name: NMDC description: "Schema for National Microbiome Data Collaborative (NMDC).\nThis schema\ \ is organized into multiple modules, such as:\n\n * a set of core types for representing\ \ data values\n * a subset of the mixs schema\n * an annotation schema\n * the NMDC\ \ schema itself, into which the other modules are imported" title: NMDC Schema notes: - 'informal ## section delimiters should be replaced with subsets ?' - commented out insdc_biosample_identifiers insdc_secondary_sample_identifiers... need better understanding of id patterns (at least) - 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 license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: CATH: prefix_prefix: CATH prefix_reference: 'https://bioregistry.io/cath:' CHEBI: prefix_prefix: CHEBI prefix_reference: http://purl.obolibrary.org/obo/CHEBI_ CHEMBL.COMPOUND: prefix_prefix: CHEMBL.COMPOUND prefix_reference: 'https://bioregistry.io/chembl.compound:' Contaminant: prefix_prefix: Contaminant prefix_reference: http://example.org/contaminant/ DRUGBANK: prefix_prefix: DRUGBANK prefix_reference: 'https://bioregistry.io/drugbank:' EC: prefix_prefix: EC prefix_reference: 'https://bioregistry.io/eccode:' EFO: prefix_prefix: EFO prefix_reference: http://www.ebi.ac.uk/efo/ EGGNOG: prefix_prefix: EGGNOG prefix_reference: 'https://bioregistry.io/eggnog:' ENVO: prefix_prefix: ENVO prefix_reference: http://purl.obolibrary.org/obo/ENVO_ FBcv: prefix_prefix: FBcv prefix_reference: http://purl.obolibrary.org/obo/FBcv_ GO: prefix_prefix: GO prefix_reference: http://purl.obolibrary.org/obo/GO_ HMDB: prefix_prefix: HMDB prefix_reference: 'https://bioregistry.io/hmdb:' ISA: prefix_prefix: ISA prefix_reference: http://example.org/isa/ KEGG.ORTHOLOGY: prefix_prefix: KEGG.ORTHOLOGY prefix_reference: 'https://bioregistry.io/kegg.orthology:' MASSIVE: prefix_prefix: MASSIVE prefix_reference: 'https://bioregistry.io/reference/massive:' MESH: prefix_prefix: MESH prefix_reference: 'https://bioregistry.io/mesh:' MS: prefix_prefix: MS prefix_reference: http://purl.obolibrary.org/obo/MS_ MetaNetX: prefix_prefix: MetaNetX prefix_reference: http://example.org/metanetx/ NCBITaxon: prefix_prefix: NCBITaxon prefix_reference: http://purl.obolibrary.org/obo/NCBITaxon_ NCIT: prefix_prefix: NCIT prefix_reference: http://purl.obolibrary.org/obo/NCIT_ PANTHER.FAMILY: prefix_prefix: PANTHER.FAMILY prefix_reference: 'https://bioregistry.io/panther.family:' PFAM: prefix_prefix: PFAM prefix_reference: 'https://bioregistry.io/pfam:' PO: prefix_prefix: PO prefix_reference: http://purl.obolibrary.org/obo/PO_ PR: prefix_prefix: PR prefix_reference: http://purl.obolibrary.org/obo/PR_ PUBCHEM.COMPOUND: prefix_prefix: PUBCHEM.COMPOUND prefix_reference: 'https://bioregistry.io/pubchem.compound:' RO: prefix_prefix: RO prefix_reference: http://purl.obolibrary.org/obo/RO_ RetroRules: prefix_prefix: RetroRules prefix_reference: http://example.org/retrorules/ SUPFAM: prefix_prefix: SUPFAM prefix_reference: 'https://bioregistry.io/supfam:' TIGRFAM: prefix_prefix: TIGRFAM prefix_reference: 'https://bioregistry.io/tigrfam:' UBERON: prefix_prefix: UBERON prefix_reference: http://purl.obolibrary.org/obo/UBERON_ UO: prefix_prefix: UO prefix_reference: http://purl.obolibrary.org/obo/UO_ biosample: prefix_prefix: biosample prefix_reference: 'https://bioregistry.io/biosample:' cas: prefix_prefix: cas prefix_reference: 'https://bioregistry.io/cas:' doi: prefix_prefix: doi prefix_reference: 'https://bioregistry.io/doi:' emsl.project: prefix_prefix: emsl.project prefix_reference: 'https://bioregistry.io/emsl.project:' generic: prefix_prefix: generic prefix_reference: https://example.org/generic/ gnps.task: prefix_prefix: gnps.task prefix_reference: 'https://bioregistry.io/gnps.task:' gtpo: prefix_prefix: gtpo prefix_reference: http://example.org/gtpo/ igsn: prefix_prefix: igsn prefix_reference: https://app.geosamples.org/sample/igsn/ img.taxon: prefix_prefix: img.taxon prefix_reference: 'https://bioregistry.io/img.taxon:' jgi.proposal: prefix_prefix: jgi.proposal prefix_reference: 'https://bioregistry.io/jgi.proposal:' jgi: prefix_prefix: jgi prefix_reference: http://example.org/jgi/ kegg: prefix_prefix: kegg prefix_reference: 'https://bioregistry.io/kegg:' linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ mgnify.proj: prefix_prefix: