rdfs:range linkml:Integer . + rdfs:label "host_dry_mass" ; + dcterms:title "host dry mass" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "host dry mass" ; + skos:definition "Measurement of dry mass" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "kilogram, gram" . -nmdc:num_t_rna a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "num_t_rna" ; - rdfs:range linkml:Integer . + rdfs:label "host_family_relation" ; + dcterms:title "host family relationship" ; + rdfs:range linkml:String ; + rdfs:subPropertyOf ; + skos:altLabel "host family relationship" ; + skos:definition "Familial relationships to other hosts in the same study; can include multiple relationships" ; + skos:inScheme ; + nmdc:expected_value "relationship type;arbitrary identifier" ; + nmdc:occurrence "m" . -nmdc:number_of_contig a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "number_of_contig" ; - rdfs:range linkml:Integer . + rdfs:label "host_genotype" ; + dcterms:title "host genotype" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "host genotype" ; + skos:definition "Observed genotype" ; + skos:inScheme ; + nmdc:expected_value "genotype" ; + nmdc:occurrence "1" . -nmdc:objective a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "objective" ; - rdfs:range linkml:String ; - skos:definition "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract." ; - skos:exactMatch . + rdfs:label "host_growth_cond" ; + dcterms:title "host growth conditions" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "host growth conditions" ; + skos:definition "Literature reference giving growth conditions of the host" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI,url or free text" ; + nmdc:occurrence "1" . -nmdc:omics_processing_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "omics_processing_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:external_database_identifiers . + rdfs:label "host_height" ; + dcterms:title "host height" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "host height" ; + skos:definition "The height of subject" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "centimeter, millimeter, meter" . -nmdc:omics_processing_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "omics_processing_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:OmicsProcessing ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of omics processings within it." . + rdfs:label "host_last_meal" ; + dcterms:title "host last meal" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "host last meal" ; + skos:definition "Content of last meal and time since feeding; can include multiple values" ; + skos:inScheme ; + nmdc:expected_value "content;duration" ; + nmdc:occurrence "m" . -nmdc:omics_type a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "omics_type" ; - rdfs:range nmdc:ControlledTermValue ; - skos:definition "The type of omics data" . + rdfs:label "host_length" ; + dcterms:title "host length" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "host length" ; + skos:definition "The length of subject" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "centimeter, millimeter, meter" . -nmdc:orcid a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "orcid" ; - rdfs:domain nmdc:PersonValue ; - rdfs:range linkml:String ; - skos:definition "The ORCID of a person." . + rdfs:label "host_life_stage" ; + dcterms:title "host life stage" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "host life stage" ; + skos:definition "Description of life stage of host" ; + skos:inScheme ; + nmdc:expected_value "stage" ; + nmdc:occurrence "1" . -nmdc:org_nitro_method a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "org_nitro_method" ; - dcterms:title "organic nitrogen method" ; - rdfs:range linkml:String ; - skos:definition "Method used for obtaining organic nitrogen" . + rdfs:label "host_phenotype" ; + dcterms:title "host phenotype" ; + rdfs:range nmdc:ControlledTermValue ; + rdfs:subPropertyOf ; + skos:altLabel "host phenotype" ; + skos:definition "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP" ; + skos:inScheme ; + nmdc:expected_value "PATO or HP" ; + nmdc:occurrence "1" . -nmdc:other_treatment a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "other_treatment" ; - dcterms:title "other treatments" ; - rdfs:range linkml:String ; - skos:definition "Other treatments applied to your samples that are not applicable to the provided fields" . + rdfs:label "host_sex" ; + dcterms:title "host sex" ; + rdfs:range nmdc:HostSexEnum ; + rdfs:subPropertyOf ; + skos:altLabel "host sex" ; + skos:definition "Gender or physical sex of the host." ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:output_base_count a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "output_base_count" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:read_qc_analysis_statistic ; - skos:definition "After QC analysis nucleotide base count number." . + rdfs:label "host_shape" ; + dcterms:title "host shape" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "host shape" ; + skos:definition "Morphological shape of host" ; + skos:inScheme ; + nmdc:expected_value "shape" ; + nmdc:occurrence "1" . -nmdc:output_read_bases a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "output_read_bases" ; - rdfs:range linkml:Float ; - skos:definition "TODO" . + rdfs:label "host_subject_id" ; + dcterms:title "host subject id" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "host subject id" ; + skos:definition "A unique identifier by which each subject can be referred to, de-identified." ; + skos:inScheme ; + nmdc:expected_value "unique identifier" ; + nmdc:occurrence "1" . -nmdc:output_read_count a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "output_read_count" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:read_qc_analysis_statistic ; - skos:definition "After QC analysis sequence count number." . + rdfs:label "host_subspecf_genlin" ; + dcterms:title "host subspecific genetic lineage" ; + rdfs:range linkml:String ; + rdfs:subPropertyOf ; + skos:altLabel "host subspecific genetic lineage" ; + skos:definition "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123." ; + skos:inScheme ; + nmdc:expected_value "Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar." ; + nmdc:occurrence "m" . -nmdc:pcr_cycles a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "pcr_cycles" ; - rdfs:range linkml:Integer ; - skos:exactMatch . + rdfs:label "host_substrate" ; + dcterms:title "host substrate" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "host substrate" ; + skos:definition "The growth substrate of the host." ; + skos:inScheme ; + nmdc:expected_value "substrate name" ; + nmdc:occurrence "1" . -nmdc:peptide_sequence a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "peptide_sequence" ; - rdfs:range linkml:String . + rdfs:label "host_symbiont" ; + dcterms:title "observed host symbionts" ; + rdfs:range linkml:String ; + rdfs:subPropertyOf ; + skos:altLabel "observed host symbionts" ; + skos:definition "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host." ; + skos:inScheme ; + nmdc:expected_value "species name or common name" ; + nmdc:occurrence "m" . -nmdc:peptide_sequence_count a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "peptide_sequence_count" ; - rdfs:range linkml:Integer ; - skos:definition "count of peptide sequences grouped to the best_protein" . + 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" . -nmdc:peptide_spectral_count a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "peptide_spectral_count" ; - rdfs:range linkml:Integer ; - skos:definition "sum of filter passing MS2 spectra associated with the peptide sequence within a given LC-MS/MS data file" . + rdfs:label "host_tot_mass" ; + dcterms:title "host total mass" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "host total mass" ; + skos:definition "Total mass of the host at collection, the unit depends on host" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "kilogram, gram" . -nmdc:peptide_sum_masic_abundance a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "peptide_sum_masic_abundance" ; - rdfs:range linkml:Integer ; - skos:definition "combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the peptide sequence from a given LC-MS/MS data file using the MASIC tool" . + rdfs:label "host_wet_mass" ; + dcterms:title "host wet mass" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "host wet mass" ; + skos:definition "Measurement of wet mass" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "kilogram, gram" . -nmdc:phase a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "phase" ; - rdfs:range linkml:Integer ; - skos:definition "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; - skos:exactMatch . + rdfs:label "humidity" ; + dcterms:title "humidity" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "humidity" ; + skos:definition "Amount of water vapour in the air, at the time of sampling" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "gram per cubic meter" . -nmdc:pooling_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "pooling_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:Pooling ; - rdfs:subPropertyOf nmdc:object_set . + 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" . -nmdc:processed_sample_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "processed_sample_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:ProcessedSample ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of processed samples within it." . - -nmdc:profile_image_url a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "profile_image_url" ; - rdfs:domain nmdc:PersonValue ; - rdfs:range linkml:String ; - skos:definition "A url that points to an image of a person." . + rdfs:label "indoor_space" ; + dcterms:title "indoor space" ; + rdfs:range nmdc:IndoorSpaceEnum ; + rdfs:subPropertyOf ; + skos:altLabel "indoor space" ; + skos:definition "A distinguishable space within a structure, the purpose for which discrete areas of a building is used" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:project_id a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "project_id" ; - dcterms:title "project ID" ; - rdfs:range linkml:String ; - skos:definition "Proposal IDs or names associated with dataset" . + rdfs:label "indoor_surf" ; + dcterms:title "indoor surface" ; + rdfs:range nmdc:IndoorSurfEnum ; + rdfs:subPropertyOf ; + skos:altLabel "indoor surface" ; + skos:definition "Type of indoor surface" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:proport_woa_temperature a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "proport_woa_temperature" ; - rdfs:range linkml:String . + rdfs:label "indust_eff_percent" ; + dcterms:title "industrial effluent percent" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "industrial effluent percent" ; + skos:definition "Percentage of industrial effluents received by wastewater treatment plant" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "percentage" . -nmdc:proposal_dna a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "proposal_dna" ; - dcterms:title "DNA proposal ID" ; - rdfs:range linkml:String . + rdfs:label "inorg_particles" ; + dcterms:title "inorganic particles" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "inorganic particles" ; + skos:definition "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles" ; + skos:inScheme ; + nmdc:expected_value "inorganic particle name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "mole per liter, milligram per liter" . -nmdc:proposal_rna a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "proposal_rna" ; - dcterms:title "RNA proposal ID" ; - rdfs:range linkml:String . + rdfs:label "inside_lux" ; + dcterms:title "inside lux light" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "inside lux light" ; + skos:definition "The recorded value at sampling time (power density)" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "kilowatt per square metre" . -nmdc:protein_spectral_count a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "protein_spectral_count" ; - rdfs:range linkml:Integer ; - skos:definition "sum of filter passing MS2 spectra associated with the best protein within a given LC-MS/MS data file" . + rdfs:label "int_wall_cond" ; + dcterms:title "interior wall condition" ; + rdfs:range nmdc:IntWallCondEnum ; + rdfs:subPropertyOf ; + skos:altLabel "interior wall condition" ; + skos:definition "The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:protein_sum_masic_abundance a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "protein_sum_masic_abundance" ; - rdfs:range linkml:Integer ; - skos:definition "combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the best protein from a given LC-MS/MS data file using the MASIC tool" . + rdfs:label "iw_bt_date_well" ; + dcterms:title "injection water breakthrough date of specific well" ; + rdfs:range nmdc:TimestampValue ; + rdfs:subPropertyOf ; + skos:altLabel "injection water breakthrough date of specific well" ; + skos:definition "Injection water breakthrough date per well following a secondary and/or tertiary recovery" ; + skos:inScheme ; + nmdc:expected_value "timestamp" ; + nmdc:occurrence "1" . -nmdc:protocol_link a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "protocol_link" ; - rdfs:range nmdc:Protocol . + rdfs:label "iwf" ; + dcterms:title "injection water fraction" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "injection water fraction" ; + skos:definition "Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "percent" . -nmdc:publication_dois a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "publication_dois" ; - rdfs:range linkml:Uriorcurie ; - rdfs:subPropertyOf nmdc:dois ; - skos:definition "One or more DOIs that links a study, or similar entity, to a publication." . + rdfs:label "last_clean" ; + dcterms:title "last time swept/mopped/vacuumed" ; + rdfs:range nmdc:TimestampValue ; + rdfs:subPropertyOf ; + skos:altLabel "last time swept/mopped/vacuumed" ; + skos:definition "The last time the floor was cleaned (swept, mopped, vacuumed)" ; + skos:inScheme ; + nmdc:expected_value "timestamp" ; + nmdc:occurrence "1" . -nmdc:publications a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "publications" ; - rdfs:range linkml:String ; - skos:definition "A list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible." . + 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" . -nmdc:quality_control_report a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "quality_control_report" ; - rdfs:range nmdc:QualityControlReport . + rdfs:label "light_intensity" ; + dcterms:title "light intensity" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "light intensity" ; + skos:definition "Measurement of light intensity" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "lux" . -nmdc:reaction_activity_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "reaction_activity_set" ; - rdfs:range nmdc:ReactionActivity . + 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" . -nmdc:reaction_aided_by a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "reaction_aided_by" ; - dcterms:title "reaction aided by" ; - rdfs:range nmdc:LabDevice ; - skos:altLabel "shaker" . + rdfs:label "light_type" ; + dcterms:title "light type" ; + rdfs:range nmdc:LightTypeEnum ; + rdfs:subPropertyOf ; + skos:altLabel "light type" ; + skos:definition "Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "m" . -nmdc:reaction_temperature a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "reaction_temperature" ; - rdfs:range linkml:String . + rdfs:label "link_addit_analys" ; + dcterms:title "links to additional analysis" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "links to additional analysis" ; + skos:definition "Link to additional analysis results performed on the sample" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . -nmdc:reaction_time a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "reaction_time" ; - rdfs:range nmdc:QuantityValue . + rdfs:label "link_class_info" ; + dcterms:title "link to classification information" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "link to classification information" ; + skos:definition "Link to digitized soil maps or other soil classification information" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . -nmdc:read_based_taxonomy_analysis_activity_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "read_based_taxonomy_analysis_activity_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:ReadBasedTaxonomyAnalysisActivity ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of read based analysis activities." . + rdfs:label "link_climate_info" ; + dcterms:title "link to climate information" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "link to climate information" ; + skos:definition "Link to climate resource" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . -nmdc:read_qc_analysis_activity_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "read_qc_analysis_activity_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:ReadQcAnalysisActivity ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of read QC analysis activities." . + rdfs:label "lithology" ; + dcterms:title "lithology" ; + rdfs:range nmdc:LithologyEnum ; + rdfs:subPropertyOf ; + skos:altLabel "lithology" ; + skos:definition "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:related_identifiers a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "related_identifiers" ; - dcterms:title "Related Identifiers" ; - rdfs:range linkml:String ; - skos:definition "Identifiers assigned to a thing that is similar to that which is represented in NMDC. Related identifier are not an identical match and may have some variation." . + rdfs:label "local_class" ; + dcterms:title "soil_taxonomic/local classification" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "soil_taxonomic/local classification" ; + skos:definition "Soil classification based on local soil classification system" ; + skos:inScheme ; + nmdc:expected_value "local classification name" ; + nmdc:occurrence "1" . -nmdc:relevant_protocols a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "relevant_protocols" ; - rdfs:range linkml:String . + rdfs:label "local_class_meth" ; + dcterms:title "soil_taxonomic/local classification method" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "soil_taxonomic/local classification method" ; + skos:definition "Reference or method used in determining the local soil classification" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . -nmdc:replicate_number a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "replicate_number" ; - dcterms:title "replicate number" ; - rdfs:range linkml:String ; - skos:definition "If sending biological replicates, indicate the rep number here." . + rdfs:label "magnesium" ; + dcterms:title "magnesium" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "magnesium" ; + skos:definition "Concentration of magnesium in the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "mole per liter, milligram per liter, parts per million, micromole per kilogram" . -nmdc:right_participants a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "right_participants" ; - rdfs:range nmdc:ReactionParticipant ; - rdfs:subPropertyOf nmdc:has_participants . + rdfs:label "max_occup" ; + dcterms:title "maximum occupancy" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "maximum occupancy" ; + skos:definition "The maximum amount of people allowed in the indoor environment" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" . -nmdc:rna_absorb1 a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rna_absorb1" ; - dcterms:title "RNA absorbance 260/280" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:biomaterial_purity ; - skos:definition "260/280 measurement of RNA sample purity" . + rdfs:label "mean_frict_vel" ; + dcterms:title "mean friction velocity" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "mean friction velocity" ; + skos:definition "Measurement of mean friction velocity" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "meter per second" . -nmdc:rna_absorb2 a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rna_absorb2" ; - dcterms:title "RNA absorbance 260/230" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:biomaterial_purity ; - skos:definition "260/230 measurement of RNA sample purity" . - -nmdc:rna_collect_site a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "rna_collect_site" ; - dcterms:title "RNA collection site" ; - rdfs:range linkml:String ; - skos:definition "Provide information on the site your RNA sample was collected from" . - -nmdc:rna_concentration a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "rna_concentration" ; - dcterms:title "RNA concentration in ng/ul" ; - rdfs:range linkml:Float . - -nmdc:rna_cont_type a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "rna_cont_type" ; - dcterms:title "RNA container type" ; - rdfs:range nmdc:JgiContTypeEnum ; - skos:definition "Tube or plate (96-well)" . + rdfs:label "mean_peak_frict_vel" ; + dcterms:title "mean peak friction velocity" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "mean peak friction velocity" ; + skos:definition "Measurement of mean peak friction velocity" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "meter per second" . -nmdc:rna_cont_well a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rna_cont_well" ; - dcterms:title "RNA plate position" ; - rdfs:range linkml:String . + rdfs:label "mech_struc" ; + dcterms:title "mechanical structure" ; + rdfs:range nmdc:MechStrucEnum ; + rdfs:subPropertyOf ; + skos:altLabel "mechanical structure" ; + skos:definition "mechanical structure: a moving structure" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:rna_container_id a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rna_container_id" ; - dcterms:title "RNA container label" ; - rdfs:range linkml:String . + rdfs:label "mechanical_damage" ; + dcterms:title "mechanical damage" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "mechanical damage" ; + skos:definition "Information about any mechanical damage exerted on the plant; can include multiple damages and sites" ; + skos:inScheme ; + nmdc:expected_value "damage type;body site" ; + nmdc:occurrence "m" . -nmdc:rna_isolate_meth a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rna_isolate_meth" ; - dcterms:title "RNA isolation method" ; - rdfs:range linkml:String ; - skos:definition "Describe the method/protocol/kit used to extract DNA/RNA." . + rdfs:label "methane" ; + dcterms:title "methane" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "methane" ; + skos:definition "Methane (gas) amount or concentration at the time of sampling" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter, parts per billion, parts per million" . -nmdc:rna_organisms a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rna_organisms" ; - dcterms:title "RNA expected organisms" ; + rdfs:label "micro_biomass_meth" ; + dcterms:title "microbial biomass method" ; rdfs:range linkml:String ; - skos:definition "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture." . - -nmdc:rna_project_contact a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "rna_project_contact" ; - dcterms:title "RNA seq project contact" ; - rdfs:range linkml:String . + rdfs:subPropertyOf ; + skos:altLabel "microbial biomass method" ; + skos:definition "Reference or method used in determining microbial biomass" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . -nmdc:rna_samp_id a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rna_samp_id" ; - dcterms:title "RNA sample ID" ; - rdfs:range linkml:String . + rdfs:label "microbial_biomass" ; + dcterms:title "microbial biomass" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "microbial biomass" ; + skos:definition "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "ton, kilogram, gram per kilogram soil" . -nmdc:rna_sample_format a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rna_sample_format" ; - dcterms:title "RNA sample format" ; - rdfs:range nmdc:RnaSampleFormatEnum ; - skos:definition "Solution in which the RNA sample has been suspended" . + rdfs:label "mineral_nutr_regm" ; + dcterms:title "mineral nutrient regimen" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "mineral nutrient regimen" ; + skos:definition "Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens" ; + skos:inScheme ; + nmdc:expected_value "mineral nutrient name;mineral nutrient amount;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram, mole per liter, milligram per liter" . -nmdc:rna_sample_name a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rna_sample_name" ; - dcterms:title "RNA sample name" ; - rdfs:range linkml:String ; - skos:definition "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only." . + rdfs:label "misc_param" ; + dcterms:title "miscellaneous parameter" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "miscellaneous parameter" ; + skos:definition "Any other measurement performed or parameter collected, that is not listed here" ; + skos:inScheme ; + nmdc:expected_value "parameter name;measurement value" ; + nmdc:occurrence "m" . -nmdc:rna_seq_project a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rna_seq_project" ; - dcterms:title "RNA seq project ID" ; - rdfs:range linkml:String . + rdfs:label "n_alkanes" ; + dcterms:title "n-alkanes" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "n-alkanes" ; + skos:definition "Concentration of n-alkanes; can include multiple n-alkanes" ; + skos:inScheme ; + nmdc:expected_value "n-alkane name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "micromole per liter" . -nmdc:rna_seq_project_name a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rna_seq_project_name" ; - dcterms:title "RNA seq project name" ; - rdfs:range linkml:String . + rdfs:label "nitrate" ; + dcterms:title "nitrate" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "nitrate" ; + skos:definition "Concentration of nitrate in the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . -nmdc:rna_seq_project_pi a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rna_seq_project_pi" ; - dcterms:title "RNA seq project PI" ; - rdfs:range linkml:String . + rdfs:label "nitrite" ; + dcterms:title "nitrite" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "nitrite" ; + skos:definition "Concentration of nitrite in the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . -nmdc:rna_volume a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rna_volume" ; - dcterms:title "RNA volume in ul" ; - rdfs:range linkml:Float . + rdfs:label "nitro" ; + dcterms:title "nitrogen" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "nitrogen" ; + skos:definition "Concentration of nitrogen (total)" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter" . -nmdc:salinity_category a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "salinity_category" ; + rdfs:label "non_min_nutr_regm" ; + dcterms:title "non-mineral nutrient regimen" ; rdfs:range linkml:String ; - skos:definition "Categorical description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline" . + rdfs:subPropertyOf ; + skos:altLabel "non-mineral nutrient regimen" ; + skos:definition "Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens" ; + skos:inScheme ; + nmdc:expected_value "non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram, mole per liter, milligram per liter" . -nmdc:sample_collection_site a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sample_collection_site" ; - rdfs:range linkml:String . + rdfs:label "nucl_acid_amp" ; + dcterms:title "nucleic acid amplification" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "nucleic acid amplification" ; + skos:definition "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids" ; + skos:inScheme ; + nmdc:expected_value "PMID, DOI or URL" . -nmdc:sample_link a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sample_link" ; - dcterms:title "sample linkage" ; - rdfs:range linkml:String ; - skos:definition "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample." . + rdfs:label "nucl_acid_ext" ; + dcterms:title "nucleic acid extraction" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "nucleic acid extraction" ; + skos:definition "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample" ; + skos:inScheme ; + nmdc:expected_value "PMID, DOI or URL" . -nmdc:sample_shipped a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sample_shipped" ; - dcterms:title "sample shipped amount" ; - rdfs:range linkml:String ; - skos:definition "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL." . + rdfs:label "number_pets" ; + dcterms:title "number of pets" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "number of pets" ; + skos:definition "The number of pets residing in the sampled space" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" . -nmdc:sample_type a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sample_type" ; - dcterms:title "sample type" ; - rdfs:range nmdc:SampleTypeEnum ; - skos:definition "Type of sample being submitted" . + rdfs:label "number_plants" ; + dcterms:title "number of houseplants" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "number of houseplants" ; + skos:definition "The number of plant(s) in the sampling space" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" . -nmdc:sampling_method a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sampling_method" ; - dcterms:title "sampling method" ; - rdfs:range nmdc:SamplingMethodEnum . + rdfs:label "number_resident" ; + dcterms:title "number of residents" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "number of residents" ; + skos:definition "The number of individuals currently occupying in the sampling location" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" . -nmdc:seqid a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "seqid" ; - rdfs:range linkml:String ; - skos:definition "The ID of the landmark used to establish the coordinate system for the current feature." . + rdfs:label "occup_density_samp" ; + dcterms:title "occupant density at sampling" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "occupant density at sampling" ; + skos:definition "Average number of occupants at time of sampling per square footage" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" . -nmdc:smarts_string a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "smarts_string" ; - rdfs:range linkml:String . + rdfs:label "occup_document" ; + dcterms:title "occupancy documentation" ; + rdfs:range nmdc:OccupDocumentEnum ; + rdfs:subPropertyOf ; + skos:altLabel "occupancy documentation" ; + skos:definition "The type of documentation of occupancy" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . -nmdc:smiles a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "smiles" ; - rdfs:range linkml:String ; - skos:definition "A string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol." . + rdfs:label "occup_samp" ; + dcterms:title "occupancy at sampling" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "occupancy at sampling" ; + skos:definition "Number of occupants present at time of sample within the given space" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" . -nmdc:soluble_iron_micromol a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "soluble_iron_micromol" ; - rdfs:range linkml:String . - -nmdc:start a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "start" ; - rdfs:range linkml:Integer ; - rdfs:subPropertyOf nmdc:gff_coordinate ; - skos:closeMatch ; - skos:definition "The start of the feature in positive 1-based integer coordinates" . - -nmdc:start_date a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "start_date" ; - rdfs:range linkml:String ; - skos:definition "The date on which any process or activity was started" . - -nmdc:start_date_inc a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "start_date_inc" ; - dcterms:title "incubation start date" ; - rdfs:range linkml:String ; - skos:definition "Date the incubation was started. Only relevant for incubation samples." . + rdfs:label "org_carb" ; + dcterms:title "organic carbon" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "organic carbon" ; + skos:definition "Concentration of organic carbon" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter" . -nmdc:start_time_inc a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "start_time_inc" ; - dcterms:title "incubation start time, GMT" ; + rdfs:label "org_count_qpcr_info" ; + dcterms:title "organism count qPCR information" ; rdfs:range linkml:String ; - skos:definition "Time the incubation was started. Only relevant for incubation samples." . + rdfs:subPropertyOf ; + skos:altLabel "organism count qPCR information" ; + skos:definition "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)" ; + skos:inScheme ; + nmdc:expected_value "gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "number of cells per gram (or ml or cm^2)" . -nmdc:status a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "status" ; - rdfs:range nmdc:StatusEnum . + rdfs:label "org_matter" ; + dcterms:title "organic matter" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "organic matter" ; + skos:definition "Concentration of organic matter" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "microgram per liter" . -nmdc:stoichiometry a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "stoichiometry" ; - rdfs:range linkml:Integer ; - skos:definition "from reaction participant class" . + rdfs:label "org_nitro" ; + dcterms:title "organic nitrogen" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "organic nitrogen" ; + skos:definition "Concentration of organic nitrogen" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "microgram per liter" . -nmdc:strand a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "strand" ; - rdfs:range linkml:String ; - skos:definition "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; - skos:exactMatch . + rdfs:label "org_particles" ; + dcterms:title "organic particles" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "organic particles" ; + skos:definition "Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc." ; + skos:inScheme ; + nmdc:expected_value "particle name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram per liter" . -nmdc:study_category a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "study_category" ; - rdfs:range nmdc:StudyCategoryEnum ; - skos:definition "The type of research initiative" . + rdfs:label "organism_count" ; + dcterms:title "organism count" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "organism count" ; + skos:definition "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)" ; + skos:inScheme ; + nmdc:expected_value "organism name;measurement value;enumeration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" . -nmdc:study_image a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "study_image" ; - rdfs:domain nmdc:Study ; - rdfs:range nmdc:ImageValue ; - skos:definition "Links a study to one or more images." . + rdfs:label "owc_tvdss" ; + dcterms:title "oil water contact depth" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "oil water contact depth" ; + skos:definition "Depth of the original oil water contact (OWC) zone (average) (m TVDSS)" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "meter" . -nmdc:study_set a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "study_set" ; - rdfs:domain nmdc:Database ; - rdfs:range nmdc:Study ; - rdfs:subPropertyOf nmdc:object_set ; - skos:definition "This property links a database object to the set of studies within it." . + 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" . -nmdc:subject a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range nmdc:GeneProduct . + rdfs:label "oxygen" ; + dcterms:title "oxygen" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "oxygen" ; + skos:definition "Oxygen (gas) amount or concentration at the time of sampling" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter, parts per million" . -nmdc:subsurface_depth a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "subsurface_depth" ; - rdfs:range nmdc:QuantityValue . + rdfs:label "part_org_carb" ; + dcterms:title "particulate organic carbon" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "particulate organic carbon" ; + skos:definition "Concentration of particulate organic carbon" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "microgram per liter" . -nmdc:technical_reps a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "technical_reps" ; - dcterms:title "number technical replicate" ; - rdfs:range linkml:String ; - skos:definition "If sending technical replicates of the same sample, indicate the replicate count." . + rdfs:label "part_org_nitro" ; + dcterms:title "particulate organic nitrogen" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "particulate organic nitrogen" ; + skos:definition "Concentration of particulate organic nitrogen" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "microgram per liter, micromole per liter" . -nmdc:title a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study." ; - skos:exactMatch dcterms:title . + rdfs:label "particle_class" ; + dcterms:title "particle classification" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "particle classification" ; + skos:definition "Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values" ; + skos:inScheme ; + nmdc:expected_value "particle name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "micrometer" . -nmdc:too_short_contig_num a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "too_short_contig_num" ; - rdfs:range linkml:Integer . + rdfs:label "pcr_cond" ; + dcterms:title "pcr conditions" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "pcr conditions" ; + skos:definition "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'" ; + skos:inScheme ; + nmdc:expected_value "initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles" . -nmdc:total_bases a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "total_bases" ; - rdfs:range linkml:String . + rdfs:label "pcr_primers" ; + dcterms:title "pcr primers" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "pcr primers" ; + skos:definition "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters" ; + skos:inScheme ; + nmdc:expected_value "FWD: forward primer sequence;REV:reverse primer sequence" . -nmdc:unbinned_contig_num a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "unbinned_contig_num" ; - rdfs:range linkml:Integer . + rdfs:label "permeability" ; + dcterms:title "permeability" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "permeability" ; + skos:definition "Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))" ; + skos:inScheme ; + nmdc:expected_value "measurement value range" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "mD" . -nmdc:version a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "version" ; - rdfs:range linkml:String . + rdfs:label "perturbation" ; + dcterms:title "perturbation" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "perturbation" ; + skos:definition "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types" ; + skos:inScheme ; + nmdc:expected_value "perturbation type name;perturbation interval and duration" ; + nmdc:occurrence "m" . -nmdc:was_informed_by a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "was_informed_by" ; - rdfs:range nmdc:Activity ; - skos:exactMatch prov:wasInformedBy . + rdfs:label "pesticide_regm" ; + dcterms:title "pesticide regimen" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "pesticide regimen" ; + skos:definition "Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens" ; + skos:inScheme ; + nmdc:expected_value "pesticide name;pesticide amount;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram, mole per liter, milligram per liter" . -nmdc:zinc a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "zinc" ; - dcterms:title "zinc" ; + rdfs:label "petroleum_hydrocarb" ; + dcterms:title "petroleum hydrocarbon" ; rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf nmdc:attribute ; - skos:altLabel "zinc" ; - skos:definition "Concentration of zinc in the sample" ; + rdfs:subPropertyOf ; + skos:altLabel "petroleum hydrocarbon" ; + skos:definition "Concentration of petroleum hydrocarbon" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "mg/kg (ppm)" . - -CHEBI:17790 a owl:Class, - nmdc:SolventEnum ; - rdfs:label "methanol" . - -CHEBI:35255 a owl:Class, - nmdc:SolventEnum ; - rdfs:label "chloroform" . - - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Principal Investigator" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "email" ; - rdfs:range linkml:String ; - skos:definition "An email address for an entity such as a person. This should be the primary email address used." ; - skos:exactMatch . - -EFO:0001741 a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Submitter" . + nmdc:preferred_unit "micromole per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "latitude" ; - rdfs:domain nmdc:GeolocationValue ; - rdfs:range nmdc:DecimalDegree ; - skos:definition "latitude" ; - skos:exactMatch , - . + rdfs:label "ph" ; + dcterms:title "pH" ; + rdfs:range linkml:Double ; + rdfs:subPropertyOf ; + skos:altLabel "pH" ; + skos:definition "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "longitude" ; - rdfs:domain nmdc:GeolocationValue ; - rdfs:range nmdc:DecimalDegree ; - skos:definition "longitude" ; - skos:exactMatch , - . + 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" . -prov:hadRole a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "applied_role" ; - rdfs:domain nmdc:CreditAssociation ; - rdfs:range nmdc:CreditEnum ; - skos:exactMatch prov:hadRole . + rdfs:label "ph_regm" ; + dcterms:title "pH regimen" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "pH regimen" ; + skos:definition "Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen" ; + skos:inScheme ; + nmdc:expected_value "measurement value;treatment interval and duration" ; + nmdc:occurrence "m" . -prov:qualifiedAssociation a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "has_credit_associations" ; - rdfs:domain nmdc:Study ; - rdfs:range nmdc:CreditAssociation ; - skos:definition "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study" ; - skos:exactMatch prov:qualifiedAssociation ; - nmdc:display_hint "Other researchers associated with this study." . - - a owl:Class, - nmdc:BiosampleCategoryEnum ; - rdfs:label "FICUS" . - - a owl:Class, - nmdc:BiosampleCategoryEnum ; - rdfs:label "LTER" . - - a owl:Class, - nmdc:ProcessingInstitutionEnum ; - rdfs:label "UCSD" . - - a owl:Class, - nmdc:ProcessingInstitutionEnum ; - rdfs:label "Battelle" . - - a owl:Class, - nmdc:ProcessingInstitutionEnum ; - rdfs:label "EMSL" . - - a owl:Class, - nmdc:ProcessingInstitutionEnum ; - rdfs:label "JGI" . - - a owl:Class, - nmdc:ProcessingInstitutionEnum ; - rdfs:label "ANL" . - - a owl:Class, - nmdc:BiosampleCategoryEnum ; - rdfs:label "SFA" . + rdfs:label "phaeopigments" ; + dcterms:title "phaeopigments" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "phaeopigments" ; + skos:definition "Concentration of phaeopigments; can include multiple phaeopigments" ; + skos:inScheme ; + nmdc:expected_value "phaeopigment name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "milligram per cubic meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_size" ; - dcterms:title "amount or size of sample collected" ; + rdfs:label "phosphate" ; + dcterms:title "phosphate" ; 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:exactMatch ; + rdfs:subPropertyOf ; + skos:altLabel "phosphate" ; + skos:definition "Concentration of phosphate" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; - nmdc:preferred_unit "millliter, gram, milligram, liter" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "samp_collec_device" ; - dcterms:title "sample collection device" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf ; - skos:altLabel "sample collection device" ; - skos:definition "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)." ; - skos:exactMatch ; - nmdc:expected_value "device name" . + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter" . - 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" ; - skos:exactMatch ; - nmdc:expected_value "text or EFO and/or OBI" . + rdfs:label "phosplipid_fatt_acid" ; + dcterms:title "phospholipid fatty acid" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "phospholipid fatty acid" ; + skos:definition "Concentration of phospholipid fatty acids; can include multiple values" ; + skos:inScheme ; + nmdc:expected_value "phospholipid fatty acid name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "mole per gram, mole per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "collection_date" ; - dcterms:title "collection date" ; - rdfs:range nmdc:TimestampValue ; - rdfs:subPropertyOf ; - skos:altLabel "collection date" ; - skos:definition "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant" ; - skos:exactMatch ; - nmdc:expected_value "date and time" . + rdfs:label "photon_flux" ; + dcterms:title "photon flux" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "photon flux" ; + skos:definition "Measurement of photon flux" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "number of photons per second per unit area" . - a owl:ObjectProperty, + 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:exactMatch ; - 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." . + rdfs:label "plant_growth_med" ; + dcterms:title "plant growth medium" ; + rdfs:range nmdc:ControlledTermValue ; + rdfs:subPropertyOf ; + skos:altLabel "plant growth medium" ; + skos:definition "Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary" ; + skos:inScheme ; + nmdc:expected_value "EO or enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + 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:exactMatch ; - nmdc:expected_value "Environmental entities having causal influences upon the entity at time of sampling." . + rdfs:label "plant_product" ; + dcterms:title "plant product" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "plant product" ; + skos:definition "Substance produced by the plant, where the sample was obtained from" ; + skos:inScheme ; + nmdc:expected_value "product name" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + 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:exactMatch ; - nmdc:expected_value "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." . + rdfs:label "plant_sex" ; + dcterms:title "plant sex" ; + rdfs:range nmdc:PlantSexEnum ; + rdfs:subPropertyOf ; + skos:altLabel "plant sex" ; + skos:definition "Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite." ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_mat_process" ; - dcterms:title "sample material processing" ; + rdfs:label "plant_struc" ; + dcterms:title "plant structure" ; rdfs:range nmdc:ControlledTermValue ; - rdfs:subPropertyOf ; - skos:altLabel "sample material processing" ; - skos:definition "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed." ; - skos:exactMatch ; - nmdc:expected_value "text" . + rdfs:subPropertyOf ; + skos:altLabel "plant structure" ; + skos:definition "Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here." ; + skos:inScheme ; + nmdc:expected_value "PO" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "size_frac" ; - dcterms:title "size fraction selected" ; + rdfs:label "pollutants" ; + dcterms:title "pollutants" ; rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "size fraction selected" ; - skos:definition "Filtering pore size used in sample preparation" ; - skos:exactMatch ; - nmdc:expected_value "filter size value range" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "depth" ; - dcterms:title "depth" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "depth" ; - skos:definition "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples." ; - skos:exactMatch ; - nmdc:expected_value "measurement value" . + rdfs:subPropertyOf ; + skos:altLabel "pollutants" ; + skos:definition "Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant" ; + skos:inScheme ; + nmdc:expected_value "pollutant name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram, mole per liter, milligram per liter, microgram per cubic meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "source_mat_id" ; - dcterms:title "source material identifiers" ; + rdfs:label "pool_dna_extracts" ; + dcterms:title "pooling of DNA extracts (if done)" ; 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:exactMatch ; - 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 "biotic_relationship" ; - dcterms:title "observed biotic relationship" ; - rdfs:range ; - 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:exactMatch ; - nmdc:expected_value "enumeration" . + rdfs:subPropertyOf ; + skos:altLabel "pooling of DNA extracts (if done)" ; + skos:definition "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given" ; + skos:inScheme ; + nmdc:expected_value "pooling status;number of pooled extracts" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "alt" ; - dcterms:title "altitude" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "altitude" ; - skos:definition "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" . + rdfs:label "porosity" ; + dcterms:title "porosity" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "porosity" ; + skos:definition "Porosity of deposited sediment is volume of voids divided by the total volume of sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value or range" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "percentage" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "barometric_press" ; - dcterms:title "barometric pressure" ; + rdfs:label "potassium" ; + dcterms:title "potassium" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "barometric pressure" ; - skos:definition "Force per unit area exerted against a surface by the weight of air above that surface" ; - skos:exactMatch ; + skos:altLabel "potassium" ; + skos:definition "Concentration of potassium in the sample" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "millibar" . + nmdc:preferred_unit "milligram per liter, parts per million" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "carb_dioxide" ; - dcterms:title "carbon dioxide" ; + rdfs:label "pour_point" ; + dcterms:title "pour point" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "carbon dioxide" ; - skos:definition "Carbon dioxide (gas) amount or concentration at the time of sampling" ; - skos:exactMatch ; + skos:altLabel "pour point" ; + skos:definition "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter, parts per million" . + nmdc:preferred_unit "degree Celsius" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "carb_monoxide" ; - dcterms:title "carbon monoxide" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "pre_treatment" ; + dcterms:title "pre-treatment" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "carbon monoxide" ; - skos:definition "Carbon monoxide (gas) amount or concentration at the time of sampling" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter, parts per million" . + skos:altLabel "pre-treatment" ; + skos:definition "The process of pre-treatment removes materials that can be easily collected from the raw wastewater" ; + skos:inScheme ; + nmdc:expected_value "pre-treatment type" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "org_count_qpcr_info" ; - dcterms:title "organism count qPCR information" ; - rdfs:range linkml:String ; + rdfs:label "pres_animal_insect" ; + dcterms:title "presence of pets, animals, or insects" ; + rdfs:range [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^(cat|dog|rodent|snake|other);\\d+$" ] ) ] ) ] ; rdfs:subPropertyOf ; - skos:altLabel "organism count qPCR information" ; - skos:definition "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)" ; - skos:exactMatch ; - nmdc:expected_value "gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "number of cells per gram (or ml or cm^2)" . + skos:altLabel "presence of pets, animals, or insects" ; + skos:definition "The type and number of animals or insects present in the sampling space." ; + skos:inScheme ; + nmdc:expected_value "enumeration;count" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "humidity" ; - dcterms:title "humidity" ; + rdfs:label "pressure" ; + dcterms:title "pressure" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "humidity" ; - skos:definition "Amount of water vapour in the air, at the time of sampling" ; - skos:exactMatch ; + skos:altLabel "pressure" ; + skos:definition "Pressure to which the sample is subject to, in atmospheres" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "gram per cubic meter" . + nmdc:preferred_unit "atmosphere" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "methane" ; - dcterms:title "methane" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "prev_land_use_meth" ; + dcterms:title "history/previous land use method" ; + rdfs:range linkml:String ; rdfs:subPropertyOf ; - skos:altLabel "methane" ; - skos:definition "Methane (gas) amount or concentration at the time of sampling" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter, parts per billion, parts per million" . + skos:altLabel "history/previous land use method" ; + skos:definition "Reference or method used in determining previous land use and dates" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tot_nitro" ; - dcterms:title "total nitrogen concentration" ; + rdfs:label "previous_land_use" ; + dcterms:title "history/previous land use" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "history/previous land use" ; + skos:definition "Previous land use and dates" ; + skos:inScheme ; + nmdc:expected_value "land use name;date" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "primary_prod" ; + dcterms:title "primary production" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "total nitrogen concentration" ; - skos:definition "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen" ; - skos:exactMatch ; + skos:altLabel "primary production" ; + skos:definition "Measurement of primary production, generally measured as isotope uptake" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter, micromole per liter, milligram per liter" . + nmdc:preferred_unit "milligram per cubic meter per day, gram per square meter per day" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "organism_count" ; - dcterms:title "organism count" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "primary_treatment" ; + dcterms:title "primary treatment" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "organism count" ; - skos:definition "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)" ; - skos:exactMatch ; - nmdc:expected_value "organism name;measurement value;enumeration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" . + skos:altLabel "primary treatment" ; + skos:definition "The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed" ; + skos:inScheme ; + nmdc:expected_value "primary treatment type" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "oxygen" ; - dcterms:title "oxygen" ; + rdfs:label "prod_rate" ; + dcterms:title "production rate" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "oxygen" ; - skos:definition "Oxygen (gas) amount or concentration at the time of sampling" ; - skos:exactMatch ; + skos:altLabel "production rate" ; + skos:definition "Oil and/or gas production rates per well (e.g. 524 m3 / day)" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter, parts per million" . + nmdc:preferred_unit "cubic meter per day" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tot_iron" ; - dcterms:title "total iron" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "prod_start_date" ; + dcterms:title "production start date" ; + rdfs:range nmdc:TimestampValue ; rdfs:subPropertyOf ; - skos:altLabel "total iron" ; - skos:definition "Concentration of total iron in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter, milligram per kilogram" . + skos:altLabel "production start date" ; + skos:definition "Date of field's first production" ; + skos:inScheme ; + nmdc:expected_value "timestamp" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "diss_inorg_phosp" ; - dcterms:title "dissolved inorganic phosphorus" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "profile_position" ; + dcterms:title "profile position" ; + rdfs:range nmdc:ProfilePositionEnum ; rdfs:subPropertyOf ; - skos:altLabel "dissolved inorganic phosphorus" ; - skos:definition "Concentration of dissolved inorganic phosphorus in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter, milligram per liter, parts per million" . + skos:altLabel "profile position" ; + skos:definition "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "pollutants" ; - dcterms:title "pollutants" ; + rdfs:label "quad_pos" ; + dcterms:title "quadrant position" ; + rdfs:range nmdc:QuadPosEnum ; + rdfs:subPropertyOf ; + skos:altLabel "quadrant position" ; + skos:definition "The quadrant position of the sampling room within the building" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "radiation_regm" ; + dcterms:title "radiation regimen" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "pollutants" ; - skos:definition "Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant" ; - skos:exactMatch ; - nmdc:expected_value "pollutant name;measurement value" ; + skos:altLabel "radiation regimen" ; + skos:definition "Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens" ; + skos:inScheme ; + nmdc:expected_value "radiation type name;radiation amount;treatment interval and duration" ; nmdc:occurrence "m" ; - nmdc:preferred_unit "gram, mole per liter, milligram per liter, microgram per cubic meter" . + nmdc:preferred_unit "rad, gray" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "air_PM_concen" ; - dcterms:title "air particulate matter concentration" ; + rdfs:label "rainfall_regm" ; + dcterms:title "rainfall regimen" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "air particulate matter concentration" ; - skos:definition "Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM" ; - skos:exactMatch ; - nmdc:expected_value "particulate matter name;measurement value" ; + skos:altLabel "rainfall regimen" ; + skos:definition "Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens" ; + skos:inScheme ; + nmdc:expected_value "measurement value;treatment interval and duration" ; nmdc:occurrence "m" ; - nmdc:preferred_unit "micrograms per cubic meter" . + nmdc:preferred_unit "millimeter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_store_temp" ; - dcterms:title "sample storage temperature" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "reactor_type" ; + dcterms:title "reactor type" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "sample storage temperature" ; - skos:definition "Temperature at which sample was stored, e.g. -80 degree Celsius" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "degree Celsius" . + skos:altLabel "reactor type" ; + skos:definition "Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage" ; + skos:inScheme ; + nmdc:expected_value "reactor type name" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "solar_irradiance" ; - dcterms:title "solar irradiance" ; + rdfs:label "redox_potential" ; + dcterms:title "redox potential" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "solar irradiance" ; - skos:definition "The amount of solar energy that arrives at a specific area of a surface during a specific time interval" ; - skos:exactMatch ; + skos:altLabel "redox potential" ; + skos:definition "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "kilowatts per square meter per day, ergs per square centimeter per second" . + nmdc:preferred_unit "millivolt" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "temp" ; - dcterms:title "temperature" ; + rdfs:label "rel_air_humidity" ; + dcterms:title "relative air humidity" ; rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "temperature" ; - skos:definition "Temperature of the sample at the time of sampling." ; - skos:exactMatch ; + rdfs:subPropertyOf ; + skos:altLabel "relative air humidity" ; + skos:definition "Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; - nmdc:preferred_unit "degree Celsius" . + nmdc:occurrence "1" ; + nmdc:preferred_unit "percentage" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ventilation_rate" ; - dcterms:title "ventilation rate" ; + rdfs:label "rel_humidity_out" ; + dcterms:title "outside relative humidity" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "ventilation rate" ; - skos:definition "Ventilation rate of the system in the sampled premises" ; - skos:exactMatch ; + skos:altLabel "outside relative humidity" ; + skos:definition "The recorded outside relative humidity value at the time of sampling" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "cubic meter per minute, liters per second" . + nmdc:preferred_unit "gram of air, kilogram of air" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "volatile_org_comp" ; - dcterms:title "volatile organic compounds" ; - rdfs:range nmdc:TextValue ; + rdfs:label "rel_samp_loc" ; + dcterms:title "relative sampling location" ; + rdfs:range nmdc:RelSampLocEnum ; rdfs:subPropertyOf ; - skos:altLabel "volatile organic compounds" ; - skos:definition "Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound" ; - skos:exactMatch ; - nmdc:expected_value "volatile organic compound name;measurement value" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "microgram per cubic meter, parts per million, nanogram per liter" . + skos:altLabel "relative sampling location" ; + skos:definition "The sampling location within the train car" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_store_dur" ; - dcterms:title "sample storage duration" ; + rdfs:label "reservoir" ; + dcterms:title "reservoir name" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "sample storage duration" ; - skos:definition "Duration for which the sample was stored" ; - skos:exactMatch ; - nmdc:expected_value "duration" ; + skos:altLabel "reservoir name" ; + skos:definition "Name of the reservoir (e.g. Carapebus)" ; + skos:inScheme ; + nmdc:expected_value "name" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tot_phosp" ; - dcterms:title "total phosphorus" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "resins_pc" ; + dcterms:title "resins wt%" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "total phosphorus" ; - skos:definition "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "resins wt%" ; + skos:definition "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" ; + skos:inScheme ; + nmdc:expected_value "name;measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . + nmdc:preferred_unit "percent" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "wind_speed" ; - dcterms:title "wind speed" ; + rdfs:label "room_air_exch_rate" ; + dcterms:title "room air exchange rate" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "wind speed" ; - skos:definition "Speed of wind measured at the time of sampling" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "room air exchange rate" ; + skos:definition "The rate at which outside air replaces indoor air in a given space" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "meter per second, kilometer per hour" . + nmdc:preferred_unit "liter per hour" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "diss_oxygen" ; - dcterms:title "dissolved oxygen" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "room_architec_elem" ; + dcterms:title "room architectural elements" ; + rdfs:range linkml:String ; rdfs:subPropertyOf ; - skos:altLabel "dissolved oxygen" ; - skos:definition "Concentration of dissolved oxygen" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per kilogram, milligram per liter" . + skos:altLabel "room architectural elements" ; + skos:definition "The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure" ; + skos:inScheme ; + nmdc:expected_value "free text" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tan" ; - dcterms:title "total acid number" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "room_condt" ; + dcterms:title "room condition" ; + rdfs:range nmdc:RoomCondtEnum ; rdfs:subPropertyOf ; - skos:altLabel "total acid number" ; - skos:definition "Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter" . + skos:altLabel "room condition" ; + skos:definition "The condition of the room at the time of sampling" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rel_air_humidity" ; - dcterms:title "relative air humidity" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "room_connected" ; + dcterms:title "rooms connected by a doorway" ; + rdfs:range nmdc:RoomConnectedEnum ; rdfs:subPropertyOf ; - skos:altLabel "relative air humidity" ; - skos:definition "Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "percentage" . + skos:altLabel "rooms connected by a doorway" ; + skos:definition "List of rooms connected to the sampling room by a doorway" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "abs_air_humidity" ; - dcterms:title "absolute air humidity" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "room_count" ; + dcterms:title "room count" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "absolute air humidity" ; - skos:definition "Actual mass of water vapor - mh20 - present in the air water vapor mixture" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "gram per gram, kilogram per kilogram, kilogram, pound" . + skos:altLabel "room count" ; + skos:definition "The total count of rooms in the built structure including all room types" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "surf_humidity" ; - dcterms:title "surface humidity" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "room_dim" ; + dcterms:title "room dimensions" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "surface humidity" ; - skos:definition "Surfaces: water activity as a function of air and material moisture" ; - skos:exactMatch ; + skos:altLabel "room dimensions" ; + skos:definition "The length, width and height of sampling room" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "percentage" . + nmdc:preferred_unit "meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "air_temp" ; - dcterms:title "air temperature" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "room_door_dist" ; + dcterms:title "room door distance" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "air temperature" ; - skos:definition "Temperature of the air at the time of sampling" ; - skos:exactMatch ; + skos:altLabel "room door distance" ; + skos:definition "Distance between doors (meters) in the hallway between the sampling room and adjacent rooms" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "degree Celsius" . + nmdc:preferred_unit "meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "surf_temp" ; - dcterms:title "surface temperature" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "room_door_share" ; + dcterms:title "rooms that share a door with sampling room" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "surface temperature" ; - skos:definition "Temperature of the surface at the time of sampling" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "degree Celsius" . + skos:altLabel "rooms that share a door with sampling room" ; + skos:definition "List of room(s) (room number, room name) sharing a door with the sampling room" ; + skos:inScheme ; + nmdc:expected_value "room name;room number" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "viscosity" ; - dcterms:title "viscosity" ; + rdfs:label "room_hallway" ; + dcterms:title "rooms that are on the same hallway" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "viscosity" ; - skos:definition "A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C)" ; - skos:exactMatch ; - nmdc:expected_value "measurement value;measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "cP at degree Celsius" . + skos:altLabel "rooms that are on the same hallway" ; + skos:definition "List of room(s) (room number, room name) located in the same hallway as sampling room" ; + skos:inScheme ; + nmdc:expected_value "room name;room number" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "pour_point" ; - dcterms:title "pour point" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "room_loc" ; + dcterms:title "room location in building" ; + rdfs:range nmdc:RoomLocEnum ; rdfs:subPropertyOf ; - skos:altLabel "pour point" ; - skos:definition "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "degree Celsius" . + skos:altLabel "room location in building" ; + skos:definition "The position of the room within the building" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "surf_moisture" ; - dcterms:title "surface moisture" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "room_moist_dam_hist" ; + dcterms:title "room moisture damage or mold history" ; + rdfs:range linkml:Integer ; rdfs:subPropertyOf ; - skos:altLabel "surface moisture" ; - skos:definition "Water held on a surface" ; - skos:exactMatch ; + skos:altLabel "room moisture damage or mold history" ; + skos:definition "The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "room_net_area" ; + dcterms:title "room net area" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "room net area" ; + skos:definition "The net floor area of sampling room. Net area excludes wall thicknesses" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "parts per million, gram per cubic meter, gram per square meter" . + nmdc:preferred_unit "square feet, square meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dew_point" ; - dcterms:title "dew point" ; + rdfs:label "room_occup" ; + dcterms:title "room occupancy" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "dew point" ; - skos:definition "The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water." ; - skos:exactMatch ; + skos:altLabel "room occupancy" ; + skos:definition "Count of room occupancy at time of sampling" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "degree Celsius" . + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "saturates_pc" ; - dcterms:title "saturates wt%" ; - rdfs:range nmdc:TextValue ; + rdfs:label "room_samp_pos" ; + dcterms:title "room sampling position" ; + rdfs:range nmdc:RoomSampPosEnum ; rdfs:subPropertyOf ; - skos:altLabel "saturates wt%" ; - skos:definition "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" ; - skos:exactMatch ; - nmdc:expected_value "name;measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "percent" . + skos:altLabel "room sampling position" ; + skos:definition "The horizontal sampling position in the room relative to architectural elements" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "aromatics_pc" ; - dcterms:title "aromatics wt%" ; - rdfs:range nmdc:TextValue ; + rdfs:label "room_type" ; + dcterms:title "room type" ; + rdfs:range nmdc:RoomTypeEnum ; rdfs:subPropertyOf ; - skos:altLabel "aromatics wt%" ; - skos:definition "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" ; - skos:exactMatch ; - nmdc:expected_value "name;measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "percent" . + skos:altLabel "room type" ; + skos:definition "The main purpose or activity of the sampling room. A room is any distinguishable space within a structure" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "resins_pc" ; - dcterms:title "resins wt%" ; + rdfs:label "room_vol" ; + dcterms:title "room volume" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "resins wt%" ; - skos:definition "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" ; - skos:exactMatch ; - nmdc:expected_value "name;measurement value" ; + skos:altLabel "room volume" ; + skos:definition "Volume of sampling room" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "percent" . + nmdc:preferred_unit "cubic feet, cubic meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "asphaltenes_pc" ; - dcterms:title "asphaltenes wt%" ; + rdfs:label "room_wall_share" ; + dcterms:title "rooms that share a wall with sampling room" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "asphaltenes wt%" ; - skos:definition "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" ; - skos:exactMatch ; - nmdc:expected_value "name;measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "percent" . + skos:altLabel "rooms that share a wall with sampling room" ; + skos:definition "List of room(s) (room number, room name) sharing a wall with the sampling room" ; + skos:inScheme ; + nmdc:expected_value "room name;room number" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_loc_corr_rate" ; - dcterms:title "corrosion rate at sample location" ; + rdfs:label "room_window_count" ; + dcterms:title "room window count" ; + rdfs:range linkml:Integer ; + rdfs:subPropertyOf ; + skos:altLabel "room window count" ; + skos:definition "Number of windows in the room" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "root_cond" ; + dcterms:title "rooting conditions" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "corrosion rate at sample location" ; - skos:definition "Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays" ; - skos:exactMatch ; - nmdc:expected_value "measurement value range" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "millimeter per year" . + skos:altLabel "rooting conditions" ; + skos:definition "Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container." ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI,url or free text" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "glucosidase_act" ; - dcterms:title "glucosidase activity" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "root_med_carbon" ; + dcterms:title "rooting medium carbon" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "glucosidase activity" ; - skos:definition "Measurement of glucosidase activity" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "rooting medium carbon" ; + skos:definition "Source of organic carbon in the culture rooting medium; e.g. sucrose." ; + skos:inScheme ; + nmdc:expected_value "carbon source name;measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "mol per liter per hour" . + nmdc:preferred_unit "milligram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "diss_iron" ; - dcterms:title "dissolved iron" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "dissolved iron" ; - skos:definition "Concentration of dissolved iron in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + rdfs:label "root_med_macronutr" ; + dcterms:title "rooting medium macronutrients" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "rooting medium macronutrients" ; + skos:definition "Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L)." ; + skos:inScheme ; + nmdc:expected_value "macronutrient name;measurement value" ; nmdc:occurrence "1" ; nmdc:preferred_unit "milligram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "amount_light" ; - dcterms:title "amount of light" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "root_med_micronutr" ; + dcterms:title "rooting medium micronutrients" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "amount of light" ; - skos:definition "The unit of illuminance and luminous emittance, measuring luminous flux per unit area" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "rooting medium micronutrients" ; + skos:definition "Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L)." ; + skos:inScheme ; + nmdc:expected_value "micronutrient name;measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "lux, lumens per square meter" . + nmdc:preferred_unit "milligram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "avg_dew_point" ; - dcterms:title "average dew point" ; + rdfs:label "root_med_ph" ; + dcterms:title "rooting medium pH" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "average dew point" ; - skos:definition "The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day" ; - skos:exactMatch ; + skos:altLabel "rooting medium pH" ; + skos:definition "pH measurement of the culture rooting medium; e.g. 5.5." ; + skos:inScheme ; nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "degree Celsius" . + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "avg_temp" ; - dcterms:title "average temperature" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "root_med_regl" ; + dcterms:title "rooting medium regulators" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "average temperature" ; - skos:definition "The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "rooting medium regulators" ; + skos:definition "Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA." ; + skos:inScheme ; + nmdc:expected_value "regulator name;measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "degree Celsius" . + nmdc:preferred_unit "milligram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ceil_thermal_mass" ; - dcterms:title "ceiling thermal mass" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "root_med_solid" ; + dcterms:title "rooting medium solidifier" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "ceiling thermal mass" ; - skos:definition "The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "joule per degree Celsius" . + skos:altLabel "rooting medium solidifier" ; + skos:definition "Specification of the solidifying agent in the culture rooting medium; e.g. agar." ; + skos:inScheme ; + nmdc:expected_value "name" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "exp_duct" ; - dcterms:title "exposed ductwork" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "root_med_suppl" ; + dcterms:title "rooting medium organic supplements" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "exposed ductwork" ; - skos:definition "The amount of exposed ductwork in the room" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "rooting medium organic supplements" ; + skos:definition "Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L)." ; + skos:inScheme ; + nmdc:expected_value "supplement name;measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "square meter" . + nmdc:preferred_unit "milligram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "built_struc_age" ; - dcterms:title "built structure age" ; + rdfs:label "salinity" ; + dcterms:title "salinity" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "built structure age" ; - skos:definition "The age of the built structure since construction" ; - skos:exactMatch ; - nmdc:expected_value "value" ; + skos:altLabel "salinity" ; + skos:definition "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater." ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "year" . + nmdc:preferred_unit "practical salinity unit, percentage" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ceil_area" ; - dcterms:title "ceiling area" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "salinity_meth" ; + dcterms:title "salinity method" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "ceiling area" ; - skos:definition "The area of the ceiling space within the room" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "square meter" . + 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, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "suspend_solids" ; - dcterms:title "suspended solids" ; + rdfs:label "salt_regm" ; + dcterms:title "salt regimen" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "suspended solids" ; - skos:definition "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances" ; - skos:exactMatch ; - nmdc:expected_value "suspended solid name;measurement value" ; + skos:altLabel "salt regimen" ; + skos:definition "Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens" ; + skos:inScheme ; + nmdc:expected_value "salt name;salt amount;treatment interval and duration" ; nmdc:occurrence "m" ; - nmdc:preferred_unit "gram, microgram, milligram per liter, mole per liter, gram per liter, part per million" . + nmdc:preferred_unit "gram, microgram, mole per liter, gram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "vfa" ; - dcterms:title "volatile fatty acids" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "samp_capt_status" ; + dcterms:title "sample capture status" ; + rdfs:range nmdc:SampCaptStatusEnum ; rdfs:subPropertyOf ; - skos:altLabel "volatile fatty acids" ; - skos:definition "Concentration of Volatile Fatty Acids in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter, parts per million" . + skos:altLabel "sample capture status" ; + skos:definition "Reason for the sample" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "benzene" ; - dcterms:title "benzene" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "benzene" ; - skos:definition "Concentration of benzene in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter, parts per million" . + rdfs:label "samp_collec_device" ; + dcterms:title "sample collection device" ; + rdfs:range linkml:String ; + rdfs:subPropertyOf ; + skos:altLabel "sample collection device" ; + skos:definition "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)." ; + skos:inScheme ; + nmdc:expected_value "device name" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "toluene" ; - dcterms:title "toluene" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "toluene" ; - skos:definition "Concentration of toluene in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter, parts per million" . + 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, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ethylbenzene" ; - dcterms:title "ethylbenzene" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "samp_collect_point" ; + dcterms:title "sample collection point" ; + rdfs:range nmdc:SampCollectPointEnum ; rdfs:subPropertyOf ; - skos:altLabel "ethylbenzene" ; - skos:definition "Concentration of ethylbenzene in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter, parts per million" . + skos:altLabel "sample collection point" ; + skos:definition "Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "xylene" ; - dcterms:title "xylene" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "samp_dis_stage" ; + dcterms:title "sample disease stage" ; + rdfs:range nmdc:SampDisStageEnum ; rdfs:subPropertyOf ; - skos:altLabel "xylene" ; - skos:definition "Concentration of xylene in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter, parts per million" . + skos:altLabel "sample disease stage" ; + skos:definition "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen." ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "api" ; - dcterms:title "API gravity" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "samp_floor" ; + dcterms:title "sampling floor" ; + rdfs:range nmdc:SampFloorEnum ; rdfs:subPropertyOf ; - skos:altLabel "API gravity" ; - skos:definition "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API)" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "degrees API" . + skos:altLabel "sampling floor" ; + skos:definition "The floor of the building, where the sampling room is located" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "door_size" ; - dcterms:title "door area or size" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "samp_loc_corr_rate" ; + dcterms:title "corrosion rate at sample location" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "door area or size" ; - skos:definition "The size of the door" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "corrosion rate at sample location" ; + skos:definition "Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays" ; + skos:inScheme ; + nmdc:expected_value "measurement value range" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "square meter" . + nmdc:preferred_unit "millimeter per year" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "diss_org_nitro" ; - dcterms:title "dissolved organic nitrogen" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "dissolved organic nitrogen" ; - skos:definition "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter, milligram per liter" . + rdfs:label "samp_mat_process" ; + dcterms:title "sample material processing" ; + rdfs:range nmdc:ControlledTermValue ; + rdfs:subPropertyOf ; + skos:altLabel "sample material processing" ; + skos:definition "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed." ; + skos:inScheme ; + nmdc:expected_value "text" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "floor_age" ; - dcterms:title "floor age" ; + rdfs:label "samp_md" ; + dcterms:title "sample measured depth" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "floor age" ; - skos:definition "The time period since installment of the carpet or flooring" ; - skos:exactMatch ; - nmdc:expected_value "value" ; + skos:altLabel "sample measured depth" ; + skos:definition "In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field" ; + skos:inScheme ; + nmdc:expected_value "measurement value;enumeration" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "years, weeks, days" . + nmdc:preferred_unit "meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "floor_area" ; - dcterms:title "floor area" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "floor area" ; - skos:definition "The area of the floor space within the room" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "square meter" . + 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" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "floor_thermal_mass" ; - dcterms:title "floor thermal mass" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "samp_preserv" ; + dcterms:title "preservative added to sample" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "floor thermal mass" ; - skos:definition "The ability of the floor to provide inertia against temperature fluctuations" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "preservative added to sample" ; + skos:definition "Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)" ; + skos:inScheme ; + nmdc:expected_value "name;measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "joule per degree Celsius" . + nmdc:preferred_unit "milliliter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "height_carper_fiber" ; - dcterms:title "height carpet fiber mat" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "samp_room_id" ; + dcterms:title "sampling room ID or name" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "height carpet fiber mat" ; - skos:definition "The average carpet fiber height in the indoor environment" ; - skos:exactMatch ; + 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:preferred_unit "centimeter" . + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "inside_lux" ; - dcterms:title "inside lux light" ; + rdfs:label "samp_size" ; + dcterms:title "amount or size of sample collected" ; rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "inside lux light" ; - skos:definition "The recorded value at sampling time (power density)" ; - skos:exactMatch ; + 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:occurrence "1" ; - nmdc:preferred_unit "kilowatt per square metre" . + nmdc:preferred_unit "millliter, gram, milligram, liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_air_exch_rate" ; - dcterms:title "room air exchange rate" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "samp_sort_meth" ; + dcterms:title "sample size sorting method" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "room air exchange rate" ; - skos:definition "The rate at which outside air replaces indoor air in a given space" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "liter per hour" . + skos:altLabel "sample size sorting method" ; + skos:definition "Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor." ; + skos:inScheme ; + nmdc:expected_value "description of method" ; + nmdc:occurrence "m" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ext_door" ; - dcterms:title "exterior door count" ; + rdfs:label "samp_store_dur" ; + dcterms:title "sample storage duration" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "exterior door count" ; - skos:definition "The number of exterior doors in the built structure" ; - skos:exactMatch ; - nmdc:expected_value "value" ; + skos:altLabel "sample storage duration" ; + skos:definition "Duration for which the sample was stored" ; + skos:inScheme ; + nmdc:expected_value "duration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "aminopept_act" ; - dcterms:title "aminopeptidase activity" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "samp_store_loc" ; + dcterms:title "sample storage location" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "aminopeptidase activity" ; - skos:definition "Measurement of aminopeptidase activity" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "mole per liter per hour" . + skos:altLabel "sample storage location" ; + skos:definition "Location at which sample was stored, usually name of a specific freezer/room" ; + skos:inScheme ; + nmdc:expected_value "location name" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "bacteria_carb_prod" ; - dcterms:title "bacterial carbon production" ; + rdfs:label "samp_store_temp" ; + dcterms:title "sample storage temperature" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "bacterial carbon production" ; - skos:definition "Measurement of bacterial carbon production" ; - skos:exactMatch ; + skos:altLabel "sample storage temperature" ; + skos:definition "Temperature at which sample was stored, e.g. -80 degree Celsius" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "nanogram per hour" . + nmdc:preferred_unit "degree Celsius" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "biomass" ; - dcterms:title "biomass" ; - rdfs:range nmdc:TextValue ; + rdfs:label "samp_subtype" ; + dcterms:title "sample subtype" ; + rdfs:range nmdc:SampSubtypeEnum ; rdfs:subPropertyOf ; - skos:altLabel "biomass" ; - skos:definition "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements" ; - skos:exactMatch ; - nmdc:expected_value "biomass type;measurement value" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "ton, kilogram, gram" . + skos:altLabel "sample subtype" ; + skos:definition "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "bishomohopanol" ; - dcterms:title "bishomohopanol" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "samp_taxon_id" ; + dcterms:title "Taxonomy ID of DNA sample" ; + rdfs:range nmdc:ControlledIdentifiedTermValue ; + rdfs:subPropertyOf ; + skos:altLabel "Taxonomy ID of DNA sample" ; + skos:definition "NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome’ for mock community/positive controls, or 'blank sample' for negative controls." ; + skos:inScheme ; + skos:note "coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value" ; + nmdc:expected_value "Taxonomy ID" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "samp_time_out" ; + dcterms:title "sampling time outside" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "bishomohopanol" ; - skos:definition "Concentration of bishomohopanol" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "sampling time outside" ; + skos:definition "The recent and long term history of outside sampling" ; + skos:inScheme ; + nmdc:expected_value "time" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter, microgram per gram" . + nmdc:preferred_unit "hour" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "bromide" ; - dcterms:title "bromide" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "samp_transport_cond" ; + dcterms:title "sample transport conditions" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "bromide" ; - skos:definition "Concentration of bromide" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "sample transport conditions" ; + skos:definition "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C)" ; + skos:inScheme ; + nmdc:expected_value "measurement value;measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "parts per million" . + nmdc:preferred_unit "days;degree Celsius" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "chlorophyll" ; - dcterms:title "chlorophyll" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "samp_tvdss" ; + dcterms:title "sample true vertical depth subsea" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "chlorophyll" ; - skos:definition "Concentration of chlorophyll" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "sample true vertical depth subsea" ; + skos:definition "Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m" ; + skos:inScheme ; + nmdc:expected_value "measurement value or measurement value range" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per cubic meter, microgram per liter" . + nmdc:preferred_unit "meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "diether_lipids" ; - dcterms:title "diether lipids" ; + rdfs:label "samp_type" ; + dcterms:title "sample type" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "diether lipids" ; - skos:definition "Concentration of diether lipids; can include multiple types of diether lipids" ; - skos:exactMatch ; - nmdc:expected_value "diether lipid name;measurement value" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "nanogram per liter" . + skos:altLabel "sample type" ; + skos:definition "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246)." ; + skos:inScheme ; + nmdc:expected_value "GENEPIO:0001246" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "diss_hydrogen" ; - dcterms:title "dissolved hydrogen" ; + rdfs:label "samp_vol_we_dna_ext" ; + dcterms:title "sample volume or weight for DNA extraction" ; rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "dissolved hydrogen" ; - skos:definition "Concentration of dissolved hydrogen" ; - skos:exactMatch ; + rdfs:subPropertyOf ; + skos:altLabel "sample volume or weight for DNA extraction" ; + skos:definition "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)." ; + skos:inScheme ; nmdc:expected_value "measurement value" ; + nmdc:preferred_unit "millliter, gram, milligram, square centimeter" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "samp_weather" ; + dcterms:title "sampling day weather" ; + rdfs:range nmdc:SampWeatherEnum ; + rdfs:subPropertyOf ; + skos:altLabel "sampling day weather" ; + skos:definition "The weather on the sampling day" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "samp_well_name" ; + dcterms:title "sample well name" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "sample well name" ; + skos:definition "Name of the well (e.g. BXA1123) where sample was taken" ; + skos:inScheme ; + nmdc:expected_value "name" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "saturates_pc" ; + dcterms:title "saturates wt%" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "saturates wt%" ; + skos:definition "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)" ; + skos:inScheme ; + nmdc:expected_value "name;measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter" . + nmdc:preferred_unit "percent" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "phaeopigments" ; - dcterms:title "phaeopigments" ; + rdfs:label "season" ; + dcterms:title "season" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "phaeopigments" ; - skos:definition "Concentration of phaeopigments; can include multiple phaeopigments" ; - skos:exactMatch ; - nmdc:expected_value "phaeopigment name;measurement value" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "milligram per cubic meter" . + skos:altLabel "season" ; + skos:definition "The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729)." ; + skos:inScheme ; + nmdc:expected_value "NCIT:C94729" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "phosplipid_fatt_acid" ; - dcterms:title "phospholipid fatty acid" ; + rdfs:label "season_environment" ; + dcterms:title "seasonal environment" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "phospholipid fatty acid" ; - skos:definition "Concentration of phospholipid fatty acids; can include multiple values" ; - skos:exactMatch ; - nmdc:expected_value "phospholipid fatty acid name;measurement value" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "mole per gram, mole per liter" . + skos:altLabel "seasonal environment" ; + skos:definition "Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment" ; + skos:inScheme ; + nmdc:expected_value "seasonal environment name;treatment interval and duration" ; + nmdc:occurrence "m" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "redox_potential" ; - dcterms:title "redox potential" ; + rdfs:label "season_precpt" ; + dcterms:title "mean seasonal precipitation" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "redox potential" ; - skos:definition "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential" ; - skos:exactMatch ; + 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 "millivolt" . + nmdc:preferred_unit "millimeter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "salinity" ; - dcterms:title "salinity" ; + rdfs:label "season_temp" ; + dcterms:title "mean seasonal temperature" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "salinity" ; - skos:definition "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater." ; - skos:exactMatch ; + skos:altLabel "mean seasonal temperature" ; + skos:definition "Mean seasonal temperature" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "practical salinity unit, percentage" . + nmdc:preferred_unit "degree Celsius" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "silicate" ; - dcterms:title "silicate" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "season_use" ; + dcterms:title "seasonal use" ; + rdfs:range nmdc:SeasonUseEnum ; rdfs:subPropertyOf ; - skos:altLabel "silicate" ; - skos:definition "Concentration of silicate" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter" . + skos:altLabel "seasonal use" ; + skos:definition "The seasons the space is occupied" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "water_content" ; - dcterms:title "water content" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "secondary_treatment" ; + dcterms:title "secondary treatment" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "water content" ; - skos:definition "Water content measurement" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "gram per gram or cubic centimeter per cubic centimeter" . + skos:altLabel "secondary treatment" ; + skos:definition "The process for substantially degrading the biological content of the sewage" ; + skos:inScheme ; + nmdc:expected_value "secondary treatment type" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rel_humidity_out" ; - dcterms:title "outside relative humidity" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "sediment_type" ; + dcterms:title "sediment type" ; + rdfs:range nmdc:SedimentTypeEnum ; rdfs:subPropertyOf ; - skos:altLabel "outside relative humidity" ; - skos:definition "The recorded outside relative humidity value at the time of sampling" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "gram of air, kilogram of air" . + skos:altLabel "sediment type" ; + skos:definition "Information about the sediment type based on major constituents" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "turbidity" ; - dcterms:title "turbidity" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "turbidity" ; - skos:definition "Measure of the amount of cloudiness or haziness in water caused by individual particles" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "formazin turbidity unit, formazin nephelometric units" . + rdfs:label "seq_meth" ; + dcterms:title "sequencing method" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "sequencing method" ; + skos:definition "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)." ; + skos:inScheme ; + nmdc:expected_value "Text or OBI" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_dim" ; - dcterms:title "room dimensions" ; + rdfs:label "seq_quality_check" ; + dcterms:title "sequence quality check" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "sequence quality check" ; + skos:definition "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA" ; + skos:inScheme ; + nmdc:expected_value "none or manually edited" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "sewage_type" ; + dcterms:title "sewage type" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "room dimensions" ; - skos:definition "The length, width and height of sampling room" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "meter" . + skos:altLabel "sewage type" ; + skos:definition "Type of wastewater treatment plant as municipial or industrial" ; + skos:inScheme ; + nmdc:expected_value "sewage type name" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_door_dist" ; - dcterms:title "room door distance" ; + rdfs:label "shad_dev_water_mold" ; + dcterms:title "shading device signs of water/mold" ; + rdfs:range linkml:String ; + rdfs:subPropertyOf ; + skos:altLabel "shading device signs of water/mold" ; + skos:definition "Signs of the presence of mold or mildew on the shading device" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "shading_device_cond" ; + dcterms:title "shading device condition" ; + rdfs:range nmdc:ShadingDeviceCondEnum ; + rdfs:subPropertyOf ; + skos:altLabel "shading device condition" ; + skos:definition "The physical condition of the shading device at the time of sampling" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "shading_device_loc" ; + dcterms:title "shading device location" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "room door distance" ; - skos:definition "Distance between doors (meters) in the hallway between the sampling room and adjacent rooms" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "meter" . + skos:altLabel "shading device location" ; + skos:definition "The location of the shading device in relation to the built structure" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_net_area" ; - dcterms:title "room net area" ; + rdfs:label "shading_device_mat" ; + dcterms:title "shading device material" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "room net area" ; - skos:definition "The net floor area of sampling room. Net area excludes wall thicknesses" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "square feet, square meter" . + skos:altLabel "shading device material" ; + skos:definition "The material the shading device is composed of" ; + skos:inScheme ; + nmdc:expected_value "material name" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_vol" ; - dcterms:title "room volume" ; + rdfs:label "shading_device_type" ; + dcterms:title "shading device type" ; + rdfs:range nmdc:ShadingDeviceTypeEnum ; + rdfs:subPropertyOf ; + skos:altLabel "shading device type" ; + skos:definition "The type of shading device" ; + skos:inScheme ; + 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 "room volume" ; - skos:definition "Volume of sampling room" ; - skos:exactMatch ; + 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" ; + dcterms:title "silicate" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "silicate" ; + skos:definition "Concentration of silicate" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "cubic feet, cubic meter" . + nmdc:preferred_unit "micromole per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_time_out" ; - dcterms:title "sampling time outside" ; + rdfs:label "size_frac" ; + dcterms:title "size fraction selected" ; rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf ; + skos:altLabel "size fraction selected" ; + skos:definition "Filtering pore size used in sample preparation" ; + skos:inScheme ; + nmdc:expected_value "filter size value range" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "size_frac_low" ; + dcterms:title "size-fraction lower threshold" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "sampling time outside" ; - skos:definition "The recent and long term history of outside sampling" ; - skos:exactMatch ; - nmdc:expected_value "time" ; + skos:altLabel "size-fraction lower threshold" ; + skos:definition "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample" ; + skos:inScheme ; + nmdc:expected_value "value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "hour" . + nmdc:preferred_unit "micrometer" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "temp_out" ; - dcterms:title "temperature outside house" ; + rdfs:label "size_frac_up" ; + dcterms:title "size-fraction upper threshold" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "temperature outside house" ; - skos:definition "The recorded temperature value at sampling time outside" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "size-fraction upper threshold" ; + skos:definition "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample" ; + skos:inScheme ; + nmdc:expected_value "value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "degree Celsius" . + nmdc:preferred_unit "micrometer" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "wall_area" ; - dcterms:title "wall area" ; + rdfs:label "slope_aspect" ; + dcterms:title "slope aspect" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "wall area" ; - skos:definition "The total area of the sampled room's walls" ; - skos:exactMatch ; + 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 "square meter" . + nmdc:preferred_unit "degree" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "water_current" ; - dcterms:title "water current" ; + rdfs:label "slope_gradient" ; + dcterms:title "slope gradient" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "water current" ; - skos:definition "Measurement of magnitude and direction of flow within a fluid" ; - skos:exactMatch ; + 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 "cubic meter per second, knots" . + nmdc:preferred_unit "percentage" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "org_matter" ; - dcterms:title "organic matter" ; + rdfs:label "sludge_retent_time" ; + dcterms:title "sludge retention time" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "organic matter" ; - skos:definition "Concentration of organic matter" ; - skos:exactMatch ; + skos:altLabel "sludge retention time" ; + skos:definition "The time activated sludge remains in reactor" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter" . + nmdc:preferred_unit "hours" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "org_nitro" ; - dcterms:title "organic nitrogen" ; + rdfs:label "sodium" ; + dcterms:title "sodium" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "organic nitrogen" ; - skos:definition "Concentration of organic nitrogen" ; - skos:exactMatch ; + skos:altLabel "sodium" ; + skos:definition "Sodium concentration in the sample" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter" . + nmdc:preferred_unit "milligram per liter, parts per million" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "particle_class" ; - dcterms:title "particle classification" ; - rdfs:range nmdc:TextValue ; + rdfs:label "soil_horizon" ; + dcterms:title "soil horizon" ; + rdfs:range nmdc:SoilHorizonEnum ; rdfs:subPropertyOf ; - skos:altLabel "particle classification" ; - skos:definition "Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values" ; - skos:exactMatch ; - nmdc:expected_value "particle name;measurement value" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "micrometer" . + skos:altLabel "soil horizon" ; + skos:definition "Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "porosity" ; - dcterms:title "porosity" ; - rdfs:range nmdc:TextValue ; + rdfs:label "soil_text_measure" ; + dcterms:title "soil texture measurement" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "porosity" ; - skos:definition "Porosity of deposited sediment is volume of voids divided by the total volume of sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value or range" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "percentage" . + skos:altLabel "soil texture measurement" ; + skos:definition "The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional." ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "specific_humidity" ; - dcterms:title "specific humidity" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "soil_texture_meth" ; + dcterms:title "soil texture method" ; + rdfs:range linkml:String ; rdfs:subPropertyOf ; - skos:altLabel "specific humidity" ; - skos:definition "The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound." ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "gram of air, kilogram of air" . + skos:altLabel "soil texture method" ; + skos:definition "Reference or method used in determining soil texture" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sewage_type" ; - dcterms:title "sewage type" ; + rdfs:label "soil_type" ; + dcterms:title "soil type" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "sewage type" ; - skos:definition "Type of wastewater treatment plant as municipial or industrial" ; - skos:exactMatch ; - nmdc:expected_value "sewage type name" ; + skos:altLabel "soil type" ; + skos:definition "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes." ; + skos:inScheme ; + nmdc:expected_value "ENVO_00001998" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_sort_meth" ; - dcterms:title "sample size sorting method" ; + rdfs:label "soil_type_meth" ; + dcterms:title "soil type method" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "sample size sorting method" ; - skos:definition "Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor." ; - skos:exactMatch ; - nmdc:expected_value "description of method" ; - nmdc:occurrence "m" . + skos:altLabel "soil type method" ; + skos:definition "Reference or method used in determining soil series name or other lower-level classification" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI or url" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "occup_density_samp" ; - dcterms:title "occupant density at sampling" ; + rdfs:label "solar_irradiance" ; + dcterms:title "solar irradiance" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "occupant density at sampling" ; - skos:definition "Average number of occupants at time of sampling per square footage" ; - skos:exactMatch ; + skos:altLabel "solar irradiance" ; + skos:definition "The amount of solar energy that arrives at a specific area of a surface during a specific time interval" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" . + nmdc:occurrence "1" ; + nmdc:preferred_unit "kilowatts per square meter per day, ergs per square centimeter per second" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "address" ; - dcterms:title "address" ; + rdfs:label "soluble_inorg_mat" ; + dcterms:title "soluble inorganic material" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "address" ; - skos:definition "The street name and building number where the sampling occurred." ; - skos:exactMatch ; - nmdc:expected_value "value" ; - nmdc:occurrence "1" . + skos:altLabel "soluble inorganic material" ; + skos:definition "Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc." ; + skos:inScheme ; + nmdc:expected_value "soluble inorganic material name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram, microgram, mole per liter, gram per liter, parts per million" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "adj_room" ; - dcterms:title "adjacent rooms" ; + rdfs:label "soluble_org_mat" ; + dcterms:title "soluble organic material" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "adjacent rooms" ; - skos:definition "List of rooms (room number, room name) immediately adjacent to the sampling room" ; - skos:exactMatch ; - nmdc:expected_value "room name;room number" ; - nmdc:occurrence "1" . + skos:altLabel "soluble organic material" ; + skos:definition "Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc." ; + skos:inScheme ; + nmdc:expected_value "soluble organic material name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram, microgram, mole per liter, gram per liter, parts per million" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "exp_pipe" ; - dcterms:title "exposed pipes" ; + rdfs:label "soluble_react_phosp" ; + dcterms:title "soluble reactive phosphorus" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "exposed pipes" ; - skos:definition "The number of exposed pipes in the room" ; - skos:exactMatch ; + skos:altLabel "soluble reactive phosphorus" ; + skos:definition "Concentration of soluble reactive phosphorus" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" . + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "wall_height" ; - dcterms:title "wall height" ; - rdfs:range nmdc:QuantityValue ; + 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" ; + dcterms:title "space typical state" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "wall height" ; - skos:definition "The average height of the walls in the sampled room" ; - skos:exactMatch ; - nmdc:expected_value "value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "centimeter" . + skos:altLabel "space typical state" ; + skos:definition "Customary or normal state of the space" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "wall_thermal_mass" ; - dcterms:title "wall thermal mass" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "specific" ; + dcterms:title "specifications" ; + rdfs:range nmdc:SpecificEnum ; rdfs:subPropertyOf ; - skos:altLabel "wall thermal mass" ; - skos:definition "The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "joule per degree Celsius" . + skos:altLabel "specifications" ; + skos:definition "The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "water_feat_size" ; - dcterms:title "water feature size" ; + rdfs:label "specific_humidity" ; + dcterms:title "specific humidity" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "water feature size" ; - skos:definition "The size of the water feature" ; - skos:exactMatch ; + skos:altLabel "specific humidity" ; + skos:definition "The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound." ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "square meter" . + nmdc:preferred_unit "gram of air, kilogram of air" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "window_size" ; - dcterms:title "window area/size" ; - rdfs:range nmdc:TextValue ; + rdfs:label "sr_dep_env" ; + dcterms:title "source rock depositional environment" ; + rdfs:range nmdc:SrDepEnvEnum ; rdfs:subPropertyOf ; - skos:altLabel "window area/size" ; - skos:definition "The window's length and width" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "inch, meter" . + skos:altLabel "source rock depositional environment" ; + skos:definition "Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "floor_count" ; - dcterms:title "floor count" ; - rdfs:range nmdc:TextValue ; + rdfs:label "sr_geol_age" ; + dcterms:title "source rock geological age" ; + rdfs:range nmdc:SrGeolAgeEnum ; rdfs:subPropertyOf ; - skos:altLabel "floor count" ; - skos:definition "The number of floors in the building, including basements and mechanical penthouse" ; - skos:exactMatch ; - nmdc:expected_value "value" ; + skos:altLabel "source rock geological age" ; + skos:definition "Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "freq_clean" ; - dcterms:title "frequency of cleaning" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "sr_kerog_type" ; + dcterms:title "source rock kerogen type" ; + rdfs:range nmdc:SrKerogTypeEnum ; rdfs:subPropertyOf ; - skos:altLabel "frequency of cleaning" ; - skos:definition "The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually." ; - skos:exactMatch ; - nmdc:expected_value "enumeration or {text}" ; + skos:altLabel "source rock kerogen type" ; + skos:definition "Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "freq_cook" ; - dcterms:title "frequency of cooking" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "sr_lithology" ; + dcterms:title "source rock lithology" ; + rdfs:range nmdc:SrLithologyEnum ; rdfs:subPropertyOf ; - skos:altLabel "frequency of cooking" ; - skos:definition "The number of times a meal is cooked per week" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "source rock lithology" ; + skos:definition "Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "hall_count" ; - dcterms:title "hallway/corridor count" ; + rdfs:label "standing_water_regm" ; + dcterms:title "standing water regimen" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "hallway/corridor count" ; - skos:definition "The total count of hallways and cooridors in the built structure" ; - skos:exactMatch ; - nmdc:expected_value "value" ; - nmdc:occurrence "1" . + skos:altLabel "standing water regimen" ; + skos:definition "Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens" ; + skos:inScheme ; + nmdc:expected_value "standing water type;treatment interval and duration" ; + nmdc:occurrence "m" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "max_occup" ; - dcterms:title "maximum occupancy" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "store_cond" ; + dcterms:title "storage conditions" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "maximum occupancy" ; - skos:definition "The maximum amount of people allowed in the indoor environment" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "storage conditions" ; + skos:definition "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)." ; + skos:inScheme ; + nmdc:expected_value "storage condition type;duration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "number_plants" ; - dcterms:title "number of houseplants" ; + rdfs:label "substructure_type" ; + dcterms:title "substructure type" ; + rdfs:range nmdc:SubstructureTypeEnum ; + rdfs:subPropertyOf ; + skos:altLabel "substructure type" ; + skos:definition "The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "m" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "sulfate" ; + dcterms:title "sulfate" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "number of houseplants" ; - skos:definition "The number of plant(s) in the sampling space" ; - skos:exactMatch ; + skos:altLabel "sulfate" ; + skos:definition "Concentration of sulfate in the sample" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" . + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "number_pets" ; - dcterms:title "number of pets" ; + rdfs:label "sulfate_fw" ; + dcterms:title "sulfate in formation water" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "number of pets" ; - skos:definition "The number of pets residing in the sampled space" ; - skos:exactMatch ; + skos:altLabel "sulfate in formation water" ; + skos:definition "Original sulfate concentration in the hydrocarbon resource" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" . + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "number_resident" ; - dcterms:title "number of residents" ; + rdfs:label "sulfide" ; + dcterms:title "sulfide" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "number of residents" ; - skos:definition "The number of individuals currently occupying in the sampling location" ; - skos:exactMatch ; + skos:altLabel "sulfide" ; + skos:definition "Concentration of sulfide in the sample" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" . + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_architec_elem" ; - dcterms:title "room architectural elements" ; - rdfs:range linkml:String ; + rdfs:label "surf_air_cont" ; + dcterms:title "surface-air contaminant" ; + rdfs:range nmdc:SurfAirContEnum ; rdfs:subPropertyOf ; - skos:altLabel "room architectural elements" ; - skos:definition "The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure" ; - skos:exactMatch ; - nmdc:expected_value "free text" ; - nmdc:occurrence "1" . + skos:altLabel "surface-air contaminant" ; + skos:definition "Contaminant identified on surface" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "m" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_count" ; - dcterms:title "room count" ; - rdfs:range nmdc:TextValue ; + rdfs:label "surf_humidity" ; + dcterms:title "surface humidity" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "room count" ; - skos:definition "The total count of rooms in the built structure including all room types" ; - skos:exactMatch ; - nmdc:expected_value "value" ; - nmdc:occurrence "1" . + skos:altLabel "surface humidity" ; + skos:definition "Surfaces: water activity as a function of air and material moisture" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "percentage" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_moist_dam_hist" ; - dcterms:title "room moisture damage or mold history" ; - rdfs:range linkml:Integer ; + rdfs:label "surf_material" ; + dcterms:title "surface material" ; + rdfs:range nmdc:SurfMaterialEnum ; rdfs:subPropertyOf ; - skos:altLabel "room moisture damage or mold history" ; - skos:definition "The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed" ; - skos:exactMatch ; - nmdc:expected_value "value" ; + skos:altLabel "surface material" ; + skos:definition "Surface materials at the point of sampling" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_occup" ; - dcterms:title "room occupancy" ; + rdfs:label "surf_moisture" ; + dcterms:title "surface moisture" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "room occupancy" ; - skos:definition "Count of room occupancy at time of sampling" ; - skos:exactMatch ; + skos:altLabel "surface moisture" ; + skos:definition "Water held on a surface" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" . + nmdc:occurrence "1" ; + nmdc:preferred_unit "parts per million, gram per cubic meter, gram per square meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_window_count" ; - dcterms:title "room window count" ; - rdfs:range linkml:Integer ; + rdfs:label "surf_moisture_ph" ; + dcterms:title "surface moisture pH" ; + rdfs:range linkml:Double ; rdfs:subPropertyOf ; - skos:altLabel "room window count" ; - skos:definition "Number of windows in the room" ; - skos:exactMatch ; - nmdc:expected_value "value" ; + skos:altLabel "surface moisture pH" ; + skos:definition "ph measurement of surface" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_hallway" ; - dcterms:title "rooms that are on the same hallway" ; - rdfs:range nmdc:TextValue ; + rdfs:label "surf_temp" ; + dcterms:title "surface temperature" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "rooms that are on the same hallway" ; - skos:definition "List of room(s) (room number, room name) located in the same hallway as sampling room" ; - skos:exactMatch ; - nmdc:expected_value "room name;room number" ; - nmdc:occurrence "1" . + skos:altLabel "surface temperature" ; + skos:definition "Temperature of the surface at the time of sampling" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "degree Celsius" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_door_share" ; - dcterms:title "rooms that share a door with sampling room" ; - rdfs:range nmdc:TextValue ; + rdfs:label "suspend_part_matter" ; + dcterms:title "suspended particulate matter" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "rooms that share a door with sampling room" ; - skos:definition "List of room(s) (room number, room name) sharing a door with the sampling room" ; - skos:exactMatch ; - nmdc:expected_value "room name;room number" ; - nmdc:occurrence "1" . + skos:altLabel "suspended particulate matter" ; + skos:definition "Concentration of suspended particulate matter" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_wall_share" ; - dcterms:title "rooms that share a wall with sampling room" ; + rdfs:label "suspend_solids" ; + dcterms:title "suspended solids" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "rooms that share a wall with sampling room" ; - skos:definition "List of room(s) (room number, room name) sharing a wall with the sampling room" ; - skos:exactMatch ; - nmdc:expected_value "room name;room number" ; - nmdc:occurrence "1" . + skos:altLabel "suspended solids" ; + skos:definition "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances" ; + skos:inScheme ; + nmdc:expected_value "suspended solid name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "gram, microgram, milligram per liter, mole per liter, gram per liter, part per million" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_room_id" ; - dcterms:title "sampling room ID or name" ; - rdfs:range nmdc:TextValue ; + rdfs:label "tan" ; + dcterms:title "total acid number" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - 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:exactMatch ; - nmdc:expected_value "value" ; - nmdc:occurrence "1" . + skos:altLabel "total acid number" ; + skos:definition "Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "shading_device_mat" ; - dcterms:title "shading device material" ; + rdfs:label "target_gene" ; + dcterms:title "target gene" ; rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "shading device material" ; - skos:definition "The material the shading device is composed of" ; - skos:exactMatch ; - nmdc:expected_value "material name" ; - nmdc:occurrence "1" . + rdfs:subPropertyOf ; + skos:altLabel "target gene" ; + skos:definition "Targeted gene or locus name for marker gene studies" ; + skos:inScheme ; + nmdc:expected_value "gene name" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "window_open_freq" ; - dcterms:title "window open frequency" ; + rdfs:label "target_subfragment" ; + dcterms:title "target subfragment" ; rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "window open frequency" ; - skos:definition "The number of times windows are opened per week" ; - skos:exactMatch ; - nmdc:expected_value "value" ; - nmdc:occurrence "1" . + rdfs:subPropertyOf ; + skos:altLabel "target subfragment" ; + skos:definition "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA" ; + skos:inScheme ; + nmdc:expected_value "gene fragment name" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ances_data" ; - dcterms:title "ancestral data" ; - rdfs:range nmdc:TextValue ; + rdfs:label "temp" ; + dcterms:title "temperature" ; + rdfs:range nmdc:QuantityValue ; + rdfs:subPropertyOf ; + skos:altLabel "temperature" ; + skos:definition "Temperature of the sample at the time of sampling." ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:preferred_unit "degree Celsius" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "temp_out" ; + dcterms:title "temperature outside house" ; + rdfs:range nmdc:QuantityValue ; 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:exactMatch ; - nmdc:expected_value "free text" ; - nmdc:occurrence "1" . + skos:altLabel "temperature outside house" ; + skos:definition "The recorded temperature value at sampling time outside" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "degree Celsius" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_common_name" ; - dcterms:title "host common name" ; + rdfs:label "tertiary_treatment" ; + dcterms:title "tertiary treatment" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "host common name" ; - skos:definition "Common name of the host." ; - skos:exactMatch ; - nmdc:expected_value "common name" ; + skos:altLabel "tertiary treatment" ; + skos:definition "The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment" ; + skos:inScheme ; + nmdc:expected_value "tertiary treatment type" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_dis_stage" ; - dcterms:title "sample disease stage" ; - rdfs:range ; + rdfs:label "tidal_stage" ; + dcterms:title "tidal stage" ; + rdfs:range nmdc:TidalStageEnum ; rdfs:subPropertyOf ; - skos:altLabel "sample disease stage" ; - skos:definition "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen." ; - skos:exactMatch ; + skos:altLabel "tidal stage" ; + skos:definition "Stage of tide" ; + skos:inScheme ; nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_taxid" ; - dcterms:title "host taxid" ; - rdfs:range nmdc:ControlledIdentifiedTermValue ; + rdfs:label "tillage" ; + dcterms:title "history/tillage" ; + rdfs:range nmdc:TillageEnum ; rdfs:subPropertyOf ; - skos:altLabel "host taxid" ; - skos:definition "NCBI taxon id of the host, e.g. 9606" ; - skos:exactMatch ; - nmdc:expected_value "NCBI taxon identifier" ; - nmdc:occurrence "1" . + skos:altLabel "history/tillage" ; + skos:definition "Note method(s) used for tilling" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "m" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_life_stage" ; - dcterms:title "host life stage" ; + rdfs:label "tiss_cult_growth_med" ; + dcterms:title "tissue culture growth media" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "host life stage" ; - skos:definition "Description of life stage of host" ; - skos:exactMatch ; - nmdc:expected_value "stage" ; + skos:altLabel "tissue culture growth media" ; + skos:definition "Description of plant tissue culture growth media used" ; + skos:inScheme ; + nmdc:expected_value "PMID,DOI,url or free text" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_substrate" ; - dcterms:title "host substrate" ; - rdfs:range nmdc:TextValue ; + rdfs:label "toluene" ; + dcterms:title "toluene" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "host substrate" ; - skos:definition "The growth substrate of the host." ; - skos:exactMatch ; - nmdc:expected_value "substrate name" ; - nmdc:occurrence "1" . + skos:altLabel "toluene" ; + skos:definition "Concentration of toluene in the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter, parts per million" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_age" ; - dcterms:title "host age" ; + rdfs:label "tot_carb" ; + dcterms:title "total carbon" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "host age" ; - skos:definition "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees" ; - skos:exactMatch ; - nmdc:expected_value "value" ; + skos:altLabel "total carbon" ; + skos:definition "Total carbon content" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "year, day, hour" . + nmdc:preferred_unit "microgram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_length" ; - dcterms:title "host length" ; + rdfs:label "tot_depth_water_col" ; + dcterms:title "total depth of water column" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "host length" ; - skos:definition "The length of subject" ; - skos:exactMatch ; + skos:altLabel "total depth of water column" ; + skos:definition "Measurement of total depth of water column" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "centimeter, millimeter, meter" . + nmdc:preferred_unit "meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_dry_mass" ; - dcterms:title "host dry mass" ; + rdfs:label "tot_diss_nitro" ; + dcterms:title "total dissolved nitrogen" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "host dry mass" ; - skos:definition "Measurement of dry mass" ; - skos:exactMatch ; + skos:altLabel "total dissolved nitrogen" ; + skos:definition "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "kilogram, gram" . + nmdc:preferred_unit "microgram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "blood_press_diast" ; - dcterms:title "host blood pressure diastolic" ; + rdfs:label "tot_inorg_nitro" ; + dcterms:title "total inorganic nitrogen" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "host blood pressure diastolic" ; - skos:definition "Resting diastolic blood pressure, measured as mm mercury" ; - skos:exactMatch ; + skos:altLabel "total inorganic nitrogen" ; + skos:definition "Total inorganic nitrogen content" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "millimeter mercury" . + nmdc:preferred_unit "microgram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "blood_press_syst" ; - dcterms:title "host blood pressure systolic" ; + rdfs:label "tot_iron" ; + dcterms:title "total iron" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "host blood pressure systolic" ; - skos:definition "Resting systolic blood pressure, measured as mm mercury" ; - skos:exactMatch ; + skos:altLabel "total iron" ; + skos:definition "Concentration of total iron in the sample" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "millimeter mercury" . + nmdc:preferred_unit "milligram per liter, milligram per kilogram" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_color" ; - dcterms:title "host color" ; - rdfs:range nmdc:TextValue ; + rdfs:label "tot_nitro" ; + dcterms:title "total nitrogen concentration" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "host color" ; - skos:definition "The color of host" ; - skos:exactMatch ; - nmdc:expected_value "color" ; - nmdc:occurrence "1" . + skos:altLabel "total nitrogen concentration" ; + skos:definition "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen" ; + 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, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_shape" ; - dcterms:title "host shape" ; - rdfs:range nmdc:TextValue ; + rdfs:label "tot_nitro_cont_meth" ; + dcterms:title "total nitrogen content method" ; + rdfs:range linkml:String ; rdfs:subPropertyOf ; - skos:altLabel "host shape" ; - skos:definition "Morphological shape of host" ; - skos:exactMatch ; - nmdc:expected_value "shape" ; + 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, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_tot_mass" ; - dcterms:title "host total mass" ; + rdfs:label "tot_nitro_content" ; + dcterms:title "total nitrogen content" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "host total mass" ; - skos:definition "Total mass of the host at collection, the unit depends on host" ; - skos:exactMatch ; + 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 "kilogram, gram" . + nmdc:preferred_unit "microgram per liter, micromole per liter, milligram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_height" ; - dcterms:title "host height" ; + 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 "host height" ; - skos:definition "The height of subject" ; - skos:exactMatch ; + 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 "centimeter, millimeter, meter" . + nmdc:preferred_unit "gram Carbon per kilogram sample material" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_body_temp" ; - dcterms:title "host body temperature" ; + rdfs:label "tot_part_carb" ; + dcterms:title "total particulate carbon" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "host body temperature" ; - skos:definition "Core body temperature of the host when sample was collected" ; - skos:exactMatch ; + skos:altLabel "total particulate carbon" ; + skos:definition "Total particulate carbon content" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "degree Celsius" . + nmdc:preferred_unit "microgram per liter, micromole per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "basin" ; - dcterms:title "basin name" ; - rdfs:range nmdc:TextValue ; + rdfs:label "tot_phosp" ; + dcterms:title "total phosphorus" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "basin name" ; - skos:definition "Name of the basin (e.g. Campos)" ; - skos:exactMatch ; - nmdc:expected_value "name" ; - nmdc:occurrence "1" . + skos:altLabel "total phosphorus" ; + skos:definition "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "field" ; - dcterms:title "field name" ; - rdfs:range nmdc:TextValue ; + rdfs:label "tot_phosphate" ; + dcterms:title "total phosphate" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "field name" ; - skos:definition "Name of the hydrocarbon field (e.g. Albacora)" ; - skos:exactMatch ; - nmdc:expected_value "name" ; - nmdc:occurrence "1" . + skos:altLabel "total phosphate" ; + skos:definition "Total amount or concentration of phosphate" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "microgram per liter, micromole per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_well_name" ; - dcterms:title "sample well name" ; - rdfs:range nmdc:TextValue ; + rdfs:label "tot_sulfur" ; + dcterms:title "total sulfur" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "sample well name" ; - skos:definition "Name of the well (e.g. BXA1123) where sample was taken" ; - skos:exactMatch ; - nmdc:expected_value "name" ; - nmdc:occurrence "1" . + skos:altLabel "total sulfur" ; + skos:definition "Concentration of total sulfur in the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter, parts per million" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "win" ; - dcterms:title "well identification number" ; - rdfs:range nmdc:TextValue ; + rdfs:label "train_line" ; + dcterms:title "train line" ; + rdfs:range nmdc:TrainLineEnum ; rdfs:subPropertyOf ; - skos:altLabel "well identification number" ; - skos:definition "A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)" ; - skos:exactMatch ; - nmdc:expected_value "text" ; + skos:altLabel "train line" ; + skos:definition "The subway line name" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "alkalinity_method" ; - dcterms:title "alkalinity method" ; - rdfs:range nmdc:TextValue ; + rdfs:label "train_stat_loc" ; + dcterms:title "train station collection location" ; + rdfs:range nmdc:TrainStatLocEnum ; rdfs:subPropertyOf ; - skos:altLabel "alkalinity method" ; - skos:definition "Method used for alkalinity measurement" ; - skos:exactMatch ; - nmdc:expected_value "description of method" ; + skos:altLabel "train station collection location" ; + skos:definition "The train station collection location" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "additional_info" ; - dcterms:title "additional info" ; - rdfs:range nmdc:TextValue ; + rdfs:label "train_stop_loc" ; + dcterms:title "train stop collection location" ; + rdfs:range nmdc:TrainStopLocEnum ; rdfs:subPropertyOf ; - skos:altLabel "additional info" ; - skos:definition "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary" ; - skos:exactMatch ; - nmdc:expected_value "text" ; + skos:altLabel "train stop collection location" ; + skos:definition "The train stop collection location" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "reservoir" ; - dcterms:title "reservoir name" ; - rdfs:range nmdc:TextValue ; + rdfs:label "turbidity" ; + dcterms:title "turbidity" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "reservoir name" ; - skos:definition "Name of the reservoir (e.g. Carapebus)" ; - skos:exactMatch ; - nmdc:expected_value "name" ; - nmdc:occurrence "1" . + skos:altLabel "turbidity" ; + skos:definition "Measure of the amount of cloudiness or haziness in water caused by individual particles" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "formazin turbidity unit, formazin nephelometric units" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "carb_nitro_ratio" ; - dcterms:title "carbon/nitrogen ratio" ; + rdfs:label "tvdss_of_hcr_press" ; + dcterms:title "depth (TVDSS) of hydrocarbon resource pressure" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "carbon/nitrogen ratio" ; - skos:definition "Ratio of amount or concentrations of carbon to nitrogen" ; - skos:exactMatch ; + skos:altLabel "depth (TVDSS) of hydrocarbon resource pressure" ; + skos:definition "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m)." ; + skos:inScheme ; nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" . + nmdc:occurrence "1" ; + nmdc:preferred_unit "meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "cur_vegetation_meth" ; - dcterms:title "current vegetation method" ; - rdfs:range nmdc:TextValue ; + rdfs:label "tvdss_of_hcr_temp" ; + dcterms:title "depth (TVDSS) of hydrocarbon resource temperature" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "current vegetation method" ; - skos:definition "Reference or method used in vegetation classification" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . + skos:altLabel "depth (TVDSS) of hydrocarbon resource temperature" ; + skos:definition "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m)." ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "previous_land_use" ; - dcterms:title "history/previous land use" ; - rdfs:range nmdc:TextValue ; + rdfs:label "typ_occup_density" ; + dcterms:title "typical occupant density" ; + rdfs:range linkml:Double ; rdfs:subPropertyOf ; - skos:altLabel "history/previous land use" ; - skos:definition "Previous land use and dates" ; - skos:exactMatch ; - nmdc:expected_value "land use name;date" ; + skos:altLabel "typical occupant density" ; + skos:definition "Customary or normal density of occupants" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "prev_land_use_meth" ; - dcterms:title "history/previous land use method" ; - rdfs:range linkml:String ; + rdfs:label "ventilation_rate" ; + dcterms:title "ventilation rate" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "history/previous land use method" ; - skos:definition "Reference or method used in determining previous land use and dates" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . + skos:altLabel "ventilation rate" ; + skos:definition "Ventilation rate of the system in the sampled premises" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "cubic meter per minute, liters per second" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "crop_rotation" ; - dcterms:title "history/crop rotation" ; + rdfs:label "ventilation_type" ; + dcterms:title "ventilation type" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "history/crop rotation" ; - skos:definition "Whether or not crop is rotated, and if yes, rotation schedule" ; - skos:exactMatch ; - nmdc:expected_value "crop rotation status;schedule" ; + skos:altLabel "ventilation type" ; + skos:definition "Ventilation system used in the sampled premises" ; + skos:inScheme ; + nmdc:expected_value "ventilation type name" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "flooding" ; - dcterms:title "history/flooding" ; - rdfs:range nmdc:TimestampValue ; + rdfs:label "vfa" ; + dcterms:title "volatile fatty acids" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "history/flooding" ; - skos:definition "Historical and/or physical evidence of flooding" ; - skos:exactMatch ; - nmdc:expected_value "date" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extreme_event" ; - dcterms:title "history/extreme events" ; - rdfs:range nmdc:TimestampValue ; + skos:altLabel "volatile fatty acids" ; + skos:definition "Concentration of Volatile Fatty Acids in the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter, parts per million" . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "vfa_fw" ; + dcterms:title "vfa in formation water" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "history/extreme events" ; - skos:definition "Unusual physical events that may have affected microbial populations" ; - skos:exactMatch ; - nmdc:expected_value "date" ; - nmdc:occurrence "1" . + skos:altLabel "vfa in formation water" ; + skos:definition "Original volatile fatty acid concentration in the hydrocarbon resource" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "milligram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "horizon_meth" ; - dcterms:title "soil horizon method" ; - rdfs:range nmdc:TextValue ; + rdfs:label "vis_media" ; + dcterms:title "visual media" ; + rdfs:range nmdc:VisMediaEnum ; rdfs:subPropertyOf ; - skos:altLabel "soil horizon method" ; - skos:definition "Reference or method used in determining the horizon" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; + skos:altLabel "visual media" ; + skos:definition "The building visual media" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sieving" ; - dcterms:title "composite design/sieving" ; + rdfs:label "viscosity" ; + dcterms:title "viscosity" ; 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:exactMatch ; - nmdc:expected_value "design name and/or size;amount" ; - nmdc:occurrence "1" . + skos:altLabel "viscosity" ; + skos:definition "A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C)" ; + skos:inScheme ; + nmdc:expected_value "measurement value;measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "cP at degree Celsius" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "water_cont_soil_meth" ; - dcterms:title "water content method" ; - rdfs:range linkml:String ; + rdfs:label "volatile_org_comp" ; + dcterms:title "volatile organic compounds" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "water content method" ; - skos:definition "Reference or method used in determining the water content of soil" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . + skos:altLabel "volatile organic compounds" ; + skos:definition "Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound" ; + skos:inScheme ; + nmdc:expected_value "volatile organic compound name;measurement value" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "microgram per cubic meter, parts per million, nanogram per liter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "al_sat_meth" ; - dcterms:title "extreme_unusual_properties/Al saturation method" ; - rdfs:range nmdc:TextValue ; + rdfs:label "wall_area" ; + dcterms:title "wall area" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "extreme_unusual_properties/Al saturation method" ; - skos:definition "Reference or method used in determining Al saturation" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or URL" ; - nmdc:occurrence "1" . + skos:altLabel "wall area" ; + skos:definition "The total area of the sampled room's walls" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "square meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "pool_dna_extracts" ; - dcterms:title "pooling of DNA extracts (if done)" ; - rdfs:range nmdc:TextValue ; + rdfs:label "wall_const_type" ; + dcterms:title "wall construction type" ; + rdfs:range nmdc:WallConstTypeEnum ; rdfs:subPropertyOf ; - skos:altLabel "pooling of DNA extracts (if done)" ; - skos:definition "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given" ; - skos:exactMatch ; - nmdc:expected_value "pooling status;number of pooled extracts" ; + skos:altLabel "wall construction type" ; + skos:definition "The building class of the wall defined by the composition of the building elements and fire-resistance rating." ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "store_cond" ; - dcterms:title "storage conditions" ; - rdfs:range nmdc:TextValue ; + rdfs:label "wall_finish_mat" ; + dcterms:title "wall finish material" ; + rdfs:range nmdc:WallFinishMatEnum ; rdfs:subPropertyOf ; - skos:altLabel "storage conditions" ; - skos:definition "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other)." ; - skos:exactMatch ; - nmdc:expected_value "storage condition type;duration" ; + skos:altLabel "wall finish material" ; + skos:definition "The material utilized to finish the outer most layer of the wall" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "link_climate_info" ; - dcterms:title "link to climate information" ; - rdfs:range nmdc:TextValue ; + rdfs:label "wall_height" ; + dcterms:title "wall height" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "link to climate information" ; - skos:definition "Link to climate resource" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . + skos:altLabel "wall height" ; + skos:definition "The average height of the walls in the sampled room" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "centimeter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "link_class_info" ; - dcterms:title "link to classification information" ; - rdfs:range nmdc:TextValue ; + rdfs:label "wall_loc" ; + dcterms:title "wall location" ; + rdfs:range nmdc:WallLocEnum ; rdfs:subPropertyOf ; - skos:altLabel "link to classification information" ; - skos:definition "Link to digitized soil maps or other soil classification information" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; + skos:altLabel "wall location" ; + skos:definition "The relative location of the wall within the room" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "local_class_meth" ; - dcterms:title "soil_taxonomic/local classification method" ; - rdfs:range nmdc:TextValue ; + rdfs:label "wall_surf_treatment" ; + dcterms:title "wall surface treatment" ; + rdfs:range nmdc:WallSurfTreatmentEnum ; rdfs:subPropertyOf ; - skos:altLabel "soil_taxonomic/local classification method" ; - skos:definition "Reference or method used in determining the local soil classification" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; + skos:altLabel "wall surface treatment" ; + skos:definition "The surface treatment of interior wall" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "soil_type_meth" ; - dcterms:title "soil type method" ; - rdfs:range nmdc:TextValue ; + rdfs:label "wall_texture" ; + dcterms:title "wall texture" ; + rdfs:range nmdc:WallTextureEnum ; rdfs:subPropertyOf ; - skos:altLabel "soil type method" ; - skos:definition "Reference or method used in determining soil series name or other lower-level classification" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; + skos:altLabel "wall texture" ; + skos:definition "The feel, appearance, or consistency of a wall surface" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "soil_text_measure" ; - dcterms:title "soil texture measurement" ; + rdfs:label "wall_thermal_mass" ; + dcterms:title "wall thermal mass" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "soil texture measurement" ; - skos:definition "The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional." ; - skos:exactMatch ; + skos:altLabel "wall thermal mass" ; + skos:definition "The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" . + nmdc:occurrence "1" ; + nmdc:preferred_unit "joule per degree Celsius" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "soil_texture_meth" ; - dcterms:title "soil texture method" ; - rdfs:range linkml:String ; + rdfs:label "wall_water_mold" ; + dcterms:title "wall signs of water/mold" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "soil texture method" ; - skos:definition "Reference or method used in determining soil texture" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; + skos:altLabel "wall signs of water/mold" ; + skos:definition "Signs of the presence of mold or mildew on a wall" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tot_org_c_meth" ; - dcterms:title "total organic carbon method" ; + rdfs:label "wastewater_type" ; + dcterms:title "wastewater type" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "total organic carbon method" ; - skos:definition "Reference or method used in determining total organic carbon" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; + skos:altLabel "wastewater type" ; + skos:definition "The origin of wastewater such as human waste, rainfall, storm drains, etc." ; + skos:inScheme ; + nmdc:expected_value "wastewater type name" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tot_nitro_cont_meth" ; - dcterms:title "total nitrogen content method" ; + rdfs:label "water_cont_soil_meth" ; + dcterms:title "water 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:exactMatch ; + 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, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "micro_biomass_meth" ; - dcterms:title "microbial biomass method" ; - rdfs:range linkml:String ; + rdfs:label "water_content" ; + dcterms:title "water content" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "microbial biomass method" ; - skos:definition "Reference or method used in determining microbial biomass" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . + 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, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "link_addit_analys" ; - dcterms:title "links to additional analysis" ; - rdfs:range nmdc:TextValue ; + rdfs:label "water_current" ; + dcterms:title "water current" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "links to additional analysis" ; - skos:definition "Link to additional analysis results performed on the sample" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . + skos:altLabel "water current" ; + skos:definition "Measurement of magnitude and direction of flow within a fluid" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "cubic meter per second, knots" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "salinity_meth" ; - dcterms:title "salinity method" ; - rdfs:range nmdc:TextValue ; + rdfs:label "water_cut" ; + dcterms:title "water cut" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "salinity method" ; - skos:definition "Reference or method used in determining salinity" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . + skos:altLabel "water cut" ; + skos:definition "Current amount of water (%) in a produced fluid stream; or the average of the combined streams" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "percent" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "heavy_metals_meth" ; - dcterms:title "extreme_unusual_properties/heavy metals method" ; - rdfs:range nmdc:TextValue ; + rdfs:label "water_feat_size" ; + dcterms:title "water feature size" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "extreme_unusual_properties/heavy metals method" ; - skos:definition "Reference or method used in determining heavy metals" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . + skos:altLabel "water feature size" ; + skos:definition "The size of the water feature" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "square meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "pre_treatment" ; - dcterms:title "pre-treatment" ; - rdfs:range nmdc:TextValue ; + rdfs:label "water_feat_type" ; + dcterms:title "water feature type" ; + rdfs:range nmdc:WaterFeatTypeEnum ; rdfs:subPropertyOf ; - skos:altLabel "pre-treatment" ; - skos:definition "The process of pre-treatment removes materials that can be easily collected from the raw wastewater" ; - skos:exactMatch ; - nmdc:expected_value "pre-treatment type" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "primary_treatment" ; - dcterms:title "primary treatment" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "primary treatment" ; - skos:definition "The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed" ; - skos:exactMatch ; - nmdc:expected_value "primary treatment type" ; + skos:altLabel "water feature type" ; + skos:definition "The type of water feature present within the building being sampled" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "reactor_type" ; - dcterms:title "reactor type" ; - rdfs:range nmdc:TextValue ; + rdfs:label "water_prod_rate" ; + dcterms:title "water production rate" ; + rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "reactor type" ; - skos:definition "Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage" ; - skos:exactMatch ; - nmdc:expected_value "reactor type name" ; - nmdc:occurrence "1" . + skos:altLabel "water production rate" ; + skos:definition "Water production rates per well (e.g. 987 m3 / day)" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; + nmdc:occurrence "1" ; + nmdc:preferred_unit "cubic meter per day" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "secondary_treatment" ; - dcterms:title "secondary treatment" ; + rdfs:label "water_temp_regm" ; + dcterms:title "water temperature regimen" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "secondary treatment" ; - skos:definition "The process for substantially degrading the biological content of the sewage" ; - skos:exactMatch ; - nmdc:expected_value "secondary treatment type" ; - nmdc:occurrence "1" . + skos:altLabel "water temperature regimen" ; + skos:definition "Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens" ; + skos:inScheme ; + nmdc:expected_value "measurement value;treatment interval and duration" ; + nmdc:occurrence "m" ; + nmdc:preferred_unit "degree Celsius" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tertiary_treatment" ; - dcterms:title "tertiary treatment" ; + rdfs:label "watering_regm" ; + dcterms:title "watering regimen" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "tertiary treatment" ; - skos:definition "The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment" ; - skos:exactMatch ; - nmdc:expected_value "tertiary treatment type" ; - nmdc:occurrence "1" . + 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:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "wastewater_type" ; - dcterms:title "wastewater type" ; - rdfs:range nmdc:TextValue ; + rdfs:label "weekday" ; + dcterms:title "weekday" ; + rdfs:range nmdc:WeekdayEnum ; rdfs:subPropertyOf ; - skos:altLabel "wastewater type" ; - skos:definition "The origin of wastewater such as human waste, rainfall, storm drains, etc." ; - skos:exactMatch ; - nmdc:expected_value "wastewater type name" ; + skos:altLabel "weekday" ; + skos:definition "The day of the week when sampling occurred" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_genotype" ; - dcterms:title "host genotype" ; + rdfs:label "win" ; + dcterms:title "well identification number" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "host genotype" ; - skos:definition "Observed genotype" ; - skos:exactMatch ; - nmdc:expected_value "genotype" ; + skos:altLabel "well identification number" ; + skos:definition "A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)" ; + skos:inScheme ; + nmdc:expected_value "text" ; nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "hcr_temp" ; - dcterms:title "hydrocarbon resource original temperature" ; + rdfs:label "wind_direction" ; + dcterms:title "wind direction" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "hydrocarbon resource original temperature" ; - skos:definition "Original temperature of the hydrocarbon resource" ; - skos:exactMatch ; - nmdc:expected_value "measurement value range" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "degree Celsius" . + skos:altLabel "wind direction" ; + skos:definition "Wind direction is the direction from which a wind originates" ; + skos:inScheme ; + nmdc:expected_value "wind direction name" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tvdss_of_hcr_temp" ; - dcterms:title "depth (TVDSS) of hydrocarbon resource temperature" ; + rdfs:label "wind_speed" ; + dcterms:title "wind speed" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "depth (TVDSS) of hydrocarbon resource temperature" ; - skos:definition "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m)." ; - skos:exactMatch ; + skos:altLabel "wind speed" ; + skos:definition "Speed of wind measured at the time of sampling" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "meter" . + nmdc:preferred_unit "meter per second, kilometer per hour" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "hcr_pressure" ; - dcterms:title "hydrocarbon resource original pressure" ; - rdfs:range nmdc:TextValue ; + rdfs:label "window_cond" ; + dcterms:title "window condition" ; + rdfs:range nmdc:WindowCondEnum ; rdfs:subPropertyOf ; - skos:altLabel "hydrocarbon resource original pressure" ; - skos:definition "Original pressure of the hydrocarbon resource" ; - skos:exactMatch ; - nmdc:expected_value "measurement value range" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "atmosphere, kilopascal" . + skos:altLabel "window condition" ; + skos:definition "The physical condition of the window at the time of sampling" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tvdss_of_hcr_press" ; - dcterms:title "depth (TVDSS) of hydrocarbon resource pressure" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "window_cover" ; + dcterms:title "window covering" ; + rdfs:range nmdc:WindowCoverEnum ; rdfs:subPropertyOf ; - skos:altLabel "depth (TVDSS) of hydrocarbon resource pressure" ; - skos:definition "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m)." ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "meter" . + skos:altLabel "window covering" ; + skos:definition "The type of window covering" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "permeability" ; - dcterms:title "permeability" ; - rdfs:range nmdc:TextValue ; + rdfs:label "window_horiz_pos" ; + dcterms:title "window horizontal position" ; + rdfs:range nmdc:WindowHorizPosEnum ; rdfs:subPropertyOf ; - skos:altLabel "permeability" ; - skos:definition "Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))" ; - skos:exactMatch ; - nmdc:expected_value "measurement value range" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "mD" . + skos:altLabel "window horizontal position" ; + skos:definition "The horizontal position of the window on the wall" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "owc_tvdss" ; - dcterms:title "oil water contact depth" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "window_loc" ; + dcterms:title "window location" ; + rdfs:range nmdc:WindowLocEnum ; rdfs:subPropertyOf ; - skos:altLabel "oil water contact depth" ; - skos:definition "Depth of the original oil water contact (OWC) zone (average) (m TVDSS)" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "meter" . + skos:altLabel "window location" ; + skos:definition "The relative location of the window within the room" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "hcr_fw_salinity" ; - dcterms:title "formation water salinity" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "window_mat" ; + dcterms:title "window material" ; + rdfs:range nmdc:WindowMatEnum ; rdfs:subPropertyOf ; - skos:altLabel "formation water salinity" ; - skos:definition "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter" . + skos:altLabel "window material" ; + skos:definition "The type of material used to finish a window" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sulfate_fw" ; - dcterms:title "sulfate in formation water" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "window_open_freq" ; + dcterms:title "window open frequency" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "sulfate in formation water" ; - skos:definition "Original sulfate concentration in the hydrocarbon resource" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter" . + skos:altLabel "window open frequency" ; + skos:definition "The number of times windows are opened per week" ; + skos:inScheme ; + nmdc:expected_value "value" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "vfa_fw" ; - dcterms:title "vfa in formation water" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "window_size" ; + dcterms:title "window area/size" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "vfa in formation water" ; - skos:definition "Original volatile fatty acid concentration in the hydrocarbon resource" ; - skos:exactMatch ; + skos:altLabel "window area/size" ; + skos:definition "The window's length and width" ; + skos:inScheme ; nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter" . + nmdc:preferred_unit "inch, meter" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_tvdss" ; - dcterms:title "sample true vertical depth subsea" ; + rdfs:label "window_status" ; + dcterms:title "window status" ; rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "sample true vertical depth subsea" ; - skos:definition "Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m" ; - skos:exactMatch ; - nmdc:expected_value "measurement value or measurement value range" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "meter" . + skos:altLabel "window status" ; + skos:definition "Defines whether the windows were open or closed during environmental testing" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_transport_cond" ; - dcterms:title "sample transport conditions" ; - rdfs:range nmdc:TextValue ; + rdfs:label "window_type" ; + dcterms:title "window type" ; + rdfs:range nmdc:WindowTypeEnum ; rdfs:subPropertyOf ; - skos:altLabel "sample transport conditions" ; - skos:definition "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C)" ; - skos:exactMatch ; - nmdc:expected_value "measurement value;measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "days;degree Celsius" . + skos:altLabel "window type" ; + skos:definition "The type of windows" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "pressure" ; - dcterms:title "pressure" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "window_vert_pos" ; + dcterms:title "window vertical position" ; + rdfs:range nmdc:WindowVertPosEnum ; rdfs:subPropertyOf ; - skos:altLabel "pressure" ; - skos:definition "Pressure to which the sample is subject to, in atmospheres" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "atmosphere" . + skos:altLabel "window vertical position" ; + skos:definition "The vertical position of the window on the wall" ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_md" ; - dcterms:title "sample measured depth" ; - rdfs:range nmdc:QuantityValue ; + rdfs:label "window_water_mold" ; + dcterms:title "window signs of water/mold" ; + rdfs:range nmdc:TextValue ; rdfs:subPropertyOf ; - skos:altLabel "sample measured depth" ; - skos:definition "In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field" ; - skos:exactMatch ; - nmdc:expected_value "measurement value;enumeration" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "meter" . + skos:altLabel "window signs of water/mold" ; + skos:definition "Signs of the presence of mold or mildew on the window." ; + skos:inScheme ; + nmdc:expected_value "enumeration" ; + nmdc:occurrence "1" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tot_sulfur" ; - dcterms:title "total sulfur" ; + rdfs:label "xylene" ; + dcterms:title "xylene" ; rdfs:range nmdc:QuantityValue ; rdfs:subPropertyOf ; - skos:altLabel "total sulfur" ; - skos:definition "Concentration of total sulfur in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; + skos:altLabel "xylene" ; + skos:definition "Concentration of xylene in the sample" ; + skos:inScheme ; + nmdc:expected_value "measurement value" ; nmdc:occurrence "1" ; nmdc:preferred_unit "milligram per liter, parts per million" . - a owl:ObjectProperty, +nmdc:AnalyticalSample a owl:Class, + linkml:ClassDefinition ; + rdfs:label "AnalyticalSample" ; + dcterms:title "Analytical Sample" ; + rdfs:subClassOf [ 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 . + +nmdc:BooleanValue a owl:Class, + linkml:ClassDefinition ; + rdfs:label "BooleanValue" ; + rdfs:subClassOf nmdc:AttributeValue ; + skos:definition "A value that is a boolean" ; + skos:inScheme nmdc:core . + +nmdc:EnvironmentalMaterialTerm a owl:Class, + linkml:ClassDefinition ; + rdfs:label "EnvironmentalMaterialTerm" ; + rdfs:subClassOf nmdc:OntologyClass ; + skos:inScheme nmdc:core . + +nmdc:Instrument a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Instrument" ; + 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 ], + nmdc:NamedThing ; + skos:altLabel "device" ; + skos:definition "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI]." ; + skos:exactMatch ; + skos:inScheme nmdc:core . + +nmdc:IntegerValue a owl:Class, + linkml:ClassDefinition ; + rdfs:label "IntegerValue" ; + rdfs:subClassOf nmdc:AttributeValue ; + skos:definition "A value that is an integer" ; + skos:inScheme nmdc:core . + +nmdc:MetatranscriptomeAnnotationActivity a owl:Class, + linkml:ClassDefinition ; + rdfs:label "MetatranscriptomeAnnotationActivity" ; + rdfs:subClassOf [ 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:WorkflowExecutionActivity ; + skos:inScheme nmdc:workflow_execution_activity . + +nmdc:MetatranscriptomeAssembly a owl:Class, + linkml:ClassDefinition ; + rdfs:label "MetatranscriptomeAssembly" ; + rdfs:subClassOf [ 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:WorkflowExecutionActivity ; + skos:inScheme nmdc:workflow_execution_activity . + +nmdc:OrthologyGroup a owl:Class, + linkml:ClassDefinition ; + rdfs:label "OrthologyGroup" ; + rdfs:subClassOf nmdc:FunctionalAnnotationTerm ; + skos:definition "A set of genes or gene products in which all members are orthologous" ; + skos:editorialNote "KEGG.ORTHOLOGY prefix is used for KO numbers" ; + skos:exactMatch ; + skos:inScheme nmdc:annotation . + +nmdc:Pathway a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Pathway" ; + rdfs:subClassOf nmdc:FunctionalAnnotationTerm ; + skos:altLabel "biological process", + "metabolic pathway", + "signaling pathway" ; + skos:definition "A pathway is a sequence of steps/reactions carried out by an organism or community of organisms" ; + skos:exactMatch ; + skos:inScheme nmdc:annotation . + +nmdc:ProteinQuantification a owl:Class, + linkml:ClassDefinition ; + rdfs:label "ProteinQuantification" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:best_protein ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:all_proteins ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:best_protein ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:best_protein ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:all_proteins ] ; + skos:definition "This is used to link a metaproteomics analysis workflow to a specific protein" ; + skos:inScheme nmdc:core . + +nmdc:UrlValue a owl:Class, + linkml:ClassDefinition ; + rdfs:label "UrlValue" ; + rdfs:subClassOf nmdc:AttributeValue ; + skos:definition "A value that is a string that conforms to URL syntax" ; + skos:inScheme nmdc:core . + +nmdc:activity_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "alkalinity" ; - dcterms:title "alkalinity" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "alkalinity" ; - skos:definition "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milliequivalent per liter, milligram per liter" . + rdfs:label "activity_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:WorkflowExecutionActivity ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of workflow activities." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:activity_speed a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sulfate" ; - dcterms:title "sulfate" ; + rdfs:label "activity_speed" ; + dcterms:title "activity speed" ; rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "sulfate" ; - skos:definition "Concentration of sulfate in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . + skos:altLabel "shake_speed" ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:activity_temperature a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sulfide" ; - dcterms:title "sulfide" ; + rdfs:label "activity_temperature" ; rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "sulfide" ; - skos:definition "Concentration of sulfide in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:activity_time a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "nitrate" ; - dcterms:title "nitrate" ; + rdfs:label "activity_time" ; + dcterms:title "activity time" ; rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "nitrate" ; - skos:definition "Concentration of nitrate in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . + skos:altLabel "shake_time" ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:add_date a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "nitrite" ; - dcterms:title "nitrite" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "nitrite" ; - skos:definition "Concentration of nitrite in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . + rdfs:label "add_date" ; + rdfs:range linkml:String ; + skos:definition "The date on which the information was added to the database." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:alternate_emails a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ammonium" ; - dcterms:title "ammonium" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "ammonium" ; - skos:definition "Concentration of ammonium in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . + rdfs:label "alternate_emails" ; + rdfs:range linkml:String ; + skos:definition "One or more other email addresses for an entity." ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:alternative_descriptions a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sodium" ; - dcterms:title "sodium" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "sodium" ; - skos:definition "Sodium concentration in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter, parts per million" . + rdfs:label "alternative_descriptions" ; + rdfs:range linkml:String ; + skos:definition "A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific." ; + skos:inScheme nmdc:basic_slots . - a owl:ObjectProperty, +nmdc:alternative_titles a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "chloride" ; - dcterms:title "chloride" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "chloride" ; - skos:definition "Concentration of chloride in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter, parts per million" . + rdfs:label "alternative_titles" ; + rdfs:range linkml:String ; + skos:definition "A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific." ; + skos:exactMatch dcterms:alternative ; + skos:inScheme nmdc:basic_slots . - a owl:ObjectProperty, +nmdc:ammonium_nitrogen a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "potassium" ; - dcterms:title "potassium" ; + rdfs:label "ammonium_nitrogen" ; + dcterms:title "ammonium nitrogen" ; rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "potassium" ; - skos:definition "Concentration of potassium in the sample" ; - skos:exactMatch ; + rdfs:seeAlso ; + rdfs:subPropertyOf nmdc:attribute ; + 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 "milligram per liter, parts per million" . + nmdc:preferred_unit "mg/kg" . - a owl:ObjectProperty, +nmdc:analysis_type a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "magnesium" ; - dcterms:title "magnesium" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "magnesium" ; - skos:definition "Concentration of magnesium in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "mole per liter, milligram per liter, parts per million, micromole per kilogram" . + rdfs:label "analysis_type" ; + dcterms:title "analysis/data type" ; + rdfs:range nmdc:AnalysisTypeEnum ; + rdfs:seeAlso ; + skos:definition "Select all the data types associated or available for this biosample" ; + skos:inScheme ; + sh:order 3 . - a owl:ObjectProperty, +nmdc:applied_role a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "calcium" ; - dcterms:title "calcium" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "calcium" ; - skos:definition "Concentration of calcium in the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter, micromole per liter, parts per million" . + rdfs:label "applied_role" ; + rdfs:domain nmdc:CreditAssociation ; + rdfs:range nmdc:CreditEnum ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:applied_roles a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "diss_org_carb" ; - dcterms:title "dissolved organic carbon" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "dissolved organic carbon" ; - skos:definition "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter, milligram per liter" . + rdfs:label "applied_roles" ; + rdfs:domain nmdc:CreditAssociation ; + rdfs:range nmdc:CreditEnum ; + skos:inScheme nmdc:nmdc ; + nmdc:display_hint "Identify all CRediT roles associated with this contributor. CRediT Information: https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/" . - a owl:ObjectProperty, +nmdc:applies_to_person a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "diss_inorg_carb" ; - dcterms:title "dissolved inorganic carbon" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "dissolved inorganic carbon" ; - skos:definition "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter, milligram per liter, parts per million" . + rdfs:label "applies_to_person" ; + rdfs:domain nmdc:CreditAssociation ; + rdfs:range nmdc:PersonValue ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:asm_score a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "density" ; - dcterms:title "density" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "density" ; - skos:definition "Density of the sample, which is its mass per unit volume (aka volumetric mass density)" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "gram per cubic meter, gram per cubic centimeter" . + rdfs:label "asm_score" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "A score for comparing metagenomic assembly quality from same sample." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:award_dois a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "diss_carb_dioxide" ; - dcterms:title "dissolved carbon dioxide" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "dissolved carbon dioxide" ; - skos:definition "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter, milligram per liter" . + rdfs:label "award_dois" ; + rdfs:subPropertyOf nmdc:dois ; + skos:definition "One or more DOIs that links a study, or similar entiry, to information about the funding authority." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:bin_name a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "diss_oxygen_fluid" ; - dcterms:title "dissolved oxygen in fluids" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "dissolved oxygen in fluids" ; - skos:definition "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic)." ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per kilogram, milligram per liter" . + rdfs:label "bin_name" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:bin_quality a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "prod_rate" ; - dcterms:title "production rate" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "production rate" ; - skos:definition "Oil and/or gas production rates per well (e.g. 524 m3 / day)" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "cubic meter per day" . + rdfs:label "bin_quality" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:binned_contig_num a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "water_prod_rate" ; - dcterms:title "water production rate" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "water production rate" ; - skos:definition "Water production rates per well (e.g. 987 m3 / day)" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "cubic meter per day" . + rdfs:label "binned_contig_num" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:biogas_retention_time a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "water_cut" ; - dcterms:title "water cut" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "water cut" ; - skos:definition "Current amount of water (%) in a produced fluid stream; or the average of the combined streams" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "percent" . + rdfs:label "biogas_retention_time" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:biogas_temperature a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "iwf" ; - dcterms:title "injection water fraction" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "injection water fraction" ; - skos:definition "Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "percent" . + rdfs:label "biogas_temperature" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:biosample_categories a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "biocide_admin_method" ; - dcterms:title "biocide administration method" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "biocide administration method" ; - skos:definition "Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)" ; - skos:exactMatch ; - nmdc:expected_value "measurement value;frequency;duration;duration" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter" . + rdfs:label "biosample_categories" ; + dcterms:title "Categories the biosample belongs to" ; + rdfs:range nmdc:BiosampleCategoryEnum ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:biosample_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "chem_treat_method" ; - dcterms:title "chemical treatment method" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf ; - skos:altLabel "chemical treatment method" ; - skos:definition "Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)" ; - skos:exactMatch ; - nmdc:expected_value "measurement value;frequency;duration;duration" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter" . + rdfs:label "biosample_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:Biosample ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of samples within it." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:canary a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_preserv" ; - dcterms:title "preservative added to sample" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "preservative added to sample" ; - skos:definition "Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)" ; - skos:exactMatch ; - nmdc:expected_value "name;measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milliliter" . + rdfs:label "canary" ; + skos:definition "a slot that can be added and removed as evidence that schema changes have propagated to other systems" ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:chemical a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "alkyl_diethers" ; - dcterms:title "alkyl diethers" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "alkyl diethers" ; - skos:definition "Concentration of alkyl diethers" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "mole per liter" . + rdfs:label "chemical" ; + rdfs:range nmdc:ChemicalEntity ; + skos:definition "from reaction participant class" ; + skos:inScheme nmdc:annotation . - a owl:ObjectProperty, +nmdc:chemical_formula a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "mean_frict_vel" ; - dcterms:title "mean friction velocity" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "mean friction velocity" ; - skos:definition "Measurement of mean friction velocity" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "meter per second" . + rdfs:label "chemical_formula" ; + rdfs:range linkml:String ; + skos:definition "A generic grouping for molecular formulae and empirical formulae" ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:collected_from a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "mean_peak_frict_vel" ; - dcterms:title "mean peak friction velocity" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "mean peak friction velocity" ; - skos:definition "Measurement of mean peak friction velocity" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "meter per second" . + rdfs:label "collected_from" ; + rdfs:domain nmdc:Biosample ; + rdfs:range nmdc:FieldResearchSite ; + skos:definition "The Site from which a Biosample was collected" ; + skos:inScheme nmdc:nmdc ; + skos:note "this illustrates implementing a Biosample relation with a (binary) slot" . - a owl:ObjectProperty, +nmdc:collecting_biosamples_from_site_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "n_alkanes" ; - dcterms:title "n-alkanes" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "n-alkanes" ; - skos:definition "Concentration of n-alkanes; can include multiple n-alkanes" ; - skos:exactMatch ; - nmdc:expected_value "n-alkane name;measurement value" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "micromole per liter" . + rdfs:label "collecting_biosamples_from_site_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:CollectingBiosamplesFromSite ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:collection_date_inc a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "nitro" ; - dcterms:title "nitrogen" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "nitrogen" ; - skos:definition "Concentration of nitrogen (total)" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter" . + rdfs:label "collection_date_inc" ; + dcterms:title "incubation collection date" ; + skos:definition "Date the incubation was harvested/collected/ended. Only relevant for incubation samples." ; + skos:editorialNote "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" ; + skos:inScheme ; + skos:note "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." ; + sh:order 2 . - a owl:ObjectProperty, +nmdc:collection_time 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:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter" . + rdfs:label "collection_time" ; + dcterms:title "collection time, GMT" ; + skos:definition "The time of sampling, either as an instance (single point) or interval." ; + skos:editorialNote "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" ; + skos:inScheme ; + skos:note "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" ; + sh:order 1 . - a owl:ObjectProperty, +nmdc:collection_time_inc a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "org_carb" ; - dcterms:title "organic carbon" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "organic carbon" ; - skos:definition "Concentration of organic carbon" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter" . + rdfs:label "collection_time_inc" ; + dcterms:title "incubation collection time, GMT" ; + skos:definition "Time the incubation was harvested/collected/ended. Only relevant for incubation samples." ; + skos:editorialNote "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" ; + skos:inScheme ; + skos:note "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" ; + sh:order 3 . - a owl:ObjectProperty, +nmdc:community a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "part_org_carb" ; - dcterms:title "particulate organic carbon" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "particulate organic carbon" ; - skos:definition "Concentration of particulate organic carbon" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter" . + rdfs:label "community" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:completeness a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "petroleum_hydrocarb" ; - dcterms:title "petroleum hydrocarbon" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "petroleum hydrocarbon" ; - skos:definition "Concentration of petroleum hydrocarbon" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter" . + rdfs:label "completeness" ; + rdfs:range linkml:Float ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:completion_date 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:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter" . + rdfs:label "completion_date" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:compression_type 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:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter, micromole per liter, milligram per liter" . + rdfs:label "compression_type" ; + rdfs:range linkml:String ; + skos:definition "If provided, specifies the compression type" ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:container_size 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:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "gram Carbon per kilogram sample material" . + rdfs:label "container_size" ; + dcterms:title "container size" ; + rdfs:range nmdc:QuantityValue ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:container_type 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:exactMatch ; - nmdc:expected_value "temperature value;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "meter" . + rdfs:label "container_type" ; + dcterms:title "container type" ; + rdfs:range nmdc:ContainerTypeEnum ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:contamination a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "antibiotic_regm" ; - dcterms:title "antibiotic regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "antibiotic regimen" ; - skos:definition "Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens" ; - skos:exactMatch ; - nmdc:expected_value "antibiotic name;antibiotic amount;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "milligram" . + rdfs:label "contamination" ; + rdfs:range linkml:Float ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:contig_bp a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "chem_mutagen" ; - dcterms:title "chemical mutagen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "chemical mutagen" ; - skos:definition "Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens" ; - skos:exactMatch ; - nmdc:expected_value "mutagen name;mutagen amount;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "milligram per liter" . + rdfs:label "contig_bp" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Total size in bp of all contigs." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:contigs a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "fertilizer_regm" ; - dcterms:title "fertilizer regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "fertilizer regimen" ; - skos:definition "Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens" ; - skos:exactMatch ; - nmdc:expected_value "fertilizer name;fertilizer amount;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram, mole per liter, milligram per liter" . + rdfs:label "contigs" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase" ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:count a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "fungicide_regm" ; - dcterms:title "fungicide regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "fungicide regimen" ; - skos:definition "Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens" ; - skos:exactMatch ; - nmdc:expected_value "fungicide name;fungicide amount;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram, mole per liter, milligram per liter" . + rdfs:label "count" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:ctg_l50 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:exactMatch ; - nmdc:expected_value "gaseous compound name;gaseous compound amount;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "micromole per liter" . + rdfs:label "ctg_l50" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:ctg_l90 a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gravity" ; - dcterms:title "gravity" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "gravity" ; - skos:definition "Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments" ; - skos:exactMatch ; - nmdc:expected_value "gravity factor value;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "meter per square second, g" . + rdfs:label "ctg_l90" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:ctg_logsum a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "growth_hormone_regm" ; - dcterms:title "growth hormone regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "growth hormone regimen" ; - skos:definition "Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens" ; - skos:exactMatch ; - nmdc:expected_value "growth hormone name;growth hormone amount;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram, mole per liter, milligram per liter" . + rdfs:label "ctg_logsum" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Maximum contig length." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:ctg_max a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "herbicide_regm" ; - dcterms:title "herbicide regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "herbicide regimen" ; - skos:definition "Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens" ; - skos:exactMatch ; - nmdc:expected_value "herbicide name;herbicide amount;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram, mole per liter, milligram per liter" . + rdfs:label "ctg_max" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Maximum contig length." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:ctg_n50 a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_wet_mass" ; - dcterms:title "host wet mass" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "host wet mass" ; - skos:definition "Measurement of wet mass" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "kilogram, gram" . + rdfs:label "ctg_n50" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:ctg_n90 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:exactMatch ; - nmdc:expected_value "humidity value;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram per cubic meter" . + rdfs:label "ctg_n90" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:ctg_powsum 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:exactMatch ; - nmdc:expected_value "exposure type;light intensity;light quality" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "lux; micrometer, nanometer, angstrom" . + rdfs:label "ctg_powsum" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25)." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:data_object_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "mineral_nutr_regm" ; - dcterms:title "mineral nutrient regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "mineral nutrient regimen" ; - skos:definition "Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens" ; - skos:exactMatch ; - nmdc:expected_value "mineral nutrient name;mineral nutrient amount;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram, mole per liter, milligram per liter" . + rdfs:label "data_object_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:DataObject ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of data objects within it." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:data_object_type a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "non_min_nutr_regm" ; - dcterms:title "non-mineral nutrient regimen" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf ; - skos:altLabel "non-mineral nutrient regimen" ; - skos:definition "Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens" ; - skos:exactMatch ; - nmdc:expected_value "non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram, mole per liter, milligram per liter" . + rdfs:label "data_object_type" ; + rdfs:range nmdc:FileTypeEnum ; + skos:definition "The type of file represented by the data object." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:dataset_dois a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "pesticide_regm" ; - dcterms:title "pesticide regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "pesticide regimen" ; - skos:definition "Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens" ; - skos:exactMatch ; - nmdc:expected_value "pesticide name;pesticide amount;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram, mole per liter, milligram per liter" . + rdfs:label "dataset_dois" ; + rdfs:subPropertyOf nmdc:dois ; + skos:definition "One or more DOIs that links a study, or similar entity, to the generated data." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:device_type a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "radiation_regm" ; - dcterms:title "radiation regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "radiation regimen" ; - skos:definition "Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens" ; - skos:exactMatch ; - nmdc:expected_value "radiation type name;radiation amount;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "rad, gray" . + rdfs:label "device_type" ; + dcterms:title "device type" ; + rdfs:range nmdc:DeviceTypeEnum ; + skos:altLabel "shaker type" ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:direction a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rainfall_regm" ; - dcterms:title "rainfall regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "rainfall regimen" ; - skos:definition "Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens" ; - skos:exactMatch ; - nmdc:expected_value "measurement value;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "millimeter" . + rdfs:label "direction" ; + skos:definition "One of l->r, r->l, bidirectional, neutral" ; + skos:inScheme nmdc:annotation . - a owl:ObjectProperty, +nmdc:display_order a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "root_med_carbon" ; - dcterms:title "rooting medium carbon" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "rooting medium carbon" ; - skos:definition "Source of organic carbon in the culture rooting medium; e.g. sucrose." ; - skos:exactMatch ; - nmdc:expected_value "carbon source name;measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter" . + rdfs:label "display_order" ; + rdfs:subPropertyOf nmdc:attribute ; + skos:definition "When rendering information, this attribute to specify the order in which the information should be rendered." ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:dissolution_aided_by a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "root_med_macronutr" ; - dcterms:title "rooting medium macronutrients" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "rooting medium macronutrients" ; - skos:definition "Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L)." ; - skos:exactMatch ; - nmdc:expected_value "macronutrient name;measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter" . + rdfs:label "dissolution_aided_by" ; + dcterms:title "dissolution aided by" ; + rdfs:range nmdc:LabDevice ; + skos:altLabel "shaker" ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:dissolution_reagent a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "root_med_micronutr" ; - dcterms:title "rooting medium micronutrients" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "rooting medium micronutrients" ; - skos:definition "Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L)." ; - skos:exactMatch ; - nmdc:expected_value "micronutrient name;measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter" . + rdfs:label "dissolution_reagent" ; + dcterms:title "dissolution reagent" ; + rdfs:range nmdc:SolventEnum ; + skos:altLabel "solvent" ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:dissolution_volume a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "root_med_suppl" ; - dcterms:title "rooting medium organic supplements" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "rooting medium organic supplements" ; - skos:definition "Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L)." ; - skos:exactMatch ; - nmdc:expected_value "supplement name;measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter" . + rdfs:label "dissolution_volume" ; + dcterms:title "dissolution volume" ; + rdfs:range nmdc:QuantityValue ; + skos:altLabel "volume" ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:dissolved_in a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "root_med_regl" ; - dcterms:title "rooting medium regulators" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "rooting medium regulators" ; - skos:definition "Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA." ; - skos:exactMatch ; - nmdc:expected_value "regulator name;measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter" . + rdfs:label "dissolved_in" ; + dcterms:title "dissolved in" ; + rdfs:range nmdc:MaterialContainer ; + skos:altLabel "container" ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:dissolving_activity_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "salt_regm" ; - dcterms:title "salt regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "salt regimen" ; - skos:definition "Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens" ; - skos:exactMatch ; - nmdc:expected_value "salt name;salt amount;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram, microgram, mole per liter, gram per liter" . + rdfs:label "dissolving_activity_set" ; + dcterms:title "dissolving activity set" ; + rdfs:range nmdc:DissolvingActivity ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:dna_absorb1 a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "water_temp_regm" ; - dcterms:title "water temperature regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "water temperature regimen" ; - skos:definition "Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens" ; - skos:exactMatch ; - nmdc:expected_value "measurement value;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "degree Celsius" . + rdfs:label "dna_absorb1" ; + dcterms:title "DNA absorbance 260/280" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:biomaterial_purity ; + skos:definition "260/280 measurement of DNA sample purity" ; + skos:inScheme ; + skos:note "Recommended value is between 1 and 3." ; + sh:order 7 . - a owl:ObjectProperty, +nmdc:dna_absorb2 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:exactMatch ; - nmdc:expected_value "measurement value;treatment interval and duration" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "milliliter, liter" . + rdfs:label "dna_absorb2" ; + dcterms:title "DNA absorbance 260/230" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:biomaterial_purity ; + skos:definition "260/230 measurement of DNA sample purity" ; + skos:inScheme ; + skos:note "Recommended value is between 1 and 3." ; + sh:order 8 . - a owl:ObjectProperty, +nmdc:dna_collect_site 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:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "percentage" . + rdfs:label "dna_collect_site" ; + dcterms:title "DNA collection site" ; + skos:definition "Provide information on the site your DNA sample was collected from" ; + skos:inScheme ; + sh:order 15 . - a owl:ObjectProperty, +nmdc:dna_concentration a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tot_depth_water_col" ; - dcterms:title "total depth of water column" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "total depth of water column" ; - skos:definition "Measurement of total depth of water column" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "meter" . + rdfs:label "dna_concentration" ; + dcterms:title "DNA concentration in ng/ul" ; + rdfs:range [ 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 ] ) ] ) ] ; + rdfs:seeAlso nmdc:nucleic_acid_concentration ; + skos:inScheme ; + 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 . - a owl:ObjectProperty, +nmdc:dna_cont_type a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "agrochem_addition" ; - dcterms:title "history/agrochemical additions" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "history/agrochemical additions" ; - skos:definition "Addition of fertilizers, pesticides, etc. - amount and time of applications" ; - skos:exactMatch ; - nmdc:expected_value "agrochemical name;agrochemical amount;timestamp" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram, mole per liter, milligram per liter" . + rdfs:label "dna_cont_type" ; + dcterms:title "DNA container type" ; + rdfs:range nmdc:JgiContTypeEnum ; + skos:definition "Tube or plate (96-well)" ; + skos:inScheme ; + sh:order 10 . - a owl:ObjectProperty, +nmdc:dna_cont_well a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "annual_temp" ; - dcterms:title "mean annual temperature" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "mean annual temperature" ; - skos:definition "Mean annual temperature" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "degree Celsius" . + 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 . - a owl:ObjectProperty, +nmdc:dna_container_id a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "season_temp" ; - dcterms:title "mean seasonal temperature" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "mean seasonal temperature" ; - skos:definition "Mean seasonal temperature" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "degree Celsius" . + rdfs:label "dna_container_id" ; + dcterms:title "DNA container label" ; + skos:inScheme ; + skos:note "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." ; + sh:order 9 . - a owl:ObjectProperty, +nmdc:dna_dnase 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:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "millimeter" . + rdfs:label "dna_dnase" ; + dcterms:title "DNase treatment DNA" ; + rdfs:range nmdc:YesNoEnum ; + skos:inScheme ; + skos:note "Note DNase treatment is required for all RNA samples." ; + sh:order 13 . - a owl:ObjectProperty, +nmdc:dna_isolate_meth 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:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "millimeter" . + rdfs:label "dna_isolate_meth" ; + dcterms:title "DNA isolation method" ; + skos:definition "Describe the method/protocol/kit used to extract DNA/RNA." ; + skos:inScheme ; + sh:order 16 . - a owl:ObjectProperty, +nmdc:dna_organisms 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:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "percentage" . + rdfs:label "dna_organisms" ; + dcterms:title "DNA expected organisms" ; + skos:definition "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture." ; + skos:inScheme ; + sh:order 14 . - a owl:ObjectProperty, +nmdc:dna_project_contact 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:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "degree" . + rdfs:label "dna_project_contact" ; + dcterms:title "DNA seq project contact" ; + skos:inScheme ; + skos:note "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." ; + sh:order 18 . - a owl:ObjectProperty, +nmdc:dna_samp_id a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "microbial_biomass" ; - dcterms:title "microbial biomass" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "microbial biomass" ; - skos:definition "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "ton, kilogram, gram per kilogram soil" . + rdfs:label "dna_samp_id" ; + dcterms:title "DNA sample ID" ; + skos:inScheme ; + skos:note "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." ; + sh:order 3 . - a owl:ObjectProperty, +nmdc:dna_sample_format 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:exactMatch ; - nmdc:expected_value "heavy metal name;measurement value unit" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "microgram per gram" . + rdfs:label "dna_sample_format" ; + dcterms:title "DNA sample format" ; + rdfs:range nmdc:DnaSampleFormatEnum ; + skos:definition "Solution in which the DNA sample has been suspended" ; + skos:inScheme ; + sh:order 12 . - a owl:ObjectProperty, +nmdc:dna_sample_name a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "biochem_oxygen_dem" ; - dcterms:title "biochemical oxygen demand" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "biochemical oxygen demand" ; - skos:definition "Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter" . + rdfs:label "dna_sample_name" ; + dcterms:title "DNA sample name" ; + skos:definition "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only." ; + skos:inScheme ; + sh:order 4 . - a owl:ObjectProperty, +nmdc:dna_seq_project a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "chem_oxygen_dem" ; - dcterms:title "chemical oxygen demand" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "chemical oxygen demand" ; - skos:definition "A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter" . + rdfs:label "dna_seq_project" ; + dcterms:title "DNA seq project ID" ; + skos:inScheme ; + skos:note "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." ; + sh:order 1 . - a owl:ObjectProperty, +nmdc:dna_seq_project_name a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "efficiency_percent" ; - dcterms:title "efficiency percent" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "efficiency percent" ; - skos:definition "Percentage of volatile solids removed from the anaerobic digestor" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter" . + rdfs:label "dna_seq_project_name" ; + dcterms:title "DNA seq project name" ; + skos:inScheme ; + skos:note "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." ; + sh:order 2 . - a owl:ObjectProperty, +nmdc:dna_seq_project_pi a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "emulsions" ; - dcterms:title "emulsions" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "emulsions" ; - skos:definition "Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types" ; - skos:exactMatch ; - nmdc:expected_value "emulsion name;measurement value" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram per liter" . + rdfs:label "dna_seq_project_pi" ; + dcterms:title "DNA seq project PI" ; + skos:inScheme ; + skos:note "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." ; + sh:order 17 . - a owl:ObjectProperty, +nmdc:dna_volume a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gaseous_substances" ; - dcterms:title "gaseous substances" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "gaseous substances" ; - skos:definition "Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances" ; - skos:exactMatch ; - nmdc:expected_value "gaseous substance name;measurement value" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "micromole per liter" . + rdfs:label "dna_volume" ; + dcterms:title "DNA volume in ul" ; + rdfs:range [ 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 ] ) ] ) ] ; + skos:inScheme ; + skos:note "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" ; + sh:order 6 . - a owl:ObjectProperty, +nmdc:dnase_rna a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "indust_eff_percent" ; - dcterms:title "industrial effluent percent" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "industrial effluent percent" ; - skos:definition "Percentage of industrial effluents received by wastewater treatment plant" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "percentage" . + rdfs:label "dnase_rna" ; + dcterms:title "DNase treated" ; + rdfs:range nmdc:YesNoEnum ; + skos:inScheme ; + skos:note "Note DNase treatment is required for all RNA samples." ; + sh:order 13 . - a owl:ObjectProperty, +nmdc:ecosystem a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "inorg_particles" ; - dcterms:title "inorganic particles" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "inorganic particles" ; - skos:definition "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles" ; - skos:exactMatch ; - nmdc:expected_value "inorganic particle name;measurement value" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "mole per liter, milligram per liter" . + 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." . - a owl:ObjectProperty, +nmdc:ecosystem_category a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "org_particles" ; - dcterms:title "organic particles" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "organic particles" ; - skos:definition "Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc." ; - skos:exactMatch ; - nmdc:expected_value "particle name;measurement value" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram per liter" . + 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." . - a owl:ObjectProperty, +nmdc:ecosystem_path_id a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sludge_retent_time" ; - dcterms:title "sludge retention time" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "sludge retention time" ; - skos:definition "The time activated sludge remains in reactor" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "hours" . + rdfs:label "ecosystem_path_id" ; + rdfs:range linkml:String ; + skos:definition "A unique id representing the GOLD classifiers associated with a sample." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:ecosystem_subtype a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "soluble_inorg_mat" ; - dcterms:title "soluble inorganic material" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "soluble inorganic material" ; - skos:definition "Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc." ; - skos:exactMatch ; - nmdc:expected_value "soluble inorganic material name;measurement value" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram, microgram, mole per liter, gram per liter, parts per million" . + 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." . - a owl:ObjectProperty, +nmdc:ecosystem_type a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "soluble_org_mat" ; - dcterms:title "soluble organic material" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "soluble organic material" ; - skos:definition "Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc." ; - skos:exactMatch ; - nmdc:expected_value "soluble organic material name;measurement value" ; - nmdc:occurrence "m" ; - nmdc:preferred_unit "gram, microgram, mole per liter, gram per liter, parts per million" . + 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." . - a owl:ObjectProperty, +nmdc:embargoed a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "bac_prod" ; - dcterms:title "bacterial production" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "bacterial production" ; - skos:definition "Bacterial production in the water column measured by isotope uptake" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per cubic meter per day" . + rdfs:label "embargoed" ; + rdfs:range linkml:Boolean ; + skos:definition "If true, the data are embargoed and not available for public access." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:emsl_biosample_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "bac_resp" ; - dcterms:title "bacterial respiration" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "bacterial respiration" ; - skos:definition "Measurement of bacterial respiration in the water column" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per cubic meter per day, micromole oxygen per liter per hour" . + rdfs:label "emsl_biosample_identifiers" ; + dcterms:title "EMSL Biosample Identifiers" ; + rdfs:subPropertyOf nmdc:biosample_identifiers, + nmdc:emsl_identifiers ; + skos:definition "A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database." ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:emsl_project_dois a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tot_phosphate" ; - dcterms:title "total phosphate" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "total phosphate" ; - skos:definition "Total amount or concentration of phosphate" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter, micromole per liter" . + rdfs:label "emsl_project_dois" ; + dcterms:title "EMSL Project DOI" ; + rdfs:subPropertyOf nmdc:dois, + nmdc:emsl_identifiers ; + skos:definition "One or more DOIs that links to an EMSL Research Campaign page." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:emsl_store_temp a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "conduc" ; - dcterms:title "conductivity" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "conductivity" ; - skos:definition "Electrical conductivity of water" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milliSiemens per centimeter" . + rdfs:label "emsl_store_temp" ; + dcterms:title "EMSL sample storage temperature, deg. C" ; + skos:definition "The temperature at which the sample should be stored upon delivery to EMSL" ; + skos:inScheme ; + skos:note "Enter a temperature in celsius. Numeric portion only." ; + sh:order 4 . - a owl:ObjectProperty, +nmdc:encodes a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "diss_inorg_nitro" ; - dcterms:title "dissolved inorganic nitrogen" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "dissolved inorganic nitrogen" ; - skos:definition "Concentration of dissolved inorganic nitrogen" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter, micromole per liter" . + rdfs:label "encodes" ; + rdfs:range nmdc:GeneProduct ; + skos:definition "The gene product encoded by this feature. Typically this is used for a CDS feature or gene feature which will encode a protein. It can also be used by a nc transcript ot gene feature that encoded a ncRNA" ; + skos:inScheme nmdc:annotation . - a owl:ObjectProperty, +nmdc:end_date a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "down_par" ; - dcterms:title "downward PAR" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "downward PAR" ; - skos:definition "Visible waveband radiance and irradiance measurements in the water column" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microEinstein per square meter per second, microEinstein per square centimeter per second" . + rdfs:label "end_date" ; + rdfs:range linkml:String ; + skos:definition "The date on which any process or activity was ended" ; + skos:inScheme nmdc:basic_slots ; + skos:note "The date should be formatted as YYYY-MM-DD", + "We are using string representations of dates until all components of our ecosystem can handle ISO 8610 dates" . - a owl:ObjectProperty, +nmdc:env_package a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "fluor" ; - dcterms:title "fluorescence" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "fluorescence" ; - skos:definition "Raw or converted fluorescence of water" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram chlorophyll a per cubic meter, volts" . + rdfs:label "env_package" ; + rdfs:range nmdc:TextValue ; + rdfs:subPropertyOf nmdc:attribute ; + skos:altLabel "environmental package" ; + skos:definition "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported" ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:ess_dive_datasets a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "light_intensity" ; - dcterms:title "light intensity" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "light intensity" ; - skos:definition "Measurement of light intensity" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "lux" . + rdfs:label "ess_dive_datasets" ; + skos:definition "List of ESS-DIVE dataset DOIs" ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:experimental_factor_other a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "part_org_nitro" ; - dcterms:title "particulate organic nitrogen" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "particulate organic nitrogen" ; - skos:definition "Concentration of particulate organic nitrogen" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter, micromole per liter" . + rdfs:label "experimental_factor_other" ; + dcterms:title "experimental factor- other" ; + skos:definition "Other details about your sample that you feel can't be accurately represented in the available columns." ; + skos:inScheme ; + skos:note "Provided pairs will be considered for inclusion as future slots/terms in this data collection template.", + "This slot accepts open-ended text about your sample.", + "We recommend using key:value pairs." ; + sh:order 7 . - a owl:ObjectProperty, +nmdc:extraction_method a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "built_struc_type" ; - dcterms:title "built structure type" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "built structure type" ; - skos:definition "A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads" ; - skos:exactMatch ; - nmdc:expected_value "free text" ; - nmdc:occurrence "1" . + rdfs:label "extraction_method" ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:extraction_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "photon_flux" ; - dcterms:title "photon flux" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "photon flux" ; - skos:definition "Measurement of photon flux" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "number of photons per second per unit area" . + rdfs:label "extraction_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:Extraction ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of extractions within it." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:extraction_target a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "primary_prod" ; - dcterms:title "primary production" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "primary production" ; - skos:definition "Measurement of primary production, generally measured as isotope uptake" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per cubic meter per day, gram per square meter per day" . + rdfs:label "extraction_target" ; + rdfs:range nmdc:ExtractionTargetEnum ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:feature_type a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "size_frac_low" ; - dcterms:title "size-fraction lower threshold" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "size-fraction lower threshold" ; - skos:definition "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample" ; - skos:exactMatch ; - nmdc:expected_value "value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micrometer" . + rdfs:label "feature_type" ; + skos:definition "TODO: Yuri to write" ; + skos:inScheme nmdc:annotation . - a owl:ObjectProperty, +nmdc:field_research_site_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "size_frac_up" ; - dcterms:title "size-fraction upper threshold" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "size-fraction upper threshold" ; - skos:definition "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample" ; - skos:exactMatch ; - nmdc:expected_value "value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micrometer" . + rdfs:label "field_research_site_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:FieldResearchSite ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:file_size_bytes a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "soluble_react_phosp" ; - dcterms:title "soluble reactive phosphorus" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "soluble reactive phosphorus" ; - skos:definition "Concentration of soluble reactive phosphorus" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "micromole per liter, milligram per liter, parts per million" . + rdfs:label "file_size_bytes" ; + rdfs:range nmdc:bytes ; + rdfs:subPropertyOf nmdc:attribute ; + skos:definition "Size of the file in bytes" ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:filter_method a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "suspend_part_matter" ; - dcterms:title "suspended particulate matter" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "suspended particulate matter" ; - skos:definition "Concentration of suspended particulate matter" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "milligram per liter" . + rdfs:label "filter_method" ; + dcterms:title "filter method" ; + skos:definition "Type of filter used or how the sample was filtered" ; + skos:inScheme ; + skos:note "describe the filter or provide a catalog number and manufacturer" ; + sh:order 6 . - a owl:ObjectProperty, +nmdc:functional_annotation_agg a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tot_diss_nitro" ; - dcterms:title "total dissolved nitrogen" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "total dissolved nitrogen" ; - skos:definition "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter" . + rdfs:label "functional_annotation_agg" ; + rdfs:range nmdc:FunctionalAnnotationAggMember ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:functional_annotation_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tot_inorg_nitro" ; - dcterms:title "total inorganic nitrogen" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "total inorganic nitrogen" ; - skos:definition "Total inorganic nitrogen content" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter" . + rdfs:label "functional_annotation_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:FunctionalAnnotation ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of all functional annotations" ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:funding_sources a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tot_part_carb" ; - dcterms:title "total particulate carbon" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "total particulate carbon" ; - skos:definition "Total particulate carbon content" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" ; - nmdc:preferred_unit "microgram per liter, micromole per liter" . + rdfs:label "funding_sources" ; + rdfs:range linkml:String ; + skos:closeMatch NCIT:C39409 ; + skos:definition "A list of organizations, along with the award numbers, that underwrite financial support for projects of a particular type. Typically, they process applications and award funds to the chosen qualified applicants." ; + skos:inScheme nmdc:nmdc ; + skos:note "Include only the name of the funding organization and the award or contract number." . - a owl:ObjectProperty, +nmdc:gap_pct a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tidal_stage" ; - dcterms:title "tidal stage" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "tidal stage" ; - skos:definition "Stage of tide" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "gap_pct" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "The gap size percentage of all scaffolds." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:gc_avg a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "chem_administration" ; - dcterms:title "chemical administration" ; - rdfs:range nmdc:ControlledTermValue ; - rdfs:subPropertyOf ; - skos:altLabel "chemical administration" ; - skos:definition "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi" ; - skos:exactMatch ; - nmdc:expected_value "CHEBI;timestamp" ; - nmdc:occurrence "m" . + rdfs:label "gc_avg" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Average of GC content of all contigs." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:gc_std a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "misc_param" ; - dcterms:title "miscellaneous parameter" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "miscellaneous parameter" ; - skos:definition "Any other measurement performed or parameter collected, that is not listed here" ; - skos:exactMatch ; - nmdc:expected_value "parameter name;measurement value" ; - nmdc:occurrence "m" . + rdfs:label "gc_std" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Standard deviation of GC content of all contigs." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:gene_count a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "oxy_stat_samp" ; - dcterms:title "oxygenation status of sample" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "oxygenation status of sample" ; - skos:definition "Oxygenation status of sample" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "gene_count" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:gene_function_id a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "perturbation" ; - dcterms:title "perturbation" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "perturbation" ; - skos:definition "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types" ; - skos:exactMatch ; - nmdc:expected_value "perturbation type name;perturbation interval and duration" ; - nmdc:occurrence "m" . + rdfs:label "gene_function_id" ; + rdfs:range linkml:Uriorcurie ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:genome_feature_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_store_loc" ; - dcterms:title "sample storage location" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "sample storage location" ; - skos:definition "Location at which sample was stored, usually name of a specific freezer/room" ; - skos:exactMatch ; - nmdc:expected_value "location name" ; - nmdc:occurrence "1" . + rdfs:label "genome_feature_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:GenomeFeature ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of all features" ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:gnps_task_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ventilation_type" ; - dcterms:title "ventilation type" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "ventilation type" ; - skos:definition "Ventilation system used in the sampled premises" ; - skos:exactMatch ; - nmdc:expected_value "ventilation type name" ; - nmdc:occurrence "1" . + rdfs:label "gnps_task_identifiers" ; + dcterms:title "GNPS task identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^gnps\\.task:[a-f0-9]+$" ] ) ] ; + rdfs:seeAlso ; + rdfs:subPropertyOf nmdc:gnps_identifiers, + nmdc:study_identifiers ; + skos:definition "identifiers that link a NMDC study to a web-based report about metabolomics analysis progress and results" ; + skos:inScheme nmdc:external_identifiers ; + skos:note "this could be considered a related identifier, as the metabolomics progress and results aren't a study per se", + "this identifier was registered with bioregistry but not identifiers.org" . - a owl:ObjectProperty, +nmdc:gold_analysis_project_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "wind_direction" ; - dcterms:title "wind direction" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "wind direction" ; - skos:definition "Wind direction is the direction from which a wind originates" ; - skos:exactMatch ; - nmdc:expected_value "wind direction name" ; - nmdc:occurrence "1" . + rdfs:label "gold_analysis_project_identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^gold:Ga[0-9]+$" ] ) ] ; + rdfs:subPropertyOf nmdc:analysis_identifiers, + nmdc:gold_identifiers ; + skos:definition "identifiers for corresponding analysis project in GOLD" ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:gold_sequencing_project_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "surf_material" ; - dcterms:title "surface material" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "surface material" ; - skos:definition "Surface materials at the point of sampling" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "gold_sequencing_project_identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^gold:Gp[0-9]+$" ] ) ] ; + rdfs:subPropertyOf nmdc:gold_identifiers, + nmdc:omics_processing_identifiers ; + skos:definition "identifiers for corresponding sequencing project in GOLD" ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:gold_study_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "surf_air_cont" ; - dcterms:title "surface-air contaminant" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "surface-air contaminant" ; - skos:definition "Contaminant identified on surface" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "m" . + rdfs:label "gold_study_identifiers" ; + dcterms:title "GOLD Study Identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^gold:Gs[0-9]+$" ] ) ] ; + rdfs:seeAlso ; + rdfs:subPropertyOf nmdc:gold_identifiers, + nmdc:study_identifiers ; + skos:definition "identifiers for corresponding project(s) in GOLD" ; + skos:inScheme nmdc:external_identifiers ; + skos:note "uses the prefix GS (but possibly in a different case)" . - a owl:ObjectProperty, +nmdc:gtdbtk_class a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "surf_moisture_ph" ; - dcterms:title "surface moisture pH" ; - rdfs:range linkml:Double ; - rdfs:subPropertyOf ; - skos:altLabel "surface moisture pH" ; - skos:definition "ph measurement of surface" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" . + rdfs:label "gtdbtk_class" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:gtdbtk_domain a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "build_occup_type" ; - dcterms:title "building occupancy type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "building occupancy type" ; - skos:definition "The primary function for which a building or discrete part of a building is intended to be used" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "m" . + rdfs:label "gtdbtk_domain" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:gtdbtk_family a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "indoor_space" ; - dcterms:title "indoor space" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "indoor space" ; - skos:definition "A distinguishable space within a structure, the purpose for which discrete areas of a building is used" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "gtdbtk_family" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:gtdbtk_genus a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "indoor_surf" ; - dcterms:title "indoor surface" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "indoor surface" ; - skos:definition "Type of indoor surface" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "gtdbtk_genus" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:gtdbtk_order a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "filter_type" ; - dcterms:title "filter type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "filter type" ; - skos:definition "A device which removes solid particulates or airborne molecular contaminants" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "m" . + rdfs:label "gtdbtk_order" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:gtdbtk_phylum a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "heat_cool_type" ; - dcterms:title "heating and cooling system type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "heating and cooling system type" ; - skos:definition "Methods of conditioning or heating a room or building" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "m" . + rdfs:label "gtdbtk_phylum" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:gtdbtk_species a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "substructure_type" ; - dcterms:title "substructure type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "substructure type" ; - skos:definition "The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "m" . + rdfs:label "gtdbtk_species" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:habitat a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "building_setting" ; - dcterms:title "building setting" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "building setting" ; - skos:definition "A location (geography) where a building is set" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "habitat" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:has_boolean_value a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "light_type" ; - dcterms:title "light type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "light type" ; - skos:definition "Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "m" . + rdfs:label "has_boolean_value" ; + rdfs:range linkml:Boolean ; + skos:definition "Links a quantity value to a boolean" ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:has_calibration a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "space_typ_state" ; - dcterms:title "space typical state" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "space typical state" ; - skos:definition "Customary or normal state of the space" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "has_calibration" ; + rdfs:range linkml:String ; + skos:definition "A reference to a file that holds calibration information." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:has_credit_associations a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "typ_occup_density" ; - dcterms:title "typical occupant density" ; - rdfs:range linkml:Double ; - rdfs:subPropertyOf ; - skos:altLabel "typical occupant density" ; - skos:definition "Customary or normal density of occupants" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" . + rdfs:label "has_credit_associations" ; + rdfs:domain nmdc:Study ; + rdfs:range nmdc:CreditAssociation ; + skos:definition "This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study" ; + skos:editorialNote "had just been \"inlined: true\"" ; + skos:inScheme nmdc:nmdc ; + nmdc:display_hint "Other researchers associated with this study." . - a owl:ObjectProperty, +nmdc:has_maximum_numeric_value a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "occup_samp" ; - dcterms:title "occupancy at sampling" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "occupancy at sampling" ; - skos:definition "Number of occupants present at time of sample within the given space" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" . + rdfs:label "has_maximum_numeric_value" ; + rdfs:subPropertyOf nmdc:has_numeric_value ; + skos:definition "The maximum value part, expressed as number, of the quantity value when the value covers a range." ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:has_metabolite_quantifications a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "aero_struc" ; - dcterms:title "aerospace structure" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "aerospace structure" ; - skos:definition "Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "has_metabolite_quantifications" ; + rdfs:range nmdc:MetaboliteQuantification ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:has_minimum_numeric_value a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "arch_struc" ; - dcterms:title "architectural structure" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "architectural structure" ; - skos:definition "An architectural structure is a human-made, free-standing, immobile outdoor construction" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "has_minimum_numeric_value" ; + rdfs:subPropertyOf nmdc:has_numeric_value ; + skos:definition "The minimum value part, expressed as number, of the quantity value when the value covers a range." ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:has_part a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "avg_occup" ; - dcterms:title "average daily occupancy" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "average daily occupancy" ; - skos:definition "Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room." ; - skos:exactMatch ; - nmdc:expected_value "value" ; - nmdc:occurrence "1" . + rdfs:label "has_part" ; + rdfs:range nmdc:Reaction ; + skos:definition "A pathway can be broken down to a series of reaction step" ; + skos:inScheme nmdc:annotation . - a owl:ObjectProperty, +nmdc:has_peptide_quantifications a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "bathroom_count" ; - dcterms:title "bathroom count" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "bathroom count" ; - skos:definition "The number of bathrooms in the building" ; - skos:exactMatch ; - nmdc:expected_value "value" ; - nmdc:occurrence "1" . + rdfs:label "has_peptide_quantifications" ; + rdfs:range nmdc:PeptideQuantification ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:highest_similarity_score a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "bedroom_count" ; - dcterms:title "bedroom count" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "bedroom count" ; - skos:definition "The number of bedrooms in the building" ; - skos:exactMatch ; - nmdc:expected_value "value" ; - nmdc:occurrence "1" . + rdfs:label "highest_similarity_score" ; + rdfs:range linkml:Float ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:host_name a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "built_struc_set" ; - dcterms:title "built structure setting" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "built structure setting" ; - skos:definition "The characterization of the location of the built structure as high or low human density" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "host_name" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:igsn_biosample_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ceil_cond" ; - dcterms:title "ceiling condition" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "ceiling condition" ; - skos:definition "The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "igsn_biosample_identifiers" ; + dcterms:title "IGSN Biosample Identifiers" ; + rdfs:subPropertyOf nmdc:biosample_identifiers, + nmdc:igsn_identifiers ; + skos:definition "A list of identifiers for the biosample from the IGSN database." ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:img_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ceil_finish_mat" ; - dcterms:title "ceiling finish material" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "ceiling finish material" ; - skos:definition "The type of material used to finish a ceiling" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "img_identifiers" ; + dcterms:title "IMG Identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$" ] ) ] ; + rdfs:subPropertyOf nmdc:external_database_identifiers ; + skos:definition "A list of identifiers that relate the biosample to records in the IMG database." ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:inchi a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ceil_water_mold" ; - dcterms:title "ceiling signs of water/mold" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "ceiling signs of water/mold" ; - skos:definition "Signs of the presence of mold or mildew on the ceiling" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "inchi" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:inchi_key a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ceil_struc" ; - dcterms:title "ceiling structure" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "ceiling structure" ; - skos:definition "The construction format of the ceiling" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "inchi_key" ; + rdfs:range linkml:String ; + skos:editorialNote "key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental testing. J Cheminform. 4:12" ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:input_base_count a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ceil_texture" ; - dcterms:title "ceiling texture" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "ceiling texture" ; - skos:definition "The feel, appearance, or consistency of a ceiling surface" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "input_base_count" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:read_qc_analysis_statistic ; + skos:definition "The nucleotide base count number of input reads for QC analysis." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:input_contig_num a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ceil_type" ; - dcterms:title "ceiling type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "ceiling type" ; - skos:definition "The type of ceiling according to the ceiling's appearance or construction" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "input_contig_num" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:input_mass a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "cool_syst_id" ; - dcterms:title "cooling system identifier" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "cooling system identifier" ; - skos:definition "The cooling system identifier" ; - skos:exactMatch ; - nmdc:expected_value "unique identifier" ; - nmdc:occurrence "1" . + rdfs:label "input_mass" ; + dcterms:title "sample mass used" ; + rdfs:range nmdc:QuantityValue ; + skos:altLabel "sample mass", + "sample weight" ; + skos:definition "Total mass of sample used in activity." ; + skos:exactMatch MS:1000004 ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:input_read_bases a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "date_last_rain" ; - dcterms:title "date last rain" ; - rdfs:range nmdc:TimestampValue ; - rdfs:subPropertyOf ; - skos:altLabel "date last rain" ; - skos:definition "The date of the last time it rained" ; - skos:exactMatch ; - nmdc:expected_value "timestamp" ; - nmdc:occurrence "1" . + rdfs:label "input_read_bases" ; + rdfs:range linkml:Float ; + skos:definition "TODO " ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:input_read_count a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "build_docs" ; - dcterms:title "design, construction, and operation documents" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "design, construction, and operation documents" ; - skos:definition "The building design, construction and operation documents" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "input_read_count" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:read_qc_analysis_statistic ; + skos:definition "The sequence count number of input reads for QC analysis." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:insdc_analysis_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "door_cond" ; - dcterms:title "door condition" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "door condition" ; - skos:definition "The phsical condition of the door" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "insdc_analysis_identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^insdc.sra:(E|D|S)RR[0-9]{6,}$" ] ) ] ; + rdfs:subPropertyOf nmdc:analysis_identifiers, + nmdc:insdc_identifiers ; + skos:inScheme nmdc:external_identifiers ; + skos:note "in INSDC this is a run but it corresponds to a GOLD analysis" . - a owl:ObjectProperty, +nmdc:insdc_assembly_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "door_direct" ; - dcterms:title "door direction of opening" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "door direction of opening" ; - skos:definition "The direction the door opens" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "insdc_assembly_identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$" ] ) ] ; + rdfs:subPropertyOf nmdc:assembly_identifiers, + nmdc:insdc_identifiers ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:insdc_biosample_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "door_loc" ; - dcterms:title "door location" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "door location" ; - skos:definition "The relative location of the door in the room" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "insdc_biosample_identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^biosample:SAM[NED]([A-Z])?[0-9]+$" ] ) ] ; + rdfs:seeAlso , + , + , + ; + rdfs:subPropertyOf nmdc:biosample_identifiers, + nmdc:insdc_identifiers ; + skos:altLabel "DDBJ biosample identifiers", + "EBI biosample identifiers", + "NCBI biosample identifiers" ; + skos:definition "identifiers for corresponding sample in INSDC" ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:insdc_experiment_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "door_mat" ; - dcterms:title "door material" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "door material" ; - skos:definition "The material the door is composed of" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "door_move" ; - dcterms:title "door movement" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "door movement" ; - skos:definition "The type of movement of the door" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "insdc_experiment_identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^insdc.sra:(E|D|S)RX[0-9]{6,}$" ] ) ] ; + rdfs:subPropertyOf nmdc:external_database_identifiers, + nmdc:insdc_identifiers ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:insdc_secondary_sample_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "door_water_mold" ; - dcterms:title "door signs of water/mold" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "door signs of water/mold" ; - skos:definition "Signs of the presence of mold or mildew on a door" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "insdc_secondary_sample_identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^biosample:(E|D|S)RS[0-9]{6,}$" ] ) ] ; + rdfs:subPropertyOf nmdc:biosample_identifiers, + nmdc:insdc_identifiers ; + skos:definition "secondary identifiers for corresponding sample in INSDC" ; + skos:inScheme nmdc:external_identifiers ; + skos:note "ENA redirects these to primary IDs, e.g. https://www.ebi.ac.uk/ena/browser/view/DRS166340 -> SAMD00212331", + "MGnify uses these as their primary sample IDs" . - a owl:ObjectProperty, +nmdc:insdc_sra_ena_study_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "door_type" ; - dcterms:title "door type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "door type" ; - skos:definition "The type of door material" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "insdc_sra_ena_study_identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^insdc.sra:(E|D|S)RP[0-9]{6,}$" ] ) ] ; + rdfs:seeAlso , + ; + rdfs:subPropertyOf nmdc:insdc_identifiers, + nmdc:study_identifiers ; + skos:altLabel "DDBJ SRA identifiers", + "EBI ENA study identifiers", + "NCBI SRA identifiers" ; + skos:definition "identifiers for corresponding project in INSDC SRA / ENA" ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:instrument_name a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "door_comp_type" ; - dcterms:title "door type, composite" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "door type, composite" ; - skos:definition "The composite type of the door" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "instrument_name" ; + skos:definition "The name of the instrument that was used for processing the sample." ; + skos:inScheme nmdc:basic_slots . - a owl:ObjectProperty, +nmdc:is_balanced a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "door_type_metal" ; - dcterms:title "door type, metal" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "door type, metal" ; - skos:definition "The type of metal door" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "is_balanced" ; + rdfs:range linkml:Boolean ; + skos:inScheme nmdc:annotation . - a owl:ObjectProperty, +nmdc:is_diastereoselective a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "door_type_wood" ; - dcterms:title "door type, wood" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "door type, wood" ; - skos:definition "The type of wood door" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "is_diastereoselective" ; + rdfs:range linkml:Boolean ; + skos:inScheme nmdc:annotation . - a owl:ObjectProperty, +nmdc:is_fully_characterized a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "drawings" ; - dcterms:title "drawings" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "drawings" ; - skos:definition "The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "is_fully_characterized" ; + rdfs:range linkml:Boolean ; + skos:definition "False if includes R-groups" ; + skos:inScheme nmdc:annotation . - a owl:ObjectProperty, +nmdc:is_stereo a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "elevator" ; - dcterms:title "elevator count" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "elevator count" ; - skos:definition "The number of elevators within the built structure" ; - skos:exactMatch ; - nmdc:expected_value "value" ; - nmdc:occurrence "1" . + rdfs:label "is_stereo" ; + rdfs:range linkml:Boolean ; + skos:inScheme nmdc:annotation . - a owl:ObjectProperty, +nmdc:is_transport a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "escalator" ; - dcterms:title "escalator count" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "escalator count" ; - skos:definition "The number of escalators within the built structure" ; - skos:exactMatch ; - nmdc:expected_value "value" ; - nmdc:occurrence "1" . + rdfs:label "is_transport" ; + rdfs:range linkml:Boolean ; + skos:inScheme nmdc:annotation . - a owl:ObjectProperty, +nmdc:isotope_exposure a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "fireplace_type" ; - dcterms:title "fireplace type" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "fireplace type" ; - skos:definition "A firebox with chimney" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "isotope_exposure" ; + dcterms:title "isotope exposure/addition" ; + skos:definition "List isotope exposure or addition applied to your sample." ; + skos:inScheme ; + skos:note "This is required when your experimental design includes the use of isotopically labeled compounds" ; + sh:order 16 . - a owl:ObjectProperty, +nmdc:jgi_portal_study_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "floor_cond" ; - dcterms:title "floor condition" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "floor condition" ; - skos:definition "The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "jgi_portal_study_identifiers" ; + dcterms:title "JGI Portal Study identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^jgi.proposal:\\d+$" ] ) ] ; + rdfs:subPropertyOf nmdc:jgi_portal_identifiers, + nmdc:study_identifiers ; + skos:definition "Identifiers that link a NMDC study to a website hosting raw and analyzed data for a JGI proposal. The suffix of the curie can used to query the GOLD API and is interoperable with an award DOI from OSTI and a GOLD study identifier." ; + skos:inScheme nmdc:external_identifiers ; + skos:note "Could this could be considered a related identifier?", + "Curie suffix is the Site Award Number from an OSTI award page", + "Site Award Number 507130 == award doi doi:10.46936/10.25585/60000017 -- GOLD study identifier gold:Gs0154044", + "bioregistry.io/jgi.proposal:507130 ==https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html" . - a owl:ObjectProperty, +nmdc:keywords a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "floor_finish_mat" ; - dcterms:title "floor finish material" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "floor finish material" ; - skos:definition "The floor covering type; the finished surface that is walked on" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "keywords" ; + rdfs:range linkml:String ; + skos:definition "A list of keywords that used to associate the entity. Keywords SHOULD come from controlled vocabularies, including MESH, ENVO." ; + skos:inScheme nmdc:core ; + skos:mappingRelation dcterms:subject . - a owl:ObjectProperty, +nmdc:language a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "floor_water_mold" ; - dcterms:title "floor signs of water/mold" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "floor signs of water/mold" ; - skos:definition "Signs of the presence of mold or mildew in a room" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "language" ; + rdfs:range nmdc:language_code ; + skos:definition "Should use ISO 639-1 code e.g. \"en\", \"fr\"" ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:lbc_thirty a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "floor_struc" ; - dcterms:title "floor structure" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "floor structure" ; - skos:definition "Refers to the structural elements and subfloor upon which the finish flooring is installed" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "lbc_thirty" ; + dcterms:title "lime buffer capacity (at 30 minutes)" ; + rdfs:range nmdc:QuantityValue ; + rdfs:seeAlso , + ; + rdfs:subPropertyOf nmdc:attribute ; + 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" . - a owl:ObjectProperty, +nmdc:lbceq a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "furniture" ; - dcterms:title "furniture" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "furniture" ; - skos:definition "The types of furniture present in the sampled room" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "lbceq" ; + dcterms:title "lime buffer capacity (after 5 day incubation)" ; + rdfs:range nmdc:QuantityValue ; + rdfs:seeAlso ; + rdfs:subPropertyOf nmdc:attribute ; + 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" . - a owl:ObjectProperty, +nmdc:left_participants a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gender_restroom" ; - dcterms:title "gender of restroom" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "gender of restroom" ; - skos:definition "The gender type of the restroom" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "left_participants" ; + rdfs:range nmdc:ReactionParticipant ; + rdfs:subPropertyOf nmdc:has_participants ; + skos:inScheme nmdc:annotation . - a owl:ObjectProperty, +nmdc:library_preparation_kit a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "handidness" ; - dcterms:title "handidness" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "handidness" ; - skos:definition "The handidness of the individual sampled" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "library_preparation_kit" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:library_preparation_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "heat_deliv_loc" ; - dcterms:title "heating delivery locations" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "heating delivery locations" ; - skos:definition "The location of heat delivery within the room" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "library_preparation_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:LibraryPreparation ; + rdfs:subPropertyOf nmdc:object_set ; + skos:altLabel "library_construction_set" ; + skos:definition "This property links a database object to the set of DNA extractions within it." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:library_type a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_sex" ; - dcterms:title "host sex" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "host sex" ; - skos:definition "Gender or physical sex of the host." ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "library_type" ; + dcterms:title "library type" ; + rdfs:range nmdc:LibraryTypeEnum ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:location a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "heat_sys_deliv_meth" ; - dcterms:title "heating system delivery method" ; + rdfs:label "location" ; rdfs:range linkml:String ; - rdfs:subPropertyOf ; - skos:altLabel "heating system delivery method" ; - skos:definition "The method by which the heat is delivered through the system" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:low_depth_contig_num a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "int_wall_cond" ; - dcterms:title "interior wall condition" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "interior wall condition" ; - skos:definition "The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "low_depth_contig_num" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:mags_activity_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "last_clean" ; - dcterms:title "last time swept/mopped/vacuumed" ; - rdfs:range nmdc:TimestampValue ; - rdfs:subPropertyOf ; - skos:altLabel "last time swept/mopped/vacuumed" ; - skos:definition "The last time the floor was cleaned (swept, mopped, vacuumed)" ; - skos:exactMatch ; - nmdc:expected_value "timestamp" ; - nmdc:occurrence "1" . + rdfs:label "mags_activity_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:MagsAnalysisActivity ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of MAGs analysis activities." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:mags_list a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "mech_struc" ; - dcterms:title "mechanical structure" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "mechanical structure" ; - skos:definition "mechanical structure: a moving structure" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "mags_list" ; + rdfs:range nmdc:MagBin ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:manganese a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "occup_document" ; - dcterms:title "occupancy documentation" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "occupancy documentation" ; - skos:definition "The type of documentation of occupancy" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "manganese" ; + dcterms:title "manganese" ; + rdfs:range nmdc:QuantityValue ; + rdfs:seeAlso ; + rdfs:subPropertyOf nmdc:attribute ; + 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)" . - a owl:ObjectProperty, +nmdc:massive_study_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ext_wall_orient" ; - dcterms:title "orientations of exterior wall" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "orientations of exterior wall" ; - skos:definition "The orientation of the exterior wall" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "massive_study_identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^MASSIVE:" ] ) ] ; + rdfs:seeAlso ; + rdfs:subPropertyOf nmdc:massive_identifiers, + nmdc:study_identifiers ; + skos:definition "identifiers for corresponding study in MASSIVE" ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:material_sample_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ext_window_orient" ; - dcterms:title "orientations of exterior window" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "orientations of exterior window" ; - skos:definition "The compass direction the exterior window of the room is facing" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "material_sample_set" ; + dcterms:title "material sample set" ; + rdfs:range nmdc:MaterialSample ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:material_sampling_activity_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "pres_animal_insect" ; - dcterms:title "presence of pets, animals, or insects" ; + rdfs:label "material_sampling_activity_set" ; + dcterms:title "material sampling activity set" ; + rdfs:range nmdc:MaterialSamplingActivity ; + skos:inScheme nmdc:sample_prep . + +nmdc:md5_checksum a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "md5_checksum" ; rdfs:range linkml:String ; - rdfs:subPropertyOf ; - skos:altLabel "presence of pets, animals, or insects" ; - skos:definition "The type and number of animals or insects present in the sampling space." ; - skos:exactMatch ; - nmdc:expected_value "enumeration;count" ; - nmdc:occurrence "1" . + rdfs:subPropertyOf nmdc:attribute ; + skos:definition "MD5 checksum of file (pre-compressed)" ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:members_id a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "quad_pos" ; - dcterms:title "quadrant position" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "quadrant position" ; - skos:definition "The quadrant position of the sampling room within the building" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "members_id" ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:metabolite_quantified a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "rel_samp_loc" ; - dcterms:title "relative sampling location" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "relative sampling location" ; - skos:definition "The sampling location within the train car" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "metabolite_quantified" ; + rdfs:range nmdc:ChemicalEntity ; + skos:definition "the specific metabolite identifier" ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:metabolomics_analysis_activity_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_condt" ; - dcterms:title "room condition" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "room condition" ; - skos:definition "The condition of the room at the time of sampling" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "metabolomics_analysis_activity_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:MetabolomicsAnalysisActivity ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of metabolomics analysis activities." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:metagenome_annotation_activity_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_loc" ; - dcterms:title "room location in building" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "room location in building" ; - skos:definition "The position of the room within the building" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "metagenome_annotation_activity_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:MetagenomeAnnotationActivity ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of metagenome annotation activities." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:metagenome_annotation_id a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_samp_pos" ; - dcterms:title "room sampling position" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "room sampling position" ; - skos:definition "The horizontal sampling position in the room relative to architectural elements" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "metagenome_annotation_id" ; + rdfs:range nmdc:WorkflowExecutionActivity ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:metagenome_assembly_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_type" ; - dcterms:title "room type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "room type" ; - skos:definition "The main purpose or activity of the sampling room. A room is any distinguishable space within a structure" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "metagenome_assembly_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:MetagenomeAssembly ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of metagenome assembly activities." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:metagenome_sequencing_activity_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "room_connected" ; - dcterms:title "rooms connected by a doorway" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "rooms connected by a doorway" ; - skos:definition "List of rooms connected to the sampling room by a doorway" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "metagenome_sequencing_activity_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:MetagenomeSequencingActivity ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of metagenome sequencing activities." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:metaproteomics_analysis_activity_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_weather" ; - dcterms:title "sampling day weather" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "sampling day weather" ; - skos:definition "The weather on the sampling day" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "metaproteomics_analysis_activity_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:MetaproteomicsAnalysisActivity ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of metaproteomics analysis activities." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:mgnify_analysis_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_floor" ; - dcterms:title "sampling floor" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "sampling floor" ; - skos:definition "The floor of the building, where the sampling room is located" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "mgnify_analysis_identifiers" ; + rdfs:subPropertyOf nmdc:analysis_identifiers, + nmdc:mgnify_identifiers ; + skos:editorialNote "removed pattern: \"^mgnify:MGYA[0-9]+$\" ## TODO https://github.com/bioregistry/bioregistry/issues/109" ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:mgnify_project_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "season" ; - dcterms:title "season" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "season" ; - skos:definition "The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729)." ; - skos:exactMatch ; - nmdc:expected_value "NCIT:C94729" ; - nmdc:occurrence "1" . + rdfs:label "mgnify_project_identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^mgnify.proj:[A-Z]+[0-9]+$" ] ) ] ; + rdfs:subPropertyOf nmdc:mgnify_identifiers, + nmdc:study_identifiers ; + skos:definition "identifiers for corresponding project in MGnify" ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:micro_biomass_c_meth a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "season_use" ; - dcterms:title "seasonal use" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "seasonal use" ; - skos:definition "The seasons the space is occupied" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "micro_biomass_c_meth" ; + dcterms:title "microbial biomass carbon method" ; + skos:definition "Reference or method used in determining microbial biomass carbon" ; + skos:inScheme ; + skos:note "required if \"microbial_biomass_c\" is provided" ; + sh:order 11 . - a owl:ObjectProperty, +nmdc:micro_biomass_n_meth a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "shading_device_cond" ; - dcterms:title "shading device condition" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "shading device condition" ; - skos:definition "The physical condition of the shading device at the time of sampling" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "micro_biomass_n_meth" ; + dcterms:title "microbial biomass nitrogen method" ; + skos:definition "Reference or method used in determining microbial biomass nitrogen" ; + skos:inScheme ; + skos:note "required if \"microbial_biomass_n\" is provided" ; + sh:order 13 . - a owl:ObjectProperty, +nmdc:microbial_biomass_c a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "shading_device_loc" ; - dcterms:title "shading device location" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "shading device location" ; - skos:definition "The location of the shading device in relation to the built structure" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "microbial_biomass_c" ; + dcterms:title "microbial biomass carbon" ; + skos:definition "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer." ; + skos:inScheme ; + skos:note "If you provide this, correction factors used for conversion to the final units and method are required" ; + sh:order 10 . - a owl:ObjectProperty, +nmdc:microbial_biomass_n a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "heat_system_id" ; - dcterms:title "heating system identifier" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "heating system identifier" ; - skos:definition "The heating system identifier" ; - skos:exactMatch ; - nmdc:expected_value "unique identifier" ; - nmdc:occurrence "1" . + rdfs:label "microbial_biomass_n" ; + dcterms:title "microbial biomass nitrogen" ; + skos:definition "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer." ; + skos:inScheme ; + skos:note "If you provide this, correction factors used for conversion to the final units and method are required" ; + sh:order 12 . - a owl:ObjectProperty, +nmdc:min_q_value a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "shad_dev_water_mold" ; - dcterms:title "shading device signs of water/mold" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf ; - skos:altLabel "shading device signs of water/mold" ; - skos:definition "Signs of the presence of mold or mildew on the shading device" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "min_q_value" ; + rdfs:range linkml:Float ; + rdfs:seeAlso ; + skos:definition "smallest Q-Value associated with the peptide sequence as provided by MSGFPlus tool" ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:mod_date a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "shading_device_type" ; - dcterms:title "shading device type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "shading device type" ; - skos:definition "The type of shading device" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "mod_date" ; + rdfs:range linkml:String ; + skos:definition "The last date on which the database information was modified." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:ncbi_project_name a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "specific" ; - dcterms:title "specifications" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "specifications" ; - skos:definition "The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "ncbi_project_name" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:ncbi_taxonomy_name a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "train_line" ; - dcterms:title "train line" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "train line" ; - skos:definition "The subway line name" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "ncbi_taxonomy_name" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:neon_biosample_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "train_stat_loc" ; - dcterms:title "train station collection location" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "train station collection location" ; - skos:definition "The train station collection location" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "neon_biosample_identifiers" ; + rdfs:subPropertyOf nmdc:biosample_identifiers, + nmdc:neon_identifiers ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:neon_deims_sdr_link a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "train_stop_loc" ; - dcterms:title "train stop collection location" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "train stop collection location" ; - skos:definition "The train stop collection location" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "neon_deims_sdr_link" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:neon_eco_type a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "vis_media" ; - dcterms:title "visual media" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "visual media" ; - skos:definition "The building visual media" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "neon_eco_type" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:neon_soil_type a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "wall_const_type" ; - dcterms:title "wall construction type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "wall construction type" ; - skos:definition "The building class of the wall defined by the composition of the building elements and fire-resistance rating." ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "neon_soil_type" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:neon_study_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "wall_finish_mat" ; - dcterms:title "wall finish material" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "wall finish material" ; - skos:definition "The material utilized to finish the outer most layer of the wall" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "neon_study_identifiers" ; + rdfs:subPropertyOf nmdc:neon_identifiers, + nmdc:study_identifiers ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:nitrate_nitrogen a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "wall_loc" ; - dcterms:title "wall location" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "wall location" ; - skos:definition "The relative location of the wall within the room" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "nitrate_nitrogen" ; + dcterms:title "nitrate_nitrogen" ; + rdfs:range nmdc:QuantityValue ; + rdfs:seeAlso ; + rdfs:subPropertyOf nmdc:attribute ; + 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" . - a owl:ObjectProperty, +nmdc:nitrite_nitrogen a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "wall_water_mold" ; - dcterms:title "wall signs of water/mold" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "wall signs of water/mold" ; - skos:definition "Signs of the presence of mold or mildew on a wall" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "nitrite_nitrogen" ; + dcterms:title "nitrite_nitrogen" ; + rdfs:range nmdc:QuantityValue ; + rdfs:seeAlso ; + rdfs:subPropertyOf nmdc:attribute ; + 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" . - a owl:ObjectProperty, +nmdc:nom_analysis_activity_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "wall_surf_treatment" ; - dcterms:title "wall surface treatment" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "wall surface treatment" ; - skos:definition "The surface treatment of interior wall" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "nom_analysis_activity_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:NomAnalysisActivity ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of natural organic matter (NOM) analysis activities." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:non_microb_biomass a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "wall_texture" ; - dcterms:title "wall texture" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "wall texture" ; - skos:definition "The feel, appearance, or consistency of a wall surface" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "non_microb_biomass" ; + dcterms:title "non-microbial biomass" ; + skos:definition "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;" ; + skos:inScheme ; + sh:order 8 . - a owl:ObjectProperty, +nmdc:non_microb_biomass_method a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "water_feat_type" ; - dcterms:title "water feature type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "water feature type" ; - skos:definition "The type of water feature present within the building being sampled" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "non_microb_biomass_method" ; + dcterms:title "non-microbial biomass method" ; + skos:definition "Reference or method used in determining biomass" ; + skos:inScheme ; + skos:note "required if \"non-microbial biomass\" is provided" ; + sh:order 9 . - a owl:ObjectProperty, +nmdc:num_16s a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "weekday" ; - dcterms:title "weekday" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "weekday" ; - skos:definition "The day of the week when sampling occurred" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "num_16s" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:num_23s a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "window_cond" ; - dcterms:title "window condition" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "window condition" ; - skos:definition "The physical condition of the window at the time of sampling" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "num_23s" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:num_5s a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "window_cover" ; - dcterms:title "window covering" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "window covering" ; - skos:definition "The type of window covering" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "num_5s" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:num_aligned_reads a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "window_horiz_pos" ; - dcterms:title "window horizontal position" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "window horizontal position" ; - skos:definition "The horizontal position of the window on the wall" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "num_aligned_reads" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "The sequence count number of input reads aligned to assembled contigs." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:num_input_reads a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "window_loc" ; - dcterms:title "window location" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "window location" ; - skos:definition "The relative location of the window within the room" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "num_input_reads" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "The sequence count number of input reads for assembly." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:num_t_rna a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "window_mat" ; - dcterms:title "window material" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "window material" ; - skos:definition "The type of material used to finish a window" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "num_t_rna" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:number_of_contig a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "window_water_mold" ; - dcterms:title "window signs of water/mold" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "window signs of water/mold" ; - skos:definition "Signs of the presence of mold or mildew on the window." ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "number_of_contig" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:objective a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "window_status" ; - dcterms:title "window status" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "window status" ; - skos:definition "Defines whether the windows were open or closed during environmental testing" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "objective" ; + rdfs:range linkml:String ; + skos:definition "The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract." ; + skos:inScheme nmdc:core ; + skos:mappingRelation . - a owl:ObjectProperty, +nmdc:omics_processing_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "window_type" ; - dcterms:title "window type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "window type" ; - skos:definition "The type of windows" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "omics_processing_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:OmicsProcessing ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of omics processings within it." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:omics_type a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "window_vert_pos" ; - dcterms:title "window vertical position" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "window vertical position" ; - skos:definition "The vertical position of the window on the wall" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "omics_type" ; + rdfs:range nmdc:ControlledTermValue ; + skos:definition "The type of omics data" ; + skos:editorialNote "was the range string at one point? the values in MongoDB don't look like NMDC classes" ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:org_nitro_method a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "biol_stat" ; - dcterms:title "biological status" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "biological status" ; - skos:definition "The level of genome modification." ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "org_nitro_method" ; + dcterms:title "organic nitrogen method" ; + skos:definition "Method used for obtaining organic nitrogen" ; + skos:inScheme ; + skos:note "required if \"org_nitro\" is provided" ; + sh:order 14 . - a owl:ObjectProperty, +nmdc:other_treatment a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "genetic_mod" ; - dcterms:title "genetic modification" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "genetic modification" ; - skos:definition "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI,url or free text" ; - nmdc:occurrence "1" . + rdfs:label "other_treatment" ; + dcterms:title "other treatments" ; + skos:definition "Other treatments applied to your samples that are not applicable to the provided fields" ; + skos:inScheme ; + skos:note "This is an open text field to provide any treatments that cannot be captured in the provided slots." ; + sh:order 15 . - a owl:ObjectProperty, +nmdc:output_base_count a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_capt_status" ; - dcterms:title "sample capture status" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "sample capture status" ; - skos:definition "Reason for the sample" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . - - a owl:ObjectProperty, + rdfs:label "output_base_count" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:read_qc_analysis_statistic ; + skos:definition "After QC analysis nucleotide base count number." ; + skos:inScheme nmdc:workflow_execution_activity . + +nmdc:output_read_bases a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_subject_id" ; - dcterms:title "host subject id" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "host subject id" ; - skos:definition "A unique identifier by which each subject can be referred to, de-identified." ; - skos:exactMatch ; - nmdc:expected_value "unique identifier" ; - nmdc:occurrence "1" . + rdfs:label "output_read_bases" ; + rdfs:range linkml:Float ; + skos:definition "TODO" ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:output_read_count a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_body_habitat" ; - dcterms:title "host body habitat" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "host body habitat" ; - skos:definition "Original body habitat where the sample was obtained from" ; - skos:exactMatch ; - nmdc:expected_value "free text" ; - nmdc:occurrence "1" . + rdfs:label "output_read_count" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:read_qc_analysis_statistic ; + skos:definition "After QC analysis sequence count number." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:ObjectProperty, +nmdc:pcr_cycles a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_body_site" ; - dcterms:title "host body site" ; - rdfs:range nmdc:ControlledTermValue ; - rdfs:subPropertyOf ; - skos:altLabel "host body site" ; - skos:definition "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON" ; - skos:exactMatch ; - nmdc:expected_value "FMA or UBERON" ; - nmdc:occurrence "1" . + rdfs:label "pcr_cycles" ; + rdfs:range linkml:Integer ; + skos:exactMatch ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:peptide_sequence a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_diet" ; - dcterms:title "host diet" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "host diet" ; - skos:definition "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types" ; - skos:exactMatch ; - nmdc:expected_value "diet type" ; - nmdc:occurrence "m" . + rdfs:label "peptide_sequence" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:peptide_sequence_count a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_last_meal" ; - dcterms:title "host last meal" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "host last meal" ; - skos:definition "Content of last meal and time since feeding; can include multiple values" ; - skos:exactMatch ; - nmdc:expected_value "content;duration" ; - nmdc:occurrence "m" . + rdfs:label "peptide_sequence_count" ; + rdfs:range linkml:Integer ; + skos:definition "count of peptide sequences grouped to the best_protein" ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:peptide_spectral_count a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_growth_cond" ; - dcterms:title "host growth conditions" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "host growth conditions" ; - skos:definition "Literature reference giving growth conditions of the host" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI,url or free text" ; - nmdc:occurrence "1" . + rdfs:label "peptide_spectral_count" ; + rdfs:range linkml:Integer ; + skos:definition "sum of filter passing MS2 spectra associated with the peptide sequence within a given LC-MS/MS data file" ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:peptide_sum_masic_abundance a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_family_relation" ; - dcterms:title "host family relationship" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf ; - skos:altLabel "host family relationship" ; - skos:definition "Familial relationships to other hosts in the same study; can include multiple relationships" ; - skos:exactMatch ; - nmdc:expected_value "relationship type;arbitrary identifier" ; - nmdc:occurrence "m" . + rdfs:label "peptide_sum_masic_abundance" ; + rdfs:range linkml:Integer ; + skos:definition "combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the peptide sequence from a given LC-MS/MS data file using the MASIC tool" ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:phase a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_phenotype" ; - dcterms:title "host phenotype" ; - rdfs:range nmdc:ControlledTermValue ; - rdfs:subPropertyOf ; - skos:altLabel "host phenotype" ; - skos:definition "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP" ; - skos:exactMatch ; - nmdc:expected_value "PATO or HP" ; - nmdc:occurrence "1" . + rdfs:label "phase" ; + rdfs:range [ 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 ] ) ] ) ] ; + skos:definition "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; + skos:exactMatch ; + skos:inScheme nmdc:annotation . - a owl:ObjectProperty, +nmdc:pooling_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gravidity" ; - dcterms:title "gravidity" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "gravidity" ; - skos:definition "Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used" ; - skos:exactMatch ; - nmdc:expected_value "gravidity status;timestamp" ; - nmdc:occurrence "1" . + rdfs:label "pooling_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:Pooling ; + rdfs:subPropertyOf nmdc:object_set ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:principal_investigator a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_body_product" ; - dcterms:title "host body product" ; - rdfs:range nmdc:ControlledTermValue ; - rdfs:subPropertyOf ; - skos:altLabel "host body product" ; - skos:definition "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon" ; - skos:exactMatch ; - nmdc:expected_value "FMA or UBERON" ; - nmdc:occurrence "1" . + rdfs:label "principal_investigator" ; + rdfs:range nmdc:PersonValue ; + rdfs:subPropertyOf nmdc:attribute ; + skos:altLabel "PI" ; + skos:definition "Principal Investigator who led the study and/or generated the dataset." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:processed_sample_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "hcr" ; - dcterms:title "hydrocarbon resource type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "hydrocarbon resource type" ; - skos:definition "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "processed_sample_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:ProcessedSample ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of processed samples within it." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:processing_institution a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "hc_produced" ; - dcterms:title "hydrocarbon type produced" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "hydrocarbon type produced" ; - skos:definition "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "processing_institution" ; + rdfs:range nmdc:ProcessingInstitutionEnum ; + skos:definition "The organization that processed the sample." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:profile_image_url a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "lithology" ; - dcterms:title "lithology" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "lithology" ; - skos:definition "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "profile_image_url" ; + rdfs:domain nmdc:PersonValue ; + rdfs:range linkml:String ; + skos:definition "A url that points to an image of a person." ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:project_id a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "depos_env" ; - dcterms:title "depositional environment" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "depositional environment" ; - skos:definition "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "project_id" ; + dcterms:title "project ID" ; + skos:definition "Proposal IDs or names associated with dataset" ; + skos:inScheme ; + sh:order 1 . - a owl:ObjectProperty, +nmdc:proport_woa_temperature a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "hcr_geol_age" ; - dcterms:title "hydrocarbon resource geological age" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "hydrocarbon resource geological age" ; - skos:definition "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "proport_woa_temperature" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:proposal_dna a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sr_kerog_type" ; - dcterms:title "source rock kerogen type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "source rock kerogen type" ; - skos:definition "Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "proposal_dna" ; + dcterms:title "DNA proposal ID" ; + skos:inScheme ; + skos:note "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." ; + sh:order 19 . - a owl:ObjectProperty, +nmdc:proposal_rna a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sr_lithology" ; - dcterms:title "source rock lithology" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "source rock lithology" ; - skos:definition "Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "proposal_rna" ; + dcterms:title "RNA proposal ID" ; + skos:inScheme ; + skos:note "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." ; + sh:order 19 . - a owl:ObjectProperty, +nmdc:protein_spectral_count a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sr_dep_env" ; - dcterms:title "source rock depositional environment" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "source rock depositional environment" ; - skos:definition "Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "protein_spectral_count" ; + rdfs:range linkml:Integer ; + skos:definition "sum of filter passing MS2 spectra associated with the best protein within a given LC-MS/MS data file" ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:protein_sum_masic_abundance a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sr_geol_age" ; - dcterms:title "source rock geological age" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "source rock geological age" ; - skos:definition "Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "protein_sum_masic_abundance" ; + rdfs:range linkml:Integer ; + skos:definition "combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the best protein from a given LC-MS/MS data file using the MASIC tool" ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:protocol_link a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_type" ; - dcterms:title "sample type" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "sample type" ; - skos:definition "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246)." ; - skos:exactMatch ; - nmdc:expected_value "GENEPIO:0001246" ; - nmdc:occurrence "1" . + rdfs:label "protocol_link" ; + rdfs:range nmdc:Protocol ; + skos:inScheme nmdc:basic_slots . - a owl:ObjectProperty, +nmdc:publication_dois a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_subtype" ; - dcterms:title "sample subtype" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "sample subtype" ; - skos:definition "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "publication_dois" ; + rdfs:subPropertyOf nmdc:dois ; + skos:definition "One or more DOIs that links a study, or similar entity, to a publication." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:publications a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ph" ; - dcterms:title "pH" ; - rdfs:range linkml:Double ; - rdfs:subPropertyOf ; - skos:altLabel "pH" ; - skos:definition "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid" ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" . + rdfs:label "publications" ; + rdfs:range linkml:String ; + skos:definition "A list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible." ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, +nmdc:quality_control_report a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "prod_start_date" ; - dcterms:title "production start date" ; - rdfs:range nmdc:TimestampValue ; - rdfs:subPropertyOf ; - skos:altLabel "production start date" ; - skos:definition "Date of field's first production" ; - skos:exactMatch ; - nmdc:expected_value "timestamp" ; - nmdc:occurrence "1" . + rdfs:label "quality_control_report" ; + rdfs:range nmdc:QualityControlReport ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:reaction_activity_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "add_recov_method" ; - dcterms:title "secondary and tertiary recovery methods and start date" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "secondary and tertiary recovery methods and start date" ; - skos:definition "Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field" ; - skos:exactMatch ; - nmdc:expected_value "enumeration;timestamp" ; - nmdc:occurrence "1" . + rdfs:label "reaction_activity_set" ; + rdfs:range nmdc:ReactionActivity ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:reaction_aided_by a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "iw_bt_date_well" ; - dcterms:title "injection water breakthrough date of specific well" ; - rdfs:range nmdc:TimestampValue ; - rdfs:subPropertyOf ; - skos:altLabel "injection water breakthrough date of specific well" ; - skos:definition "Injection water breakthrough date per well following a secondary and/or tertiary recovery" ; - skos:exactMatch ; - nmdc:expected_value "timestamp" ; - nmdc:occurrence "1" . + rdfs:label "reaction_aided_by" ; + dcterms:title "reaction aided by" ; + rdfs:range nmdc:LabDevice ; + skos:altLabel "shaker" ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:reaction_temperature a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "biocide" ; - dcterms:title "biocide administration" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "biocide administration" ; - skos:definition "List of biocides (commercial name of product and supplier) and date of administration" ; - skos:exactMatch ; - nmdc:expected_value "name;name;timestamp" ; - nmdc:occurrence "1" . + rdfs:label "reaction_temperature" ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:read_based_taxonomy_analysis_activity_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "chem_treatment" ; - dcterms:title "chemical treatment" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "chemical treatment" ; - skos:definition "List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included" ; - skos:exactMatch ; - nmdc:expected_value "name;name;timestamp" ; - nmdc:occurrence "1" . + rdfs:label "read_based_taxonomy_analysis_activity_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:ReadBasedTaxonomyAnalysisActivity ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of read based analysis activities." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:read_qc_analysis_activity_set a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_collect_point" ; - dcterms:title "sample collection point" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "sample collection point" ; - skos:definition "Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "read_qc_analysis_activity_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:ReadQcAnalysisActivity ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of read QC analysis activities." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:relevant_protocols 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:exactMatch ; - nmdc:expected_value "free text" ; - nmdc:occurrence "1" . + rdfs:label "relevant_protocols" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:replicate_number 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:exactMatch ; - nmdc:expected_value "climate name;treatment interval and duration" ; - nmdc:occurrence "m" . + rdfs:label "replicate_number" ; + dcterms:title "replicate number" ; + skos:definition "If sending biological replicates, indicate the rep number here." ; + skos:inScheme ; + skos:note "This will guide staff in ensuring your samples are blocked & randomized correctly" ; + sh:order 6 . - a owl:ObjectProperty, +nmdc:right_participants a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "cult_root_med" ; - dcterms:title "culture rooting medium" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "culture rooting medium" ; - skos:definition "Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors." ; - skos:exactMatch ; - nmdc:expected_value "name, PMID,DOI or url" ; - nmdc:occurrence "1" . + rdfs:label "right_participants" ; + rdfs:range nmdc:ReactionParticipant ; + rdfs:subPropertyOf nmdc:has_participants ; + skos:inScheme nmdc:annotation . - a owl:ObjectProperty, +nmdc:rna_absorb1 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:exactMatch ; - nmdc:expected_value "free text or CO" ; - nmdc:occurrence "1" . + rdfs:label "rna_absorb1" ; + dcterms:title "RNA absorbance 260/280" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:biomaterial_purity ; + skos:definition "260/280 measurement of RNA sample purity" ; + skos:inScheme ; + skos:note "Recommended value is between 1 and 3." ; + sh:order 7 . - a owl:ObjectProperty, +nmdc:rna_absorb2 a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "growth_habit" ; - dcterms:title "growth habit" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "growth habit" ; - skos:definition "Characteristic shape, appearance or growth form of a plant species" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "rna_absorb2" ; + dcterms:title "RNA absorbance 260/230" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:biomaterial_purity ; + skos:definition "260/230 measurement of RNA sample purity" ; + skos:inScheme ; + skos:note "Recommended value is between 1 and 3." ; + sh:order 8 . - a owl:ObjectProperty, +nmdc:rna_collect_site a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "mechanical_damage" ; - dcterms:title "mechanical damage" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "mechanical damage" ; - skos:definition "Information about any mechanical damage exerted on the plant; can include multiple damages and sites" ; - skos:exactMatch ; - nmdc:expected_value "damage type;body site" ; - nmdc:occurrence "m" . + rdfs:label "rna_collect_site" ; + dcterms:title "RNA collection site" ; + skos:definition "Provide information on the site your RNA sample was collected from" ; + skos:inScheme ; + sh:order 15 . - a owl:ObjectProperty, +nmdc:rna_concentration a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "ph_regm" ; - dcterms:title "pH regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "pH regimen" ; - skos:definition "Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen" ; - skos:exactMatch ; - nmdc:expected_value "measurement value;treatment interval and duration" ; - nmdc:occurrence "m" . + rdfs:label "rna_concentration" ; + dcterms:title "RNA concentration in ng/ul" ; + rdfs:range [ 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 ] ) ] ) ] ; + rdfs:seeAlso nmdc:nucleic_acid_concentration ; + skos:inScheme ; + 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 . - a owl:ObjectProperty, +nmdc:rna_cont_type a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "plant_growth_med" ; - dcterms:title "plant growth medium" ; - rdfs:range nmdc:ControlledTermValue ; - rdfs:subPropertyOf ; - skos:altLabel "plant growth medium" ; - skos:definition "Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary" ; - skos:exactMatch ; - nmdc:expected_value "EO or enumeration" ; - nmdc:occurrence "1" . + rdfs:label "rna_cont_type" ; + dcterms:title "RNA container type" ; + rdfs:range nmdc:JgiContTypeEnum ; + skos:definition "Tube or plate (96-well)" ; + skos:inScheme ; + sh:order 10 . - a owl:ObjectProperty, +nmdc:rna_cont_well a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "plant_product" ; - dcterms:title "plant product" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "plant product" ; - skos:definition "Substance produced by the plant, where the sample was obtained from" ; - skos:exactMatch ; - nmdc:expected_value "product name" ; - nmdc:occurrence "1" . + rdfs:label "rna_cont_well" ; + dcterms:title "RNA 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 . - a owl:ObjectProperty, +nmdc:rna_container_id a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "plant_sex" ; - dcterms:title "plant sex" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "plant sex" ; - skos:definition "Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite." ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "rna_container_id" ; + dcterms:title "RNA container label" ; + skos:inScheme ; + skos:note "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." ; + sh:order 9 . - a owl:ObjectProperty, +nmdc:rna_isolate_meth a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "plant_struc" ; - dcterms:title "plant structure" ; - rdfs:range nmdc:ControlledTermValue ; - rdfs:subPropertyOf ; - skos:altLabel "plant structure" ; - skos:definition "Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here." ; - skos:exactMatch ; - nmdc:expected_value "PO" ; - nmdc:occurrence "1" . + rdfs:label "rna_isolate_meth" ; + dcterms:title "RNA isolation method" ; + skos:definition "Describe the method/protocol/kit used to extract DNA/RNA." ; + skos:inScheme ; + sh:order 16 . - a owl:ObjectProperty, +nmdc:rna_organisms a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "root_cond" ; - dcterms:title "rooting conditions" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "rooting conditions" ; - skos:definition "Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container." ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI,url or free text" ; - nmdc:occurrence "1" . + rdfs:label "rna_organisms" ; + dcterms:title "RNA expected organisms" ; + skos:definition "List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture." ; + skos:inScheme ; + sh:order 14 . - a owl:ObjectProperty, +nmdc:rna_project_contact a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "root_med_ph" ; - dcterms:title "rooting medium pH" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "rooting medium pH" ; - skos:definition "pH measurement of the culture rooting medium; e.g. 5.5." ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:occurrence "1" . + rdfs:label "rna_project_contact" ; + dcterms:title "RNA seq project contact" ; + skos:inScheme ; + skos:note "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." ; + sh:order 18 . - a owl:ObjectProperty, +nmdc:rna_samp_id a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "root_med_solid" ; - dcterms:title "rooting medium solidifier" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "rooting medium solidifier" ; - skos:definition "Specification of the solidifying agent in the culture rooting medium; e.g. agar." ; - skos:exactMatch ; - nmdc:expected_value "name" ; - nmdc:occurrence "1" . + rdfs:label "rna_samp_id" ; + dcterms:title "RNA sample ID" ; + skos:inScheme ; + skos:note "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." ; + sh:order 3 . - a owl:ObjectProperty, +nmdc:rna_sample_format a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "season_environment" ; - dcterms:title "seasonal environment" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "seasonal environment" ; - skos:definition "Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment" ; - skos:exactMatch ; - nmdc:expected_value "seasonal environment name;treatment interval and duration" ; - nmdc:occurrence "m" . + rdfs:label "rna_sample_format" ; + dcterms:title "RNA sample format" ; + rdfs:range nmdc:RnaSampleFormatEnum ; + skos:definition "Solution in which the RNA sample has been suspended" ; + skos:inScheme ; + sh:order 12 . - a owl:ObjectProperty, +nmdc:rna_sample_name a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "standing_water_regm" ; - dcterms:title "standing water regimen" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "standing water regimen" ; - skos:definition "Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens" ; - skos:exactMatch ; - nmdc:expected_value "standing water type;treatment interval and duration" ; - nmdc:occurrence "m" . + rdfs:label "rna_sample_name" ; + dcterms:title "RNA sample name" ; + rdfs:range [ 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 ] ) ] ) ] ; + skos:definition "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only." ; + skos:inScheme ; + sh:order 4 . - a owl:ObjectProperty, +nmdc:rna_seq_project a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tiss_cult_growth_med" ; - dcterms:title "tissue culture growth media" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "tissue culture growth media" ; - skos:definition "Description of plant tissue culture growth media used" ; - skos:exactMatch ; - nmdc:expected_value "PMID,DOI,url or free text" ; - nmdc:occurrence "1" . + rdfs:label "rna_seq_project" ; + dcterms:title "RNA seq project ID" ; + skos:inScheme ; + skos:note "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." ; + sh:order 1 . - a owl:ObjectProperty, +nmdc:rna_seq_project_name a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sediment_type" ; - dcterms:title "sediment type" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "sediment type" ; - skos:definition "Information about the sediment type based on major constituents" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "rna_seq_project_name" ; + dcterms:title "RNA seq project name" ; + skos:inScheme ; + skos:note "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." ; + sh:order 2 . - a owl:ObjectProperty, +nmdc:rna_seq_project_pi a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "cur_land_use" ; - dcterms:title "current land use" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "current land use" ; - skos:definition "Present state of sample site" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "rna_seq_project_pi" ; + dcterms:title "RNA seq project PI" ; + skos:inScheme ; + skos:note "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." ; + sh:order 17 . - a owl:ObjectProperty, +nmdc:rna_volume a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "tillage" ; - dcterms:title "history/tillage" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "history/tillage" ; - skos:definition "Note method(s) used for tilling" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "m" . + rdfs:label "rna_volume" ; + dcterms:title "RNA volume in ul" ; + rdfs:range [ 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 ] ) ] ) ] ; + skos:inScheme ; + skos:note "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" ; + sh:order 6 . - a owl:ObjectProperty, +nmdc:salinity_category a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "soil_horizon" ; - dcterms:title "soil horizon" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "soil horizon" ; - skos:definition "Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "salinity_category" ; + rdfs:range linkml:String ; + rdfs:seeAlso ; + skos:definition "Categorical description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline" ; + skos:editorialNote "maps to gold:salinity" ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:sample_collection_day a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "fao_class" ; - dcterms:title "soil_taxonomic/FAO classification" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "soil_taxonomic/FAO classification" ; - skos:definition "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "sample_collection_day" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:sample_collection_hour a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "profile_position" ; - dcterms:title "profile position" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "profile position" ; - skos:definition "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "sample_collection_hour" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:sample_collection_minute a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "drainage_class" ; - dcterms:title "drainage classification" ; - rdfs:range ; - rdfs:subPropertyOf ; - skos:altLabel "drainage classification" ; - skos:definition "Drainage classification from a standard system such as the USDA system" ; - skos:exactMatch ; - nmdc:expected_value "enumeration" ; - nmdc:occurrence "1" . + rdfs:label "sample_collection_minute" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:sample_collection_month 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:exactMatch ; - nmdc:expected_value "date" ; - nmdc:occurrence "1" . + rdfs:label "sample_collection_month" ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:sample_collection_site a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "atmospheric_data" ; - dcterms:title "atmospheric data" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "atmospheric data" ; - skos:definition "Measurement of atmospheric data; can include multiple data" ; - skos:exactMatch ; - nmdc:expected_value "atmospheric data name;measurement value" ; - nmdc:occurrence "m" . + rdfs:label "sample_collection_site" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:sample_collection_year 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:exactMatch ; - nmdc:expected_value "PMID,DOI or url" ; - nmdc:occurrence "1" . + rdfs:label "sample_collection_year" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:sample_link a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_name" ; - dcterms:title "sample name" ; + rdfs:label "sample_link" ; + dcterms:title "sample linkage" ; 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:exactMatch ; - nmdc:expected_value "text" . + skos:definition "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample." ; + skos:inScheme ; + skos:note "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" ; + sh:order 5 . - a owl:ObjectProperty, +nmdc:sample_shipped 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:exactMatch ; - nmdc:expected_value "PMID,DOI,url , or text" . + rdfs:label "sample_shipped" ; + dcterms:title "sample shipped amount" ; + skos:definition "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL." ; + skos:inScheme ; + skos:note "This field is only required when completing metadata for samples being submitted to EMSL for analyses." ; + sh:order 3 . - a owl:ObjectProperty, +nmdc:sample_type a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_symbiont" ; - dcterms:title "observed host symbionts" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf ; - skos:altLabel "observed host symbionts" ; - skos:definition "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host." ; - skos:exactMatch ; - nmdc:expected_value "species name or common name" ; - nmdc:occurrence "m" . + rdfs:label "sample_type" ; + dcterms:title "sample type" ; + rdfs:range nmdc:SampleTypeEnum ; + skos:definition "Type of sample being submitted" ; + skos:inScheme ; + skos:note "This can vary from 'environmental package' if the sample is an extraction." ; + sh:order 2 . - a owl:ObjectProperty, +nmdc:sampling_method a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "host_subspecf_genlin" ; - dcterms:title "host subspecific genetic lineage" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf ; - skos:altLabel "host subspecific genetic lineage" ; - skos:definition "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123." ; - skos:exactMatch ; - nmdc:expected_value "Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar." ; - nmdc:occurrence "m" . + rdfs:label "sampling_method" ; + dcterms:title "sampling method" ; + rdfs:range nmdc:SamplingMethodEnum ; + skos:inScheme nmdc:sample_prep . - a owl:ObjectProperty, +nmdc:scaf_bp a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "samp_taxon_id" ; - dcterms:title "Taxonomy ID of DNA sample" ; - rdfs:range nmdc:ControlledIdentifiedTermValue ; - rdfs:subPropertyOf ; - skos:altLabel "Taxonomy ID of DNA sample" ; - skos:definition "NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome’ for mock community/positive controls, or 'blank sample' for negative controls." ; - skos:exactMatch ; - nmdc:expected_value "Taxonomy ID" . - - a owl:Class, - ; - rdfs:label "building" . + rdfs:label "scaf_bp" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Total size in bp of all scaffolds." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "home" . +nmdc:scaf_l50 a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "scaf_l50" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "shed" . +nmdc:scaf_l90 a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "scaf_l90" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "breeder's line" . +nmdc:scaf_l_gt50k a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "scaf_l_gt50k" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Total size in bp of all scaffolds greater than 50 KB." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "clonal selection" . +nmdc:scaf_logsum a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "scaf_logsum" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase" ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "hybrid" . +nmdc:scaf_max a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "scaf_max" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Maximum scaffold length." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "inbred line" . +nmdc:scaf_n50 a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "scaf_n50" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "mutant" . +nmdc:scaf_n90 a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "scaf_n90" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "natural" . +nmdc:scaf_n_gt50k a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "scaf_n_gt50k" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Total sequence count of scaffolds greater than 50 KB." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "semi-natural" . +nmdc:scaf_pct_gt50k a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "scaf_pct_gt50k" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Total sequence size percentage of scaffolds greater than 50 KB." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "wild" . +nmdc:scaf_powsum a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "scaf_powsum" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25)." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "commensal" . +nmdc:scaffolds a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "scaffolds" ; + rdfs:range linkml:Float ; + rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; + skos:definition "Total sequence count of all scaffolds." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "free living" . +nmdc:smarts_string a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "smarts_string" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:annotation . - a owl:Class, - ; - rdfs:label "parasite" . +nmdc:smiles a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "smiles" ; + rdfs:range linkml:String ; + skos:definition "A string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol." ; + skos:inScheme nmdc:core . - a owl:Class, - ; - rdfs:label "symbiont" . +nmdc:soil_annual_season_temp a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "soil_annual_season_temp" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:Class, - ; - rdfs:label "building information model" . +nmdc:soluble_iron_micromol a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "soluble_iron_micromol" ; + rdfs:range linkml:String ; + skos:inScheme nmdc:nmdc . - a owl:Class, - ; - rdfs:label "commissioning report" . +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." . - a owl:Class, - ; - rdfs:label "complaint logs" . +nmdc:start_date a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "start_date" ; + rdfs:range linkml:String ; + skos:definition "The date on which any process or activity was started" ; + skos:inScheme nmdc:basic_slots ; + skos:note "The date should be formatted as YYYY-MM-DD", + "We are using string representations of dates until all components of our ecosystem can handle ISO 8610 dates" . - a owl:Class, - ; - rdfs:label "contract administration" . +nmdc:start_date_inc a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "start_date_inc" ; + dcterms:title "incubation start date" ; + skos:definition "Date the incubation was started. Only relevant for incubation samples." ; + skos:editorialNote "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" ; + skos:inScheme ; + skos:note "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." ; + sh:order 4 . - a owl:Class, - ; - rdfs:label "cost estimate" . +nmdc:start_time_inc a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "start_time_inc" ; + dcterms:title "incubation start time, GMT" ; + skos:definition "Time the incubation was started. Only relevant for incubation samples." ; + skos:editorialNote "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" ; + skos:inScheme ; + skos:note "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" ; + sh:order 5 . - a owl:Class, - ; - rdfs:label "janitorial schedules or logs" . +nmdc:status a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "status" ; + rdfs:range nmdc:StatusEnum ; + skos:inScheme nmdc:nmdc . - a owl:Class, - ; - rdfs:label "maintenance plans" . - - a owl:Class, - ; - rdfs:label "schedule" . +nmdc:stoichiometry a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "stoichiometry" ; + rdfs:range linkml:Integer ; + skos:definition "from reaction participant class" ; + skos:inScheme nmdc:annotation . - a owl:Class, - ; - rdfs:label "sections" . +nmdc:strand a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "strand" ; + skos:definition "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; + skos:exactMatch ; + skos:inScheme nmdc:annotation . - a owl:Class, - ; - rdfs:label "shop drawings" . +nmdc:study_category a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "study_category" ; + rdfs:range nmdc:StudyCategoryEnum ; + skos:definition "The type of research initiative" ; + skos:inScheme nmdc:nmdc . - a owl:Class, - ; - rdfs:label "submittals" . +nmdc:study_image a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "study_image" ; + rdfs:domain nmdc:Study ; + rdfs:range nmdc:ImageValue ; + skos:definition "Links a study to one or more images." ; + skos:inScheme nmdc:nmdc . - a owl:Class, - ; - rdfs:label "ventilation system" . +nmdc:study_set a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "study_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:Study ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of studies within it." ; + skos:inScheme nmdc:nmdc . - a owl:Class, - ; - rdfs:label "windows" . +nmdc:subject a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "subject" ; + rdfs:range nmdc:GeneProduct ; + skos:inScheme nmdc:annotation . - a owl:Class, - ; - rdfs:label "airport" . +nmdc:subsurface_depth a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "subsurface_depth" ; + rdfs:range nmdc:QuantityValue ; + skos:inScheme nmdc:nmdc . - a owl:Class, - ; - rdfs:label "commercial" . +nmdc:technical_reps a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "technical_reps" ; + dcterms:title "number technical replicate" ; + skos:definition "If sending technical replicates of the same sample, indicate the replicate count." ; + skos:inScheme ; + skos:note "This field is only required when completing metadata for samples being submitted to EMSL for analyses." ; + sh:order 5 . - a owl:Class, - ; - rdfs:label "health care" . +nmdc:title a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "title" ; + rdfs:range linkml:String ; + skos:definition "A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study." ; + skos:exactMatch dcterms:title ; + skos:inScheme nmdc:basic_slots . - a owl:Class, - ; - rdfs:label "high rise" . +nmdc:too_short_contig_num a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "too_short_contig_num" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "low rise" . +nmdc:total_bases a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "total_bases" ; + skos:inScheme nmdc:core . - a owl:Class, - ; - rdfs:label "market" . +nmdc:unbinned_contig_num a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "unbinned_contig_num" ; + rdfs:range linkml:Integer ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "office" . +nmdc:url a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "url" ; + rdfs:range linkml:String ; + rdfs:subPropertyOf nmdc:attribute ; + skos:editorialNote "See issue 207 - this clashes with the mixs field" ; + skos:inScheme nmdc:core . - a owl:Class, - ; - rdfs:label "residence" . +nmdc:version a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "version" ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "residential" . +nmdc:was_informed_by a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "was_informed_by" ; + rdfs:range nmdc:Activity ; + skos:inScheme nmdc:prov ; + skos:mappingRelation prov:wasInformedBy . - a owl:Class, - ; - rdfs:label "restaurant" . +nmdc:zinc a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "zinc" ; + dcterms:title "zinc" ; + rdfs:range nmdc:QuantityValue ; + rdfs:seeAlso ; + rdfs:subPropertyOf nmdc:attribute ; + 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, - ; - rdfs:label "school" . +nmdc:CollectingBiosamplesFromSite a owl:Class, + linkml:ClassDefinition ; + rdfs:label "CollectingBiosamplesFromSite" ; + dcterms:title "Collecting Biosamples From Site" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:has_output ], + [ 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:allValuesFrom nmdc:Site ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:Biosample ; + owl:onProperty nmdc:has_output ], + nmdc:PlannedProcess ; + skos:closeMatch ; + skos:inScheme nmdc:nmdc ; + skos:note "this illustrates implementing a Biosample relation with a process class" . - a owl:Class, - ; - rdfs:label "sports complex" . + a owl:Class, + nmdc:ContainerTypeEnum ; + rdfs:label "screw_top_conical" . - a owl:Class, - ; - rdfs:label "wood framed" . +nmdc:DataObject a owl:Class, + linkml:ClassDefinition ; + rdfs:label "DataObject" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:description ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:description ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:description ], + 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:editorialNote "removed previous id_prefixes value of GOLD, since we are now using pattern-based id validation" ; + skos:inScheme nmdc:nmdc ; + skos:note "removed id_prefixes value of GOLD, since we are now using pattern-based id validation" . - a owl:Class, - ; - rdfs:label "exurban" . +nmdc:DissolvingActivity a owl:Class, + linkml:ClassDefinition ; + rdfs:label "DissolvingActivity" ; + dcterms:title "Dissolving activity" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:material_output ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:material_input ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:material_output ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:material_output ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:material_input ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:material_input ] ; + skos:altLabel "dissolution-activity" ; + skos:exactMatch ; + skos:inScheme nmdc:sample_prep . - a owl:Class, - ; - rdfs:label "rural" . +nmdc:Extraction a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Extraction" ; + 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:minCardinality 1 ; + owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_output ], + nmdc:BiosampleProcessing ; + skos:definition "A material separation in which a desired component of an input material is separated from the remainder." ; + skos:exactMatch ; + skos:inScheme nmdc:nmdc . - a owl:Class, - ; - rdfs:label "suburban" . +nmdc:FunctionalAnnotation a owl:Class, + linkml:ClassDefinition ; + rdfs:label "FunctionalAnnotation" ; + rdfs:seeAlso , + ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:was_generated_by ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_function ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:was_generated_by ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:OntologyClass ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:MetagenomeAnnotationActivity ; + owl:onProperty nmdc:was_generated_by ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:has_function ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_function ] ; + 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 . - a owl:Class, - ; - rdfs:label "urban" . +nmdc:FunctionalAnnotationAggMember a owl:Class, + linkml:ClassDefinition ; + rdfs:label "FunctionalAnnotationAggMember" ; + skos:inScheme nmdc:nmdc . - a owl:Class, - ; - rdfs:label "damaged" . +nmdc:GenomeFeature a owl:Class, + linkml:ClassDefinition ; + rdfs:label "GenomeFeature" ; + rdfs:seeAlso ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:start ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:start ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:seqid ], + [ a owl:Restriction ; + 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:start ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:OntologyClass ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:end ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:seqid ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:end ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:seqid ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:type ] ; + skos:definition "A feature localized to an interval along a genome" ; + skos:inScheme nmdc:annotation ; + skos:note "corresponds to an entry in GFF3" . - a owl:Class, - ; - rdfs:label "needs repair" . +nmdc:ImageValue a owl:Class, + linkml:ClassDefinition ; + rdfs:label "ImageValue" ; + rdfs:subClassOf nmdc:AttributeValue ; + skos:definition "An attribute value representing an image." ; + skos:inScheme nmdc:core . - a owl:Class, - ; - rdfs:label "new" . +nmdc:InstrumentValue a owl:Class, + linkml:ClassDefinition ; + rdfs:label "InstrumentValue" ; + rdfs:subClassOf nmdc:AttributeValue ; + skos:inScheme nmdc:core . - a owl:Class, - ; - rdfs:label "rupture" . +nmdc:LibraryPreparation a owl:Class, + linkml:ClassDefinition ; + rdfs:label "LibraryPreparation" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:has_input ], + [ 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:has_output ], + [ 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:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_input ], + nmdc:BiosampleProcessing ; + skos:altLabel "LibraryConstruction" ; + skos:closeMatch ; + skos:inScheme nmdc:nmdc ; + skos:note "OBI:0000711 specifies a DNA input (but not ONLY a DNA input)" . - a owl:Class, - ; - rdfs:label "visible wear" . +nmdc:MagBin a owl:Class, + linkml:ClassDefinition ; + rdfs:label "MagBin" ; + skos:inScheme nmdc:core . - a owl:Class, - ; - rdfs:label "PVC" . +nmdc:MagsAnalysisActivity a owl:Class, + linkml:ClassDefinition ; + rdfs:label "MagsAnalysisActivity" ; + dcterms:title "Metagenome-Assembled Genome analysis activity" ; + 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:id ], + 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 . - a owl:Class, - ; - rdfs:label "drywall" . +nmdc:MaterialSamplingActivity a owl:Class, + linkml:ClassDefinition ; + rdfs:label "MaterialSamplingActivity" ; + dcterms:title "Material sampling activity" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:material_output ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:collected_into ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:material_output ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:amount_collected ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:material_output ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:collected_into ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:amount_collected ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:amount_collected ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:collected_into ] ; + skos:altLabel "weighing-activity" ; + skos:exactMatch ; + skos:inScheme nmdc:sample_prep . - a owl:Class, - ; - rdfs:label "fiberglass" . +nmdc:MetaboliteQuantification a owl:Class, + linkml:ClassDefinition ; + rdfs:label "MetaboliteQuantification" ; + skos:definition "This is used to link a metabolomics analysis workflow to a specific metabolite" ; + skos:inScheme nmdc:core . - a owl:Class, - ; - rdfs:label "metal" . +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:maxCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], + nmdc:WorkflowExecutionActivity ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "mineral fibre" . +nmdc:MetagenomeAssembly a owl:Class, + linkml:ClassDefinition ; + rdfs:label "MetagenomeAssembly" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], + nmdc:WorkflowExecutionActivity ; + skos:definition "A workflow execution activity that converts sequencing reads into an assembled metagenome." ; + skos:inScheme nmdc:workflow_execution_activity ; + skos:note "instances of this class may use a de novo assembly strategy in most or all cases relevant to NMDC" . - a owl:Class, - ; - rdfs:label "mineral wool/calcium silicate" . +nmdc:MetagenomeSequencingActivity a owl:Class, + linkml:ClassDefinition ; + rdfs:label "MetagenomeSequencingActivity" ; + dcterms:title "Metagenome sequencing activity" ; + 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 ], + nmdc:WorkflowExecutionActivity ; + skos:definition "Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data." ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "plasterboard" . +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: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 ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:used ], + nmdc:WorkflowExecutionActivity ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "stucco" . +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:minCardinality 1 ; + owl:onProperty nmdc:id ], + [ 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 . - a owl:Class, - ; - rdfs:label "tiles" . +nmdc:NomAnalysisActivity a owl:Class, + linkml:ClassDefinition ; + rdfs:label "NomAnalysisActivity" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:used ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:used ], + [ 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:used ], + nmdc:WorkflowExecutionActivity ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "wood" . +nmdc:OmicsProcessing a owl:Class, + linkml:ClassDefinition ; + rdfs:label "OmicsProcessing" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_input ], + [ 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:PlannedProcess ; + skos:altLabel "experiment", + "omics assay", + "sequencing project" ; + skos:broadMatch ISA:Assay, + ; + skos:definition "The methods and processes used to generate omics data from a biosample or organism." ; + skos:inScheme nmdc:nmdc ; + skos:note "The ID prefix for objects coming from GOLD will be gold:Gp" . - a owl:Class, - ; - rdfs:label "Santa-Fe texture" . +nmdc:PeptideQuantification a owl:Class, + linkml:ClassDefinition ; + rdfs:label "PeptideQuantification" ; + skos:definition "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information" ; + skos:inScheme nmdc:core . - a owl:Class, - ; - rdfs:label "crows feet" . +nmdc:Pooling a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Pooling" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], + nmdc:BiosampleProcessing ; + skos:definition "physical combination of several instances of like material." ; + skos:exactMatch ; + skos:inScheme nmdc:nmdc . - a owl:Class, - ; - rdfs:label "crows-foot stomp" . +nmdc:ProcessedSample a owl:Class, + linkml:ClassDefinition ; + 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 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + nmdc:MaterialEntity ; + skos:inScheme nmdc:core . - a owl:Class, - ; - rdfs:label "double skip" . +nmdc:Protocol a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Protocol" ; + skos:inScheme nmdc:nmdc . - a owl:Class, - ; - rdfs:label "hawk and trowel" . +nmdc:QualityControlReport a owl:Class, + linkml:ClassDefinition ; + rdfs:label "QualityControlReport" ; + skos:inScheme nmdc:nmdc . - a owl:Class, - ; - rdfs:label "knockdown" . +nmdc:Reaction a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Reaction" ; + rdfs:subClassOf 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 ; + skos:inScheme nmdc:annotation . - a owl:Class, - ; - rdfs:label "orange peel" . +nmdc:ReactionActivity a owl:Class, + linkml:ClassDefinition ; + rdfs:label "ReactionActivity" ; + dcterms:title "Reaction activity" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:reaction_time ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:reaction_time ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:reaction_time ] ; + skos:altLabel "reaction-activity" ; + skos:inScheme nmdc:sample_prep . - a owl:Class, - ; - rdfs:label "popcorn" . +nmdc:ReadBasedTaxonomyAnalysisActivity a owl:Class, + linkml:ClassDefinition ; + rdfs:label "ReadBasedTaxonomyAnalysisActivity" ; + dcterms:title "Read based analysis activity" ; + rdfs:subClassOf [ 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 ], + nmdc:WorkflowExecutionActivity ; + skos:definition "A workflow execution activity that performs taxonomy classification using sequencing reads" ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "rosebud stomp" . +nmdc:ReadQcAnalysisActivity a owl:Class, + linkml:ClassDefinition ; + rdfs:label "ReadQcAnalysisActivity" ; + dcterms:title "Read quality control analysis activity" ; + 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:id ], + 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 . - a owl:Class, - ; - rdfs:label "skip trowel" . + a owl:Class, + nmdc:SamplingMethodEnum ; + rdfs:label "weighing" . - a owl:Class, - ; - rdfs:label "smooth" . +nmdc:assembly_identifiers a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "assembly_identifiers" ; + skos:inScheme nmdc:external_identifiers . - a owl:Class, - ; - rdfs:label "stomp knockdown" . +nmdc:external_identifier a owl:Class, + linkml:TypeDefinition ; + rdfs:subClassOf linkml:Uriorcurie . - a owl:Class, - ; - rdfs:label "swirl" . +nmdc:gnps_identifiers a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "gnps_identifiers" ; + skos:inScheme nmdc:external_identifiers . - a owl:Class, - ; - rdfs:label "barrel-shaped" . +nmdc:igsn_identifiers a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "igsn_identifiers" ; + skos:inScheme nmdc:external_identifiers . - a owl:Class, - ; - rdfs:label "cathedral" . +nmdc:jgi_portal_identifiers a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "jgi_portal_identifiers" ; + skos:definition "identifiers for entities according to JGI Portal" ; + skos:inScheme nmdc:external_identifiers . - a owl:Class, - ; - rdfs:label "coffered" . +nmdc:massive_identifiers a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "massive_identifiers" ; + skos:definition "identifiers for entities according to MASSIVE" ; + skos:inScheme nmdc:external_identifiers . - a owl:Class, - ; - rdfs:label "concave" . +nmdc:omics_processing_identifiers a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "omics_processing_identifiers" ; + rdfs:subPropertyOf nmdc:external_database_identifiers ; + skos:inScheme nmdc:external_identifiers . - a owl:Class, - ; - rdfs:label "cove" . +CHEBI:17790 a owl:Class, + nmdc:SolventEnum ; + rdfs:label "methanol" . - a owl:Class, - ; - rdfs:label "dropped" . +CHEBI:35255 a owl:Class, + nmdc:SolventEnum ; + rdfs:label "chloroform" . - a owl:Class, - ; - rdfs:label "stretched" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Principal Investigator" . - a owl:Class, - ; - rdfs:label "badlands" . +EFO:0001741 a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Submitter" . - a owl:Class, - ; - rdfs:label "cities" . + a owl:Class, + nmdc:BiosampleCategoryEnum ; + rdfs:label "FICUS" . - a owl:Class, - ; - rdfs:label "conifers" . + a owl:Class, + nmdc:BiosampleCategoryEnum ; + rdfs:label "LTER" . - a owl:Class, - ; - rdfs:label "crop trees" . + a owl:Class, + nmdc:ProcessingInstitutionEnum ; + rdfs:label "UCSD" . - a owl:Class, - ; - rdfs:label "farmstead" . + a owl:Class, + nmdc:ProcessingInstitutionEnum ; + rdfs:label "Battelle" . - a owl:Class, - ; - rdfs:label "gravel" . + a owl:Class, + nmdc:ProcessingInstitutionEnum ; + rdfs:label "EMSL" . - a owl:Class, - ; - rdfs:label "hardwoods" . + a owl:Class, + nmdc:ProcessingInstitutionEnum ; + rdfs:label "JGI" . - a owl:Class, - ; - rdfs:label "hayland" . + a owl:Class, + nmdc:ProcessingInstitutionEnum ; + rdfs:label "ANL" . - a owl:Class, - ; - rdfs:label "horticultural plants" . + a owl:Class, + nmdc:BiosampleCategoryEnum ; + rdfs:label "SFA" . - a owl:Class, - ; - rdfs:label "industrial areas" . + a owl:Class, + nmdc:AnalysisTypeEnum ; + rdfs:label "metabolomics" . - a owl:Class, - ; - rdfs:label "intermixed hardwood and conifers" . + a owl:Class, + nmdc:AnalysisTypeEnum ; + rdfs:label "metagenomics" . - a owl:Class, - ; - rdfs:label "marshlands" . + a owl:Class, + nmdc:AnalysisTypeEnum ; + rdfs:label "metaproteomics" . - a owl:Class, - ; - rdfs:label "meadows" . + a owl:Class, + nmdc:AnalysisTypeEnum ; + rdfs:label "metatranscriptomics" . - a owl:Class, - ; - rdfs:label "mines/quarries" . + a owl:Class, + nmdc:AnalysisTypeEnum ; + rdfs:label "natural organic matter" . - a owl:Class, - ; - rdfs:label "mudflats" . + a owl:Class, + nmdc:ArchStrucEnum ; + rdfs:label "building" . - a owl:Class, - ; - rdfs:label "oil waste areas" . + a owl:Class, + nmdc:ArchStrucEnum ; + rdfs:label "home" . - a owl:Class, - ; - rdfs:label "pastureland" . + a owl:Class, + nmdc:ArchStrucEnum ; + rdfs:label "shed" . - a owl:Class, - ; - rdfs:label "permanent snow or ice" . + a owl:Class, + nmdc:BiolStatEnum ; + rdfs:label "breeder's line" . - a owl:Class, - ; - rdfs:label "rainforest" . + a owl:Class, + nmdc:BiolStatEnum ; + rdfs:label "clonal selection" . - a owl:Class, - ; - rdfs:label "rangeland" . + a owl:Class, + nmdc:BiolStatEnum ; + rdfs:label "hybrid" . - a owl:Class, - ; - rdfs:label "roads/railroads" . + a owl:Class, + nmdc:BiolStatEnum ; + rdfs:label "inbred line" . - a owl:Class, - ; - rdfs:label "rock" . + a owl:Class, + nmdc:BiolStatEnum ; + rdfs:label "mutant" . - a owl:Class, - ; - rdfs:label "row crops" . + a owl:Class, + nmdc:BiolStatEnum ; + rdfs:label "natural" . - a owl:Class, - ; - rdfs:label "saline seeps" . + a owl:Class, + nmdc:BiolStatEnum ; + rdfs:label "semi-natural" . - a owl:Class, - ; - rdfs:label "salt flats" . + a owl:Class, + nmdc:BiolStatEnum ; + rdfs:label "wild" . - a owl:Class, - ; - rdfs:label "sand" . + a owl:Class, + nmdc:BiosampleCategoryEnum ; + rdfs:label "SIP" . - a owl:Class, - ; - rdfs:label "shrub crops" . + a owl:Class, + nmdc:BioticRelationshipEnum ; + rdfs:label "commensal" . - a owl:Class, - ; - rdfs:label "shrub land" . + a owl:Class, + nmdc:BioticRelationshipEnum ; + rdfs:label "free living" . - a owl:Class, - ; - rdfs:label "small grains" . + a owl:Class, + nmdc:BioticRelationshipEnum ; + rdfs:label "parasite" . - a owl:Class, - ; - rdfs:label "successional shrub land" . + a owl:Class, + nmdc:BioticRelationshipEnum ; + rdfs:label "symbiont" . - a owl:Class, - ; - rdfs:label "swamp" . + a owl:Class, + nmdc:BuildDocsEnum ; + rdfs:label "building information model" . - a owl:Class, - ; - rdfs:label "tropical" . + a owl:Class, + nmdc:BuildDocsEnum ; + rdfs:label "commissioning report" . - a owl:Class, - ; - rdfs:label "tundra" . + a owl:Class, + nmdc:BuildDocsEnum ; + rdfs:label "complaint logs" . - a owl:Class, - ; - rdfs:label "vegetable crops" . + a owl:Class, + nmdc:BuildDocsEnum ; + rdfs:label "contract administration" . - a owl:Class, - ; - rdfs:label "vine crops" . + a owl:Class, + nmdc:BuildDocsEnum ; + rdfs:label "cost estimate" . - a owl:Class, - ; - rdfs:label "Continental - Aeolian" . + a owl:Class, + nmdc:BuildDocsEnum ; + rdfs:label "janitorial schedules or logs" . - a owl:Class, - ; - rdfs:label "Continental - Alluvial" . + a owl:Class, + nmdc:BuildDocsEnum ; + rdfs:label "maintenance plans" . - a owl:Class, - ; - rdfs:label "Continental - Fluvial" . + a owl:Class, + nmdc:BuildDocsEnum ; + rdfs:label "schedule" . - a owl:Class, - ; - rdfs:label "Continental - Lacustrine" . + a owl:Class, + nmdc:BuildDocsEnum ; + rdfs:label "sections" . - a owl:Class, - ; - rdfs:label "Marine - Deep" . + a owl:Class, + nmdc:BuildDocsEnum ; + rdfs:label "shop drawings" . - a owl:Class, - ; - rdfs:label "Marine - Reef" . + a owl:Class, + nmdc:BuildDocsEnum ; + rdfs:label "submittals" . - a owl:Class, - ; - rdfs:label "Marine - Shallow" . + a owl:Class, + nmdc:BuildDocsEnum ; + rdfs:label "ventilation system" . - a owl:Class, - ; - rdfs:label "Other - Evaporite" . + a owl:Class, + nmdc:BuildDocsEnum ; + rdfs:label "windows" . - a owl:Class, - ; - rdfs:label "Other - Glacial" . + a owl:Class, + nmdc:BuildOccupTypeEnum ; + rdfs:label "airport" . - a owl:Class, - ; - rdfs:label "Other - Volcanic" . + a owl:Class, + nmdc:BuildOccupTypeEnum ; + rdfs:label "commercial" . - a owl:Class, - ; - rdfs:label "Transitional - Beach" . + a owl:Class, + nmdc:BuildOccupTypeEnum ; + rdfs:label "health care" . - a owl:Class, - ; - rdfs:label "Transitional - Deltaic" . + a owl:Class, + nmdc:BuildOccupTypeEnum ; + rdfs:label "high rise" . - a owl:Class, - ; - rdfs:label "Transitional - Lagoonal" . + a owl:Class, + nmdc:BuildOccupTypeEnum ; + rdfs:label "low rise" . - a owl:Class, - ; - rdfs:label "Transitional - Lake" . + a owl:Class, + nmdc:BuildOccupTypeEnum ; + rdfs:label "market" . - a owl:Class, - ; - rdfs:label "Transitional - Tidal" . + a owl:Class, + nmdc:BuildOccupTypeEnum ; + rdfs:label "office" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:BuildOccupTypeEnum ; + rdfs:label "residence" . - a owl:Class, - ; - rdfs:label "metal covered" . + a owl:Class, + nmdc:BuildOccupTypeEnum ; + rdfs:label "residential" . - a owl:Class, - ; - rdfs:label "revolving" . + a owl:Class, + nmdc:BuildOccupTypeEnum ; + rdfs:label "restaurant" . - a owl:Class, - ; - rdfs:label "sliding" . + a owl:Class, + nmdc:BuildOccupTypeEnum ; + rdfs:label "school" . - a owl:Class, - ; - rdfs:label "telescopic" . + a owl:Class, + nmdc:BuildOccupTypeEnum ; + rdfs:label "sports complex" . + + a owl:Class, + nmdc:BuildOccupTypeEnum ; + rdfs:label "wood framed" . + + a owl:Class, + nmdc:BuildingSettingEnum ; + rdfs:label "exurban" . + + a owl:Class, + nmdc:BuildingSettingEnum ; + rdfs:label "rural" . + + a owl:Class, + nmdc:BuildingSettingEnum ; + rdfs:label "suburban" . + + a owl:Class, + nmdc:BuildingSettingEnum ; + rdfs:label "urban" . - a owl:Class, - ; + a owl:Class, + nmdc:CeilCondEnum ; rdfs:label "damaged" . - a owl:Class, - ; + a owl:Class, + nmdc:CeilCondEnum ; rdfs:label "needs repair" . - a owl:Class, - ; + a owl:Class, + nmdc:CeilCondEnum ; rdfs:label "new" . - a owl:Class, - ; + a owl:Class, + nmdc:CeilCondEnum ; rdfs:label "rupture" . - a owl:Class, - ; + a owl:Class, + nmdc:CeilCondEnum ; rdfs:label "visible wear" . - a owl:Class, - ; - rdfs:label "inward" . + a owl:Class, + nmdc:CeilFinishMatEnum ; + rdfs:label "PVC" . - a owl:Class, - ; - rdfs:label "outward" . + a owl:Class, + nmdc:CeilFinishMatEnum ; + rdfs:label "drywall" . - a owl:Class, - ; - rdfs:label "sideways" . + a owl:Class, + nmdc:CeilFinishMatEnum ; + rdfs:label "fiberglass" . - a owl:Class, - ; - rdfs:label "east" . + a owl:Class, + nmdc:CeilFinishMatEnum ; + rdfs:label "metal" . - a owl:Class, - ; - rdfs:label "north" . + a owl:Class, + nmdc:CeilFinishMatEnum ; + rdfs:label "mineral fibre" . - a owl:Class, - ; - rdfs:label "south" . + a owl:Class, + nmdc:CeilFinishMatEnum ; + rdfs:label "mineral wool/calcium silicate" . - a owl:Class, - ; - rdfs:label "west" . + a owl:Class, + nmdc:CeilFinishMatEnum ; + rdfs:label "plasterboard" . - a owl:Class, - ; - rdfs:label "aluminum" . + a owl:Class, + nmdc:CeilFinishMatEnum ; + rdfs:label "stucco" . - a owl:Class, - ; - rdfs:label "cellular PVC" . + a owl:Class, + nmdc:CeilFinishMatEnum ; + rdfs:label "tiles" . - a owl:Class, - ; - rdfs:label "engineered plastic" . + a owl:Class, + nmdc:CeilFinishMatEnum ; + rdfs:label "wood" . - a owl:Class, - ; - rdfs:label "fiberboard" . + a owl:Class, + nmdc:CeilTextureEnum ; + rdfs:label "Santa-Fe texture" . - a owl:Class, - ; - rdfs:label "fiberglass" . + a owl:Class, + nmdc:CeilTextureEnum ; + rdfs:label "crows feet" . - a owl:Class, - ; - rdfs:label "metal" . + a owl:Class, + nmdc:CeilTextureEnum ; + rdfs:label "crows-foot stomp" . - a owl:Class, - ; - rdfs:label "thermoplastic alloy" . + a owl:Class, + nmdc:CeilTextureEnum ; + rdfs:label "double skip" . - a owl:Class, - ; - rdfs:label "vinyl" . + a owl:Class, + nmdc:CeilTextureEnum ; + rdfs:label "hawk and trowel" . - a owl:Class, - ; - rdfs:label "wood" . + a owl:Class, + nmdc:CeilTextureEnum ; + rdfs:label "knockdown" . - a owl:Class, - ; - rdfs:label "wood/plastic composite" . + a owl:Class, + nmdc:CeilTextureEnum ; + rdfs:label "orange peel" . - a owl:Class, - ; - rdfs:label "collapsible" . + a owl:Class, + nmdc:CeilTextureEnum ; + rdfs:label "popcorn" . - a owl:Class, - ; - rdfs:label "folding" . + a owl:Class, + nmdc:CeilTextureEnum ; + rdfs:label "rosebud stomp" . - a owl:Class, - ; - rdfs:label "revolving" . + a owl:Class, + nmdc:CeilTextureEnum ; + rdfs:label "skip trowel" . - a owl:Class, - ; - rdfs:label "rolling shutter" . + a owl:Class, + nmdc:CeilTextureEnum ; + rdfs:label "smooth" . - a owl:Class, - ; - rdfs:label "sliding" . + a owl:Class, + nmdc:CeilTextureEnum ; + rdfs:label "stomp knockdown" . - a owl:Class, - ; - rdfs:label "swinging" . + a owl:Class, + nmdc:CeilTextureEnum ; + rdfs:label "swirl" . - a owl:Class, - ; - rdfs:label "composite" . + a owl:Class, + nmdc:CeilTypeEnum ; + rdfs:label "barrel-shaped" . - a owl:Class, - ; - rdfs:label "metal" . + a owl:Class, + nmdc:CeilTypeEnum ; + rdfs:label "cathedral" . - a owl:Class, - ; - rdfs:label "wooden" . + a owl:Class, + nmdc:CeilTypeEnum ; + rdfs:label "coffered" . - a owl:Class, - ; - rdfs:label "collapsible" . + a owl:Class, + nmdc:CeilTypeEnum ; + rdfs:label "concave" . - a owl:Class, - ; - rdfs:label "corrugated steel" . + a owl:Class, + nmdc:CeilTypeEnum ; + rdfs:label "cove" . - a owl:Class, - ; - rdfs:label "hollow" . + a owl:Class, + nmdc:CeilTypeEnum ; + rdfs:label "dropped" . - a owl:Class, - ; - rdfs:label "rolling shutters" . + a owl:Class, + nmdc:CeilTypeEnum ; + rdfs:label "stretched" . - a owl:Class, - ; - rdfs:label "steel plate" . +nmdc:ChemicalEntity a owl:Class, + linkml:ClassDefinition ; + rdfs:label "ChemicalEntity" ; + rdfs:seeAlso ; + rdfs:subClassOf nmdc:OntologyClass ; + skos:altLabel "chemical", + "chemical compound", + "chemical substance", + "metabolite" ; + skos:definition "An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states" ; + skos:exactMatch ; + skos:inScheme nmdc:core ; + skos:note "As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode to this class." . - a owl:Class, - ; - rdfs:label "battened" . +nmdc:ContainerTypeEnum a owl:Class, + linkml:EnumDefinition ; + linkml:permissible_values . - a owl:Class, - ; - rdfs:label "bettened and ledged" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Conceptualization" . - a owl:Class, - ; - rdfs:label "flush" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Data curation" . - a owl:Class, - ; - rdfs:label "framed and paneled" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Formal Analysis" . - a owl:Class, - ; - rdfs:label "glashed or sash" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Funding acquisition" . - a owl:Class, - ; - rdfs:label "ledged and braced" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Investigation" . - a owl:Class, - ; - rdfs:label "ledged and framed" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Methodology" . - a owl:Class, - ; - rdfs:label "ledged, braced and frame" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Project administration" . - a owl:Class, - ; - rdfs:label "louvered" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Resources" . - a owl:Class, - ; - rdfs:label "wire gauged" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Software" . - a owl:Class, - ; - rdfs:label "excessively drained" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Supervision" . - a owl:Class, - ; - rdfs:label "moderately well" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Validation" . - a owl:Class, - ; - rdfs:label "poorly" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Visualization" . - a owl:Class, - ; - rdfs:label "somewhat poorly" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Writing original draft" . - a owl:Class, - ; - rdfs:label "very poorly" . + a owl:Class, + nmdc:CreditEnum ; + rdfs:label "Writing review and editing" . - a owl:Class, - ; - rdfs:label "well" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "badlands" . - a owl:Class, - ; - rdfs:label "as built" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "cities" . - a owl:Class, - ; - rdfs:label "bid" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "conifers" . - a owl:Class, - ; - rdfs:label "building navigation map" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "crop trees" . - a owl:Class, - ; - rdfs:label "construction" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "farmstead" . - a owl:Class, - ; - rdfs:label "design" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "gravel" . - a owl:Class, - ; - rdfs:label "diagram" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "hardwoods" . - a owl:Class, - ; - rdfs:label "operation" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "hayland" . - a owl:Class, - ; - rdfs:label "sketch" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "horticultural plants" . - a owl:Class, - ; - rdfs:label "east" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "industrial areas" . - a owl:Class, - ; - rdfs:label "north" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "intermixed hardwood and conifers" . - a owl:Class, - ; - rdfs:label "northeast" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "marshlands" . - a owl:Class, - ; - rdfs:label "northwest" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "meadows" . - a owl:Class, - ; - rdfs:label "south" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "mines/quarries" . - a owl:Class, - ; - rdfs:label "southeast" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "mudflats" . - a owl:Class, - ; - rdfs:label "southwest" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "oil waste areas" . - a owl:Class, - ; - rdfs:label "west" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "pastureland" . - a owl:Class, - ; - rdfs:label "east" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "permanent snow or ice" . - a owl:Class, - ; - rdfs:label "north" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "rainforest" . - a owl:Class, - ; - rdfs:label "northeast" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "rangeland" . - a owl:Class, - ; - rdfs:label "northwest" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "roads/railroads" . - a owl:Class, - ; - rdfs:label "south" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "rock" . - a owl:Class, - ; - rdfs:label "southeast" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "row crops" . - a owl:Class, - ; - rdfs:label "southwest" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "saline seeps" . - a owl:Class, - ; - rdfs:label "west" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "salt flats" . - a owl:Class, - ; - rdfs:label "Acrisols" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "sand" . - a owl:Class, - ; - rdfs:label "Andosols" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "shrub crops" . - a owl:Class, - ; - rdfs:label "Arenosols" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "shrub land" . - a owl:Class, - ; - rdfs:label "Cambisols" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "small grains" . - a owl:Class, - ; - rdfs:label "Chernozems" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "successional shrub land" . - a owl:Class, - ; - rdfs:label "Ferralsols" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "swamp" . - a owl:Class, - ; - rdfs:label "Fluvisols" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "tropical" . - a owl:Class, - ; - rdfs:label "Gleysols" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "tundra" . - a owl:Class, - ; - rdfs:label "Greyzems" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "vegetable crops" . - a owl:Class, - ; - rdfs:label "Gypsisols" . + a owl:Class, + nmdc:CurLandUseEnum ; + rdfs:label "vine crops" . - a owl:Class, - ; - rdfs:label "Histosols" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Continental - Aeolian" . - a owl:Class, - ; - rdfs:label "Kastanozems" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Continental - Alluvial" . - a owl:Class, - ; - rdfs:label "Lithosols" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Continental - Fluvial" . - a owl:Class, - ; - rdfs:label "Luvisols" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Continental - Lacustrine" . - a owl:Class, - ; - rdfs:label "Nitosols" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Marine - Deep" . - a owl:Class, - ; - rdfs:label "Phaeozems" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Marine - Reef" . - a owl:Class, - ; - rdfs:label "Planosols" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Marine - Shallow" . - a owl:Class, - ; - rdfs:label "Podzols" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Other - Evaporite" . - a owl:Class, - ; - rdfs:label "Podzoluvisols" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Other - Glacial" . - a owl:Class, - ; - rdfs:label "Rankers" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Other - Volcanic" . - a owl:Class, - ; - rdfs:label "Regosols" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Transitional - Beach" . - a owl:Class, - ; - rdfs:label "Rendzinas" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Transitional - Deltaic" . - a owl:Class, - ; - rdfs:label "Solonchaks" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Transitional - Lagoonal" . - a owl:Class, - ; - rdfs:label "Solonetz" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Transitional - Lake" . - a owl:Class, - ; - rdfs:label "Vertisols" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "Transitional - Tidal" . - a owl:Class, - ; - rdfs:label "Yermosols" . + a owl:Class, + nmdc:DeposEnvEnum ; + rdfs:label "other" . - a owl:Class, - ; - rdfs:label "HEPA" . + a owl:Class, + nmdc:DeviceTypeEnum ; + rdfs:label "orbital_shaker" . - a owl:Class, - ; - rdfs:label "chemical air filter" . + a owl:Class, + nmdc:DeviceTypeEnum ; + rdfs:label "thermomixer" . - a owl:Class, - ; - rdfs:label "electrostatic" . + a owl:Class, + nmdc:DnaSampleFormatEnum ; + rdfs:label "10 mM Tris-HCl" . - a owl:Class, - ; - rdfs:label "gas-phase or ultraviolet air treatments" . + a owl:Class, + nmdc:DnaSampleFormatEnum ; + rdfs:label "DNAStable" . - a owl:Class, - ; - rdfs:label "low-MERV pleated media" . + a owl:Class, + nmdc:DnaSampleFormatEnum ; + rdfs:label "Ethanol" . - a owl:Class, - ; - rdfs:label "particulate air filter" . + a owl:Class, + nmdc:DnaSampleFormatEnum ; + rdfs:label "Gentegra-DNA" . - a owl:Class, - ; - rdfs:label "damaged" . + a owl:Class, + nmdc:DnaSampleFormatEnum ; + rdfs:label "Gentegra-RNA" . - a owl:Class, - ; - rdfs:label "needs repair" . + a owl:Class, + nmdc:DnaSampleFormatEnum ; + rdfs:label "Low EDTA TE" . - a owl:Class, - ; - rdfs:label "new" . + a owl:Class, + nmdc:DnaSampleFormatEnum ; + rdfs:label "MDA reaction buffer" . - a owl:Class, - ; - rdfs:label "rupture" . + a owl:Class, + nmdc:DnaSampleFormatEnum ; + rdfs:label "PBS" . - a owl:Class, - ; - rdfs:label "visible wear" . + a owl:Class, + nmdc:DnaSampleFormatEnum ; + rdfs:label "Pellet" . - a owl:Class, - ; - rdfs:label "bamboo" . + a owl:Class, + nmdc:DnaSampleFormatEnum ; + rdfs:label "RNAStable" . - a owl:Class, - ; - rdfs:label "carpet" . + a owl:Class, + nmdc:DnaSampleFormatEnum ; + rdfs:label "TE" . - a owl:Class, - ; - rdfs:label "clear finish" . + a owl:Class, + nmdc:DnaSampleFormatEnum ; + rdfs:label "Water" . - a owl:Class, - ; - rdfs:label "concrete" . + a owl:Class, + nmdc:DoorCompTypeEnum ; + rdfs:label "metal covered" . - a owl:Class, - ; - rdfs:label "cork" . + a owl:Class, + nmdc:DoorCompTypeEnum ; + rdfs:label "revolving" . - a owl:Class, - ; - rdfs:label "laminate wood" . + a owl:Class, + nmdc:DoorCompTypeEnum ; + rdfs:label "sliding" . - a owl:Class, - ; - rdfs:label "lineoleum" . + a owl:Class, + nmdc:DoorCompTypeEnum ; + rdfs:label "telescopic" . - a owl:Class, - ; - rdfs:label "none" . + a owl:Class, + nmdc:DoorCondEnum ; + rdfs:label "damaged" . - a owl:Class, - ; - rdfs:label "none or unfinished" . + a owl:Class, + nmdc:DoorCondEnum ; + rdfs:label "needs repair" . - a owl:Class, - ; - rdfs:label "paint" . + a owl:Class, + nmdc:DoorCondEnum ; + rdfs:label "new" . - a owl:Class, - ; - rdfs:label "rug" . + a owl:Class, + nmdc:DoorCondEnum ; + rdfs:label "rupture" . - a owl:Class, - ; - rdfs:label "sealed" . + a owl:Class, + nmdc:DoorCondEnum ; + rdfs:label "visible wear" . - a owl:Class, - ; - rdfs:label "sheet vinyl" . + a owl:Class, + nmdc:DoorDirectEnum ; + rdfs:label "inward" . - a owl:Class, - ; - rdfs:label "stone" . + a owl:Class, + nmdc:DoorDirectEnum ; + rdfs:label "outward" . - a owl:Class, - ; - rdfs:label "terrazo" . + a owl:Class, + nmdc:DoorDirectEnum ; + rdfs:label "sideways" . - a owl:Class, - ; - rdfs:label "tile" . + a owl:Class, + nmdc:DoorLocEnum ; + rdfs:label "east" . - a owl:Class, - ; - rdfs:label "vinyl composition tile" . + a owl:Class, + nmdc:DoorLocEnum ; + rdfs:label "north" . - a owl:Class, - ; - rdfs:label "wood strip or parquet" . + a owl:Class, + nmdc:DoorLocEnum ; + rdfs:label "south" . - a owl:Class, - ; - rdfs:label "balcony" . + a owl:Class, + nmdc:DoorLocEnum ; + rdfs:label "west" . - a owl:Class, - ; - rdfs:label "concrete" . + a owl:Class, + nmdc:DoorMatEnum ; + rdfs:label "aluminum" . - a owl:Class, - ; - rdfs:label "floating floor" . + a owl:Class, + nmdc:DoorMatEnum ; + rdfs:label "cellular PVC" . - a owl:Class, - ; - rdfs:label "glass floor" . + a owl:Class, + nmdc:DoorMatEnum ; + rdfs:label "engineered plastic" . - a owl:Class, - ; - rdfs:label "raised floor" . + a owl:Class, + nmdc:DoorMatEnum ; + rdfs:label "fiberboard" . - a owl:Class, - ; - rdfs:label "sprung floor" . + a owl:Class, + nmdc:DoorMatEnum ; + rdfs:label "fiberglass" . - a owl:Class, - ; - rdfs:label "wood-framed" . + a owl:Class, + nmdc:DoorMatEnum ; + rdfs:label "metal" . - a owl:Class, - ; - rdfs:label "bulging walls" . + a owl:Class, + nmdc:DoorMatEnum ; + rdfs:label "thermoplastic alloy" . - a owl:Class, - ; - rdfs:label "ceiling discoloration" . + a owl:Class, + nmdc:DoorMatEnum ; + rdfs:label "vinyl" . - a owl:Class, - ; - rdfs:label "condensation" . + a owl:Class, + nmdc:DoorMatEnum ; + rdfs:label "wood" . - a owl:Class, - ; - rdfs:label "floor discoloration" . + a owl:Class, + nmdc:DoorMatEnum ; + rdfs:label "wood/plastic composite" . - a owl:Class, - ; - rdfs:label "mold odor" . + a owl:Class, + nmdc:DoorMoveEnum ; + rdfs:label "collapsible" . - a owl:Class, - ; - rdfs:label "peeling paint or wallpaper" . + a owl:Class, + nmdc:DoorMoveEnum ; + rdfs:label "folding" . - a owl:Class, - ; - rdfs:label "wall discoloration" . + a owl:Class, + nmdc:DoorMoveEnum ; + rdfs:label "revolving" . - a owl:Class, - ; - rdfs:label "water stains" . + a owl:Class, + nmdc:DoorMoveEnum ; + rdfs:label "rolling shutter" . - a owl:Class, - ; - rdfs:label "wet floor" . + a owl:Class, + nmdc:DoorMoveEnum ; + rdfs:label "sliding" . - a owl:Class, - ; - rdfs:label "Annually" . + a owl:Class, + nmdc:DoorMoveEnum ; + rdfs:label "swinging" . - a owl:Class, - ; - rdfs:label "Daily" . + a owl:Class, + nmdc:DoorTypeEnum ; + rdfs:label "composite" . - a owl:Class, - ; - rdfs:label "Monthly" . + a owl:Class, + nmdc:DoorTypeEnum ; + rdfs:label "metal" . - a owl:Class, - ; - rdfs:label "Quarterly" . + a owl:Class, + nmdc:DoorTypeEnum ; + rdfs:label "wooden" . - a owl:Class, - ; - rdfs:label "Weekly" . + a owl:Class, + nmdc:DoorTypeMetalEnum ; + rdfs:label "collapsible" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:DoorTypeMetalEnum ; + rdfs:label "corrugated steel" . - a owl:Class, - ; - rdfs:label "cabinet" . + a owl:Class, + nmdc:DoorTypeMetalEnum ; + rdfs:label "hollow" . - a owl:Class, - ; - rdfs:label "chair" . + a owl:Class, + nmdc:DoorTypeMetalEnum ; + rdfs:label "rolling shutters" . - a owl:Class, - ; - rdfs:label "desks" . + a owl:Class, + nmdc:DoorTypeMetalEnum ; + rdfs:label "steel plate" . - a owl:Class, - ; - rdfs:label "all gender" . + a owl:Class, + nmdc:DoorTypeWoodEnum ; + rdfs:label "battened" . - a owl:Class, - ; - rdfs:label "female" . + a owl:Class, + nmdc:DoorTypeWoodEnum ; + rdfs:label "bettened and ledged" . - a owl:Class, - ; - rdfs:label "gender neurtral" . + a owl:Class, + nmdc:DoorTypeWoodEnum ; + rdfs:label "flush" . - a owl:Class, - ; - rdfs:label "male" . + a owl:Class, + nmdc:DoorTypeWoodEnum ; + rdfs:label "framed and paneled" . - a owl:Class, - ; - rdfs:label "male and female" . + a owl:Class, + nmdc:DoorTypeWoodEnum ; + rdfs:label "glashed or sash" . - a owl:Class, - ; - rdfs:label "unisex" . + a owl:Class, + nmdc:DoorTypeWoodEnum ; + rdfs:label "ledged and braced" . - a owl:Class, - ; - rdfs:label "erect" . + a owl:Class, + nmdc:DoorTypeWoodEnum ; + rdfs:label "ledged and framed" . - a owl:Class, - ; - rdfs:label "prostrate" . + a owl:Class, + nmdc:DoorTypeWoodEnum ; + rdfs:label "ledged, braced and frame" . - a owl:Class, - ; - rdfs:label "semi-erect" . + a owl:Class, + nmdc:DoorTypeWoodEnum ; + rdfs:label "louvered" . - a owl:Class, - ; - rdfs:label "spreading" . + a owl:Class, + nmdc:DoorTypeWoodEnum ; + rdfs:label "wire gauged" . - a owl:Class, - ; - rdfs:label "ambidexterity" . + a owl:Class, + nmdc:DrainageClassEnum ; + rdfs:label "excessively drained" . - a owl:Class, - ; - rdfs:label "left handedness" . + a owl:Class, + nmdc:DrainageClassEnum ; + rdfs:label "moderately well" . - a owl:Class, - ; - rdfs:label "mixed-handedness" . + a owl:Class, + nmdc:DrainageClassEnum ; + rdfs:label "poorly" . - a owl:Class, - ; - rdfs:label "right handedness" . + a owl:Class, + nmdc:DrainageClassEnum ; + rdfs:label "somewhat poorly" . - a owl:Class, - ; - rdfs:label "Bitumen" . + a owl:Class, + nmdc:DrainageClassEnum ; + rdfs:label "very poorly" . - a owl:Class, - ; - rdfs:label "Coalbed Methane" . + a owl:Class, + nmdc:DrainageClassEnum ; + rdfs:label "well" . - a owl:Class, - ; - rdfs:label "Gas" . + a owl:Class, + nmdc:DrawingsEnum ; + rdfs:label "as built" . - a owl:Class, - ; - rdfs:label "Gas-Condensate" . + a owl:Class, + nmdc:DrawingsEnum ; + rdfs:label "bid" . - a owl:Class, - ; - rdfs:label "Oil" . + a owl:Class, + nmdc:DrawingsEnum ; + rdfs:label "building navigation map" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:DrawingsEnum ; + rdfs:label "construction" . - a owl:Class, - ; - rdfs:label "Coalbed" . + a owl:Class, + nmdc:DrawingsEnum ; + rdfs:label "design" . - a owl:Class, - ; - rdfs:label "Gas Reservoir" . + a owl:Class, + nmdc:DrawingsEnum ; + rdfs:label "diagram" . - a owl:Class, - ; - rdfs:label "Oil Reservoir" . + a owl:Class, + nmdc:DrawingsEnum ; + rdfs:label "operation" . - a owl:Class, - ; - rdfs:label "Oil Sand" . + a owl:Class, + nmdc:DrawingsEnum ; + rdfs:label "sketch" . - a owl:Class, - ; - rdfs:label "Shale" . + a owl:Class, + nmdc:ExtWallOrientEnum ; + rdfs:label "east" . - a owl:Class, - ; - rdfs:label "Tight Gas Reservoir" . + a owl:Class, + nmdc:ExtWallOrientEnum ; + rdfs:label "north" . - a owl:Class, - ; - rdfs:label "Tight Oil Reservoir" . + a owl:Class, + nmdc:ExtWallOrientEnum ; + rdfs:label "northeast" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:ExtWallOrientEnum ; + rdfs:label "northwest" . - a owl:Class, - ; - rdfs:label "Archean" . + a owl:Class, + nmdc:ExtWallOrientEnum ; + rdfs:label "south" . - a owl:Class, - ; - rdfs:label "Cambrian" . + a owl:Class, + nmdc:ExtWallOrientEnum ; + rdfs:label "southeast" . - a owl:Class, - ; - rdfs:label "Carboniferous" . + a owl:Class, + nmdc:ExtWallOrientEnum ; + rdfs:label "southwest" . - a owl:Class, - ; - rdfs:label "Cenozoic" . + a owl:Class, + nmdc:ExtWallOrientEnum ; + rdfs:label "west" . - a owl:Class, - ; - rdfs:label "Cretaceous" . + a owl:Class, + nmdc:ExtWindowOrientEnum ; + rdfs:label "east" . - a owl:Class, - ; - rdfs:label "Devonian" . + a owl:Class, + nmdc:ExtWindowOrientEnum ; + rdfs:label "north" . - a owl:Class, - ; - rdfs:label "Jurassic" . + a owl:Class, + nmdc:ExtWindowOrientEnum ; + rdfs:label "northeast" . - a owl:Class, - ; - rdfs:label "Mesozoic" . + a owl:Class, + nmdc:ExtWindowOrientEnum ; + rdfs:label "northwest" . - a owl:Class, - ; - rdfs:label "Neogene" . + a owl:Class, + nmdc:ExtWindowOrientEnum ; + rdfs:label "south" . - a owl:Class, - ; - rdfs:label "Ordovician" . + a owl:Class, + nmdc:ExtWindowOrientEnum ; + rdfs:label "southeast" . - a owl:Class, - ; - rdfs:label "Paleogene" . + a owl:Class, + nmdc:ExtWindowOrientEnum ; + rdfs:label "southwest" . - a owl:Class, - ; - rdfs:label "Paleozoic" . + a owl:Class, + nmdc:ExtWindowOrientEnum ; + rdfs:label "west" . - a owl:Class, - ; - rdfs:label "Permian" . + a owl:Class, + nmdc:ExtractionTargetEnum ; + rdfs:label "DNA" . - a owl:Class, - ; - rdfs:label "Precambrian" . + a owl:Class, + nmdc:ExtractionTargetEnum ; + rdfs:label "RNA" . - a owl:Class, - ; - rdfs:label "Proterozoic" . + a owl:Class, + nmdc:ExtractionTargetEnum ; + rdfs:label "metabolite" . - a owl:Class, - ; - rdfs:label "Silurian" . + a owl:Class, + nmdc:ExtractionTargetEnum ; + rdfs:label "protein" . - a owl:Class, - ; - rdfs:label "Triassic" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Acrisols" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Andosols" . - a owl:Class, - ; - rdfs:label "forced air system" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Arenosols" . - a owl:Class, - ; - rdfs:label "heat pump" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Cambisols" . - a owl:Class, - ; - rdfs:label "radiant system" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Chernozems" . - a owl:Class, - ; - rdfs:label "steam forced heat" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Ferralsols" . - a owl:Class, - ; - rdfs:label "wood stove" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Fluvisols" . - a owl:Class, - ; - rdfs:label "east" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Gleysols" . - a owl:Class, - ; - rdfs:label "north" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Greyzems" . - a owl:Class, - ; - rdfs:label "south" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Gypsisols" . - a owl:Class, - ; - rdfs:label "west" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Histosols" . - a owl:Class, - ; - rdfs:label "female" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Kastanozems" . - a owl:Class, - ; - rdfs:label "hermaphrodite" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Lithosols" . - a owl:Class, - ; - rdfs:label "male" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Luvisols" . - a owl:Class, - ; - rdfs:label "neuter" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Nitosols" . - a owl:Class, - ; - rdfs:label "bathroom" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Phaeozems" . - a owl:Class, - ; - rdfs:label "bedroom" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Planosols" . - a owl:Class, - ; - rdfs:label "elevator" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Podzols" . - a owl:Class, - ; - rdfs:label "foyer" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Podzoluvisols" . - a owl:Class, - ; - rdfs:label "hallway" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Rankers" . - a owl:Class, - ; - rdfs:label "kitchen" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Regosols" . - a owl:Class, - ; - rdfs:label "locker room" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Rendzinas" . - a owl:Class, - ; - rdfs:label "office" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Solonchaks" . - a owl:Class, - ; - rdfs:label "cabinet" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Solonetz" . - a owl:Class, - ; - rdfs:label "ceiling" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Vertisols" . - a owl:Class, - ; - rdfs:label "counter top" . + a owl:Class, + nmdc:FaoClassEnum ; + rdfs:label "Yermosols" . - a owl:Class, - ; - rdfs:label "door" . +nmdc:FieldResearchSite a owl:Class, + linkml:ClassDefinition ; + rdfs:label "FieldResearchSite" ; + dcterms:title "Field Research 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 ], + nmdc:Site ; + skos:altLabel "research plot" ; + skos:definition "A site, outside of a laboratory, from which biosamples may be collected." ; + skos:inScheme nmdc:nmdc ; + skos:note "In Bioscales, one might say that rhizosphere soil and bulk soil from around the same plant were obtained at the same site. In this case, the site would correspond to one tree.", + "Provides grouping of biosamples at level that's more specific than belonging to the same study", + "be very clear that this could be part of a larger site", + "might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833" . - a owl:Class, - ; - rdfs:label "shelving" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Annotation Amino Acid FASTA" . - a owl:Class, - ; - rdfs:label "vent cover" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Annotation Enzyme Commission" . - a owl:Class, - ; - rdfs:label "wall" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Annotation Info File" . - a owl:Class, - ; - rdfs:label "window" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Annotation KEGG Orthology" . - a owl:Class, - ; - rdfs:label "damaged" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Annotation Statistics" . - a owl:Class, - ; - rdfs:label "needs repair" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Assembly AGP" . - a owl:Class, - ; - rdfs:label "new" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Assembly Contigs" . - a owl:Class, - ; - rdfs:label "rupture" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Assembly Coverage BAM" . - a owl:Class, - ; - rdfs:label "visible wear" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Assembly Coverage Stats" . - a owl:Class, - ; - rdfs:label "desk lamp" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Assembly Info File" . - a owl:Class, - ; - rdfs:label "electric light" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Assembly Scaffolds" . - a owl:Class, - ; - rdfs:label "flourescent lights" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "CATH FunFams (Functional Families) Annotation GFF" . - a owl:Class, - ; - rdfs:label "natural light" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "CRT Annotation GFF" . - a owl:Class, - ; - rdfs:label "none" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Centrifuge Classification Report" . - a owl:Class, - ; - rdfs:label "Basement" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Centrifuge Krona Plot" . - a owl:Class, - ; - rdfs:label "Chalk" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Centrifuge Taxonomic Classification" . - a owl:Class, - ; - rdfs:label "Chert" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Centrifuge output report file" . - a owl:Class, - ; - rdfs:label "Coal" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "CheckM Statistics" . - a owl:Class, - ; - rdfs:label "Conglomerate" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Clusters of Orthologous Groups (COG) Annotation GFF" . - a owl:Class, - ; - rdfs:label "Diatomite" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Contig Mapping File" . - a owl:Class, - ; - rdfs:label "Dolomite" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Crispr Terms" . - a owl:Class, - ; - rdfs:label "Limestone" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Direct Infusion FT ICR-MS Raw Data" . - a owl:Class, - ; - rdfs:label "Sandstone" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Error Corrected Reads" . - a owl:Class, - ; - rdfs:label "Shale" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "FT ICR-MS Analysis Results" . - a owl:Class, - ; - rdfs:label "Siltstone" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Filtered Sequencing Reads" . - a owl:Class, - ; - rdfs:label "Volcanic" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Functional Annotation GFF" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "GC-MS Metabolomics Results" . - a owl:Class, - ; - rdfs:label "boat" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "GOTTCHA2 Classification Report" . - a owl:Class, - ; - rdfs:label "bus" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "GOTTCHA2 Krona Plot" . - a owl:Class, - ; - rdfs:label "car" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "GOTTCHA2 Report Full" . - a owl:Class, - ; - rdfs:label "carriage" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "GTDBTK Archaeal Summary" . - a owl:Class, - ; - rdfs:label "coach" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "GTDBTK Bacterial Summary" . - a owl:Class, - ; - rdfs:label "elevator" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Gene Phylogeny tsv" . - a owl:Class, - ; - rdfs:label "escalator" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Genemark Annotation GFF" . - a owl:Class, - ; - rdfs:label "subway" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "KO_EC Annotation GFF" . - a owl:Class, - ; - rdfs:label "train" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Kraken2 Classification Report" . - a owl:Class, - ; - rdfs:label "automated count" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Kraken2 Krona Plot" . - a owl:Class, - ; - rdfs:label "estimate" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Kraken2 Taxonomic Classification" . - a owl:Class, - ; - rdfs:label "manual count" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Metagenome Bins" . - a owl:Class, - ; - rdfs:label "videos" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Metagenome Bins Compression File" . - a owl:Class, - ; - rdfs:label "ATP" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Metagenome Bins Info File" . - a owl:Class, - ; - rdfs:label "MPN" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Metagenome Raw Read 1" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Metagenome Raw Read 2" . - a owl:Class, - ; - rdfs:label "aerobic" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Metagenome Raw Reads" . - a owl:Class, - ; - rdfs:label "anaerobic" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Metaproteomics Workflow Statistics" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Misc Annotation GFF" . - a owl:Class, - ; - rdfs:label "other artificial liquid medium" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Peptide Report" . - a owl:Class, - ; - rdfs:label "other artificial solid medium" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Pfam Annotation GFF" . - a owl:Class, - ; - rdfs:label "peat moss" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Prodigal Annotation GFF" . - a owl:Class, - ; - rdfs:label "perlite" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Product Names" . - a owl:Class, - ; - rdfs:label "pumice" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Protein Report" . - a owl:Class, - ; - rdfs:label "sand" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "QC Statistics" . - a owl:Class, - ; - rdfs:label "soil" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "QC Statistics Extended" . - a owl:Class, - ; - rdfs:label "vermiculite" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "QC non-rRNA R1" . - a owl:Class, - ; - rdfs:label "water" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "QC non-rRNA R2" . - a owl:Class, - ; - rdfs:label "Androdioecious" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "RFAM Annotation GFF" . - a owl:Class, - ; - rdfs:label "Androecious" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Raw Compressed Metagenome Interleaved Paired-End Reads" . - a owl:Class, - ; - rdfs:label "Androgynomonoecious" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Read Based Analysis Info File" . - a owl:Class, - ; - rdfs:label "Androgynous" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Read Count and RPKM" . - a owl:Class, - ; - rdfs:label "Andromonoecious" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Read Filtering Info File" . - a owl:Class, - ; - rdfs:label "Bisexual" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "SMART Annotation GFF" . - a owl:Class, - ; - rdfs:label "Dichogamous" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "SUPERFam Annotation GFF" . - a owl:Class, - ; - rdfs:label "Diclinous" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Scaffold Lineage tsv" . - a owl:Class, - ; - rdfs:label "Dioecious" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Structural Annotation GFF" . - a owl:Class, - ; - rdfs:label "Gynodioecious" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Structural Annotation Stats Json" . - a owl:Class, - ; - rdfs:label "Gynoecious" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "TIGRFam Annotation GFF" . - a owl:Class, - ; - rdfs:label "Gynomonoecious" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "TMRNA Annotation GFF" . - a owl:Class, - ; - rdfs:label "Hermaphroditic" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "TRNA Annotation GFF" . - a owl:Class, - ; - rdfs:label "Imperfect" . + a owl:Class, + nmdc:FileTypeEnum ; + rdfs:label "Unfiltered Metaproteomics Results" . - a owl:Class, - ; - rdfs:label "Monoclinous" . + a owl:Class, + nmdc:FilterTypeEnum ; + rdfs:label "HEPA" . - a owl:Class, - ; - rdfs:label "Monoecious" . + a owl:Class, + nmdc:FilterTypeEnum ; + rdfs:label "chemical air filter" . - a owl:Class, - ; - rdfs:label "Perfect" . + a owl:Class, + nmdc:FilterTypeEnum ; + rdfs:label "electrostatic" . - a owl:Class, - ; - rdfs:label "Polygamodioecious" . + a owl:Class, + nmdc:FilterTypeEnum ; + rdfs:label "gas-phase or ultraviolet air treatments" . - a owl:Class, - ; - rdfs:label "Polygamomonoecious" . + a owl:Class, + nmdc:FilterTypeEnum ; + rdfs:label "low-MERV pleated media" . - a owl:Class, - ; - rdfs:label "Polygamous" . + a owl:Class, + nmdc:FilterTypeEnum ; + rdfs:label "particulate air filter" . - a owl:Class, - ; - rdfs:label "Protandrous" . + a owl:Class, + nmdc:FloorCondEnum ; + rdfs:label "damaged" . - a owl:Class, - ; - rdfs:label "Protogynous" . + a owl:Class, + nmdc:FloorCondEnum ; + rdfs:label "needs repair" . - a owl:Class, - ; - rdfs:label "Subandroecious" . + a owl:Class, + nmdc:FloorCondEnum ; + rdfs:label "new" . - a owl:Class, - ; - rdfs:label "Subdioecious" . + a owl:Class, + nmdc:FloorCondEnum ; + rdfs:label "rupture" . - a owl:Class, - ; - rdfs:label "Subgynoecious" . + a owl:Class, + nmdc:FloorCondEnum ; + rdfs:label "visible wear" . - a owl:Class, - ; - rdfs:label "Synoecious" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "bamboo" . - a owl:Class, - ; - rdfs:label "Trimonoecious" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "carpet" . - a owl:Class, - ; - rdfs:label "Trioecious" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "clear finish" . - a owl:Class, - ; - rdfs:label "Unisexual" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "concrete" . - a owl:Class, - ; - rdfs:label "backslope" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "cork" . - a owl:Class, - ; - rdfs:label "footslope" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "laminate wood" . - a owl:Class, - ; - rdfs:label "shoulder" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "lineoleum" . - a owl:Class, - ; - rdfs:label "summit" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "none" . - a owl:Class, - ; - rdfs:label "toeslope" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "none or unfinished" . - a owl:Class, - ; - rdfs:label "East side" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "paint" . - a owl:Class, - ; - rdfs:label "North side" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "rug" . - a owl:Class, - ; - rdfs:label "South side" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "sealed" . - a owl:Class, - ; - rdfs:label "West side" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "sheet vinyl" . - a owl:Class, - ; - rdfs:label "center of car" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "stone" . - a owl:Class, - ; - rdfs:label "edge of car" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "terrazo" . - a owl:Class, - ; - rdfs:label "under a seat" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "tile" . - a owl:Class, - ; - rdfs:label "damaged" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "vinyl composition tile" . - a owl:Class, - ; - rdfs:label "needs repair" . + a owl:Class, + nmdc:FloorFinishMatEnum ; + rdfs:label "wood strip or parquet" . - a owl:Class, - ; - rdfs:label "new" . + a owl:Class, + nmdc:FloorStrucEnum ; + rdfs:label "balcony" . - a owl:Class, - ; - rdfs:label "rupture" . + a owl:Class, + nmdc:FloorStrucEnum ; + rdfs:label "concrete" . - a owl:Class, - ; - rdfs:label "visible signs of mold/mildew" . + a owl:Class, + nmdc:FloorStrucEnum ; + rdfs:label "floating floor" . - a owl:Class, - ; - rdfs:label "visible wear" . + a owl:Class, + nmdc:FloorStrucEnum ; + rdfs:label "glass floor" . - a owl:Class, - ; - rdfs:label "attic" . + a owl:Class, + nmdc:FloorStrucEnum ; + rdfs:label "raised floor" . - a owl:Class, - ; - rdfs:label "bathroom" . + a owl:Class, + nmdc:FloorStrucEnum ; + rdfs:label "sprung floor" . - a owl:Class, - ; - rdfs:label "closet" . + a owl:Class, + nmdc:FloorStrucEnum ; + rdfs:label "wood-framed" . - a owl:Class, - ; - rdfs:label "conference room" . + a owl:Class, + nmdc:FloorWaterMoldEnum ; + rdfs:label "bulging walls" . - a owl:Class, - ; - rdfs:label "elevator" . + a owl:Class, + nmdc:FloorWaterMoldEnum ; + rdfs:label "ceiling discoloration" . - a owl:Class, - ; - rdfs:label "examining room" . - - a owl:Class, - ; - rdfs:label "hallway" . + a owl:Class, + nmdc:FloorWaterMoldEnum ; + rdfs:label "condensation" . - a owl:Class, - ; - rdfs:label "kitchen" . + a owl:Class, + nmdc:FloorWaterMoldEnum ; + rdfs:label "floor discoloration" . - a owl:Class, - ; - rdfs:label "mail room" . + a owl:Class, + nmdc:FloorWaterMoldEnum ; + rdfs:label "mold odor" . - a owl:Class, - ; - rdfs:label "office" . + a owl:Class, + nmdc:FloorWaterMoldEnum ; + rdfs:label "peeling paint or wallpaper" . - a owl:Class, - ; - rdfs:label "stairwell" . + a owl:Class, + nmdc:FloorWaterMoldEnum ; + rdfs:label "wall discoloration" . - a owl:Class, - ; - rdfs:label "corner room" . + a owl:Class, + nmdc:FloorWaterMoldEnum ; + rdfs:label "water stains" . - a owl:Class, - ; - rdfs:label "exterior wall" . + a owl:Class, + nmdc:FloorWaterMoldEnum ; + rdfs:label "wet floor" . - a owl:Class, - ; - rdfs:label "interior room" . + a owl:Class, + nmdc:FreqCleanEnum ; + rdfs:label "Annually" . - a owl:Class, - ; - rdfs:label "center" . + a owl:Class, + nmdc:FreqCleanEnum ; + rdfs:label "Daily" . - a owl:Class, - ; - rdfs:label "east corner" . + a owl:Class, + nmdc:FreqCleanEnum ; + rdfs:label "Monthly" . - a owl:Class, - ; - rdfs:label "north corner" . + a owl:Class, + nmdc:FreqCleanEnum ; + rdfs:label "Quarterly" . - a owl:Class, - ; - rdfs:label "northeast corner" . + a owl:Class, + nmdc:FreqCleanEnum ; + rdfs:label "Weekly" . - a owl:Class, - ; - rdfs:label "northwest corner" . + a owl:Class, + nmdc:FreqCleanEnum ; + rdfs:label "other" . - a owl:Class, - ; - rdfs:label "south corner" . + a owl:Class, + nmdc:FurnitureEnum ; + rdfs:label "cabinet" . - a owl:Class, - ; - rdfs:label "southeast corner" . + a owl:Class, + nmdc:FurnitureEnum ; + rdfs:label "chair" . - a owl:Class, - ; - rdfs:label "southwest corner" . + a owl:Class, + nmdc:FurnitureEnum ; + rdfs:label "desks" . - a owl:Class, - ; - rdfs:label "west corner" . + a owl:Class, + nmdc:GenderRestroomEnum ; + rdfs:label "all gender" . - a owl:Class, - ; - rdfs:label ",restroom" . + a owl:Class, + nmdc:GenderRestroomEnum ; + rdfs:label "female" . - a owl:Class, - ; - rdfs:label "attic" . + a owl:Class, + nmdc:GenderRestroomEnum ; + rdfs:label "gender neurtral" . - a owl:Class, - ; - rdfs:label "auditorium" . + a owl:Class, + nmdc:GenderRestroomEnum ; + rdfs:label "male" . - a owl:Class, - ; - rdfs:label "bathroom" . + a owl:Class, + nmdc:GenderRestroomEnum ; + rdfs:label "male and female" . - a owl:Class, - ; - rdfs:label "cafe" . + a owl:Class, + nmdc:GenderRestroomEnum ; + rdfs:label "unisex" . - a owl:Class, - ; - rdfs:label "closet" . + a owl:Class, + nmdc:GrowthHabitEnum ; + rdfs:label "erect" . - a owl:Class, - ; - rdfs:label "conference room" . + a owl:Class, + nmdc:GrowthHabitEnum ; + rdfs:label "prostrate" . - a owl:Class, - ; - rdfs:label "data center" . + a owl:Class, + nmdc:GrowthHabitEnum ; + rdfs:label "semi-erect" . - a owl:Class, - ; - rdfs:label "elevator" . + a owl:Class, + nmdc:GrowthHabitEnum ; + rdfs:label "spreading" . - a owl:Class, - ; - rdfs:label "examining room" . + a owl:Class, + nmdc:HandidnessEnum ; + rdfs:label "ambidexterity" . - a owl:Class, - ; - rdfs:label "gymnasium" . + a owl:Class, + nmdc:HandidnessEnum ; + rdfs:label "left handedness" . - a owl:Class, - ; - rdfs:label "hallway" . + a owl:Class, + nmdc:HandidnessEnum ; + rdfs:label "mixed-handedness" . - a owl:Class, - ; - rdfs:label "kitchen" . + a owl:Class, + nmdc:HandidnessEnum ; + rdfs:label "right handedness" . - a owl:Class, - ; - rdfs:label "laboratory_dry" . + a owl:Class, + nmdc:HcProducedEnum ; + rdfs:label "Bitumen" . - a owl:Class, - ; - rdfs:label "laboratory_wet" . + a owl:Class, + nmdc:HcProducedEnum ; + rdfs:label "Coalbed Methane" . - a owl:Class, - ; - rdfs:label "lobby" . + a owl:Class, + nmdc:HcProducedEnum ; + rdfs:label "Gas" . - a owl:Class, - ; - rdfs:label "lockers" . + a owl:Class, + nmdc:HcProducedEnum ; + rdfs:label "Gas-Condensate" . - a owl:Class, - ; - rdfs:label "mail room" . + a owl:Class, + nmdc:HcProducedEnum ; + rdfs:label "Oil" . - a owl:Class, - ; - rdfs:label "mechanical or electrical room" . + a owl:Class, + nmdc:HcProducedEnum ; + rdfs:label "other" . - a owl:Class, - ; - rdfs:label "natatorium" . + a owl:Class, + nmdc:HcrEnum ; + rdfs:label "Coalbed" . - a owl:Class, - ; - rdfs:label "open office" . + a owl:Class, + nmdc:HcrEnum ; + rdfs:label "Gas Reservoir" . - a owl:Class, - ; - rdfs:label "private office" . + a owl:Class, + nmdc:HcrEnum ; + rdfs:label "Oil Reservoir" . - a owl:Class, - ; - rdfs:label "stairwell" . + a owl:Class, + nmdc:HcrEnum ; + rdfs:label "Oil Sand" . - a owl:Class, - ; - rdfs:label "vestibule" . + a owl:Class, + nmdc:HcrEnum ; + rdfs:label "Shale" . - a owl:Class, - ; - rdfs:label "warehouse" . + a owl:Class, + nmdc:HcrEnum ; + rdfs:label "Tight Gas Reservoir" . - a owl:Class, - ; - rdfs:label "active surveillance in response to an outbreak" . + a owl:Class, + nmdc:HcrEnum ; + rdfs:label "Tight Oil Reservoir" . - a owl:Class, - ; - rdfs:label "active surveillance not initiated by an outbreak" . + a owl:Class, + nmdc:HcrEnum ; + rdfs:label "other" . - a owl:Class, - ; - rdfs:label "farm sample" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Archean" . - a owl:Class, - ; - rdfs:label "market sample" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Cambrian" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Carboniferous" . - a owl:Class, - ; - rdfs:label "drilling rig" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Cenozoic" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Cretaceous" . - a owl:Class, - ; - rdfs:label "separator" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Devonian" . - a owl:Class, - ; - rdfs:label "storage tank" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Jurassic" . - a owl:Class, - ; - rdfs:label "test well" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Mesozoic" . - a owl:Class, - ; - rdfs:label "well" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Neogene" . - a owl:Class, - ; - rdfs:label "wellhead" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Ordovician" . - a owl:Class, - ; - rdfs:label "dissemination" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Paleogene" . - a owl:Class, - ; - rdfs:label "growth and reproduction" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Paleozoic" . - a owl:Class, - ; - rdfs:label "infection" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Permian" . - a owl:Class, - ; - rdfs:label "inoculation" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Precambrian" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Proterozoic" . - a owl:Class, - ; - rdfs:label "penetration" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Silurian" . - a owl:Class, - ; - rdfs:label "1st floor" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "Triassic" . - a owl:Class, - ; - rdfs:label "2nd floor" . + a owl:Class, + nmdc:HcrGeolAgeEnum ; + rdfs:label "other" . - a owl:Class, - ; - rdfs:label "basement" . + a owl:Class, + nmdc:HeatCoolTypeEnum ; + rdfs:label "forced air system" . - a owl:Class, - ; - rdfs:label "lobby" . + a owl:Class, + nmdc:HeatCoolTypeEnum ; + rdfs:label "heat pump" . - a owl:Class, - ; - rdfs:label "DF" . + a owl:Class, + nmdc:HeatCoolTypeEnum ; + rdfs:label "radiant system" . - a owl:Class, - ; - rdfs:label "KB" . + a owl:Class, + nmdc:HeatCoolTypeEnum ; + rdfs:label "steam forced heat" . - a owl:Class, - ; - rdfs:label "MSL" . + a owl:Class, + nmdc:HeatCoolTypeEnum ; + rdfs:label "wood stove" . - a owl:Class, - ; - rdfs:label "RT" . + a owl:Class, + nmdc:HeatDelivLocEnum ; + rdfs:label "east" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:HeatDelivLocEnum ; + rdfs:label "north" . - a owl:Class, - ; - rdfs:label "biofilm" . + a owl:Class, + nmdc:HeatDelivLocEnum ; + rdfs:label "south" . - a owl:Class, - ; - rdfs:label "not applicable" . + a owl:Class, + nmdc:HeatDelivLocEnum ; + rdfs:label "west" . - a owl:Class, - ; - rdfs:label "oil phase" . + a owl:Class, + nmdc:HostSexEnum ; + rdfs:label "female" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:HostSexEnum ; + rdfs:label "hermaphrodite" . - a owl:Class, - ; - rdfs:label "water phase" . + a owl:Class, + nmdc:HostSexEnum ; + rdfs:label "male" . - a owl:Class, - ; - rdfs:label "clear sky" . + a owl:Class, + nmdc:HostSexEnum ; + rdfs:label "neuter" . - a owl:Class, - ; - rdfs:label "cloudy" . + a owl:Class, + nmdc:IndoorSpaceEnum ; + rdfs:label "bathroom" . - a owl:Class, - ; - rdfs:label "foggy" . + a owl:Class, + nmdc:IndoorSpaceEnum ; + rdfs:label "bedroom" . - a owl:Class, - ; - rdfs:label "hail" . + a owl:Class, + nmdc:IndoorSpaceEnum ; + rdfs:label "elevator" . - a owl:Class, - ; - rdfs:label "rain" . + a owl:Class, + nmdc:IndoorSpaceEnum ; + rdfs:label "foyer" . - a owl:Class, - ; - rdfs:label "sleet" . + a owl:Class, + nmdc:IndoorSpaceEnum ; + rdfs:label "hallway" . - a owl:Class, - ; - rdfs:label "snow" . + a owl:Class, + nmdc:IndoorSpaceEnum ; + rdfs:label "kitchen" . - a owl:Class, - ; - rdfs:label "sunny" . + a owl:Class, + nmdc:IndoorSpaceEnum ; + rdfs:label "locker room" . - a owl:Class, - ; - rdfs:label "windy" . + a owl:Class, + nmdc:IndoorSpaceEnum ; + rdfs:label "office" . - a owl:Class, - ; - rdfs:label "Fall" . + a owl:Class, + nmdc:IndoorSurfEnum ; + rdfs:label "cabinet" . - a owl:Class, - ; - rdfs:label "Spring" . + a owl:Class, + nmdc:IndoorSurfEnum ; + rdfs:label "ceiling" . - a owl:Class, - ; - rdfs:label "Summer" . + a owl:Class, + nmdc:IndoorSurfEnum ; + rdfs:label "counter top" . - a owl:Class, - ; - rdfs:label "Winter" . + a owl:Class, + nmdc:IndoorSurfEnum ; + rdfs:label "door" . - a owl:Class, - ; - rdfs:label "biogenous" . + a owl:Class, + nmdc:IndoorSurfEnum ; + rdfs:label "shelving" . - a owl:Class, - ; - rdfs:label "cosmogenous" . + a owl:Class, + nmdc:IndoorSurfEnum ; + rdfs:label "vent cover" . - a owl:Class, - ; - rdfs:label "hydrogenous" . + a owl:Class, + nmdc:IndoorSurfEnum ; + rdfs:label "wall" . - a owl:Class, - ; - rdfs:label "lithogenous" . + a owl:Class, + nmdc:IndoorSurfEnum ; + rdfs:label "window" . - a owl:Class, - ; + a owl:Class, + nmdc:IntWallCondEnum ; rdfs:label "damaged" . - a owl:Class, - ; + a owl:Class, + nmdc:IntWallCondEnum ; rdfs:label "needs repair" . - a owl:Class, - ; + a owl:Class, + nmdc:IntWallCondEnum ; rdfs:label "new" . - a owl:Class, - ; + a owl:Class, + nmdc:IntWallCondEnum ; rdfs:label "rupture" . - a owl:Class, - ; + a owl:Class, + nmdc:IntWallCondEnum ; rdfs:label "visible wear" . - a owl:Class, - ; - rdfs:label "bahama shutters" . + a owl:Class, + nmdc:JgiContTypeEnum ; + rdfs:label "plate" . - a owl:Class, - ; - rdfs:label "exterior roll blind" . + a owl:Class, + nmdc:JgiContTypeEnum ; + rdfs:label "tube" . - a owl:Class, - ; - rdfs:label "gambrel awning" . +nmdc:LabDevice a owl:Class, + linkml:ClassDefinition ; + rdfs:label "LabDevice" ; + dcterms:title "Lab device" ; + skos:inScheme nmdc:sample_prep . - a owl:Class, - ; - rdfs:label "hood awning" . + a owl:Class, + nmdc:LibraryTypeEnum ; + rdfs:label "DNA" . - a owl:Class, - ; - rdfs:label "porchroller awning" . + a owl:Class, + nmdc:LibraryTypeEnum ; + rdfs:label "RNA" . - a owl:Class, - ; - rdfs:label "sarasota shutters" . + a owl:Class, + nmdc:LightTypeEnum ; + rdfs:label "desk lamp" . - a owl:Class, - ; - rdfs:label "slatted aluminum" . + a owl:Class, + nmdc:LightTypeEnum ; + rdfs:label "electric light" . - a owl:Class, - ; - rdfs:label "solid aluminum awning" . + a owl:Class, + nmdc:LightTypeEnum ; + rdfs:label "flourescent lights" . - a owl:Class, - ; - rdfs:label "sun screen" . + a owl:Class, + nmdc:LightTypeEnum ; + rdfs:label "natural light" . - a owl:Class, - ; - rdfs:label "tree" . + a owl:Class, + nmdc:LightTypeEnum ; + rdfs:label "none" . - a owl:Class, - ; - rdfs:label "trellis" . + a owl:Class, + nmdc:LithologyEnum ; + rdfs:label "Basement" . - a owl:Class, - ; - rdfs:label "venetian awning" . + a owl:Class, + nmdc:LithologyEnum ; + rdfs:label "Chalk" . - a owl:Class, - ; - rdfs:label "A horizon" . + a owl:Class, + nmdc:LithologyEnum ; + rdfs:label "Chert" . - a owl:Class, - ; - rdfs:label "B horizon" . + a owl:Class, + nmdc:LithologyEnum ; + rdfs:label "Coal" . - a owl:Class, - ; - rdfs:label "C horizon" . + a owl:Class, + nmdc:LithologyEnum ; + rdfs:label "Conglomerate" . - a owl:Class, - ; - rdfs:label "E horizon" . + a owl:Class, + nmdc:LithologyEnum ; + rdfs:label "Diatomite" . - a owl:Class, - ; - rdfs:label "M horizon" . + a owl:Class, + nmdc:LithologyEnum ; + rdfs:label "Dolomite" . - a owl:Class, - ; - rdfs:label "O horizon" . + a owl:Class, + nmdc:LithologyEnum ; + rdfs:label "Limestone" . - a owl:Class, - ; - rdfs:label "Permafrost" . + a owl:Class, + nmdc:LithologyEnum ; + rdfs:label "Sandstone" . - a owl:Class, - ; - rdfs:label "R layer" . + a owl:Class, + nmdc:LithologyEnum ; + rdfs:label "Shale" . - a owl:Class, - ; - rdfs:label "as built" . + a owl:Class, + nmdc:LithologyEnum ; + rdfs:label "Siltstone" . - a owl:Class, - ; - rdfs:label "bid" . + a owl:Class, + nmdc:LithologyEnum ; + rdfs:label "Volcanic" . - a owl:Class, - ; - rdfs:label "construction" . + a owl:Class, + nmdc:LithologyEnum ; + rdfs:label "other" . - a owl:Class, - ; - rdfs:label "design" . +nmdc:MaterialContainer a owl:Class, + linkml:ClassDefinition ; + rdfs:label "MaterialContainer" ; + dcterms:title "Material container" ; + skos:inScheme nmdc:sample_prep . - a owl:Class, - ; - rdfs:label "operation" . + a owl:Class, + nmdc:MechStrucEnum ; + rdfs:label "boat" . - a owl:Class, - ; - rdfs:label "photos" . + a owl:Class, + nmdc:MechStrucEnum ; + rdfs:label "bus" . - a owl:Class, - ; - rdfs:label "Fluvioldeltaic" . + a owl:Class, + nmdc:MechStrucEnum ; + rdfs:label "car" . - a owl:Class, - ; - rdfs:label "Fluviomarine" . + a owl:Class, + nmdc:MechStrucEnum ; + rdfs:label "carriage" . - a owl:Class, - ; - rdfs:label "Lacustine" . + a owl:Class, + nmdc:MechStrucEnum ; + rdfs:label "coach" . - a owl:Class, - ; - rdfs:label "Marine" . + a owl:Class, + nmdc:MechStrucEnum ; + rdfs:label "elevator" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:MechStrucEnum ; + rdfs:label "escalator" . - a owl:Class, - ; - rdfs:label "Archean" . + a owl:Class, + nmdc:MechStrucEnum ; + rdfs:label "subway" . - a owl:Class, - ; - rdfs:label "Cambrian" . + a owl:Class, + nmdc:MechStrucEnum ; + rdfs:label "train" . - a owl:Class, - ; - rdfs:label "Carboniferous" . +nmdc:MetagenomeAnnotationActivity a owl:Class, + linkml:ClassDefinition ; + rdfs:label "MetagenomeAnnotationActivity" ; + 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 ], + nmdc:WorkflowExecutionActivity ; + skos:definition "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs" ; + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - ; - rdfs:label "Cenozoic" . + a owl:Class, + nmdc:OccupDocumentEnum ; + rdfs:label "automated count" . - a owl:Class, - ; - rdfs:label "Cretaceous" . + a owl:Class, + nmdc:OccupDocumentEnum ; + rdfs:label "estimate" . - a owl:Class, - ; - rdfs:label "Devonian" . + a owl:Class, + nmdc:OccupDocumentEnum ; + rdfs:label "manual count" . - a owl:Class, - ; - rdfs:label "Jurassic" . + a owl:Class, + nmdc:OccupDocumentEnum ; + rdfs:label "videos" . - a owl:Class, - ; - rdfs:label "Mesozoic" . + a owl:Class, + nmdc:OrganismCountEnum ; + rdfs:label "ATP" . - a owl:Class, - ; - rdfs:label "Neogene" . + a owl:Class, + nmdc:OrganismCountEnum ; + rdfs:label "MPN" . - a owl:Class, - ; - rdfs:label "Ordovician" . + a owl:Class, + nmdc:OrganismCountEnum ; + rdfs:label "other" . - a owl:Class, - ; - rdfs:label "Paleogene" . + a owl:Class, + nmdc:OxyStatSampEnum ; + rdfs:label "aerobic" . - a owl:Class, - ; - rdfs:label "Paleozoic" . + a owl:Class, + nmdc:OxyStatSampEnum ; + rdfs:label "anaerobic" . - a owl:Class, - ; - rdfs:label "Permian" . + a owl:Class, + nmdc:OxyStatSampEnum ; + rdfs:label "other" . - a owl:Class, - ; - rdfs:label "Precambrian" . + a owl:Class, + nmdc:PlantGrowthMedEnum ; + rdfs:label "other artificial liquid medium" . - a owl:Class, - ; - rdfs:label "Proterozoic" . + a owl:Class, + nmdc:PlantGrowthMedEnum ; + rdfs:label "other artificial solid medium" . - a owl:Class, - ; - rdfs:label "Silurian" . + a owl:Class, + nmdc:PlantGrowthMedEnum ; + rdfs:label "peat moss" . - a owl:Class, - ; - rdfs:label "Triassic" . + a owl:Class, + nmdc:PlantGrowthMedEnum ; + rdfs:label "perlite" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:PlantGrowthMedEnum ; + rdfs:label "pumice" . - a owl:Class, - ; - rdfs:label "Type I" . + a owl:Class, + nmdc:PlantGrowthMedEnum ; + rdfs:label "sand" . - a owl:Class, - ; - rdfs:label "Type II" . + a owl:Class, + nmdc:PlantGrowthMedEnum ; + rdfs:label "soil" . - a owl:Class, - ; - rdfs:label "Type III" . + a owl:Class, + nmdc:PlantGrowthMedEnum ; + rdfs:label "vermiculite" . - a owl:Class, - ; - rdfs:label "Type IV" . + a owl:Class, + nmdc:PlantGrowthMedEnum ; + rdfs:label "water" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Androdioecious" . - a owl:Class, - ; - rdfs:label "Biosilicieous" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Androecious" . - a owl:Class, - ; - rdfs:label "Carbonate" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Androgynomonoecious" . - a owl:Class, - ; - rdfs:label "Clastic" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Androgynous" . - a owl:Class, - ; - rdfs:label "Coal" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Andromonoecious" . - a owl:Class, - ; - rdfs:label "other" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Bisexual" . - a owl:Class, - ; - rdfs:label "basement" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Dichogamous" . - a owl:Class, - ; - rdfs:label "crawlspace" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Diclinous" . - a owl:Class, - ; - rdfs:label "slab on grade" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Dioecious" . - a owl:Class, - ; - rdfs:label "biocides" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Gynodioecious" . - a owl:Class, - ; - rdfs:label "biological contaminants" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Gynoecious" . - a owl:Class, - ; - rdfs:label "dust" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Gynomonoecious" . - a owl:Class, - ; - rdfs:label "nutrients" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Hermaphroditic" . - a owl:Class, - ; - rdfs:label "organic matter" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Imperfect" . - a owl:Class, - ; - rdfs:label "particulate matter" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Monoclinous" . - a owl:Class, - ; - rdfs:label "radon" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Monoecious" . - a owl:Class, - ; - rdfs:label "volatile organic compounds" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Perfect" . - a owl:Class, - ; - rdfs:label "adobe" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Polygamodioecious" . - a owl:Class, - ; - rdfs:label "carpet" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Polygamomonoecious" . - a owl:Class, - ; - rdfs:label "cinder blocks" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Polygamous" . - a owl:Class, - ; - rdfs:label "concrete" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Protandrous" . - a owl:Class, - ; - rdfs:label "glass" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Protogynous" . - a owl:Class, - ; - rdfs:label "hay bales" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Subandroecious" . - a owl:Class, - ; - rdfs:label "metal" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Subdioecious" . - a owl:Class, - ; - rdfs:label "paint" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Subgynoecious" . - a owl:Class, - ; - rdfs:label "plastic" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Synoecious" . - a owl:Class, - ; - rdfs:label "stainless steel" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Trimonoecious" . - a owl:Class, - ; - rdfs:label "stone" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Trioecious" . - a owl:Class, - ; - rdfs:label "stucco" . + a owl:Class, + nmdc:PlantSexEnum ; + rdfs:label "Unisexual" . - a owl:Class, - ; - rdfs:label "tile" . + a owl:Class, + nmdc:ProfilePositionEnum ; + rdfs:label "backslope" . - a owl:Class, - ; - rdfs:label "vinyl" . + a owl:Class, + nmdc:ProfilePositionEnum ; + rdfs:label "footslope" . - a owl:Class, - ; - rdfs:label "wood" . + a owl:Class, + nmdc:ProfilePositionEnum ; + rdfs:label "shoulder" . - a owl:Class, - ; - rdfs:label "ebb tide" . + a owl:Class, + nmdc:ProfilePositionEnum ; + rdfs:label "summit" . - a owl:Class, - ; - rdfs:label "flood tide" . + a owl:Class, + nmdc:ProfilePositionEnum ; + rdfs:label "toeslope" . - a owl:Class, - ; - rdfs:label "high tide" . + a owl:Class, + nmdc:QuadPosEnum ; + rdfs:label "East side" . - a owl:Class, - ; - rdfs:label "low tide" . + a owl:Class, + nmdc:QuadPosEnum ; + rdfs:label "North side" . - a owl:Class, - ; - rdfs:label "chisel" . + a owl:Class, + nmdc:QuadPosEnum ; + rdfs:label "South side" . - a owl:Class, - ; - rdfs:label "cutting disc" . + a owl:Class, + nmdc:QuadPosEnum ; + rdfs:label "West side" . - a owl:Class, - ; - rdfs:label "disc plough" . +nmdc:ReactionParticipant a owl:Class, + linkml:ClassDefinition ; + rdfs:label "ReactionParticipant" ; + skos:definition "Instances of this link a reaction to a chemical entity participant" ; + skos:inScheme nmdc:annotation . - a owl:Class, - ; - rdfs:label "drill" . + a owl:Class, + nmdc:RelSampLocEnum ; + rdfs:label "center of car" . - a owl:Class, - ; - rdfs:label "mouldboard" . + a owl:Class, + nmdc:RelSampLocEnum ; + rdfs:label "edge of car" . - a owl:Class, - ; - rdfs:label "ridge till" . + a owl:Class, + nmdc:RelSampLocEnum ; + rdfs:label "under a seat" . - a owl:Class, - ; - rdfs:label "strip tillage" . + a owl:Class, + nmdc:RnaSampleFormatEnum ; + rdfs:label "10 mM Tris-HCl" . - a owl:Class, - ; - rdfs:label "tined" . + a owl:Class, + nmdc:RnaSampleFormatEnum ; + rdfs:label "DNAStable" . - a owl:Class, - ; - rdfs:label "zonal tillage" . + a owl:Class, + nmdc:RnaSampleFormatEnum ; + rdfs:label "Ethanol" . - a owl:Class, - ; - rdfs:label "green" . + a owl:Class, + nmdc:RnaSampleFormatEnum ; + rdfs:label "Gentegra-DNA" . - a owl:Class, - ; - rdfs:label "orange" . + a owl:Class, + nmdc:RnaSampleFormatEnum ; + rdfs:label "Gentegra-RNA" . - a owl:Class, - ; - rdfs:label "red" . + a owl:Class, + nmdc:RnaSampleFormatEnum ; + rdfs:label "Low EDTA TE" . - a owl:Class, - ; - rdfs:label "forest hills" . + a owl:Class, + nmdc:RnaSampleFormatEnum ; + rdfs:label "MDA reaction buffer" . - a owl:Class, - ; - rdfs:label "riverside" . + a owl:Class, + nmdc:RnaSampleFormatEnum ; + rdfs:label "PBS" . - a owl:Class, - ; - rdfs:label "south station above ground" . + a owl:Class, + nmdc:RnaSampleFormatEnum ; + rdfs:label "Pellet" . - a owl:Class, - ; - rdfs:label "south station amtrak" . + a owl:Class, + nmdc:RnaSampleFormatEnum ; + rdfs:label "RNAStable" . - a owl:Class, - ; - rdfs:label "south station underground" . + a owl:Class, + nmdc:RnaSampleFormatEnum ; + rdfs:label "TE" . - a owl:Class, - ; - rdfs:label "downtown" . + a owl:Class, + nmdc:RnaSampleFormatEnum ; + rdfs:label "Water" . - a owl:Class, - ; - rdfs:label "end" . + a owl:Class, + nmdc:RoomCondtEnum ; + rdfs:label "damaged" . - a owl:Class, - ; - rdfs:label "mid" . + a owl:Class, + nmdc:RoomCondtEnum ; + rdfs:label "needs repair" . - a owl:Class, - ; - rdfs:label "3D scans" . + a owl:Class, + nmdc:RoomCondtEnum ; + rdfs:label "new" . - a owl:Class, - ; - rdfs:label "commonly of the building" . + a owl:Class, + nmdc:RoomCondtEnum ; + rdfs:label "rupture" . - a owl:Class, - ; - rdfs:label "equipment" . + a owl:Class, + nmdc:RoomCondtEnum ; + rdfs:label "visible signs of mold/mildew" . - a owl:Class, - ; - rdfs:label "interiors" . + a owl:Class, + nmdc:RoomCondtEnum ; + rdfs:label "visible wear" . - a owl:Class, - ; - rdfs:label "photos" . + a owl:Class, + nmdc:RoomConnectedEnum ; + rdfs:label "attic" . - a owl:Class, - ; - rdfs:label "site context (adjacent buildings, vegetation, terrain, streets)" . + a owl:Class, + nmdc:RoomConnectedEnum ; + rdfs:label "bathroom" . - a owl:Class, - ; - rdfs:label "videos" . + a owl:Class, + nmdc:RoomConnectedEnum ; + rdfs:label "closet" . - a owl:Class, - ; - rdfs:label "fire resistive" . + a owl:Class, + nmdc:RoomConnectedEnum ; + rdfs:label "conference room" . - a owl:Class, - ; - rdfs:label "frame construction" . + a owl:Class, + nmdc:RoomConnectedEnum ; + rdfs:label "elevator" . - a owl:Class, - ; - rdfs:label "joisted masonry" . + a owl:Class, + nmdc:RoomConnectedEnum ; + rdfs:label "examining room" . - a owl:Class, - ; - rdfs:label "light noncombustible" . + a owl:Class, + nmdc:RoomConnectedEnum ; + rdfs:label "hallway" . - a owl:Class, - ; - rdfs:label "masonry noncombustible" . + a owl:Class, + nmdc:RoomConnectedEnum ; + rdfs:label "kitchen" . - a owl:Class, - ; - rdfs:label "modified fire resistive" . + a owl:Class, + nmdc:RoomConnectedEnum ; + rdfs:label "mail room" . - a owl:Class, - ; - rdfs:label "acoustical treatment" . + a owl:Class, + nmdc:RoomConnectedEnum ; + rdfs:label "office" . - a owl:Class, - ; - rdfs:label "gypsum board" . + a owl:Class, + nmdc:RoomConnectedEnum ; + rdfs:label "stairwell" . - a owl:Class, - ; - rdfs:label "gypsum plaster" . + a owl:Class, + nmdc:RoomLocEnum ; + rdfs:label "corner room" . - a owl:Class, - ; - rdfs:label "masonry" . + a owl:Class, + nmdc:RoomLocEnum ; + rdfs:label "exterior wall" . - a owl:Class, - ; - rdfs:label "metal" . + a owl:Class, + nmdc:RoomLocEnum ; + rdfs:label "interior room" . - a owl:Class, - ; - rdfs:label "plaster" . + a owl:Class, + nmdc:RoomSampPosEnum ; + rdfs:label "center" . - a owl:Class, - ; - rdfs:label "stone facing" . + a owl:Class, + nmdc:RoomSampPosEnum ; + rdfs:label "east corner" . - a owl:Class, - ; - rdfs:label "terrazzo" . + a owl:Class, + nmdc:RoomSampPosEnum ; + rdfs:label "north corner" . - a owl:Class, - ; - rdfs:label "tile" . + a owl:Class, + nmdc:RoomSampPosEnum ; + rdfs:label "northeast corner" . - a owl:Class, - ; - rdfs:label "veneer plaster" . + a owl:Class, + nmdc:RoomSampPosEnum ; + rdfs:label "northwest corner" . - a owl:Class, - ; - rdfs:label "wood" . + a owl:Class, + nmdc:RoomSampPosEnum ; + rdfs:label "south corner" . - a owl:Class, - ; - rdfs:label "east" . + a owl:Class, + nmdc:RoomSampPosEnum ; + rdfs:label "southeast corner" . - a owl:Class, - ; - rdfs:label "north" . + a owl:Class, + nmdc:RoomSampPosEnum ; + rdfs:label "southwest corner" . - a owl:Class, - ; - rdfs:label "south" . + a owl:Class, + nmdc:RoomSampPosEnum ; + rdfs:label "west corner" . - a owl:Class, - ; - rdfs:label "west" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label ",restroom" . - a owl:Class, - ; - rdfs:label "fabric" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "attic" . - a owl:Class, - ; - rdfs:label "no treatment" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "auditorium" . - a owl:Class, - ; - rdfs:label "painted" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "bathroom" . - a owl:Class, - ; - rdfs:label "paneling" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "cafe" . - a owl:Class, - ; - rdfs:label "stucco" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "closet" . - a owl:Class, - ; - rdfs:label "wall paper" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "conference room" . - a owl:Class, - ; - rdfs:label "" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "data center" . - a owl:Class, - ; - rdfs:label "Santa-Fe texture" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "elevator" . - a owl:Class, - ; - rdfs:label "crows feet" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "examining room" . - a owl:Class, - ; - rdfs:label "crows-foot stomp" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "gymnasium" . - a owl:Class, - ; - rdfs:label "double skip" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "hallway" . - a owl:Class, - ; - rdfs:label "hawk and trowel" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "kitchen" . - a owl:Class, - ; - rdfs:label "knockdown" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "laboratory_dry" . - a owl:Class, - ; - rdfs:label "orange peel" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "laboratory_wet" . - a owl:Class, - ; - rdfs:label "popcorn" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "lobby" . - a owl:Class, - ; - rdfs:label "rosebud stomp" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "lockers" . - a owl:Class, - ; - rdfs:label "skip trowel" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "mail room" . - a owl:Class, - ; - rdfs:label "smooth" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "mechanical or electrical room" . - a owl:Class, - ; - rdfs:label "stomp knockdown" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "natatorium" . - a owl:Class, - ; - rdfs:label "swirl" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "open office" . - a owl:Class, - ; - rdfs:label "fountain" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "private office" . - a owl:Class, - ; - rdfs:label "pool" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "stairwell" . - a owl:Class, - ; - rdfs:label "standing feature" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "vestibule" . - a owl:Class, - ; - rdfs:label "stream" . + a owl:Class, + nmdc:RoomTypeEnum ; + rdfs:label "warehouse" . - a owl:Class, - ; - rdfs:label "waterfall" . + a owl:Class, + nmdc:SampCaptStatusEnum ; + rdfs:label "active surveillance in response to an outbreak" . - a owl:Class, - ; - rdfs:label "Friday" . + a owl:Class, + nmdc:SampCaptStatusEnum ; + rdfs:label "active surveillance not initiated by an outbreak" . - a owl:Class, - ; - rdfs:label "Monday" . + a owl:Class, + nmdc:SampCaptStatusEnum ; + rdfs:label "farm sample" . - a owl:Class, - ; - rdfs:label "Saturday" . + a owl:Class, + nmdc:SampCaptStatusEnum ; + rdfs:label "market sample" . - a owl:Class, - ; - rdfs:label "Sunday" . + a owl:Class, + nmdc:SampCaptStatusEnum ; + rdfs:label "other" . - a owl:Class, - ; - rdfs:label "Thursday" . + a owl:Class, + nmdc:SampCollectPointEnum ; + rdfs:label "drilling rig" . - a owl:Class, - ; - rdfs:label "Tuesday" . + a owl:Class, + nmdc:SampCollectPointEnum ; + rdfs:label "other" . - a owl:Class, - ; - rdfs:label "Wednesday" . + a owl:Class, + nmdc:SampCollectPointEnum ; + rdfs:label "separator" . - a owl:Class, - ; - rdfs:label "damaged" . + a owl:Class, + nmdc:SampCollectPointEnum ; + rdfs:label "storage tank" . - a owl:Class, - ; - rdfs:label "needs repair" . + a owl:Class, + nmdc:SampCollectPointEnum ; + rdfs:label "test well" . - a owl:Class, - ; - rdfs:label "new" . + a owl:Class, + nmdc:SampCollectPointEnum ; + rdfs:label "well" . - a owl:Class, - ; - rdfs:label "rupture" . + a owl:Class, + nmdc:SampCollectPointEnum ; + rdfs:label "wellhead" . - a owl:Class, - ; - rdfs:label "visible wear" . + a owl:Class, + nmdc:SampDisStageEnum ; + rdfs:label "dissemination" . - a owl:Class, - ; - rdfs:label "blinds" . + a owl:Class, + nmdc:SampDisStageEnum ; + rdfs:label "growth and reproduction" . - a owl:Class, - ; - rdfs:label "curtains" . + a owl:Class, + nmdc:SampDisStageEnum ; + rdfs:label "infection" . - a owl:Class, - ; - rdfs:label "none" . + a owl:Class, + nmdc:SampDisStageEnum ; + rdfs:label "inoculation" . - a owl:Class, - ; - rdfs:label "left" . + a owl:Class, + nmdc:SampDisStageEnum ; + rdfs:label "other" . - a owl:Class, - ; - rdfs:label "middle" . + a owl:Class, + nmdc:SampDisStageEnum ; + rdfs:label "penetration" . - a owl:Class, - ; - rdfs:label "right" . + a owl:Class, + nmdc:SampFloorEnum ; + rdfs:label "1st floor" . - a owl:Class, - ; - rdfs:label "east" . + a owl:Class, + nmdc:SampFloorEnum ; + rdfs:label "2nd floor" . - a owl:Class, - ; - rdfs:label "north" . + a owl:Class, + nmdc:SampFloorEnum ; + rdfs:label "basement" . - a owl:Class, - ; - rdfs:label "south" . + a owl:Class, + nmdc:SampFloorEnum ; + rdfs:label "lobby" . - a owl:Class, - ; - rdfs:label "west" . + a owl:Class, + nmdc:SampMdEnum ; + rdfs:label "DF" . - a owl:Class, - ; - rdfs:label "clad" . + a owl:Class, + nmdc:SampMdEnum ; + rdfs:label "KB" . - a owl:Class, - ; - rdfs:label "fiberglass" . + a owl:Class, + nmdc:SampMdEnum ; + rdfs:label "MSL" . - a owl:Class, - ; - rdfs:label "metal" . + a owl:Class, + nmdc:SampMdEnum ; + rdfs:label "RT" . - a owl:Class, - ; - rdfs:label "vinyl" . + a owl:Class, + nmdc:SampMdEnum ; + rdfs:label "other" . - a owl:Class, - ; - rdfs:label "wood" . + a owl:Class, + nmdc:SampSubtypeEnum ; + rdfs:label "biofilm" . - a owl:Class, - ; - rdfs:label "fixed window" . + a owl:Class, + nmdc:SampSubtypeEnum ; + rdfs:label "not applicable" . - a owl:Class, - ; - rdfs:label "horizontal sash window" . + a owl:Class, + nmdc:SampSubtypeEnum ; + rdfs:label "oil phase" . - a owl:Class, - ; - rdfs:label "single-hung sash window" . + a owl:Class, + nmdc:SampSubtypeEnum ; + rdfs:label "other" . - a owl:Class, - ; - rdfs:label "bottom" . + a owl:Class, + nmdc:SampSubtypeEnum ; + rdfs:label "water phase" . - a owl:Class, - ; - rdfs:label "high" . + a owl:Class, + nmdc:SampWeatherEnum ; + rdfs:label "clear sky" . - a owl:Class, - ; - rdfs:label "low" . + a owl:Class, + nmdc:SampWeatherEnum ; + rdfs:label "cloudy" . - a owl:Class, - ; - rdfs:label "middle" . + a owl:Class, + nmdc:SampWeatherEnum ; + rdfs:label "foggy" . - a owl:Class, - ; - rdfs:label "top" . + a owl:Class, + nmdc:SampWeatherEnum ; + rdfs:label "hail" . - a owl:Class, - nmdc:AnalysisTypeEnum ; - rdfs:label "metabolomics" . + a owl:Class, + nmdc:SampWeatherEnum ; + rdfs:label "rain" . - a owl:Class, - nmdc:AnalysisTypeEnum ; - rdfs:label "metagenomics" . + a owl:Class, + nmdc:SampWeatherEnum ; + rdfs:label "sleet" . - a owl:Class, - nmdc:AnalysisTypeEnum ; - rdfs:label "metaproteomics" . + a owl:Class, + nmdc:SampWeatherEnum ; + rdfs:label "snow" . - a owl:Class, - nmdc:AnalysisTypeEnum ; - rdfs:label "metatranscriptomics" . + a owl:Class, + nmdc:SampWeatherEnum ; + rdfs:label "sunny" . - a owl:Class, - nmdc:AnalysisTypeEnum ; - rdfs:label "natural organic matter" . + a owl:Class, + nmdc:SampWeatherEnum ; + rdfs:label "windy" . - a owl:Class, - nmdc:BiosampleCategoryEnum ; - rdfs:label "SIP" . + a owl:Class, + nmdc:SampleTypeEnum ; + rdfs:label "soil" . -nmdc:Bytes a owl:Class, - linkml:TypeDefinition ; - rdfs:label "bytes" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onDataRange xsd:long ; - owl:onProperty linkml:topValue ; - owl:qualifiedCardinality 1 ] . + a owl:Class, + nmdc:SampleTypeEnum ; + rdfs:label "water_extract_soil" . -nmdc:CollectingBiosamplesFromSite a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CollectingBiosamplesFromSite" ; - dcterms:title "Collecting Biosamples From Site" ; - rdfs:subClassOf [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc:Site ; - owl:onProperty nmdc:has_input ] [ a owl:Restriction ; - owl:onProperty nmdc:has_input ; - owl:someValuesFrom nmdc:Site ] ) ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc:Biosample ; - owl:onProperty nmdc:has_output ] [ a owl:Restriction ; - owl:onProperty nmdc:has_output ; - owl:someValuesFrom nmdc:Biosample ] ) ], - nmdc:PlannedProcess ; - skos:closeMatch . +nmdc:SamplingMethodEnum a owl:Class, + linkml:EnumDefinition ; + linkml:permissible_values . - a owl:Class, - nmdc:ContainerTypeEnum ; - rdfs:label "screw_top_conical" . + a owl:Class, + nmdc:SeasonUseEnum ; + rdfs:label "Fall" . - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Conceptualization" . + a owl:Class, + nmdc:SeasonUseEnum ; + rdfs:label "Spring" . - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Data curation" . + a owl:Class, + nmdc:SeasonUseEnum ; + rdfs:label "Summer" . - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Formal Analysis" . + a owl:Class, + nmdc:SeasonUseEnum ; + rdfs:label "Winter" . - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Funding acquisition" . + a owl:Class, + nmdc:SedimentTypeEnum ; + rdfs:label "biogenous" . - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Investigation" . + a owl:Class, + nmdc:SedimentTypeEnum ; + rdfs:label "cosmogenous" . - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Methodology" . + a owl:Class, + nmdc:SedimentTypeEnum ; + rdfs:label "hydrogenous" . - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Project administration" . + a owl:Class, + nmdc:SedimentTypeEnum ; + rdfs:label "lithogenous" . - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Resources" . + a owl:Class, + nmdc:ShadingDeviceCondEnum ; + rdfs:label "damaged" . - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Software" . + a owl:Class, + nmdc:ShadingDeviceCondEnum ; + rdfs:label "needs repair" . - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Supervision" . + a owl:Class, + nmdc:ShadingDeviceCondEnum ; + rdfs:label "new" . - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Validation" . + a owl:Class, + nmdc:ShadingDeviceCondEnum ; + rdfs:label "rupture" . - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Visualization" . + a owl:Class, + nmdc:ShadingDeviceCondEnum ; + rdfs:label "visible wear" . - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Writing original draft" . + a owl:Class, + nmdc:ShadingDeviceTypeEnum ; + rdfs:label "bahama shutters" . - a owl:Class, - nmdc:CreditEnum ; - rdfs:label "Writing review and editing" . + a owl:Class, + nmdc:ShadingDeviceTypeEnum ; + rdfs:label "exterior roll blind" . -nmdc:DataObject a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DataObject" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:Activity ; - owl:onProperty nmdc:was_generated_by ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:compression_type ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:url ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:FileTypeEnum ; - owl:onProperty nmdc:data_object_type ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty nmdc:name ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:md5_checksum ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:Bytes ; - owl:onProperty nmdc:file_size_bytes ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty dcterms:description ; - owl:qualifiedCardinality 1 ], - nmdc:NamedThing ; - skos:definition "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects." . + a owl:Class, + nmdc:ShadingDeviceTypeEnum ; + rdfs:label "gambrel awning" . - a owl:Class, - nmdc:DeviceTypeEnum ; - rdfs:label "orbital_shaker" . + a owl:Class, + nmdc:ShadingDeviceTypeEnum ; + rdfs:label "hood awning" . - a owl:Class, - nmdc:DeviceTypeEnum ; - rdfs:label "thermomixer" . + a owl:Class, + nmdc:ShadingDeviceTypeEnum ; + rdfs:label "porchroller awning" . - a owl:Class, - nmdc:DnaSampleFormatEnum ; - rdfs:label "10 mM Tris-HCl" . + a owl:Class, + nmdc:ShadingDeviceTypeEnum ; + rdfs:label "sarasota shutters" . - a owl:Class, - nmdc:DnaSampleFormatEnum ; - rdfs:label "DNAStable" . + a owl:Class, + nmdc:ShadingDeviceTypeEnum ; + rdfs:label "slatted aluminum" . - a owl:Class, - nmdc:DnaSampleFormatEnum ; - rdfs:label "Ethanol" . + a owl:Class, + nmdc:ShadingDeviceTypeEnum ; + rdfs:label "solid aluminum awning" . - a owl:Class, - nmdc:DnaSampleFormatEnum ; - rdfs:label "Gentegra-DNA" . + a owl:Class, + nmdc:ShadingDeviceTypeEnum ; + rdfs:label "sun screen" . - a owl:Class, - nmdc:DnaSampleFormatEnum ; - rdfs:label "Gentegra-RNA" . + a owl:Class, + nmdc:ShadingDeviceTypeEnum ; + rdfs:label "tree" . - a owl:Class, - nmdc:DnaSampleFormatEnum ; - rdfs:label "Low EDTA TE" . + a owl:Class, + nmdc:ShadingDeviceTypeEnum ; + rdfs:label "trellis" . - a owl:Class, - nmdc:DnaSampleFormatEnum ; - rdfs:label "MDA reaction buffer" . + a owl:Class, + nmdc:ShadingDeviceTypeEnum ; + rdfs:label "venetian awning" . - a owl:Class, - nmdc:DnaSampleFormatEnum ; - rdfs:label "PBS" . +nmdc:Site a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Site" ; + dcterms:title "Site" ; + rdfs:subClassOf [ 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 ], + nmdc:MaterialEntity ; + skos:inScheme nmdc:core ; + skos:note "BCO sample collection site ?" . - a owl:Class, - nmdc:DnaSampleFormatEnum ; - rdfs:label "Pellet" . + a owl:Class, + nmdc:SoilHorizonEnum ; + rdfs:label "A horizon" . - a owl:Class, - nmdc:DnaSampleFormatEnum ; - rdfs:label "RNAStable" . + a owl:Class, + nmdc:SoilHorizonEnum ; + rdfs:label "B horizon" . - a owl:Class, - nmdc:DnaSampleFormatEnum ; - rdfs:label "TE" . + a owl:Class, + nmdc:SoilHorizonEnum ; + rdfs:label "C horizon" . - a owl:Class, - nmdc:DnaSampleFormatEnum ; - rdfs:label "Water" . + a owl:Class, + nmdc:SoilHorizonEnum ; + rdfs:label "E horizon" . -nmdc:Extraction a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Extraction" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:ProcessingInstitutionEnum ; - owl:onProperty nmdc:processing_institution ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:has_input ] [ a owl:Restriction ; - owl:onProperty nmdc:has_input ; - owl:someValuesFrom nmdc:NamedThing ] ) ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:extraction_method ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QualityControlReport ; - owl:onProperty nmdc:quality_control_report ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:has_output ] [ a owl:Restriction ; - owl:onProperty nmdc:has_output ; - owl:someValuesFrom nmdc:NamedThing ] ) ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:ExtractionTargetEnum ; - owl:onProperty nmdc:extraction_target ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty nmdc:input_mass ], - nmdc:BiosampleProcessing ; - skos:definition "A material separation in which a desired component of an input material is separated from the remainder." ; - skos:exactMatch . + a owl:Class, + nmdc:SoilHorizonEnum ; + rdfs:label "M horizon" . - a owl:Class, - nmdc:ExtractionTargetEnum ; - rdfs:label "DNA" . + a owl:Class, + nmdc:SoilHorizonEnum ; + rdfs:label "O horizon" . - a owl:Class, - nmdc:ExtractionTargetEnum ; - rdfs:label "RNA" . + a owl:Class, + nmdc:SoilHorizonEnum ; + rdfs:label "Permafrost" . - a owl:Class, - nmdc:ExtractionTargetEnum ; - rdfs:label "metabolite" . + a owl:Class, + nmdc:SoilHorizonEnum ; + rdfs:label "R layer" . - a owl:Class, - nmdc:ExtractionTargetEnum ; - rdfs:label "protein" . + a owl:Class, + nmdc:SolventEnum ; + rdfs:label "deionized_water" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Annotation Amino Acid FASTA" . + a owl:Class, + nmdc:SpecificEnum ; + rdfs:label "as built" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Annotation Enzyme Commission" . + a owl:Class, + nmdc:SpecificEnum ; + rdfs:label "bid" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Annotation Info File" . + a owl:Class, + nmdc:SpecificEnum ; + rdfs:label "construction" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Annotation KEGG Orthology" . + a owl:Class, + nmdc:SpecificEnum ; + rdfs:label "design" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Annotation Statistics" . + a owl:Class, + nmdc:SpecificEnum ; + rdfs:label "operation" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Assembly AGP" . + a owl:Class, + nmdc:SpecificEnum ; + rdfs:label "photos" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Assembly Contigs" . + a owl:Class, + nmdc:SrDepEnvEnum ; + rdfs:label "Fluvioldeltaic" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Assembly Coverage BAM" . + a owl:Class, + nmdc:SrDepEnvEnum ; + rdfs:label "Fluviomarine" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Assembly Coverage Stats" . + a owl:Class, + nmdc:SrDepEnvEnum ; + rdfs:label "Lacustine" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Assembly Info File" . + a owl:Class, + nmdc:SrDepEnvEnum ; + rdfs:label "Marine" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Assembly Scaffolds" . + a owl:Class, + nmdc:SrDepEnvEnum ; + rdfs:label "other" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "CATH FunFams (Functional Families) Annotation GFF" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Archean" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "CRT Annotation GFF" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Cambrian" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Centrifuge Classification Report" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Carboniferous" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Centrifuge Krona Plot" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Cenozoic" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Centrifuge Taxonomic Classification" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Cretaceous" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Centrifuge output report file" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Devonian" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "CheckM Statistics" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Jurassic" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Clusters of Orthologous Groups (COG) Annotation GFF" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Mesozoic" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Contig Mapping File" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Neogene" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Crispr Terms" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Ordovician" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Direct Infusion FT ICR-MS Raw Data" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Paleogene" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Error Corrected Reads" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Paleozoic" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "FT ICR-MS Analysis Results" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Permian" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Filtered Sequencing Reads" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Precambrian" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Functional Annotation GFF" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Proterozoic" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "GC-MS Metabolomics Results" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Silurian" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "GOTTCHA2 Classification Report" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "Triassic" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "GOTTCHA2 Krona Plot" . + a owl:Class, + nmdc:SrGeolAgeEnum ; + rdfs:label "other" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "GOTTCHA2 Report Full" . + a owl:Class, + nmdc:SrKerogTypeEnum ; + rdfs:label "Type I" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "GTDBTK Archaeal Summary" . + a owl:Class, + nmdc:SrKerogTypeEnum ; + rdfs:label "Type II" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "GTDBTK Bacterial Summary" . + a owl:Class, + nmdc:SrKerogTypeEnum ; + rdfs:label "Type III" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Gene Phylogeny tsv" . + a owl:Class, + nmdc:SrKerogTypeEnum ; + rdfs:label "Type IV" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Genemark Annotation GFF" . + a owl:Class, + nmdc:SrKerogTypeEnum ; + rdfs:label "other" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "KO_EC Annotation GFF" . + a owl:Class, + nmdc:SrLithologyEnum ; + rdfs:label "Biosilicieous" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Kraken2 Classification Report" . + a owl:Class, + nmdc:SrLithologyEnum ; + rdfs:label "Carbonate" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Kraken2 Krona Plot" . + a owl:Class, + nmdc:SrLithologyEnum ; + rdfs:label "Clastic" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Kraken2 Taxonomic Classification" . + a owl:Class, + nmdc:SrLithologyEnum ; + rdfs:label "Coal" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Metagenome Bins" . + a owl:Class, + nmdc:SrLithologyEnum ; + rdfs:label "other" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Metagenome Bins Compression File" . + a owl:Class, + nmdc:StatusEnum ; + rdfs:label "fail" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Metagenome Bins Info File" . + a owl:Class, + nmdc:StatusEnum ; + rdfs:label "pass" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Metagenome Raw Read 1" . + a owl:Class, + nmdc:StudyCategoryEnum ; + rdfs:label "consortium" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Metagenome Raw Read 2" . + a owl:Class, + nmdc:StudyCategoryEnum ; + rdfs:label "research_study" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Metagenome Raw Reads" . + a owl:Class, + nmdc:SubstructureTypeEnum ; + rdfs:label "basement" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Metaproteomics Workflow Statistics" . + a owl:Class, + nmdc:SubstructureTypeEnum ; + rdfs:label "crawlspace" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Misc Annotation GFF" . + a owl:Class, + nmdc:SubstructureTypeEnum ; + rdfs:label "slab on grade" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Peptide Report" . + a owl:Class, + nmdc:SurfAirContEnum ; + rdfs:label "biocides" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Pfam Annotation GFF" . + a owl:Class, + nmdc:SurfAirContEnum ; + rdfs:label "biological contaminants" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Prodigal Annotation GFF" . + a owl:Class, + nmdc:SurfAirContEnum ; + rdfs:label "dust" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Product Names" . + a owl:Class, + nmdc:SurfAirContEnum ; + rdfs:label "nutrients" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Protein Report" . + a owl:Class, + nmdc:SurfAirContEnum ; + rdfs:label "organic matter" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "QC Statistics" . + a owl:Class, + nmdc:SurfAirContEnum ; + rdfs:label "particulate matter" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "QC Statistics Extended" . + a owl:Class, + nmdc:SurfAirContEnum ; + rdfs:label "radon" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "QC non-rRNA R1" . + a owl:Class, + nmdc:SurfAirContEnum ; + rdfs:label "volatile organic compounds" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "QC non-rRNA R2" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "adobe" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "RFAM Annotation GFF" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "carpet" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Raw Compressed Metagenome Interleaved Paired-End Reads" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "cinder blocks" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Read Based Analysis Info File" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "concrete" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Read Count and RPKM" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "glass" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Read Filtering Info File" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "hay bales" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "SMART Annotation GFF" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "metal" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "SUPERFam Annotation GFF" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "paint" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Scaffold Lineage tsv" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "plastic" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Structural Annotation GFF" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "stainless steel" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Structural Annotation Stats Json" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "stone" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "TIGRFam Annotation GFF" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "stucco" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "TMRNA Annotation GFF" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "tile" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "TRNA Annotation GFF" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "vinyl" . - a owl:Class, - nmdc:FileTypeEnum ; - rdfs:label "Unfiltered Metaproteomics Results" . + a owl:Class, + nmdc:SurfMaterialEnum ; + rdfs:label "wood" . -nmdc:ImageValue a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ImageValue" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:display_order ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty dcterms:description ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:url ], - nmdc:AttributeValue ; - skos:definition "An attribute value representing an image." . + a owl:Class, + nmdc:TidalStageEnum ; + rdfs:label "ebb tide" . -nmdc:InstrumentValue a owl:Class, - linkml:ClassDefinition ; - rdfs:label "InstrumentValue" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:Unit ; - owl:onProperty nmdc:has_unit ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:has_numeric_value ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:instrument_name ], - nmdc:AttributeValue . + a owl:Class, + nmdc:TidalStageEnum ; + rdfs:label "flood tide" . - a owl:Class, - nmdc:JgiContTypeEnum ; - rdfs:label "plate" . + a owl:Class, + nmdc:TidalStageEnum ; + rdfs:label "high tide" . - a owl:Class, - nmdc:JgiContTypeEnum ; - rdfs:label "tube" . + a owl:Class, + nmdc:TidalStageEnum ; + rdfs:label "low tide" . -nmdc:LanguageCode a owl:Class, - linkml:TypeDefinition ; - rdfs:label "language code" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onDataRange xsd:language ; - owl:onProperty linkml:topValue ; - owl:qualifiedCardinality 1 ] . + a owl:Class, + nmdc:TillageEnum ; + rdfs:label "chisel" . -nmdc:LibraryPreparation a owl:Class, - linkml:ClassDefinition ; - rdfs:label "LibraryPreparation" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:pcr_cycles ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:library_preparation_kit ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:LibraryTypeEnum ; - owl:onProperty nmdc:library_type ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:has_output ] [ a owl:Restriction ; - owl:onProperty nmdc:has_output ; - owl:someValuesFrom nmdc:NamedThing ] ) ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:has_input ] [ a owl:Restriction ; - owl:onProperty nmdc:has_input ; - owl:someValuesFrom nmdc:NamedThing ] ) ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:ProcessingInstitutionEnum ; - owl:onProperty nmdc:processing_institution ], - nmdc:BiosampleProcessing ; - skos:altLabel "LibraryConstruction" ; - skos:closeMatch . + a owl:Class, + nmdc:TillageEnum ; + rdfs:label "cutting disc" . - a owl:Class, - nmdc:LibraryTypeEnum ; - rdfs:label "DNA" . + a owl:Class, + nmdc:TillageEnum ; + rdfs:label "disc plough" . - a owl:Class, - nmdc:LibraryTypeEnum ; - rdfs:label "RNA" . + a owl:Class, + nmdc:TillageEnum ; + rdfs:label "drill" . -nmdc:MagsAnalysisActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MagsAnalysisActivity" ; - dcterms:title "Metagenome-Assembled Genome analysis activity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:unbinned_contig_num ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:low_depth_contig_num ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MagBin ; - owl:onProperty nmdc:mags_list ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:binned_contig_num ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:input_contig_num ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:too_short_contig_num ], - nmdc:WorkflowExecutionActivity ; - skos:definition "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes" . + a owl:Class, + nmdc:TillageEnum ; + rdfs:label "mouldboard" . -nmdc:MetabolomicsAnalysisActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MetabolomicsAnalysisActivity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetaboliteQuantification ; - owl:onProperty nmdc:has_metabolite_quantifications ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:has_calibration ], - nmdc:WorkflowExecutionActivity . + a owl:Class, + nmdc:TillageEnum ; + rdfs:label "ridge till" . -nmdc:MetagenomeAssembly a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MetagenomeAssembly" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:gc_std ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:insdc_assembly_identifiers ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_logsum ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_n50 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:ctg_max ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:contigs ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:ctg_n50 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_pct_gt50k ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:ctg_logsum ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:gc_avg ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_max ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:ctg_l50 ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_bp ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:num_aligned_reads ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:ctg_powsum ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:contig_bp ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:num_input_reads ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_l50 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_l90 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaffolds ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_l_gt50k ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:asm_score ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_n90 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:gap_pct ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:ctg_l90 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_n_gt50k ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:ctg_n90 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:scaf_powsum ], - nmdc:WorkflowExecutionActivity ; - skos:definition "A workflow execution activity that converts sequencing reads into an assembled metagenome." . + a owl:Class, + nmdc:TillageEnum ; + rdfs:label "strip tillage" . -nmdc:MetagenomeSequencingActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MetagenomeSequencingActivity" ; - dcterms:title "Metagenome sequencing activity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - nmdc:WorkflowExecutionActivity ; - skos:definition "Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data." . + a owl:Class, + nmdc:TillageEnum ; + rdfs:label "tined" . -nmdc:MetaproteomicsAnalysisActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MetaproteomicsAnalysisActivity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:Instrument ; - owl:onProperty nmdc:used ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:PeptideQuantification ; - owl:onProperty nmdc:has_peptide_quantifications ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - nmdc:WorkflowExecutionActivity . + a owl:Class, + nmdc:TillageEnum ; + rdfs:label "zonal tillage" . -nmdc:MetatranscriptomeActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MetatranscriptomeActivity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:type ], - nmdc:WorkflowExecutionActivity ; - skos:definition "A metatranscriptome activity that e.g. pools assembly and annotation activity." . + a owl:Class, + nmdc:TrainLineEnum ; + rdfs:label "green" . -nmdc:NomAnalysisActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NomAnalysisActivity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:used ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:has_calibration ], - nmdc:WorkflowExecutionActivity . + a owl:Class, + nmdc:TrainLineEnum ; + rdfs:label "orange" . -nmdc:OmicsProcessing a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OmicsProcessing" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:PersonValue ; - owl:onProperty nmdc:principal_investigator ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:mod_date ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty dcterms:isPartOf ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:add_date ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:instrument_name ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; - owl:onProperty nmdc:gold_sequencing_project_identifiers ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:has_input ] [ a owl:Restriction ; - owl:onProperty nmdc:has_input ; - owl:someValuesFrom nmdc:NamedThing ] ) ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:ControlledTermValue ; - owl:onProperty nmdc:omics_type ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:ncbi_project_name ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; - owl:onProperty nmdc:insdc_experiment_identifiers ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:ProcessingInstitutionEnum ; - owl:onProperty nmdc:processing_institution ], - nmdc:PlannedProcess ; - skos:altLabel "experiment", - "omics assay", - "sequencing project" ; - skos:broadMatch ISA:Assay, - ; - skos:definition "The methods and processes used to generate omics data from a biosample or organism." . + a owl:Class, + nmdc:TrainLineEnum ; + rdfs:label "red" . -nmdc:Pooling a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Pooling" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:has_input ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:has_output ], - nmdc:BiosampleProcessing ; - skos:definition "physical combination of several instances of like material." ; - skos:exactMatch . + a owl:Class, + nmdc:TrainStatLocEnum ; + rdfs:label "forest hills" . -nmdc:ProcessedSample a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ProcessedSample" ; - dcterms:title "Processed Sample" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; - owl:onProperty nmdc:external_database_identifiers ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:InstrumentValue ; - owl:onProperty nmdc:nucleic_acid_concentration ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:dna_concentration ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty nmdc:biomaterial_purity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:dna_absorb1 ], - nmdc:MaterialEntity . + a owl:Class, + nmdc:TrainStatLocEnum ; + rdfs:label "riverside" . -nmdc:Reaction a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Reaction" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty nmdc:is_balanced ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty nmdc:is_diastereoselective ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:smarts_string ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:direction ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ReactionParticipant ; - owl:onProperty nmdc:left_participants ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty nmdc:is_transport ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty nmdc:is_stereo ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ReactionParticipant ; - owl:onProperty nmdc:right_participants ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty nmdc:is_fully_characterized ], - 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 . + a owl:Class, + nmdc:TrainStatLocEnum ; + rdfs:label "south station above ground" . -nmdc:ReadBasedTaxonomyAnalysisActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ReadBasedTaxonomyAnalysisActivity" ; - dcterms:title "Read based analysis activity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - nmdc:WorkflowExecutionActivity ; - skos:definition "A workflow execution activity that performs taxonomy classification using sequencing reads" . + a owl:Class, + nmdc:TrainStatLocEnum ; + rdfs:label "south station amtrak" . -nmdc:ReadQcAnalysisActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ReadQcAnalysisActivity" ; - dcterms:title "Read quality control analysis activity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:input_read_count ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:output_base_count ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:input_read_bases ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:output_read_count ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:input_base_count ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:output_read_bases ], - 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" . + a owl:Class, + nmdc:TrainStatLocEnum ; + rdfs:label "south station underground" . - a owl:Class, - nmdc:RnaSampleFormatEnum ; - rdfs:label "10 mM Tris-HCl" . + a owl:Class, + nmdc:TrainStopLocEnum ; + rdfs:label "downtown" . - a owl:Class, - nmdc:RnaSampleFormatEnum ; - rdfs:label "DNAStable" . + a owl:Class, + nmdc:TrainStopLocEnum ; + rdfs:label "end" . - a owl:Class, - nmdc:RnaSampleFormatEnum ; - rdfs:label "Ethanol" . + a owl:Class, + nmdc:TrainStopLocEnum ; + rdfs:label "mid" . - a owl:Class, - nmdc:RnaSampleFormatEnum ; - rdfs:label "Gentegra-DNA" . + a owl:Class, + nmdc:VisMediaEnum ; + rdfs:label "3D scans" . - a owl:Class, - nmdc:RnaSampleFormatEnum ; - rdfs:label "Gentegra-RNA" . + a owl:Class, + nmdc:VisMediaEnum ; + rdfs:label "commonly of the building" . - a owl:Class, - nmdc:RnaSampleFormatEnum ; - rdfs:label "Low EDTA TE" . + a owl:Class, + nmdc:VisMediaEnum ; + rdfs:label "equipment" . - a owl:Class, - nmdc:RnaSampleFormatEnum ; - rdfs:label "MDA reaction buffer" . + a owl:Class, + nmdc:VisMediaEnum ; + rdfs:label "interiors" . - a owl:Class, - nmdc:RnaSampleFormatEnum ; - rdfs:label "PBS" . + a owl:Class, + nmdc:VisMediaEnum ; + rdfs:label "photos" . - a owl:Class, - nmdc:RnaSampleFormatEnum ; - rdfs:label "Pellet" . + a owl:Class, + nmdc:VisMediaEnum ; + rdfs:label "site context (adjacent buildings, vegetation, terrain, streets)" . - a owl:Class, - nmdc:RnaSampleFormatEnum ; - rdfs:label "RNAStable" . + a owl:Class, + nmdc:VisMediaEnum ; + rdfs:label "videos" . - a owl:Class, - nmdc:RnaSampleFormatEnum ; - rdfs:label "TE" . + a owl:Class, + nmdc:WallConstTypeEnum ; + rdfs:label "fire resistive" . - a owl:Class, - nmdc:RnaSampleFormatEnum ; - rdfs:label "Water" . + a owl:Class, + nmdc:WallConstTypeEnum ; + rdfs:label "frame construction" . - a owl:Class, - nmdc:SampleTypeEnum ; - rdfs:label "soil" . + a owl:Class, + nmdc:WallConstTypeEnum ; + rdfs:label "joisted masonry" . - a owl:Class, - nmdc:SampleTypeEnum ; - rdfs:label "water_extract_soil" . + a owl:Class, + nmdc:WallConstTypeEnum ; + rdfs:label "light noncombustible" . - a owl:Class, - nmdc:SamplingMethodEnum ; - rdfs:label "weighing" . + a owl:Class, + nmdc:WallConstTypeEnum ; + rdfs:label "masonry noncombustible" . - a owl:Class, - nmdc:SolventEnum ; - rdfs:label "deionized_water" . + a owl:Class, + nmdc:WallConstTypeEnum ; + rdfs:label "modified fire resistive" . - a owl:Class, - nmdc:StatusEnum ; - rdfs:label "fail" . + a owl:Class, + nmdc:WallFinishMatEnum ; + rdfs:label "acoustical treatment" . - a owl:Class, - nmdc:StatusEnum ; - rdfs:label "pass" . + a owl:Class, + nmdc:WallFinishMatEnum ; + rdfs:label "gypsum board" . - a owl:Class, - nmdc:StudyCategoryEnum ; - rdfs:label "consortium" . + a owl:Class, + nmdc:WallFinishMatEnum ; + rdfs:label "gypsum plaster" . - a owl:Class, - nmdc:StudyCategoryEnum ; - rdfs:label "research_study" . + a owl:Class, + nmdc:WallFinishMatEnum ; + rdfs:label "masonry" . - a owl:Class, - nmdc:YesNoEnum ; - rdfs:label "no" . + a owl:Class, + nmdc:WallFinishMatEnum ; + rdfs:label "metal" . - a owl:Class, - nmdc:YesNoEnum ; - rdfs:label "yes" . + a owl:Class, + nmdc:WallFinishMatEnum ; + rdfs:label "plaster" . -nmdc:add_date a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "add_date" ; - rdfs:range linkml:String ; - skos:definition "The date on which the information was added to the database." . + a owl:Class, + nmdc:WallFinishMatEnum ; + rdfs:label "stone facing" . -nmdc:all_proteins a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "all_proteins" ; - rdfs:range nmdc:GeneProduct ; - skos:definition "the list of protein identifiers that are associated with the peptide sequence" . + a owl:Class, + nmdc:WallFinishMatEnum ; + rdfs:label "terrazzo" . -nmdc:applied_roles a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "applied_roles" ; - rdfs:domain nmdc:CreditAssociation ; - rdfs:range nmdc:CreditEnum ; - nmdc:display_hint "Identify all CRediT roles associated with this contributor. CRediT Information: https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/" . + a owl:Class, + nmdc:WallFinishMatEnum ; + rdfs:label "tile" . -nmdc:asm_score a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "asm_score" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "A score for comparing metagenomic assembly quality from same sample." . + a owl:Class, + nmdc:WallFinishMatEnum ; + rdfs:label "veneer plaster" . -nmdc:best_protein a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "best_protein" ; - rdfs:range nmdc:GeneProduct ; - skos:definition "the specific protein identifier most correctly associated with the peptide sequence" . + a owl:Class, + nmdc:WallFinishMatEnum ; + rdfs:label "wood" . -nmdc:contig_bp a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "contig_bp" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Total size in bp of all contigs." . + a owl:Class, + nmdc:WallLocEnum ; + rdfs:label "east" . -nmdc:contigs a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "contigs" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase" . + a owl:Class, + nmdc:WallLocEnum ; + rdfs:label "north" . -nmdc:ctg_l50 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ctg_l50" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length." . + a owl:Class, + nmdc:WallLocEnum ; + rdfs:label "south" . -nmdc:ctg_l90 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ctg_l90" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs." . + a owl:Class, + nmdc:WallLocEnum ; + rdfs:label "west" . -nmdc:ctg_logsum a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ctg_logsum" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Maximum contig length." . + a owl:Class, + nmdc:WallSurfTreatmentEnum ; + rdfs:label "fabric" . -nmdc:ctg_max a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ctg_max" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Maximum contig length." . + a owl:Class, + nmdc:WallSurfTreatmentEnum ; + rdfs:label "no treatment" . -nmdc:ctg_n50 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ctg_n50" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size." . + a owl:Class, + nmdc:WallSurfTreatmentEnum ; + rdfs:label "painted" . -nmdc:ctg_n90 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ctg_n90" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size." . + a owl:Class, + nmdc:WallSurfTreatmentEnum ; + rdfs:label "paneling" . -nmdc:ctg_powsum a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ctg_powsum" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25)." . + a owl:Class, + nmdc:WallSurfTreatmentEnum ; + rdfs:label "stucco" . -nmdc:dna_absorb1 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "dna_absorb1" ; - dcterms:title "DNA absorbance 260/280" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:biomaterial_purity ; - skos:definition "260/280 measurement of DNA sample purity" . + a owl:Class, + nmdc:WallSurfTreatmentEnum ; + rdfs:label "wall paper" . -nmdc:dna_concentration a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "dna_concentration" ; - dcterms:title "DNA concentration in ng/ul" ; - rdfs:range linkml:Float . + a owl:Class, + nmdc:WallTextureEnum ; + rdfs:label "" . -nmdc:ecosystem a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ecosystem" ; - rdfs:range linkml:String ; - 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." . + a owl:Class, + nmdc:WallTextureEnum ; + rdfs:label "Santa-Fe texture" . -nmdc:ecosystem_category a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ecosystem_category" ; - rdfs:range linkml:String ; - 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." . + a owl:Class, + nmdc:WallTextureEnum ; + rdfs:label "crows feet" . -nmdc:ecosystem_subtype a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ecosystem_subtype" ; - rdfs:range linkml:String ; - 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." . + a owl:Class, + nmdc:WallTextureEnum ; + rdfs:label "crows-foot stomp" . -nmdc:ecosystem_type a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ecosystem_type" ; - rdfs:range linkml:String ; - 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." . + a owl:Class, + nmdc:WallTextureEnum ; + rdfs:label "double skip" . -nmdc:emsl_identifiers a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "emsl_identifiers" ; - rdfs:range linkml:String . + a owl:Class, + nmdc:WallTextureEnum ; + rdfs:label "hawk and trowel" . -nmdc:ended_at_time a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ended_at_time" ; - rdfs:range linkml:String ; - skos:exactMatch prov:endedAtTime . + a owl:Class, + nmdc:WallTextureEnum ; + rdfs:label "knockdown" . -nmdc:gap_pct a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gap_pct" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "The gap size percentage of all scaffolds." . + a owl:Class, + nmdc:WallTextureEnum ; + rdfs:label "orange peel" . -nmdc:gc_avg a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gc_avg" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Average of GC content of all contigs." . + a owl:Class, + nmdc:WallTextureEnum ; + rdfs:label "popcorn" . -nmdc:gc_std a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gc_std" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Standard deviation of GC content of all contigs." . + a owl:Class, + nmdc:WallTextureEnum ; + rdfs:label "rosebud stomp" . -nmdc:gff_coordinate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gff_coordinate" ; - rdfs:range linkml:Integer ; - skos:definition "A positive 1-based integer coordinate indicating start or end" . + a owl:Class, + nmdc:WallTextureEnum ; + rdfs:label "skip trowel" . -nmdc:gold_analysis_project_identifiers a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gold_analysis_project_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:analysis_identifiers, - nmdc:gold_identifiers ; - skos:definition "identifiers for corresponding analysis project in GOLD" . + a owl:Class, + nmdc:WallTextureEnum ; + rdfs:label "smooth" . -nmdc:habitat a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "habitat" ; - rdfs:range linkml:String . + a owl:Class, + nmdc:WallTextureEnum ; + rdfs:label "stomp knockdown" . -nmdc:has_calibration a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "has_calibration" ; - rdfs:range linkml:String ; - skos:definition "A reference to a file that holds calibration information." . + a owl:Class, + nmdc:WallTextureEnum ; + rdfs:label "swirl" . -nmdc:has_participants a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "has_participants" ; - rdfs:range linkml:String ; - skos:exactMatch RO:0000057 . + a owl:Class, + nmdc:WaterFeatTypeEnum ; + rdfs:label "fountain" . -nmdc:has_unit a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "has_unit" ; - rdfs:range nmdc:Unit ; - skos:altLabel "scale" ; - skos:definition "Links a QuantityValue to a unit" ; - skos:exactMatch , - . + a owl:Class, + nmdc:WaterFeatTypeEnum ; + rdfs:label "pool" . -nmdc:insdc_assembly_identifiers a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "insdc_assembly_identifiers" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf nmdc:assembly_identifiers, - nmdc:insdc_identifiers . + a owl:Class, + nmdc:WaterFeatTypeEnum ; + rdfs:label "standing feature" . -nmdc:instrument_name a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "instrument_name" ; - rdfs:range linkml:String ; - skos:definition "The name of the instrument that was used for processing the sample." . + a owl:Class, + nmdc:WaterFeatTypeEnum ; + rdfs:label "stream" . -nmdc:material_input a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "material_input" ; - dcterms:title "material input" ; - rdfs:range nmdc:MaterialSample . + a owl:Class, + nmdc:WaterFeatTypeEnum ; + rdfs:label "waterfall" . -nmdc:mgnify_identifiers a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "mgnify_identifiers" ; - rdfs:range linkml:String . + a owl:Class, + nmdc:WeekdayEnum ; + rdfs:label "Friday" . -nmdc:mod_date a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "mod_date" ; - rdfs:range linkml:String ; - skos:definition "The last date on which the database information was modified." . + a owl:Class, + nmdc:WeekdayEnum ; + rdfs:label "Monday" . -nmdc:neon_identifiers a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "neon_identifiers" ; - rdfs:range linkml:String ; - skos:definition "identifiers for entities according to NEON" . + a owl:Class, + nmdc:WeekdayEnum ; + rdfs:label "Saturday" . -nmdc:num_aligned_reads a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "num_aligned_reads" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "The sequence count number of input reads aligned to assembled contigs." . + a owl:Class, + nmdc:WeekdayEnum ; + rdfs:label "Sunday" . -nmdc:num_input_reads a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "num_input_reads" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "The sequence count number of input reads for assembly." . + a owl:Class, + nmdc:WeekdayEnum ; + rdfs:label "Thursday" . -nmdc:principal_investigator a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "principal_investigator" ; - rdfs:range nmdc:PersonValue ; - rdfs:subPropertyOf nmdc:attribute ; - skos:altLabel "PI" ; - skos:definition "Principal Investigator who led the study and/or generated the dataset." . + a owl:Class, + nmdc:WeekdayEnum ; + rdfs:label "Tuesday" . -nmdc:scaf_bp a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "scaf_bp" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Total size in bp of all scaffolds." . + a owl:Class, + nmdc:WeekdayEnum ; + rdfs:label "Wednesday" . -nmdc:scaf_l50 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "scaf_l50" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length." . + a owl:Class, + nmdc:WindowCondEnum ; + rdfs:label "damaged" . -nmdc:scaf_l90 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "scaf_l90" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds." . + a owl:Class, + nmdc:WindowCondEnum ; + rdfs:label "needs repair" . -nmdc:scaf_l_gt50k a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "scaf_l_gt50k" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Total size in bp of all scaffolds greater than 50 KB." . + a owl:Class, + nmdc:WindowCondEnum ; + rdfs:label "new" . -nmdc:scaf_logsum a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "scaf_logsum" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase" . + a owl:Class, + nmdc:WindowCondEnum ; + rdfs:label "rupture" . -nmdc:scaf_max a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "scaf_max" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Maximum scaffold length." . + a owl:Class, + nmdc:WindowCondEnum ; + rdfs:label "visible wear" . -nmdc:scaf_n50 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "scaf_n50" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size." . + a owl:Class, + nmdc:WindowCoverEnum ; + rdfs:label "blinds" . -nmdc:scaf_n90 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "scaf_n90" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size." . + a owl:Class, + nmdc:WindowCoverEnum ; + rdfs:label "curtains" . -nmdc:scaf_n_gt50k a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "scaf_n_gt50k" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Total sequence count of scaffolds greater than 50 KB." . + a owl:Class, + nmdc:WindowCoverEnum ; + rdfs:label "none" . -nmdc:scaf_pct_gt50k a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "scaf_pct_gt50k" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Total sequence size percentage of scaffolds greater than 50 KB." . + a owl:Class, + nmdc:WindowHorizPosEnum ; + rdfs:label "left" . -nmdc:scaf_powsum a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "scaf_powsum" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25)." . + a owl:Class, + nmdc:WindowHorizPosEnum ; + rdfs:label "middle" . -nmdc:scaffolds a owl:ObjectProperty, + a owl:Class, + nmdc:WindowHorizPosEnum ; + rdfs:label "right" . + + a owl:Class, + nmdc:WindowLocEnum ; + rdfs:label "east" . + + a owl:Class, + nmdc:WindowLocEnum ; + rdfs:label "north" . + + a owl:Class, + nmdc:WindowLocEnum ; + rdfs:label "south" . + + a owl:Class, + nmdc:WindowLocEnum ; + rdfs:label "west" . + + a owl:Class, + nmdc:WindowMatEnum ; + rdfs:label "clad" . + + a owl:Class, + nmdc:WindowMatEnum ; + rdfs:label "fiberglass" . + + a owl:Class, + nmdc:WindowMatEnum ; + rdfs:label "metal" . + + a owl:Class, + nmdc:WindowMatEnum ; + rdfs:label "vinyl" . + + a owl:Class, + nmdc:WindowMatEnum ; + rdfs:label "wood" . + + a owl:Class, + nmdc:WindowTypeEnum ; + rdfs:label "fixed window" . + + a owl:Class, + nmdc:WindowTypeEnum ; + rdfs:label "horizontal sash window" . + + a owl:Class, + nmdc:WindowTypeEnum ; + rdfs:label "single-hung sash window" . + + a owl:Class, + nmdc:WindowVertPosEnum ; + rdfs:label "bottom" . + + a owl:Class, + nmdc:WindowVertPosEnum ; + rdfs:label "high" . + + a owl:Class, + nmdc:WindowVertPosEnum ; + rdfs:label "low" . + + a owl:Class, + nmdc:WindowVertPosEnum ; + rdfs:label "middle" . + + a owl:Class, + nmdc:WindowVertPosEnum ; + rdfs:label "top" . + + a owl:Class, + nmdc:YesNoEnum ; + rdfs:label "no" . + + a owl:Class, + nmdc:YesNoEnum ; + rdfs:label "yes" . + +nmdc:all_proteins a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "scaffolds" ; - rdfs:range linkml:Float ; - rdfs:subPropertyOf nmdc:metagenome_assembly_parameter ; - skos:definition "Total sequence count of all scaffolds." . + rdfs:label "all_proteins" ; + rdfs:range nmdc:GeneProduct ; + skos:definition "the list of protein identifiers that are associated with the peptide sequence" ; + skos:inScheme nmdc:core . -nmdc:specific_ecosystem a owl:ObjectProperty, +nmdc:alternative_names a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "specific_ecosystem" ; + rdfs:label "alternative_names" ; rdfs:range linkml:String ; - 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:definition "A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific." ; + skos:exactMatch dcterms:alternative, + skos:altLabel ; + skos:inScheme nmdc:basic_slots . -nmdc:started_at_time a owl:ObjectProperty, +nmdc:bytes a owl:Class, + linkml:TypeDefinition ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onDataRange nmdc:bytes ; + owl:onProperty linkml:topValue ; + owl:qualifiedCardinality 1 ] . + +nmdc:emsl_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "started_at_time" ; - rdfs:range linkml:String ; - skos:exactMatch prov:startedAtTime . + rdfs:label "emsl_identifiers" ; + skos:inScheme nmdc:external_identifiers . -nmdc:term a owl:ObjectProperty, +nmdc:gff_coordinate a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "term" ; - rdfs:domain nmdc:ControlledTermValue ; - rdfs:range nmdc:OntologyClass ; - skos:definition "pointer to an ontology class" . + rdfs:label "gff_coordinate" ; + rdfs:range [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Integer [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:minInclusive 1 ] ) ] ) ] ; + skos:definition "A positive 1-based integer coordinate indicating start or end" ; + skos:inScheme nmdc:annotation ; + skos:note "For features that cross the origin of a circular feature (e.g. most bacterial genomes, plasmids, and some viral genomes), the requirement for start to be less than or equal to end is satisfied by making end = the position of the end + the length of the landmark feature." . -nmdc:websites a owl:ObjectProperty, +nmdc:has_participants a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "websites" ; - rdfs:range linkml:String ; - skos:definition "A list of websites that are associated with the entity." . + rdfs:label "has_participants" ; + skos:exactMatch RO:0000057 ; + skos:inScheme nmdc:annotation . - a owl:Class, - nmdc:BiosampleCategoryEnum ; - rdfs:label "NEON" . +nmdc:language_code a owl:Class, + linkml:TypeDefinition ; + rdfs:subClassOf [ a owl:Restriction ; + owl:onDataRange nmdc:language_code ; + owl:onProperty linkml:topValue ; + owl:qualifiedCardinality 1 ] . - a owl:ObjectProperty, +nmdc:metatranscriptome_activity_set 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:exactMatch ; - nmdc:expected_value "decimal degrees, limit to 8 decimal points" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "geo_loc_name" ; - dcterms:title "geographic location (country and/or sea,region)" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "geographic location (country and/or sea,region)" ; - skos:definition "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)" ; - skos:exactMatch ; - nmdc:expected_value "country or sea name (INSDC or GAZ): region(GAZ), specific location name" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "nucl_acid_ext" ; - dcterms:title "nucleic acid extraction" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "nucleic acid extraction" ; - skos:definition "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample" ; - skos:exactMatch ; - nmdc:expected_value "PMID, DOI or URL" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "nucl_acid_amp" ; - dcterms:title "nucleic acid amplification" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "nucleic acid amplification" ; - skos:definition "A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids" ; - skos:exactMatch ; - nmdc:expected_value "PMID, DOI or URL" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "target_gene" ; - dcterms:title "target gene" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "target gene" ; - skos:definition "Targeted gene or locus name for marker gene studies" ; - skos:exactMatch ; - nmdc:expected_value "gene name" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "target_subfragment" ; - dcterms:title "target subfragment" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "target subfragment" ; - skos:definition "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA" ; - skos:exactMatch ; - nmdc:expected_value "gene fragment name" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "pcr_primers" ; - dcterms:title "pcr primers" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "pcr primers" ; - skos:definition "PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters" ; - skos:exactMatch ; - nmdc:expected_value "FWD: forward primer sequence;REV:reverse primer sequence" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "pcr_cond" ; - dcterms:title "pcr conditions" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "pcr conditions" ; - skos:definition "Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'" ; - skos:exactMatch ; - nmdc:expected_value "initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "seq_meth" ; - dcterms:title "sequencing method" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "sequencing method" ; - skos:definition "Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)." ; - skos:exactMatch ; - nmdc:expected_value "Text or OBI" . + rdfs:label "metatranscriptome_activity_set" ; + rdfs:domain nmdc:Database ; + rdfs:range nmdc:MetatranscriptomeActivity ; + rdfs:subPropertyOf nmdc:object_set ; + skos:definition "This property links a database object to the set of metatranscriptome analysis activities." ; + skos:inScheme nmdc:nmdc . - a owl:ObjectProperty, +nmdc:mgnify_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "seq_quality_check" ; - dcterms:title "sequence quality check" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "sequence quality check" ; - skos:definition "Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA" ; - skos:exactMatch ; - nmdc:expected_value "none or manually edited" . + rdfs:label "mgnify_identifiers" ; + rdfs:seeAlso ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:neon_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "chimera_check" ; - dcterms:title "chimera check software" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "chimera check software" ; - skos:definition "Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences." ; - skos:exactMatch ; - nmdc:expected_value "name and version of software, parameters used" . + rdfs:label "neon_identifiers" ; + skos:definition "identifiers for entities according to NEON" ; + skos:inScheme nmdc:external_identifiers . - a owl:ObjectProperty, +nmdc:nucleic_acid_concentration 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:exactMatch ; - nmdc:expected_value "measurement value" . + rdfs:label "nucleic_acid_concentration" ; + rdfs:range nmdc:InstrumentValue ; + skos:inScheme nmdc:basic_slots . - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "samp_vol_we_dna_ext" ; - dcterms:title "sample volume or weight for DNA extraction" ; - rdfs:range nmdc:QuantityValue ; - rdfs:subPropertyOf ; - skos:altLabel "sample volume or weight for DNA extraction" ; - skos:definition "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)." ; - skos:exactMatch ; - nmdc:expected_value "measurement value" ; - nmdc:preferred_unit "millliter, gram, milligram, square centimeter" . +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:ObjectProperty, +nmdc:websites a owl:ObjectProperty, linkml:SlotDefinition ; - 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:exactMatch ; - nmdc:expected_value "current vegetation type" ; - nmdc:occurrence "1" . + rdfs:label "websites" ; + rdfs:range linkml:String ; + skos:definition "A list of websites that are associated with the entity." ; + skos:inScheme nmdc:core . - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "local_class" ; - dcterms:title "soil_taxonomic/local classification" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "soil_taxonomic/local classification" ; - skos:definition "Soil classification based on local soil classification system" ; - skos:exactMatch ; - nmdc:expected_value "local classification name" ; - nmdc:occurrence "1" . + a owl:Class, + nmdc:BiosampleCategoryEnum ; + rdfs:label "NEON" . - a owl:ObjectProperty, + a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "soil_type" ; - dcterms:title "soil type" ; - rdfs:range nmdc:TextValue ; - rdfs:subPropertyOf ; - skos:altLabel "soil type" ; - skos:definition "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes." ; - skos:exactMatch ; - nmdc:expected_value "ENVO_00001998" ; - nmdc:occurrence "1" . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "organism_count_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . + rdfs:label "investigation field" ; + skos:definition "field describing aspect of the investigation/study to which the sample belongs" ; + skos:inScheme . nmdc:BiosampleProcessing a owl:Class, linkml:ClassDefinition ; rdfs:label "BiosampleProcessing" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom nmdc:Biosample ; owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], nmdc:PlannedProcess ; skos:altLabel "material processing" ; skos:broadMatch ; - skos:definition "A process that takes one or more biosamples as inputs and generates one or more biosamples as outputs. An example of an output includes samples cultivated from another sample." . + skos:definition "A process that takes one or more biosamples as inputs and generates one or more biosamples as outputs. An example of an output includes samples cultivated from another sample." ; + skos:inScheme nmdc:nmdc . -nmdc:ContainerTypeEnum a owl:Class, +nmdc:DeviceTypeEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "ContainerTypeEnum" ; - owl:unionOf ( ) ; - linkml:permissible_values . - -nmdc:DissolvingActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DissolvingActivity" ; - dcterms:title "Dissolving activity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:LabDevice ; - owl:onProperty nmdc:dissolution_aided_by ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:SolventEnum ; - owl:onProperty nmdc:dissolution_reagent ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:MaterialContainer ; - owl:onProperty nmdc:dissolved_in ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty nmdc:dissolution_volume ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:MaterialSample ; - owl:onProperty nmdc:material_output ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:MaterialSample ; - owl:onProperty nmdc:material_input ] ; - skos:altLabel "dissolution-activity" ; - skos:exactMatch . - -nmdc:FunctionalAnnotation a owl:Class, - linkml:ClassDefinition ; - rdfs:label "FunctionalAnnotation" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:GeneProduct ; - owl:onProperty nmdc:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:OntologyClass ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:has_function ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass 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:narrowMatch . - -nmdc:FunctionalAnnotationAggMember a owl:Class, - linkml:ClassDefinition ; - rdfs:label "FunctionalAnnotationAggMember" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:gene_function_id ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:count ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:WorkflowExecutionActivity ; - owl:onProperty nmdc:metagenome_annotation_id ] . + owl:unionOf ( ) ; + linkml:permissible_values , + . nmdc:FunctionalAnnotationTerm a owl:Class, linkml:ClassDefinition ; @@ -13044,3641 +13183,1116 @@ nmdc:FunctionalAnnotationTerm a owl:Class, rdfs:subClassOf nmdc:OntologyClass ; skos:altLabel "FunctionalAnnotation", "function" ; - skos:definition "Abstract grouping class for any term/descriptor that can be applied to a functional unit of a genome (protein, ncRNA, complex)." . - -nmdc:GenomeFeature a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GenomeFeature" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:end ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:phase ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty nmdc:seqid ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:feature_type ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:OntologyClass ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:start ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:GeneProduct ; - owl:onProperty nmdc:encodes ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:strand ] ; - skos:definition "A feature localized to an interval along a genome" . + skos:definition "Abstract grouping class for any term/descriptor that can be applied to a functional unit of a genome (protein, ncRNA, complex)." ; + skos:inScheme nmdc:annotation . -nmdc:MagBin a owl:Class, +nmdc:GeolocationValue a owl:Class, linkml:ClassDefinition ; - rdfs:label "MagBin" ; + rdfs:label "GeolocationValue" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:num_16s ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:completeness ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:gtdbtk_family ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:gtdbtk_phylum ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:bin_quality ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:gtdbtk_species ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:gtdbtk_domain ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:latitude ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:num_t_rna ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:gtdbtk_genus ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:members_id ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:number_of_contig ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:num_23s ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:total_bases ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:contamination ], + owl:minCardinality 0 ; + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:num_5s ], + owl:minCardinality 1 ; + owl:onProperty nmdc:latitude ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:bin_name ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:gtdbtk_class ], + owl:minCardinality 1 ; + owl:onProperty nmdc:longitude ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:gene_count ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:longitude ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:type ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:longitude ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:gtdbtk_order ] . + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:latitude ], + 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:MaterialSamplingActivity a owl:Class, +nmdc:LibraryTypeEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + . + +nmdc:MaterialSample a owl:Class, linkml:ClassDefinition ; - rdfs:label "MaterialSamplingActivity" ; - dcterms:title "Material sampling activity" ; + rdfs:label "MaterialSample" ; + dcterms:title "Material sample" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:SamplingMethodEnum ; - owl:onProperty nmdc:sampling_method ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:MaterialContainer ; - owl:onProperty nmdc:collected_into ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:MaterialSample ; - owl:onProperty nmdc:material_output ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty nmdc:amount_collected ] ; - skos:altLabel "weighing-activity" ; - skos:exactMatch . + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + nmdc:NamedThing ; + skos:altLabel "Material entity" ; + skos:inScheme nmdc:sample_prep . -nmdc:MetaboliteQuantification a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MetaboliteQuantification" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty nmdc:alternative_identifiers ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:highest_similarity_score ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:ChemicalEntity ; - owl:onProperty nmdc:metabolite_quantified ] ; - skos:definition "This is used to link a metabolomics analysis workflow to a specific metabolite" . - -nmdc:MetagenomeAnnotationActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MetagenomeAnnotationActivity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; - owl:onProperty nmdc:gold_analysis_project_identifiers ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:type ], - nmdc:WorkflowExecutionActivity ; - skos:definition "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs" . - -nmdc:PeptideQuantification a owl:Class, - linkml:ClassDefinition ; - rdfs:label "PeptideQuantification" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:GeneProduct ; - owl:onProperty nmdc:best_protein ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:peptide_spectral_count ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:peptide_sum_masic_abundance ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:GeneProduct ; - owl:onProperty nmdc:all_proteins ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:peptide_sequence ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:min_q_value ] ; - skos:definition "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information" . +nmdc:OrganismCountEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + . nmdc:PlannedProcess a owl:Class, linkml:ClassDefinition ; rdfs:label "PlannedProcess" ; dcterms:title "Planned Process" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:has_output ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:Protocol ; - owl:onProperty nmdc:protocol_link ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:has_input ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:start_date ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:end_date ], - nmdc:NamedThing ; - skos:exactMatch . - -nmdc:Protocol a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Protocol" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:url ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:name ] . - -nmdc:QualityControlReport a owl:Class, - linkml:ClassDefinition ; - rdfs:label "QualityControlReport" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:name ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:StatusEnum ; - owl:onProperty nmdc:status ] . - -nmdc:ReactionActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ReactionActivity" ; - dcterms:title "Reaction activity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty nmdc:reaction_time ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:MaterialSample ; - owl:onProperty nmdc:material_output ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:LabDevice ; - owl:onProperty nmdc:reaction_aided_by ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:MaterialSample ; - owl:onProperty nmdc:material_input ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:reaction_temperature ] ; - skos:altLabel "reaction-activity" . - -nmdc:SamplingMethodEnum a owl:Class, - linkml:EnumDefinition ; - rdfs:label "SamplingMethodEnum" ; - owl:unionOf ( ) ; - linkml:permissible_values . - -nmdc:Site a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Site" ; - dcterms:title "Site" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - nmdc:MaterialEntity . - -nmdc:Unit a owl:Class, - linkml:TypeDefinition ; - rdfs:label "unit" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onDataRange xsd:string ; - owl:onProperty linkml:topValue ; - owl:qualifiedCardinality 1 ] . - -nmdc:analysis_identifiers a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "analysis_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:external_database_identifiers . - -nmdc:material_output a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "material_output" ; - dcterms:title "material output" ; - rdfs:range nmdc:MaterialSample . - -nmdc:processing_institution a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "processing_institution" ; - rdfs:range nmdc:ProcessingInstitutionEnum ; - skos:definition "The organization that processed the sample." . - -nmdc:url a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "url" ; - rdfs:range linkml:String ; - rdfs:subPropertyOf nmdc:attribute . - -nmdc:used a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "used" ; - rdfs:domain nmdc:Activity ; - rdfs:range linkml:String ; - skos:exactMatch prov:used . - -nmdc:was_generated_by a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "was_generated_by" ; - rdfs:range nmdc:Activity ; - skos:exactMatch prov:wasGeneratedBy . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "investigation field" ; - rdfs:range linkml:String ; - skos:definition "field describing aspect of the investigation/study to which the sample belongs" . - -nmdc:ChemicalEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:chemical_formula ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:inchi_key ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:inchi ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:smiles ], - nmdc:OntologyClass ; - skos:altLabel "chemical", - "chemical compound", - "chemical substance", - "metabolite" ; - skos:definition "An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states" ; - skos:exactMatch . - -nmdc:DecimalDegree a owl:Class, - linkml:TypeDefinition ; - rdfs:label "decimal degree" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onDataRange xsd:decimal ; - owl:onProperty linkml:topValue ; - owl:qualifiedCardinality 1 ] . - -nmdc:DeviceTypeEnum a owl:Class, - linkml:EnumDefinition ; - rdfs:label "DeviceTypeEnum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - . - -nmdc:FieldResearchSite a owl:Class, - linkml:ClassDefinition ; - rdfs:label "FieldResearchSite" ; - dcterms:title "Field Research Site" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:GeolocationValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty dcterms:isPartOf ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:habitat ], - nmdc:Site ; - skos:altLabel "research plot" ; - skos:definition "A site, outside of a laboratory, from which biosamples may be collected." . - -nmdc:LibraryTypeEnum a owl:Class, - linkml:EnumDefinition ; - rdfs:label "LibraryTypeEnum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - . - -nmdc:MaterialEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MaterialEntity" ; - dcterms:title "Material Entity" ; rdfs:subClassOf nmdc:NamedThing ; - skos:altLabel "Material", - "Physical entity" . + skos:exactMatch ; + skos:inScheme nmdc:core . nmdc:SampleTypeEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "sample_type_enum" ; owl:unionOf ( ) ; linkml:permissible_values , . nmdc:StatusEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "StatusEnum" ; owl:unionOf ( ) ; linkml:permissible_values , . nmdc:StudyCategoryEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "StudyCategoryEnum" ; owl:unionOf ( ) ; linkml:permissible_values , . -nmdc:dois a owl:ObjectProperty, +nmdc:amount_collected a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "dois" ; - rdfs:range linkml:Uriorcurie ; - skos:altLabel "DOIs", - "digital object identifiers" ; - skos:definition "A digital object identifier, which is intended to persistantly identify some resource on the web." . + rdfs:label "amount_collected" ; + dcterms:title "amount collected" ; + rdfs:range nmdc:QuantityValue ; + skos:inScheme nmdc:sample_prep . -nmdc:gold_identifiers a owl:ObjectProperty, +nmdc:analysis_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gold_identifiers" ; - rdfs:range linkml:String . + rdfs:label "analysis_identifiers" ; + rdfs:subPropertyOf nmdc:external_database_identifiers ; + skos:inScheme nmdc:external_identifiers . -nmdc:has_raw_value a owl:ObjectProperty, +nmdc:best_protein a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "has_raw_value" ; - rdfs:domain nmdc:AttributeValue ; - rdfs:range linkml:String ; - skos:definition "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"" . + rdfs:label "best_protein" ; + rdfs:range nmdc:GeneProduct ; + skos:definition "the specific protein identifier most correctly associated with the peptide sequence" ; + skos:inScheme nmdc:core . -nmdc:read_qc_analysis_statistic a owl:ObjectProperty, +nmdc:collected_into a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "read_qc_analysis_statistic" ; - rdfs:range linkml:String . + rdfs:label "collected_into" ; + dcterms:title "collected into" ; + rdfs:range nmdc:MaterialContainer ; + skos:inScheme nmdc:sample_prep . -dcterms:description a owl:ObjectProperty, +nmdc:date_created a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "description" ; - rdfs:range linkml:String ; - skos:definition "a human-readable description of a thing" ; - skos:exactMatch dcterms:description . - -linkml:TypeDefinition a owl:Class . + rdfs:label "date_created" ; + skos:definition "from database class" ; + skos:inScheme nmdc:nmdc . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "arch_struc_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . +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 ] . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "door_direct_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . +nmdc:email a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "email" ; + rdfs:range linkml:String ; + skos:definition "An email address for an entity such as a person. This should be the primary email address used." ; + skos:inScheme nmdc:core . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "door_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . +nmdc:end a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "end" ; + rdfs:subPropertyOf nmdc:gff_coordinate ; + skos:closeMatch ; + skos:definition "The end of the feature in positive 1-based integer coordinates" ; + skos:inScheme nmdc:annotation ; + skos:note "- \"constraint: end > start\" - \"For features that cross the origin of a circular feature, end = the position of the end + the length of the landmark feature.\"" . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "furniture_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . +nmdc:ended_at_time a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "ended_at_time" ; + rdfs:range [ 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)?)?)?)?$" ] ) ] ; + skos:editorialNote "The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/ It may not be complete, but it is good enough for now." ; + skos:inScheme nmdc:prov ; + skos:mappingRelation prov:endedAtTime . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "oxy_stat_samp_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . +nmdc:etl_software_version a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "etl_software_version" ; + skos:definition "from database class" ; + skos:inScheme nmdc:nmdc . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "rel_samp_loc_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . +nmdc:execution_resource a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "execution_resource" ; + rdfs:subPropertyOf nmdc:attribute ; + skos:inScheme nmdc:core . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "room_loc_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . +nmdc:git_url a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "git_url" ; + rdfs:range linkml:String ; + rdfs:subPropertyOf nmdc:attribute ; + skos:inScheme nmdc:core . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "samp_md_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "substructure_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . +nmdc:gold_biosample_identifiers a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "gold_biosample_identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^gold:Gb[0-9]+$" ] ) ] ; + rdfs:subPropertyOf nmdc:biosample_identifiers, + nmdc:gold_identifiers ; + skos:definition "identifiers for corresponding sample in GOLD" ; + skos:inScheme nmdc:external_identifiers . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "train_line_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . +nmdc:has_function a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "has_function" ; + rdfs:range [ 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})?)$" ] ) ] ) ] ; + skos:editorialNote "and those are frequently fulltext, not CURIEs. MAM 2021-06-23", + "but is actually taking string arguments in MongoDB,", + "the range for has_function was asserted as functional_annotation_term/FunctionalAnnotationTerm," ; + skos:inScheme nmdc:annotation . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "train_stop_loc_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . +nmdc:has_unit a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "has_unit" ; + rdfs:range nmdc:unit ; + skos:altLabel "scale" ; + skos:definition "Links a QuantityValue to a unit" ; + skos:inScheme nmdc:core ; + skos:mappingRelation , + . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "window_cover_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "window_horiz_pos_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "window_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . - -nmdc:GeolocationValue a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeolocationValue" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:has_raw_value ], - [ a owl:Restriction ; - owl:onClass nmdc:DecimalDegree ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass nmdc:DecimalDegree ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - nmdc:AttributeValue ; - skos:definition "A normalized value for a location on the earth's surface" ; - skos:exactMatch . - -nmdc:LabDevice a owl:Class, - linkml:ClassDefinition ; - rdfs:label "LabDevice" ; - dcterms:title "Lab device" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty nmdc:activity_temperature ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty nmdc:activity_speed ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty nmdc:activity_time ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:DeviceTypeEnum ; - owl:onProperty nmdc:device_type ] . - -nmdc:MaterialContainer a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MaterialContainer" ; - dcterms:title "Material container" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:ContainerTypeEnum ; - owl:onProperty nmdc:container_type ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty nmdc:container_size ] . +nmdc:insdc_bioproject_identifiers a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "insdc_bioproject_identifiers" ; + rdfs:range [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^bioproject:PRJ[DEN][A-Z][0-9]+$" ] ) ] ; + rdfs:seeAlso , + ; + rdfs:subPropertyOf nmdc:insdc_identifiers, + nmdc:study_identifiers ; + skos:altLabel "DDBJ bioproject identifiers", + "NCBI bioproject identifiers" ; + skos:definition "identifiers for corresponding project in INSDC Bioproject" ; + skos:inScheme nmdc:external_identifiers ; + skos:note "these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?) one to one" . -nmdc:ReactionParticipant a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ReactionParticipant" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:ChemicalEntity ; - owl:onProperty nmdc:chemical ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty nmdc:stoichiometry ] ; - skos:definition "Instances of this link a reaction to a chemical entity participant" . +nmdc:latitude a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "latitude" ; + rdfs:domain nmdc:GeolocationValue ; + rdfs:range nmdc:decimal_degree ; + skos:definition "latitude" ; + skos:inScheme nmdc:core ; + skos:mappingRelation . -nmdc:SolventEnum a owl:Class, - linkml:EnumDefinition ; - rdfs:label "SolventEnum" ; - owl:unionOf ( CHEBI:17790 CHEBI:35255 ) ; - linkml:permissible_values CHEBI:17790, - CHEBI:35255, - . +nmdc:longitude a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "longitude" ; + rdfs:domain nmdc:GeolocationValue ; + rdfs:range nmdc:decimal_degree ; + skos:definition "longitude" ; + skos:inScheme nmdc:core ; + skos:mappingRelation . -nmdc:alternative_identifiers a owl:ObjectProperty, +nmdc:material_input a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "alternative_identifiers" ; - rdfs:range linkml:Uriorcurie ; - skos:definition "A list of alternative identifiers for the entity." . + rdfs:label "material_input" ; + dcterms:title "material input" ; + rdfs:range nmdc:MaterialSample ; + skos:inScheme nmdc:sample_prep . -nmdc:biomaterial_purity a owl:ObjectProperty, +nmdc:notes a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "biomaterial_purity" ; - rdfs:range nmdc:QuantityValue . + rdfs:label "notes" ; + skos:definition "from study class" ; + skos:inScheme nmdc:nmdc . -nmdc:gold_path_field a owl:ObjectProperty, +nmdc:orcid a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "gold_path_field" ; + rdfs:label "orcid" ; + rdfs:domain nmdc:PersonValue ; rdfs:range linkml:String ; - rdfs:subPropertyOf nmdc:attribute ; - skos:definition "This is a grouping for any of the gold path fields" . + skos:definition "The ORCID of a person." ; + skos:inScheme nmdc:core . -nmdc:has_numeric_value a owl:ObjectProperty, +nmdc:reaction_time a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "has_numeric_value" ; - rdfs:range linkml:Float ; - skos:definition "Links a quantity value to a number" ; - skos:exactMatch , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "biotic_relationship_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "building_setting_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "door_comp_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "door_loc_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "freq_clean_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "growth_habit_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "handidness_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "heat_deliv_loc_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "host_sex_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "occup_document_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "quad_pos_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "samp_floor_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "season_use_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "sediment_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "tidal_stage_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "wall_loc_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "window_loc_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . - -nmdc:Biosample a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Biosample" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:ControlledTermValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:FieldResearchSite ; - owl:onProperty nmdc:collected_from ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:sample_link ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:sample_collection_site ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:rna_volume ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:dna_absorb2 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:habitat ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty nmdc:nitrite_nitrogen ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:microbial_biomass_c ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:JgiContTypeEnum ; - owl:onProperty nmdc:rna_cont_type ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty nmdc:lbceq ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:start_date_inc ], - [ a owl:Restriction ; 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- owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + rdfs:label "reaction_time" ; + rdfs:range nmdc:QuantityValue ; + skos:inScheme nmdc:sample_prep . + +nmdc:related_identifiers a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "related_identifiers" ; + dcterms:title "Related Identifiers" ; + skos:definition "Identifiers assigned to a thing that is similar to that which is represented in NMDC. Related identifier are not an identical match and may have some variation." ; + skos:inScheme nmdc:nmdc . + +nmdc:seqid a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "seqid" ; + rdfs:range linkml:String ; + skos:definition "The ID of the landmark used to establish the coordinate system for the current feature." ; + skos:inScheme nmdc:annotation . + +nmdc:start a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "start" ; + rdfs:subPropertyOf nmdc:gff_coordinate ; + skos:closeMatch ; + skos:definition "The start of the feature in positive 1-based integer coordinates" ; + skos:inScheme nmdc:annotation . + +nmdc:started_at_time a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "started_at_time" ; + rdfs:range [ 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)?)?)?)?$" ] ) ] ; + skos:editorialNote "The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/ It may not be complete, but it is good enough for now." ; + skos:inScheme nmdc:prov ; + skos:mappingRelation prov:startedAtTime . + +nmdc:term a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "term" ; + rdfs:domain nmdc:ControlledTermValue ; + rdfs:range nmdc:OntologyClass ; + skos:definition "pointer to an ontology class" ; + skos:editorialNote "removed 'slot_uri: rdf:type'" ; + skos:inScheme nmdc:core . + +nmdc:was_generated_by a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "was_generated_by" ; + rdfs:range nmdc:Activity ; + skos:inScheme nmdc:prov ; + skos:mappingRelation prov:wasGeneratedBy . + +linkml:topValue a owl:DatatypeProperty ; + rdfs:label "value" . + +nmdc:Activity a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Activity" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:dna_container_id ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TimestampValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty nmdc:embargoed ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:collection_date_inc ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:proposal_rna ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:salinity_category ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty nmdc:zinc ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:dna_samp_id ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty nmdc:manganese ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:dna_concentration ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:start_time_inc ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:proport_woa_temperature ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:dna_project_contact ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:rna_seq_project ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:rna_cont_well ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - 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:ControlledTermValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; - owl:onProperty nmdc:img_identifiers ], + owl:onProperty nmdc:id ] ; + skos:definition "a provence-generating activity" ; + skos:editorialNote "removed was_associated_with because we are trying to avoid instantiating id-less Agents" ; + skos:inScheme nmdc:prov ; + skos:mappingRelation prov:Activity . + +nmdc:ArchStrucEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + . + +nmdc:Biosample a owl:Class, + linkml:ClassDefinition ; + rdfs:label "Biosample" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:tot_org_c_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:env_medium ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:env_medium ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:al_sat ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:climate_environment ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:alternative_identifiers ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:extreme_event ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:slope_aspect ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:tot_nitro_content ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:specific_ecosystem ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:fire ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:extreme_event ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:watering_regm ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:flooding ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:annual_precpt ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:al_sat ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:slope_aspect ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:slope_gradient ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:heavy_metals_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:tot_org_carb ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:filter_method ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:oxy_stat_samp ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:dna_volume ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:env_broad_scale ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:lat_lon ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:cur_vegetation ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:tot_org_c_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:dna_seq_project_pi ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:env_broad_scale ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:replicate_number ], + owl:minCardinality 0 ; + owl:onProperty nmdc:alternative_identifiers ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:tot_nitro_cont_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:technical_reps ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:al_sat_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:dna_isolate_meth ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:slope_gradient ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:al_sat ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:ControlledTermValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:salinity_meth ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty nmdc:sieving ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:tot_org_c_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:sieving ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 1 ; + owl:onProperty nmdc:env_local_scale ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; - owl:onProperty nmdc:insdc_biosample_identifiers ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:gold_biosample_identifiers ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:allValuesFrom nmdc:OxyStatSampEnum ; + owl:onProperty nmdc:oxy_stat_samp ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:water_content ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:source_mat_id ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:annual_precpt ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:tot_nitro_cont_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:heavy_metals ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty nmdc:ammonium_nitrogen ], + owl:minCardinality 1 ; + owl:onProperty nmdc:env_medium ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:cur_vegetation ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:tot_nitro_cont_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:rna_absorb2 ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:cur_vegetation_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:al_sat_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:flooding ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:sieving ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:heavy_metals_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:ControlledTermValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:flooding ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 1 ; + owl:onProperty nmdc:part_of ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:cur_vegetation_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:micro_biomass_c_meth ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:source_mat_id ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:ControlledTermValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:fire ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:cur_vegetation_meth ], [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], + owl:minCardinality 0 ; + owl:onProperty nmdc:tot_org_carb ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:onProperty nmdc:salinity_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:allValuesFrom nmdc:Study ; + owl:onProperty nmdc:part_of ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:source_mat_id ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:micro_biomass_n_meth ], + owl:minCardinality 0 ; + owl:onProperty nmdc:gaseous_environment ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:annual_precpt ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:ph_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:slope_gradient ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:elev ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; - owl:onProperty nmdc:neon_biosample_identifiers ], + owl:minCardinality 0 ; + owl:onProperty nmdc:tot_carb ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:gaseous_environment ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:elev ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:lat_lon ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:season_precpt ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:extreme_event ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:tot_nitro_content ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:rna_organisms ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:ph_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:al_sat_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:water_cont_soil_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:water_cont_soil_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:oxy_stat_samp ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:ControlledTermValue ; - owl:onProperty ], + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty nmdc:gold_biosample_identifiers ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:lat_lon ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:cur_vegetation ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:season_precpt ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:ControlledIdentifiedTermValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:env_local_scale ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty nmdc:gold_biosample_identifiers ], + owl:minCardinality 1 ; + owl:onProperty nmdc:env_broad_scale ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:community ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:elev ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:tot_carb ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:slope_aspect ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TimestampValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:tot_carb ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:onProperty nmdc:water_content ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:gold_biosample_identifiers ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + 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 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:watering_regm ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:ph_meth ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:climate_environment ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:tot_nitro_content ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:heavy_metals ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:salinity_meth ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:season_precpt ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:TimestampValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:env_local_scale ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:tot_org_carb ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:water_cont_soil_meth ], nmdc:MaterialEntity ; skos:altLabel "biospecimen", "material sample", "sample", "specimen" ; skos:definition "Biological source material which can be characterized by an experiment." ; + skos:editorialNote "removed previous id_prefixes value of GOLD, since we are now using pattern-based id validation" ; skos:exactMatch FBcv:0003024, NCIT:C43412, - . + ; + skos:inScheme nmdc:nmdc . nmdc:CreditAssociation a owl:Class, linkml:ClassDefinition ; rdfs:label "CreditAssociation" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass nmdc:PersonValue ; - owl:onProperty nmdc:applies_to_person ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc:CreditEnum ; - owl:onProperty nmdc:applied_roles ] [ a owl:Restriction ; - owl:onProperty nmdc:applied_roles ; - owl:someValuesFrom nmdc:CreditEnum ] ) ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:CreditEnum ; - owl:onProperty prov:hadRole ] ; skos:altLabel "associated researchers", "credit table", "study role" ; skos:definition "This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0" ; - skos:exactMatch prov:Association . + skos:exactMatch prov:Association ; + skos:inScheme nmdc:nmdc . + +nmdc:DoorDirectEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + . + +nmdc:DoorTypeEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + . + +nmdc:FurnitureEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + . + +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:JgiContTypeEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + . + +nmdc:MaterialEntity a owl:Class, + linkml:ClassDefinition ; + rdfs:label "MaterialEntity" ; + dcterms:title "Material Entity" ; + rdfs:subClassOf nmdc:NamedThing ; + skos:altLabel "Material", + "Physical entity" ; + skos:inScheme nmdc:core . + +nmdc:PersonValue a owl:Class, + linkml:ClassDefinition ; + rdfs:label "PersonValue" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_raw_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:has_raw_value ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:email ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:orcid ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:orcid ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:orcid ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_raw_value ], + [ 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:name ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:email ], + nmdc:AttributeValue ; + skos:definition "An attribute value representing a person" ; + skos:inScheme nmdc:core . + +nmdc:RelSampLocEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + . + +nmdc:RoomLocEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + . + +nmdc:SolventEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( CHEBI:17790 CHEBI:35255 ) ; + linkml:permissible_values CHEBI:17790, + CHEBI:35255, + . + +nmdc:SubstructureTypeEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + . + +nmdc:TrainLineEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + . + +nmdc:TrainStopLocEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + . -nmdc:ExtractionTargetEnum a owl:Class, +nmdc:WindowCoverEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "ExtractionTargetEnum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + . -nmdc:JgiContTypeEnum a owl:Class, +nmdc:WindowHorizPosEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "JgiContTypeEnum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + . + +nmdc:WindowTypeEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + . nmdc:YesNoEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "YesNoEnum" ; owl:unionOf ( ) ; linkml:permissible_values , . -nmdc:biosample_identifiers a owl:ObjectProperty, +nmdc:biomaterial_purity a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "biosample_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:external_database_identifiers . + rdfs:label "biomaterial_purity" ; + rdfs:range nmdc:QuantityValue ; + skos:inScheme nmdc:basic_slots . + +nmdc:dois a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "dois" ; + rdfs:range [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^doi:10.\\d{2,9}/.*$" ] ) ] ) ] ; + rdfs:seeAlso , + ; + skos:altLabel "DOIs", + "digital object identifiers" ; + skos:definition "A digital object identifier, which is intended to persistantly identify some resource on the web." ; + skos:inScheme nmdc:nmdc ; + skos:note "See especially the resourceTypeGeneral section of the DataCite pdf, on pp48-53 as of 2023-07-19" . + +nmdc:gold_identifiers a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "gold_identifiers" ; + rdfs:seeAlso ; + skos:inScheme nmdc:external_identifiers . -dcterms:isPartOf a owl:ObjectProperty, +nmdc:part_of a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "part_of" ; rdfs:domain nmdc:NamedThing ; rdfs:range nmdc:NamedThing ; skos:altLabel "is part of" ; skos:definition "Links a resource to another resource that either logically or physically includes it." ; - skos:exactMatch dcterms:isPartOf . + skos:inScheme nmdc:core . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "ceil_cond_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "door_cond_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "door_type_metal_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "floor_cond_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "heat_cool_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "int_wall_cond_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "light_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, +nmdc:read_qc_analysis_statistic a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "read_qc_analysis_statistic" ; + skos:inScheme nmdc:workflow_execution_activity . + +nmdc:BioticRelationshipEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "profile_position_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . + +nmdc:BuildingSettingEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "samp_capt_status_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . + +nmdc:ControlledIdentifiedTermValue a owl:Class, + linkml:ClassDefinition ; + rdfs:label "ControlledIdentifiedTermValue" ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:term ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:term ], + [ a owl:Restriction ; + owl:minCardinality 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:DoorCompTypeEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "samp_subtype_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . + +nmdc:DoorLocEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "shading_device_cond_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . + +nmdc:ExtractionTargetEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "sr_dep_env_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . + +nmdc:GrowthHabitEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "sr_kerog_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . + +nmdc:HandidnessEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "sr_lithology_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . + +nmdc:HeatDelivLocEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "train_stat_loc_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . + +nmdc:HostSexEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "water_feat_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . + +nmdc:OccupDocumentEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "window_cond_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . + +nmdc:OxyStatSampEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "window_mat_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + . + +nmdc:QuadPosEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "window_vert_pos_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . -nmdc:AnalysisTypeEnum a owl:Class, +nmdc:SampFloorEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "analysis_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . -nmdc:BiosampleCategoryEnum a owl:Class, +nmdc:SampMdEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "BiosampleCategoryEnum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:SeasonUseEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . -nmdc:PersonValue a owl:Class, - linkml:ClassDefinition ; - rdfs:label "PersonValue" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:orcid ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:websites ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:name ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:profile_image_url ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:has_raw_value ], - nmdc:AttributeValue ; - skos:definition "An attribute value representing a person" . +nmdc:SedimentTypeEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . nmdc:Study a owl:Class, linkml:ClassDefinition ; rdfs:label "Study" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; - owl:onProperty nmdc:jgi_portal_study_identifiers ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty nmdc:alternative_identifiers ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:alternative_titles ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty nmdc:publication_dois ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:title ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:publications ], + owl:minCardinality 0 ; + owl:onProperty nmdc:insdc_bioproject_identifiers ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:type ], + owl:minCardinality 0 ; + owl:onProperty nmdc:part_of ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ImageValue ; - owl:onProperty nmdc:study_image ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:notes ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:alternative_descriptions ], + owl:onProperty nmdc:websites ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:alternative_names ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; + owl:minCardinality 0 ; owl:onProperty nmdc:name ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:ecosystem ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:notes ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:websites ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty dcterms:description ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty nmdc:emsl_project_dois ], + owl:onProperty nmdc:notes ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty nmdc:award_dois ], + owl:minCardinality 0 ; + owl:onProperty nmdc:alternative_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:insdc_bioproject_identifiers ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:objective ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:ecosystem_category ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:ecosystem_type ], + owl:minCardinality 0 ; + owl:onProperty nmdc:related_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; - owl:onProperty nmdc:massive_study_identifiers ], + owl:allValuesFrom nmdc:Study ; + owl:onProperty nmdc:part_of ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; - owl:onProperty nmdc:gold_study_identifiers ], + owl:minCardinality 0 ; + owl:onProperty nmdc:description ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ess_dive_datasets ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; - owl:onProperty nmdc:mgnify_project_identifiers ], + owl:onProperty nmdc:related_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:funding_sources ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:related_identifiers ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:ecosystem_subtype ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:description ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty nmdc:dataset_dois ], + owl:minCardinality 0 ; + owl:onProperty nmdc:alternative_names ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; - owl:onProperty nmdc:gnps_task_identifiers ], + owl:minCardinality 0 ; + owl:onProperty nmdc:websites ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:related_identifiers ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:alternative_identifiers ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:relevant_protocols ], + owl:onProperty nmdc:name ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExternalIdentifier ; - owl:onProperty nmdc:neon_study_identifiers ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:description ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:specific_ecosystem ], + owl:minCardinality 0 ; + owl:onProperty nmdc:notes ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:PersonValue ; - owl:onProperty nmdc:principal_investigator ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:insdc_bioproject_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Study ; - owl:onProperty dcterms:isPartOf ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:name ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:StudyCategoryEnum ; - owl:onProperty nmdc:study_category ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:CreditAssociation ; - owl:onProperty prov:qualifiedAssociation ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], nmdc:NamedThing ; skos:altLabel "investigation", "project", @@ -16689,640 +14303,846 @@ nmdc:Study a owl:Class, "umbrella project" ; skos:broadMatch prov:Activity ; skos:definition "A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects." ; + skos:editorialNote "GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers, but no longer for the Study.id", + "sample GOLD link https://bioregistry.io/gold:Gs0110115", + "sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?", + "sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757" ; skos:exactMatch ISA:Investigation, NCIT:C41198, , - . + ; + skos:inScheme nmdc:nmdc ; + skos:note "The Study class can include both consortia and research studies." . -nmdc:external_database_identifiers a owl:ObjectProperty, +nmdc:TidalStageEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . + +nmdc:WallLocEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . + +nmdc:WindowLocEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + . + +nmdc:alternative_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "external_database_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:alternative_identifiers ; - skos:closeMatch skos:closeMatch ; - skos:definition "Link to corresponding identifier in external database" . + rdfs:label "alternative_identifiers" ; + rdfs:range [ 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_\\-\\/\\.,]*$" ] ) ] ) ] ; + skos:definition "A list of alternative identifiers for the entity." ; + skos:inScheme nmdc:basic_slots . -nmdc:insdc_identifiers a owl:ObjectProperty, +nmdc:gold_path_field a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "insdc_identifiers" ; + rdfs:label "gold_path_field" ; rdfs:range linkml:String ; - skos:altLabel "DDBJ identifiers", - "EBI identifiers", - "NCBI identifiers" ; - skos:definition "Any identifier covered by the International Nucleotide Sequence Database Collaboration" . + rdfs:subPropertyOf nmdc:attribute ; + skos:definition "This is a grouping for any of the gold path fields" ; + skos:inScheme nmdc:nmdc . -nmdc:name a owl:ObjectProperty, +nmdc:has_numeric_value a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "name" ; - rdfs:range linkml:String ; - skos:definition "A human readable label for an entity" . + rdfs:label "has_numeric_value" ; + rdfs:range linkml:Float ; + skos:definition "Links a quantity value to a number" ; + skos:inScheme nmdc:core ; + skos:mappingRelation , + . - a owl:Class, +nmdc:AnalysisTypeEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "door_move_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:BiosampleCategoryEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "drainage_class_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:CeilCondEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "filter_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:DoorCondEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "gender_restroom_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:DoorTypeMetalEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "hc_produced_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:FloorCondEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "room_condt_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:FreqCleanEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "samp_dis_stage_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + . + +nmdc:HeatCoolTypeEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "specific_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:IntWallCondEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "wall_const_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:LightTypeEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "wall_surf_treatment_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . -nmdc:Activity a owl:Class, +nmdc:OntologyClass a owl:Class, linkml:ClassDefinition ; - rdfs:label "Activity" ; + rdfs:label "OntologyClass" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:ended_at_time ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:name ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:used ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:started_at_time ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:Activity ; - owl:onProperty nmdc:was_informed_by ] ; - skos:definition "a provence-generating activity" ; - skos:exactMatch prov:Activity . + 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 ], + nmdc:NamedThing ; + skos:editorialNote "The identifiers for terms from external ontologies can't have their ids constrained to the nmdc namespace" ; + skos:inScheme nmdc:core . -nmdc:OntologyClass a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OntologyClass" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - nmdc:NamedThing . +nmdc:ProcessingInstitutionEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . -nmdc:study_identifiers a owl:ObjectProperty, +nmdc:ProfilePositionEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:SampCaptStatusEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:SampSubtypeEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:ShadingDeviceCondEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:SrDepEnvEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:SrKerogTypeEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:SrLithologyEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:TrainStatLocEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:WaterFeatTypeEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:WindowCondEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:WindowMatEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:WindowVertPosEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + . + +nmdc:biosample_identifiers a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "study_identifiers" ; - rdfs:range nmdc:ExternalIdentifier ; - rdfs:subPropertyOf nmdc:external_database_identifiers . + rdfs:label "biosample_identifiers" ; + rdfs:subPropertyOf nmdc:external_database_identifiers ; + skos:inScheme nmdc:external_identifiers . + +nmdc:description a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "description" ; + rdfs:range linkml:String ; + skos:definition "a human-readable description of a thing" ; + skos:inScheme nmdc:basic_slots . + +nmdc:external_database_identifiers a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "external_database_identifiers" ; + rdfs:range [ 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_\\-\\/\\.,]*$" ] ) ] ) ] ; + rdfs:subPropertyOf nmdc:alternative_identifiers ; + skos:closeMatch skos:closeMatch ; + skos:definition "Link to corresponding identifier in external database" ; + skos:editorialNote "had tried ranges of external identifier and string" ; + skos:inScheme nmdc:external_identifiers ; + skos:note "The value of this field is always a registered CURIE" . + +nmdc:material_output a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "material_output" ; + dcterms:title "material output" ; + rdfs:range nmdc:MaterialSample ; + skos:inScheme nmdc:sample_prep . + +nmdc:used a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "used" ; + rdfs:domain nmdc:Activity ; + skos:inScheme nmdc:prov ; + skos:mappingRelation prov:used . - a owl:Class, +nmdc:DoorMoveEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + . + +nmdc:DrainageClassEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + . + +nmdc:FilterTypeEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + . + +nmdc:GenderRestroomEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + . + +nmdc:HcProducedEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "ceil_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + . + +nmdc:RoomCondtEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "floor_struc_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + . + +nmdc:SampDisStageEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "plant_growth_med_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + . + +nmdc:SpecificEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "samp_collect_point_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + . + +nmdc:WallConstTypeEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "vis_media_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + . + +nmdc:WallSurfTreatmentEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "weekday_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + . + +nmdc:insdc_identifiers a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "insdc_identifiers" ; + rdfs:seeAlso , + ; + skos:altLabel "DDBJ identifiers", + "EBI identifiers", + "NCBI identifiers" ; + skos:definition "Any identifier covered by the International Nucleotide Sequence Database Collaboration" ; + skos:inScheme nmdc:external_identifiers ; + skos:note "note that we deliberately abstract over which of the partner databases accepted the initial submission", + "the first letter of the accession indicates which partner accepted the initial submission: E for ENA, D for DDBJ, or S or N for NCBI." . a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "nucleic acid sequence source field" ; - rdfs:range linkml:String . + skos:inScheme . -nmdc:MaterialSample a owl:Class, +nmdc:CeilTypeEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + . + +nmdc:FloorStrucEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + . + +nmdc:SampCollectPointEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + . + +nmdc:TimestampValue a owl:Class, linkml:ClassDefinition ; - rdfs:label "MaterialSample" ; - dcterms:title "Material sample" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - nmdc:NamedThing ; - skos:altLabel "Material entity" . + rdfs:label "TimestampValue" ; + rdfs:subClassOf nmdc:AttributeValue ; + skos:definition "A value that is a timestamp. The range should be ISO-8601" ; + skos:editorialNote "removed the following slots: year, month, day" ; + skos:inScheme nmdc:core . -nmdc:ProcessingInstitutionEnum a owl:Class, +nmdc:VisMediaEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "processing_institution_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + . + +nmdc:WeekdayEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + . + +nmdc:study_identifiers a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "study_identifiers" ; + rdfs:subPropertyOf nmdc:external_database_identifiers ; + skos:inScheme nmdc:external_identifiers . - a owl:Class, + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "sequencing field" ; + skos:inScheme . + +nmdc:BiolStatEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "biol_stat_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + . + +nmdc:DrawingsEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "drawings_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + . + +nmdc:ExtWallOrientEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "ext_wall_orient_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + . + +nmdc:ExtWindowOrientEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "ext_window_orient_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + . + +nmdc:HcrEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "hcr_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + . + +nmdc:IndoorSpaceEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "indoor_space_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + . + +nmdc:IndoorSurfEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "indoor_surf_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + . + +nmdc:PlantGrowthMedEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "soil_horizon_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + . + +nmdc:SoilHorizonEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "surf_air_cont_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + . + +nmdc:SurfAirContEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + . - a owl:ObjectProperty, +nmdc:has_raw_value a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "sequencing field" ; - rdfs:range linkml:String . - -nmdc:ControlledIdentifiedTermValue a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ControlledIdentifiedTermValue" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass nmdc:OntologyClass ; - owl:onProperty nmdc:term ; - owl:qualifiedCardinality 1 ], - nmdc:ControlledTermValue ; - skos:definition "A controlled term or class from an ontology, requiring the presence of term with an id" . + rdfs:label "has_raw_value" ; + rdfs:domain nmdc:AttributeValue ; + rdfs:range linkml:String ; + skos:definition "The value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"" ; + skos:inScheme nmdc:core . -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:exactMatch . +nmdc:name 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 . -nmdc:has_output a owl:ObjectProperty, + 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 "environment field" ; + skos:definition "field describing environmental aspect of a sample" ; + skos:inScheme . - a owl:Class, +nmdc:FloorWaterMoldEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "floor_water_mold_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + . + +nmdc:MechStrucEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "mech_struc_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + . + +nmdc:RoomSampPosEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "room_samp_pos_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + . + +nmdc:SampWeatherEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "samp_weather_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + . + +nmdc:TillageEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "tillage_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + . - a owl:ObjectProperty, +nmdc:has_output a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "environment field" ; - rdfs:range linkml:String ; - skos:definition "field describing environmental aspect of a sample" . + 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 . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "ceil_finish_mat_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - . - - a owl:Class, +nmdc:CeilFinishMatEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "door_mat_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + . + +nmdc:DoorMatEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "door_type_wood_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + . + +nmdc:DoorTypeWoodEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "room_connected_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "wall_finish_mat_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + . nmdc:AttributeValue a owl:Class, linkml:ClassDefinition ; rdfs:label "AttributeValue" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:Activity ; - owl:onProperty nmdc:was_generated_by ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; + owl:maxCardinality 1 ; owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:has_raw_value ] ; - 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" . + owl:minCardinality 0 ; + owl:onProperty nmdc:type ] ; + 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:TimestampValue a owl:Class, +nmdc:ControlledTermValue a owl:Class, linkml:ClassDefinition ; - rdfs:label "TimestampValue" ; + rdfs:label "ControlledTermValue" ; rdfs:subClassOf nmdc:AttributeValue ; - skos:definition "A value that is a timestamp. The range should be ISO-8601" . - -nmdc:has_input a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "has_input" ; - rdfs:domain nmdc:NamedThing ; - rdfs:range nmdc:NamedThing ; - skos:altLabel "input" ; - skos:definition "An input to a process." . + skos:definition "A controlled term or class from an ontology" ; + skos:inScheme nmdc:core . - a owl:Class, +nmdc:RoomConnectedEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + . + +nmdc:WallFinishMatEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "shading_device_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + . + +nmdc:type a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "type" ; + rdfs:range linkml:String ; + 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:DnaSampleFormatEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "dna_sample_format_enum" ; owl:unionOf ( ) ; linkml:permissible_values , , @@ -17339,7 +15159,6 @@ nmdc:DnaSampleFormatEnum a owl:Class, nmdc:RnaSampleFormatEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "rna_sample_format_enum" ; owl:unionOf ( ) ; linkml:permissible_values , , @@ -17354,277 +15173,250 @@ nmdc:RnaSampleFormatEnum a owl:Class, , . - a owl:Class, +nmdc:ShadingDeviceTypeEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "build_docs_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + . + +nmdc:BuildDocsEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "build_occup_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + , + . + +nmdc:BuildOccupTypeEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "ceil_texture_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + , + . + +nmdc:CeilTextureEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "lithology_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - , - . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + , + . + +nmdc:LithologyEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "wall_texture_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - , - , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + , + . + +nmdc:NamedThing a owl:Class, + linkml:ClassDefinition ; + rdfs:label "NamedThing" ; + skos:definition "a databased entity or concept/class" ; + skos:inScheme nmdc:core . nmdc:WorkflowExecutionActivity a owl:Class, linkml:ClassDefinition ; rdfs:label "WorkflowExecutionActivity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty dcterms:isPartOf ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:has_input ] [ a owl:Restriction ; - owl:onProperty nmdc:has_input ; - owl:someValuesFrom nmdc:NamedThing ] ) ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty nmdc:git_url ; - owl:qualifiedCardinality 1 ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:has_output ] [ a owl:Restriction ; - owl:onProperty nmdc:has_output ; - owl:someValuesFrom nmdc:NamedThing ] ) ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty nmdc:ended_at_time ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty nmdc:started_at_time ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty nmdc:type ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty nmdc:execution_resource ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:version ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:ended_at_time ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:git_url ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:ended_at_time ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:git_url ], + [ a owl:Restriction ; + 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:ended_at_time ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:execution_resource ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:started_at_time ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:started_at_time ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:type ], + [ 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 1 ; + owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:execution_resource ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:execution_resource ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:git_url ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:started_at_time ], nmdc:Activity ; skos:altLabel "analysis" ; - skos:definition "Represents an instance of an execution of a particular workflow" . + 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:has_input a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "has_input" ; + rdfs:domain nmdc:NamedThing ; + rdfs:range nmdc:NamedThing ; + skos:altLabel "input" ; + skos:definition "An input to a process." ; + skos:inScheme nmdc:core . + +nmdc:WallTextureEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + , + , + . + +nmdc:SurfMaterialEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + , + , + , + . nmdc:attribute a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "attribute" ; - rdfs:range linkml:String ; skos:altLabel "characteristic", "field", "key", "property", "template field" ; - skos:definition "A attribute of a biosample. Examples: depth, habitat, material. For NMDC, attributes SHOULD be mapped to terms within a MIxS template" . + skos:definition "A attribute of a biosample. Examples: depth, habitat, material. For NMDC, attributes SHOULD be mapped to terms within a MIxS template" ; + skos:inScheme nmdc:core . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "surf_material_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - , - , - , - . - -nmdc:type a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "type" ; - rdfs:range linkml:String ; - skos:definition "An optional string that specifies the type object. This is used to allow for searches for different kinds of objects." . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "depos_env_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - . - - a owl:Class, +nmdc:DeposEnvEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "floor_finish_mat_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "hcr_geol_age_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "sr_geol_age_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . nmdc:CreditEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "credit enum" ; owl:unionOf ( EFO:0001741 ) ; linkml:permissible_values , EFO:0001741, @@ -17643,297 +15435,248 @@ nmdc:CreditEnum a owl:Class, , . +nmdc:FloorFinishMatEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . + +nmdc:HcrGeolAgeEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . + +nmdc:SrGeolAgeEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . + nmdc:object_set a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "object_set" ; rdfs:domain nmdc:Database ; - rdfs:range linkml:String ; - skos:definition "Applies to a property that links a database object to a set of objects. This is necessary in a json document to provide context for a list, and to allow for a single json object that combines multiple object types" . - -nmdc:ControlledTermValue a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ControlledTermValue" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:OntologyClass ; - owl:onProperty nmdc:term ], - nmdc:AttributeValue ; - skos:definition "A controlled term or class from an ontology" . + skos:definition "Applies to a property that links a database object to a set of objects. This is necessary in a json document to provide context for a list, and to allow for a single json object that combines multiple object types" ; + skos:inScheme nmdc:nmdc . nmdc:Database a owl:Class, linkml:ClassDefinition ; rdfs:label "Database" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:date_created ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetaproteomicsAnalysisActivity ; - owl:onProperty nmdc:metaproteomics_analysis_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:DissolvingActivity ; - owl:onProperty nmdc:dissolving_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:NomAnalysisActivity ; - owl:onProperty nmdc:nom_analysis_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:Extraction ; - owl:onProperty nmdc:extraction_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:OmicsProcessing ; - owl:onProperty nmdc:omics_processing_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MaterialSample ; - owl:onProperty nmdc:material_sample_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetatranscriptomeActivity ; - owl:onProperty nmdc:metatranscriptome_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ProcessedSample ; - owl:onProperty nmdc:processed_sample_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ReactionActivity ; - owl:onProperty nmdc:reaction_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ReadBasedTaxonomyAnalysisActivity ; - owl:onProperty nmdc:read_based_taxonomy_analysis_activity_set ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; + owl:minCardinality 0 ; owl:onProperty nmdc:etl_software_version ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WorkflowExecutionActivity ; - owl:onProperty nmdc:activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:FunctionalAnnotationAggMember ; - owl:onProperty nmdc:functional_annotation_agg ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:Study ; - owl:onProperty nmdc:study_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetabolomicsAnalysisActivity ; - owl:onProperty nmdc:metabolomics_analysis_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetagenomeAnnotationActivity ; - owl:onProperty nmdc:metagenome_annotation_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MagsAnalysisActivity ; - owl:onProperty nmdc:mags_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ReadQcAnalysisActivity ; - owl:onProperty nmdc:read_qc_analysis_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:FieldResearchSite ; - owl:onProperty nmdc:field_research_site_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:DataObject ; - owl:onProperty nmdc:data_object_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetagenomeSequencingActivity ; - owl:onProperty nmdc:metagenome_sequencing_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:Biosample ; - owl:onProperty nmdc:biosample_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetagenomeAssembly ; - owl:onProperty nmdc:metagenome_assembly_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:FunctionalAnnotation ; - owl:onProperty nmdc:functional_annotation_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:date_created ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:MaterialSamplingActivity ; - owl:onProperty nmdc:material_sampling_activity_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:etl_software_version ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:CollectingBiosamplesFromSite ; - owl:onProperty nmdc:collecting_biosamples_from_site_set ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:etl_software_version ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:GenomeFeature ; - owl:onProperty nmdc:genome_feature_set ], + owl:minCardinality 0 ; + owl:onProperty nmdc:date_created ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:LibraryPreparation ; - owl:onProperty nmdc:library_preparation_set ], + owl:minCardinality 0 ; + owl:onProperty nmdc:metatranscriptome_activity_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Pooling ; - owl:onProperty nmdc:pooling_set ] ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:metatranscriptome_activity_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" . + 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" ; + skos:inScheme nmdc:nmdc . - a owl:Class, +nmdc:RoomTypeEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "room_type_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - . + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . + +nmdc:FaoClassEnum a owl:Class, + linkml:EnumDefinition ; + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . nmdc:metagenome_assembly_parameter a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "metagenome_assembly_parameter" ; - rdfs:range linkml:String . + skos:inScheme nmdc:workflow_execution_activity . - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "fao_class_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - . - - a owl:Class, +nmdc:PlantSexEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "plant_sex_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - . - -nmdc:id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "id" ; - rdfs:range linkml:Uriorcurie ; - skos:definition "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI" . - -nmdc:NamedThing a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedThing" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty dcterms:description ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty nmdc:name ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty nmdc:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty nmdc:alternative_identifiers ] ; - skos:definition "a databased entity or concept/class" . - - a owl:Class, + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . + +nmdc:CurLandUseEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "cur_land_use_enum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - . - -nmdc:ExternalIdentifier a owl:Class, - linkml:TypeDefinition ; - rdfs:label "external_identifier" ; - rdfs:subClassOf linkml:Uriorcurie . - -linkml:ClassDefinition a owl:Class . + owl:unionOf ( ) ; + linkml:permissible_values , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + . nmdc:FileTypeEnum a owl:Class, linkml:EnumDefinition ; - rdfs:label "file type enum" ; owl:unionOf ( ) ; linkml:permissible_values , , @@ -18005,49 +15748,81 @@ nmdc:FileTypeEnum a owl:Class, , . +nmdc:id a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "id" ; + rdfs:range [ 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_\\-\\/\\.,]*$" ] ) ] ) ] ; + skos:definition "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI" ; + skos:editorialNote "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", + "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", + "minting authority shoulders should probably be enumerated and checked in the pattern", + "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions" ; + skos:inScheme nmdc:basic_slots . + +nmdc:nmdc a owl:Ontology ; + rdfs:label "NMDC" ; + dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ; + dcterms:title "NMDC Schema" ; + pav:version "v8.1.0" ; + skos:definition """Schema for National Microbiome Data Collaborative (NMDC). +This schema is organized into multiple modules, such as: + + * a set of core types for representing data values + * a subset of the mixs schema + * an annotation schema + * the NMDC schema itself, into which the other modules are imported""" ; + skos:editorialNote "commented out insdc_biosample_identifiers insdc_secondary_sample_identifiers... need better understanding of id patterns (at least)", + "informal ## section delimiters should be replaced with subsets ?", + "not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1" . + nmdc:TextValue a owl:Class, linkml:ClassDefinition ; rdfs:label "TextValue" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:LanguageCode ; - owl:onProperty nmdc:language ], - nmdc:AttributeValue ; - skos:definition "A basic string value" . + rdfs:subClassOf nmdc:AttributeValue ; + skos:definition "A basic string value" ; + skos:inScheme nmdc:core . nmdc:QuantityValue a owl:Class, linkml:ClassDefinition ; rdfs:label "QuantityValue" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:has_minimum_numeric_value ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc:Unit ; + owl:minCardinality 0 ; owl:onProperty nmdc:has_unit ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; + owl:allValuesFrom linkml:Double ; owl:onProperty nmdc:has_numeric_value ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_raw_value ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_raw_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty nmdc:has_maximum_numeric_value ], + owl:minCardinality 0 ; + owl:onProperty nmdc:has_numeric_value ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_unit ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:has_numeric_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:has_unit ], nmdc:AttributeValue ; skos:definition "A simple quantity, e.g. 2cm" ; - skos:exactMatch . + skos:inScheme nmdc:core ; + skos:mappingRelation . a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "core field" ; - rdfs:range linkml:String ; - skos:definition "basic fields" . - -linkml:SlotDefinition a owl:Class . - + skos:definition "basic fields" ; + skos:inScheme . diff --git a/pyproject.toml b/pyproject.toml index 95f48a84e2..e3013ab668 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,7 +10,7 @@ license = "MIT" name = "nmdc_schema" readme = "README.md" repository = "https://github.com/microbiomedata/nmdc-schema" -version = "8.0.0" # nmdc.yaml and GH say v8.0.0 +version = "8.1.0" # nmdc.yaml and GH say v8.1.0 authors = [ "Bill Duncan ", "Chris Mungall ", diff --git a/src/schema/mixs.yaml b/src/schema/mixs.yaml index eaf9c65bdc..2ad97fa0af 100644 --- a/src/schema/mixs.yaml +++ b/src/schema/mixs.yaml @@ -33,18 +33,6 @@ subsets: description: A combination of a checklist and a package from_schema: http://w3id.org/mixs/terms enums: - door_direct_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - inward: {} - outward: {} - sideways: {} - oxy_stat_samp_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - aerobic: {} - anaerobic: {} - other: {} surf_air_cont_enum: from_schema: http://w3id.org/mixs/terms permissible_values: @@ -56,94 +44,94 @@ enums: radon: {} nutrients: {} biocides: {} - window_vert_pos_enum: + water_feat_type_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - bottom: {} - middle: {} - top: {} - low: {} - high: {} - filter_type_enum: + fountain: {} + pool: {} + standing feature: {} + stream: {} + waterfall: {} + samp_collect_point_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - particulate air filter: {} - chemical air filter: {} - low-MERV pleated media: {} - HEPA: {} - electrostatic: {} - gas-phase or ultraviolet air treatments: {} - rel_samp_loc_enum: + well: {} + test well: {} + drilling rig: {} + wellhead: {} + separator: {} + storage tank: {} + other: {} + floor_water_mold_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - edge of car: {} - center of car: {} - under a seat: {} - sediment_type_enum: + mold odor: {} + wet floor: {} + water stains: {} + wall discoloration: {} + floor discoloration: {} + ceiling discoloration: {} + peeling paint or wallpaper: {} + bulging walls: {} + condensation: {} + wall_texture_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - biogenous: {} - cosmogenous: {} - hydrogenous: {} - lithogenous: {} - occup_document_enum: + crows feet: {} + crows-foot stomp: {} + '': {} + double skip: {} + hawk and trowel: {} + knockdown: {} + popcorn: {} + orange peel: {} + rosebud stomp: {} + Santa-Fe texture: {} + skip trowel: {} + smooth: {} + stomp knockdown: {} + swirl: {} + samp_subtype_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - automated count: {} - estimate: {} - manual count: {} - videos: {} - room_connected_enum: + oil phase: {} + water phase: {} + biofilm: {} + not applicable: {} + other: {} + drainage_class_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - attic: {} - bathroom: {} - closet: {} - conference room: {} - elevator: {} - examining room: {} - hallway: {} - kitchen: {} - mail room: {} - office: {} - stairwell: {} - quad_pos_enum: + very poorly: {} + poorly: {} + somewhat poorly: {} + moderately well: {} + well: {} + excessively drained: {} + freq_clean_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - North side: {} - West side: {} - South side: {} - East side: {} - sr_geol_age_enum: + Daily: {} + Weekly: {} + Monthly: {} + Quarterly: {} + Annually: {} + other: {} + biotic_relationship_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - Archean: {} - Cambrian: {} - Carboniferous: {} - Cenozoic: {} - Cretaceous: {} - Devonian: {} - Jurassic: {} - Mesozoic: {} - Neogene: {} - Ordovician: {} - Paleogene: {} - Paleozoic: {} - Permian: {} - Precambrian: {} - Proterozoic: {} - Silurian: {} - Triassic: {} - other: {} - door_move_enum: + free living: {} + parasite: {} + commensal: {} + symbiont: {} + light_type_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - collapsible: {} - folding: {} - revolving: {} - rolling shutter: {} - sliding: {} - swinging: {} + natural light: {} + electric light: {} + desk lamp: {} + flourescent lights: {} + none: {} cur_land_use_enum: from_schema: http://w3id.org/mixs/terms permissible_values: @@ -270,211 +258,122 @@ enums: originally: vine crops (grapes) examples: - value: grapes - hcr_geol_age_enum: + drawings_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - Archean: {} - Cambrian: {} - Carboniferous: {} - Cenozoic: {} - Cretaceous: {} - Devonian: {} - Jurassic: {} - Mesozoic: {} - Neogene: {} - Ordovician: {} - Paleogene: {} - Paleozoic: {} - Permian: {} - Precambrian: {} - Proterozoic: {} - Silurian: {} - Triassic: {} - other: {} - wall_const_type_enum: + operation: {} + as built: {} + construction: {} + bid: {} + design: {} + building navigation map: {} + diagram: {} + sketch: {} + indoor_surf_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - frame construction: {} - joisted masonry: {} - light noncombustible: {} - masonry noncombustible: {} - modified fire resistive: {} - fire resistive: {} - plant_sex_enum: + cabinet: {} + ceiling: {} + counter top: {} + door: {} + shelving: {} + vent cover: {} + window: {} + wall: {} + samp_capt_status_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - Androdioecious: {} - Androecious: {} - Androgynous: {} - Androgynomonoecious: {} - Andromonoecious: {} - Bisexual: {} - Dichogamous: {} - Diclinous: {} - Dioecious: {} - Gynodioecious: {} - Gynoecious: {} - Gynomonoecious: {} - Hermaphroditic: {} - Imperfect: {} - Monoclinous: {} - Monoecious: {} - Perfect: {} - Polygamodioecious: {} - Polygamomonoecious: {} - Polygamous: {} - Protandrous: {} - Protogynous: {} - Subandroecious: {} - Subdioecious: {} - Subgynoecious: {} - Synoecious: {} - Trimonoecious: {} - Trioecious: {} - Unisexual: {} - ceil_type_enum: + active surveillance in response to an outbreak: {} + active surveillance not initiated by an outbreak: {} + farm sample: {} + market sample: {} + other: {} + room_loc_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - cathedral: {} - dropped: {} - concave: {} - barrel-shaped: {} - coffered: {} - cove: {} - stretched: {} - floor_finish_mat_enum: + corner room: {} + interior room: {} + exterior wall: {} + occup_document_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - tile: {} - wood strip or parquet: {} - carpet: {} - rug: {} - laminate wood: {} - lineoleum: {} - vinyl composition tile: {} - sheet vinyl: {} - stone: {} - bamboo: {} - cork: {} - terrazo: {} - concrete: {} - none: {} - sealed: {} - clear finish: {} - paint: {} - none or unfinished: {} - wall_loc_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - north: {} - south: {} - east: {} - west: {} - wall_surf_treatment_enum: + automated count: {} + estimate: {} + manual count: {} + videos: {} + arch_struc_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - painted: {} - wall paper: {} - no treatment: {} - paneling: {} - stucco: {} - fabric: {} - window_cond_enum: + building: {} + shed: {} + home: {} + wall_finish_mat_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - damaged: {} - needs repair: {} - new: {} - rupture: {} - visible wear: {} - door_mat_enum: + plaster: {} + gypsum plaster: {} + veneer plaster: {} + gypsum board: {} + tile: {} + terrazzo: {} + stone facing: {} + acoustical treatment: {} + wood: {} + metal: {} + masonry: {} + window_mat_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - aluminum: {} - cellular PVC: {} - engineered plastic: {} - fiberboard: {} + clad: {} fiberglass: {} metal: {} - thermoplastic alloy: {} vinyl: {} wood: {} - wood/plastic composite: {} - soil_horizon_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - O horizon: {} - A horizon: {} - E horizon: {} - B horizon: {} - C horizon: {} - R layer: {} - Permafrost: {} - M horizon: {} - ceil_finish_mat_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - drywall: {} - mineral fibre: {} - tiles: {} - PVC: {} - plasterboard: {} - metal: {} - fiberglass: {} - stucco: {} - mineral wool/calcium silicate: {} - wood: {} - shading_device_cond_enum: + int_wall_cond_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - damaged: {} - needs repair: {} new: {} - rupture: {} visible wear: {} - hc_produced_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - Oil: {} - Gas-Condensate: {} - Gas: {} - Bitumen: {} - Coalbed Methane: {} - other: {} - door_comp_type_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - metal covered: {} - revolving: {} - sliding: {} - telescopic: {} - window_loc_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - north: {} - south: {} - east: {} - west: {} - sr_lithology_enum: + needs repair: {} + damaged: {} + rupture: {} + floor_finish_mat_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - Clastic: {} - Carbonate: {} - Coal: {} - Biosilicieous: {} - other: {} - plant_growth_med_enum: + tile: {} + wood strip or parquet: {} + carpet: {} + rug: {} + laminate wood: {} + lineoleum: {} + vinyl composition tile: {} + sheet vinyl: {} + stone: {} + bamboo: {} + cork: {} + terrazo: {} + concrete: {} + none: {} + sealed: {} + clear finish: {} + paint: {} + none or unfinished: {} + build_docs_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - other artificial liquid medium: {} - other artificial solid medium: {} - peat moss: {} - perlite: {} - pumice: {} - sand: {} - soil: {} - vermiculite: {} - water: {} + building information model: {} + commissioning report: {} + complaint logs: {} + contract administration: {} + cost estimate: {} + janitorial schedules or logs: {} + maintenance plans: {} + schedule: {} + sections: {} + shop drawings: {} + submittals: {} + ventilation system: {} + windows: {} surf_material_enum: from_schema: http://w3id.org/mixs/terms permissible_values: @@ -493,199 +392,100 @@ enums: tile: {} vinyl: {} wood: {} - ceil_cond_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - new: {} - visible wear: {} - needs repair: {} - damaged: {} - rupture: {} - building_setting_enum: + tidal_stage_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - urban: {} - suburban: {} - exurban: {} - rural: {} - build_occup_type_enum: + low tide: {} + ebb tide: {} + flood tide: {} + high tide: {} + window_horiz_pos_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - office: {} - market: {} - restaurant: {} - residence: {} - school: {} - residential: {} - commercial: {} - low rise: {} - high rise: {} - wood framed: {} - health care: {} - airport: {} - sports complex: {} - depos_env_enum: + left: {} + middle: {} + right: {} + train_stop_loc_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - Continental - Alluvial: {} - Continental - Aeolian: {} - Continental - Fluvial: {} - Continental - Lacustrine: {} - Transitional - Deltaic: {} - Transitional - Tidal: {} - Transitional - Lagoonal: {} - Transitional - Beach: {} - Transitional - Lake: {} - Marine - Shallow: {} - Marine - Deep: {} - Marine - Reef: {} - Other - Evaporite: {} - Other - Glacial: {} - Other - Volcanic: {} - other: {} - profile_position_enum: + end: {} + mid: {} + downtown: {} + train_line_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - summit: {} - shoulder: {} - backslope: {} - footslope: {} - toeslope: {} - furniture_enum: + red: {} + green: {} + orange: {} + train_stat_loc_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - cabinet: {} - chair: {} - desks: {} - door_type_enum: + south station above ground: {} + south station underground: {} + south station amtrak: {} + forest hills: {} + riverside: {} + sr_dep_env_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - composite: {} - metal: {} - wooden: {} - tidal_stage_enum: + Lacustine: {} + Fluvioldeltaic: {} + Fluviomarine: {} + Marine: {} + other: {} + samp_weather_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - low tide: {} - ebb tide: {} - flood tide: {} - high tide: {} - door_type_metal_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - collapsible: {} - corrugated steel: {} - hollow: {} - rolling shutters: {} - steel plate: {} - handidness_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - ambidexterity: {} - left handedness: {} - mixed-handedness: {} - right handedness: {} - tillage_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - drill: {} - cutting disc: {} - ridge till: {} - strip tillage: {} - zonal tillage: {} - chisel: {} - tined: {} - mouldboard: {} - disc plough: {} - hcr_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - Oil Reservoir: {} - Gas Reservoir: {} - Oil Sand: {} - Coalbed: {} - Shale: {} - Tight Oil Reservoir: {} - Tight Gas Reservoir: {} - other: {} - freq_clean_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - Daily: {} - Weekly: {} - Monthly: {} - Quarterly: {} - Annually: {} - other: {} - growth_habit_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - erect: {} - semi-erect: {} - spreading: {} - prostrate: {} - season_use_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - Spring: {} - Summer: {} - Fall: {} - Winter: {} - sr_dep_env_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - Lacustine: {} - Fluvioldeltaic: {} - Fluviomarine: {} - Marine: {} - other: {} - water_feat_type_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - fountain: {} - pool: {} - standing feature: {} - stream: {} - waterfall: {} - substructure_type_enum: + clear sky: {} + cloudy: {} + foggy: {} + hail: {} + rain: {} + snow: {} + sleet: {} + sunny: {} + windy: {} + window_cover_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - crawlspace: {} - slab on grade: {} - basement: {} - indoor_space_enum: + blinds: {} + curtains: {} + none: {} + room_type_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - bedroom: {} - office: {} + attic: {} bathroom: {} - foyer: {} - kitchen: {} - locker room: {} - hallway: {} + closet: {} + conference room: {} elevator: {} - host_sex_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - female: {} - hermaphrodite: {} - male: {} - neuter: {} - window_type_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - single-hung sash window: {} - horizontal sash window: {} - fixed window: {} - specific_enum: + examining room: {} + hallway: {} + kitchen: {} + mail room: {} + private office: {} + open office: {} + stairwell: {} + ',restroom': {} + lobby: {} + vestibule: {} + mechanical or electrical room: {} + data center: {} + laboratory_wet: {} + laboratory_dry: {} + gymnasium: {} + natatorium: {} + auditorium: {} + lockers: {} + cafe: {} + warehouse: {} + sediment_type_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - operation: {} - as built: {} - construction: {} - bid: {} - design: {} - photos: {} + biogenous: {} + cosmogenous: {} + hydrogenous: {} + lithogenous: {} fao_class_enum: from_schema: http://w3id.org/mixs/terms permissible_values: @@ -715,22 +515,58 @@ enums: Solonetz: {} Vertisols: {} Yermosols: {} - floor_struc_enum: + ext_window_orient_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - balcony: {} - floating floor: {} - glass floor: {} - raised floor: {} - sprung floor: {} - wood-framed: {} - concrete: {} - wall_texture_enum: + north: {} + south: {} + east: {} + west: {} + northeast: {} + southeast: {} + southwest: {} + northwest: {} + sr_geol_age_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + Archean: {} + Cambrian: {} + Carboniferous: {} + Cenozoic: {} + Cretaceous: {} + Devonian: {} + Jurassic: {} + Mesozoic: {} + Neogene: {} + Ordovician: {} + Paleogene: {} + Paleozoic: {} + Permian: {} + Precambrian: {} + Proterozoic: {} + Silurian: {} + Triassic: {} + other: {} + door_move_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + collapsible: {} + folding: {} + revolving: {} + rolling shutter: {} + sliding: {} + swinging: {} + door_direct_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + inward: {} + outward: {} + sideways: {} + ceil_texture_enum: from_schema: http://w3id.org/mixs/terms permissible_values: crows feet: {} crows-foot stomp: {} - '': {} double skip: {} hawk and trowel: {} knockdown: {} @@ -742,69 +578,161 @@ enums: smooth: {} stomp knockdown: {} swirl: {} - train_stop_loc_enum: + samp_md_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - end: {} - mid: {} - downtown: {} - drawings_enum: + DF: {} + RT: {} + KB: {} + MSL: {} + other: {} + ceil_type_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - operation: {} - as built: {} - construction: {} - bid: {} - design: {} - building navigation map: {} - diagram: {} - sketch: {} - room_loc_enum: + cathedral: {} + dropped: {} + concave: {} + barrel-shaped: {} + coffered: {} + cove: {} + stretched: {} + wall_loc_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - corner room: {} - interior room: {} - exterior wall: {} - light_type_enum: + north: {} + south: {} + east: {} + west: {} + door_type_metal_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - natural light: {} - electric light: {} - desk lamp: {} - flourescent lights: {} - none: {} - weekday_enum: + collapsible: {} + corrugated steel: {} + hollow: {} + rolling shutters: {} + steel plate: {} + gender_restroom_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - Monday: {} - Tuesday: {} - Wednesday: {} - Thursday: {} - Friday: {} - Saturday: {} - Sunday: {} - arch_struc_enum: + all gender: {} + female: {} + gender neurtral: {} + male: {} + male and female: {} + unisex: {} + vis_media_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - building: {} - shed: {} - home: {} - heat_cool_type_enum: + photos: {} + videos: {} + commonly of the building: {} + site context (adjacent buildings, vegetation, terrain, streets): {} + interiors: {} + equipment: {} + 3D scans: {} + window_loc_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - radiant system: {} - heat pump: {} - forced air system: {} - steam forced heat: {} - wood stove: {} - samp_md_enum: + north: {} + south: {} + east: {} + west: {} + soil_horizon_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - DF: {} - RT: {} - KB: {} - MSL: {} + O horizon: {} + A horizon: {} + E horizon: {} + B horizon: {} + C horizon: {} + R layer: {} + Permafrost: {} + M horizon: {} + indoor_space_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + bedroom: {} + office: {} + bathroom: {} + foyer: {} + kitchen: {} + locker room: {} + hallway: {} + elevator: {} + door_type_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + composite: {} + metal: {} + wooden: {} + depos_env_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + Continental - Alluvial: {} + Continental - Aeolian: {} + Continental - Fluvial: {} + Continental - Lacustrine: {} + Transitional - Deltaic: {} + Transitional - Tidal: {} + Transitional - Lagoonal: {} + Transitional - Beach: {} + Transitional - Lake: {} + Marine - Shallow: {} + Marine - Deep: {} + Marine - Reef: {} + Other - Evaporite: {} + Other - Glacial: {} + Other - Volcanic: {} other: {} + sr_lithology_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + Clastic: {} + Carbonate: {} + Coal: {} + Biosilicieous: {} + other: {} + plant_sex_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + Androdioecious: {} + Androecious: {} + Androgynous: {} + Androgynomonoecious: {} + Andromonoecious: {} + Bisexual: {} + Dichogamous: {} + Diclinous: {} + Dioecious: {} + Gynodioecious: {} + Gynoecious: {} + Gynomonoecious: {} + Hermaphroditic: {} + Imperfect: {} + Monoclinous: {} + Monoecious: {} + Perfect: {} + Polygamodioecious: {} + Polygamomonoecious: {} + Polygamous: {} + Protandrous: {} + Protogynous: {} + Subandroecious: {} + Subdioecious: {} + Subgynoecious: {} + Synoecious: {} + Trimonoecious: {} + Trioecious: {} + Unisexual: {} + specific_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + operation: {} + as built: {} + construction: {} + bid: {} + design: {} + photos: {} ext_wall_orient_enum: from_schema: http://w3id.org/mixs/terms permissible_values: @@ -816,113 +744,134 @@ enums: southeast: {} southwest: {} northwest: {} - mech_struc_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - subway: {} - coach: {} - carriage: {} - elevator: {} - escalator: {} - boat: {} - train: {} - car: {} - bus: {} - ext_window_orient_enum: + door_loc_enum: from_schema: http://w3id.org/mixs/terms permissible_values: north: {} south: {} east: {} west: {} - northeast: {} - southeast: {} - southwest: {} - northwest: {} - window_cover_enum: + profile_position_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - blinds: {} - curtains: {} - none: {} - drainage_class_enum: + summit: {} + shoulder: {} + backslope: {} + footslope: {} + toeslope: {} + growth_habit_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - very poorly: {} - poorly: {} - somewhat poorly: {} - moderately well: {} - well: {} - excessively drained: {} - window_horiz_pos_enum: + erect: {} + semi-erect: {} + spreading: {} + prostrate: {} + season_use_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - left: {} - middle: {} - right: {} - samp_subtype_enum: + Spring: {} + Summer: {} + Fall: {} + Winter: {} + ceil_finish_mat_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - oil phase: {} - water phase: {} - biofilm: {} - not applicable: {} - other: {} - ceil_texture_enum: + drywall: {} + mineral fibre: {} + tiles: {} + PVC: {} + plasterboard: {} + metal: {} + fiberglass: {} + stucco: {} + mineral wool/calcium silicate: {} + wood: {} + tillage_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - crows feet: {} - crows-foot stomp: {} - double skip: {} - hawk and trowel: {} - knockdown: {} - popcorn: {} - orange peel: {} - rosebud stomp: {} - Santa-Fe texture: {} - skip trowel: {} - smooth: {} - stomp knockdown: {} - swirl: {} - room_samp_pos_enum: + drill: {} + cutting disc: {} + ridge till: {} + strip tillage: {} + zonal tillage: {} + chisel: {} + tined: {} + mouldboard: {} + disc plough: {} + window_type_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + single-hung sash window: {} + horizontal sash window: {} + fixed window: {} + ceil_cond_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + new: {} + visible wear: {} + needs repair: {} + damaged: {} + rupture: {} + hcr_geol_age_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - north corner: {} - south corner: {} - west corner: {} - east corner: {} - northeast corner: {} - northwest corner: {} - southeast corner: {} - southwest corner: {} - center: {} - indoor_surf_enum: + Archean: {} + Cambrian: {} + Carboniferous: {} + Cenozoic: {} + Cretaceous: {} + Devonian: {} + Jurassic: {} + Mesozoic: {} + Neogene: {} + Ordovician: {} + Paleogene: {} + Paleozoic: {} + Permian: {} + Precambrian: {} + Proterozoic: {} + Silurian: {} + Triassic: {} + other: {} + door_cond_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - cabinet: {} - ceiling: {} - counter top: {} - door: {} - shelving: {} - vent cover: {} - window: {} - wall: {} - organism_count_enum: + damaged: {} + needs repair: {} + new: {} + rupture: {} + visible wear: {} + lithology_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - ATP: {} - MPN: {} + Basement: {} + Chalk: {} + Chert: {} + Coal: {} + Conglomerate: {} + Diatomite: {} + Dolomite: {} + Limestone: {} + Sandstone: {} + Shale: {} + Siltstone: {} + Volcanic: {} other: {} - vis_media_enum: + heat_cool_type_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - photos: {} - videos: {} - commonly of the building: {} - site context (adjacent buildings, vegetation, terrain, streets): {} - interiors: {} - equipment: {} - 3D scans: {} + radiant system: {} + heat pump: {} + forced air system: {} + steam forced heat: {} + wood stove: {} + building_setting_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + urban: {} + suburban: {} + exurban: {} + rural: {} room_condt_enum: from_schema: http://w3id.org/mixs/terms permissible_values: @@ -932,25 +881,22 @@ enums: damaged: {} rupture: {} visible signs of mold/mildew: {} - samp_collect_point_enum: + rel_samp_loc_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - well: {} - test well: {} - drilling rig: {} - wellhead: {} - separator: {} - storage tank: {} - other: {} - samp_capt_status_enum: + edge of car: {} + center of car: {} + under a seat: {} + wall_surf_treatment_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - active surveillance in response to an outbreak: {} - active surveillance not initiated by an outbreak: {} - farm sample: {} - market sample: {} - other: {} - room_type_enum: + painted: {} + wall paper: {} + no treatment: {} + paneling: {} + stucco: {} + fabric: {} + room_connected_enum: from_schema: http://w3id.org/mixs/terms permissible_values: attic: {} @@ -962,55 +908,72 @@ enums: hallway: {} kitchen: {} mail room: {} - private office: {} - open office: {} + office: {} stairwell: {} - ',restroom': {} - lobby: {} - vestibule: {} - mechanical or electrical room: {} - data center: {} - laboratory_wet: {} - laboratory_dry: {} - gymnasium: {} - natatorium: {} - auditorium: {} - lockers: {} - cafe: {} - warehouse: {} - samp_dis_stage_enum: + window_vert_pos_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - dissemination: {} - growth and reproduction: {} - infection: {} - inoculation: {} - penetration: {} - other: {} - floor_cond_enum: + bottom: {} + middle: {} + top: {} + low: {} + high: {} + weekday_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - new: {} - visible wear: {} - needs repair: {} - damaged: {} - rupture: {} - lithology_enum: + Monday: {} + Tuesday: {} + Wednesday: {} + Thursday: {} + Friday: {} + Saturday: {} + Sunday: {} + room_samp_pos_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - Basement: {} - Chalk: {} - Chert: {} - Coal: {} - Conglomerate: {} - Diatomite: {} - Dolomite: {} - Limestone: {} - Sandstone: {} - Shale: {} - Siltstone: {} - Volcanic: {} - other: {} + north corner: {} + south corner: {} + west corner: {} + east corner: {} + northeast corner: {} + northwest corner: {} + southeast corner: {} + southwest corner: {} + center: {} + door_mat_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + aluminum: {} + cellular PVC: {} + engineered plastic: {} + fiberboard: {} + fiberglass: {} + metal: {} + thermoplastic alloy: {} + vinyl: {} + wood: {} + wood/plastic composite: {} + biol_stat_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + wild: {} + natural: {} + semi-natural: {} + inbred line: {} + breeder's line: {} + hybrid: {} + clonal selection: {} + mutant: {} + floor_struc_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + balcony: {} + floating floor: {} + glass floor: {} + raised floor: {} + sprung floor: {} + wood-framed: {} + concrete: {} door_type_wood_enum: from_schema: http://w3id.org/mixs/terms permissible_values: @@ -1024,74 +987,52 @@ enums: flush: {} louvered: {} wire gauged: {} - wall_finish_mat_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - plaster: {} - gypsum plaster: {} - veneer plaster: {} - gypsum board: {} - tile: {} - terrazzo: {} - stone facing: {} - acoustical treatment: {} - wood: {} - metal: {} - masonry: {} - gender_restroom_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - all gender: {} - female: {} - gender neurtral: {} - male: {} - male and female: {} - unisex: {} - int_wall_cond_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - new: {} - visible wear: {} - needs repair: {} - damaged: {} - rupture: {} - floor_water_mold_enum: - from_schema: http://w3id.org/mixs/terms - permissible_values: - mold odor: {} - wet floor: {} - water stains: {} - wall discoloration: {} - floor discoloration: {} - ceiling discoloration: {} - peeling paint or wallpaper: {} - bulging walls: {} - condensation: {} - samp_floor_enum: + organism_count_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - 1st floor: {} - 2nd floor: {} - basement: {} - lobby: {} - heat_deliv_loc_enum: + ATP: {} + MPN: {} + other: {} + shading_device_cond_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - north: {} - south: {} - east: {} - west: {} - biol_stat_enum: + damaged: {} + needs repair: {} + new: {} + rupture: {} + visible wear: {} + hcr_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - wild: {} - natural: {} - semi-natural: {} - inbred line: {} - breeder's line: {} - hybrid: {} - clonal selection: {} - mutant: {} + Oil Reservoir: {} + Gas Reservoir: {} + Oil Sand: {} + Coalbed: {} + Shale: {} + Tight Oil Reservoir: {} + Tight Gas Reservoir: {} + other: {} + mech_struc_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + subway: {} + coach: {} + carriage: {} + elevator: {} + escalator: {} + boat: {} + train: {} + car: {} + bus: {} + hc_produced_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + Oil: {} + Gas-Condensate: {} + Gas: {} + Bitumen: {} + Coalbed Methane: {} + other: {} shading_device_type_enum: from_schema: http://w3id.org/mixs/terms permissible_values: @@ -1107,42 +1048,44 @@ enums: tree: {} trellis: {} venetian awning: {} - train_stat_loc_enum: + quad_pos_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - south station above ground: {} - south station underground: {} - south station amtrak: {} - forest hills: {} - riverside: {} - window_mat_enum: + North side: {} + West side: {} + South side: {} + East side: {} + sr_kerog_type_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - clad: {} - fiberglass: {} - metal: {} - vinyl: {} - wood: {} - samp_weather_enum: + Type I: {} + Type II: {} + Type III: {} + Type IV: {} + other: {} + floor_cond_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - clear sky: {} - cloudy: {} - foggy: {} - hail: {} - rain: {} - snow: {} - sleet: {} - sunny: {} - windy: {} - biotic_relationship_enum: + new: {} + visible wear: {} + needs repair: {} + damaged: {} + rupture: {} + heat_deliv_loc_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - free living: {} - parasite: {} - commensal: {} - symbiont: {} - door_cond_enum: + north: {} + south: {} + east: {} + west: {} + host_sex_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + female: {} + hermaphrodite: {} + male: {} + neuter: {} + window_cond_enum: from_schema: http://w3id.org/mixs/terms permissible_values: damaged: {} @@ -1150,43 +1093,100 @@ enums: new: {} rupture: {} visible wear: {} - train_line_enum: + handidness_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - red: {} - green: {} - orange: {} - build_docs_enum: + ambidexterity: {} + left handedness: {} + mixed-handedness: {} + right handedness: {} + wall_const_type_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - building information model: {} - commissioning report: {} - complaint logs: {} - contract administration: {} - cost estimate: {} - janitorial schedules or logs: {} - maintenance plans: {} - schedule: {} - sections: {} - shop drawings: {} - submittals: {} - ventilation system: {} - windows: {} - door_loc_enum: + frame construction: {} + joisted masonry: {} + light noncombustible: {} + masonry noncombustible: {} + modified fire resistive: {} + fire resistive: {} + build_occup_type_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - north: {} - south: {} - east: {} - west: {} - sr_kerog_type_enum: + office: {} + market: {} + restaurant: {} + residence: {} + school: {} + residential: {} + commercial: {} + low rise: {} + high rise: {} + wood framed: {} + health care: {} + airport: {} + sports complex: {} + oxy_stat_samp_enum: from_schema: http://w3id.org/mixs/terms permissible_values: - Type I: {} - Type II: {} - Type III: {} - Type IV: {} + aerobic: {} + anaerobic: {} + other: {} + filter_type_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + particulate air filter: {} + chemical air filter: {} + low-MERV pleated media: {} + HEPA: {} + electrostatic: {} + gas-phase or ultraviolet air treatments: {} + samp_floor_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + 1st floor: {} + 2nd floor: {} + basement: {} + lobby: {} + furniture_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + cabinet: {} + chair: {} + desks: {} + samp_dis_stage_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + dissemination: {} + growth and reproduction: {} + infection: {} + inoculation: {} + penetration: {} other: {} + substructure_type_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + crawlspace: {} + slab on grade: {} + basement: {} + door_comp_type_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + metal covered: {} + revolving: {} + sliding: {} + telescopic: {} + plant_growth_med_enum: + from_schema: http://w3id.org/mixs/terms + permissible_values: + other artificial liquid medium: {} + other artificial solid medium: {} + peat moss: {} + perlite: {} + pumice: {} + sand: {} + soil: {} + vermiculite: {} + water: {} slots: abs_air_humidity: annotations: @@ -11212,34 +11212,34 @@ slots: slot_uri: MIXS:0000156 multivalued: false range: QuantityValue - investigation field: - description: field describing aspect of the investigation/study to which the sample belongs + has unit: + description: Example "m" + from_schema: http://w3id.org/mixs/ranges + owner: QuantityValue + sequencing field: from_schema: http://w3id.org/mixs/terms abstract: true + has raw value: + from_schema: http://w3id.org/mixs/ranges + string_serialization: '{has numeric value} {has unit}' + owner: QuantityValue core field: description: basic fields from_schema: http://w3id.org/mixs/terms abstract: true - nucleic acid sequence source field: + environment field: + description: field describing environmental aspect of a sample from_schema: http://w3id.org/mixs/terms abstract: true has numeric value: from_schema: http://w3id.org/mixs/ranges owner: QuantityValue range: double - environment field: - description: field describing environmental aspect of a sample + nucleic acid sequence source field: from_schema: http://w3id.org/mixs/terms abstract: true - has unit: - description: Example "m" - from_schema: http://w3id.org/mixs/ranges - owner: QuantityValue - sequencing field: + investigation field: + description: field describing aspect of the investigation/study to which the sample belongs from_schema: http://w3id.org/mixs/terms abstract: true - has raw value: - from_schema: http://w3id.org/mixs/ranges - string_serialization: '{has numeric value} {has unit}' - owner: QuantityValue source_file: assets/other_mixs_yaml_files/mixs_template.yaml diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml index bfdea0a947..12179ae105 100644 --- a/src/schema/nmdc.yaml +++ b/src/schema/nmdc.yaml @@ -17,7 +17,7 @@ description: >- * the NMDC schema itself, into which the other modules are imported license: https://creativecommons.org/publicdomain/zero/1.0/ -version: v8.0.0 # GH uses same version string # pyproject.toml says "8.0.0" +version: v8.1.0 # GH uses same version string # pyproject.toml says "8.1.0" imports: - annotation diff --git a/src/schema/workflow_execution_activity.yaml b/src/schema/workflow_execution_activity.yaml index 6c2a3003a1..6794da3e07 100644 --- a/src/schema/workflow_execution_activity.yaml +++ b/src/schema/workflow_execution_activity.yaml @@ -292,7 +292,7 @@ classes: - has_peptide_quantifications slot_usage: used: - range: Instrument + # range: Instrument description: The instrument used to collect the data used in the analysis id: required: true