mgnify.proj prefix_reference: 'https://bioregistry.io/mgnify.proj:' neon.identifier: prefix_prefix: neon.identifier prefix_reference: http://example.org/neon/identifier/ neon.schema: prefix_prefix: neon.schema prefix_reference: http://example.org/neon/schema/ nmdc: prefix_prefix: nmdc prefix_reference: https://w3id.org/nmdc/ prov: prefix_prefix: prov prefix_reference: http://www.w3.org/ns/prov# rdf: prefix_prefix: rdf prefix_reference: http://www.w3.org/1999/02/22-rdf-syntax-ns# rdfs: prefix_prefix: rdfs prefix_reference: http://www.w3.org/2000/01/rdf-schema# skos: prefix_prefix: skos prefix_reference: http://www.w3.org/2004/02/skos/core# xsd: prefix_prefix: xsd prefix_reference: http://www.w3.org/2001/XMLSchema# emsl: prefix_prefix: emsl prefix_reference: http://example.org/emsl_biosample_in_mongodb/ emsl_biosample_uuid_like: prefix_prefix: emsl_biosample_uuid_like prefix_reference: http://example.org/emsl_biosample_uuid_like/ KEGG.COMPOUND: prefix_prefix: KEGG.COMPOUND prefix_reference: 'https://bioregistry.io/kegg.compound:' SIO: prefix_prefix: SIO prefix_reference: http://semanticscience.org/resource/SIO_ UniProtKB: prefix_prefix: UniProtKB prefix_reference: 'https://bioregistry.io/uniprot:' biolink: prefix_prefix: biolink prefix_reference: https://w3id.org/biolink/vocab/ dcterms: prefix_prefix: dcterms prefix_reference: http://purl.org/dc/terms/ qud: prefix_prefix: qud prefix_reference: http://qudt.org/1.1/schema/qudt# schema: prefix_prefix: schema prefix_reference: http://schema.org/ wgs84: prefix_prefix: wgs84 prefix_reference: http://www.w3.org/2003/01/geo/wgs84_pos# gold: prefix_prefix: gold prefix_reference: 'https://bioregistry.io/gold:' CHMO: prefix_prefix: CHMO prefix_reference: http://purl.obolibrary.org/obo/CHMO_ OBI: prefix_prefix: OBI prefix_reference: http://purl.obolibrary.org/obo/OBI_ shex: prefix_prefix: shex prefix_reference: http://www.w3.org/ns/shex# MIXS: prefix_prefix: MIXS prefix_reference: https://w3id.org/mixs/ MIXS_yaml: prefix_prefix: MIXS_yaml prefix_reference: https://raw.githubusercontent.com/microbiomedata/mixs/main/model/schema/ COG: prefix_prefix: COG prefix_reference: 'https://bioregistry.io/cog:' KEGG.REACTION: prefix_prefix: KEGG.REACTION prefix_reference: 'https://bioregistry.io/kegg.reaction:' KEGG_PATHWAY: prefix_prefix: KEGG_PATHWAY prefix_reference: 'https://bioregistry.io/kegg.pathway:' MetaCyc: prefix_prefix: MetaCyc prefix_reference: 'https://bioregistry.io/metacyc.compound:' RHEA: prefix_prefix: RHEA prefix_reference: 'https://bioregistry.io/rhea:' SEED: prefix_prefix: SEED prefix_reference: 'https://bioregistry.io/seed:' emit_prefixes: - KEGG.ORTHOLOGY - MASSIVE - biosample - cas - doi - gnps.task - gold - img.taxon - jgi.proposal - kegg - rdf - rdfs - skos - xsd default_prefix: nmdc default_range: string subsets: sample subset: name: sample subset description: Subset consisting of entities linked to the processing of samples. Currently, this subset consists of study, omics process, and biosample. from_schema: https://w3id.org/nmdc/nmdc data object subset: name: data object subset description: Subset consisting of the data objects that either inputs or outputs of processes or workflows. from_schema: https://w3id.org/nmdc/nmdc workflow subset: name: workflow subset description: Subset consisting of just the workflow execution activities from_schema: https://w3id.org/nmdc/nmdc environment: name: environment from_schema: https://w3id.org/nmdc/nmdc investigation: name: investigation from_schema: https://w3id.org/nmdc/nmdc nucleic acid sequence source: name: nucleic acid sequence source from_schema: https://w3id.org/nmdc/nmdc sequencing: name: sequencing from_schema: https://w3id.org/nmdc/nmdc mixs_environmental_triad: name: mixs_environmental_triad title: MIxS Environmental Triad from_schema: https://w3id.org/nmdc/nmdc mixs extension: name: mixs extension from_schema: https://w3id.org/nmdc/nmdc checklist: name: checklist description: A MIxS checklist. These can be combined with packages from_schema: https://w3id.org/nmdc/nmdc package: name: package description: A MIxS package. These can be combined with checklists from_schema: https://w3id.org/nmdc/nmdc checklist_package_combination: name: checklist_package_combination description: A combination of a checklist and a package from_schema: https://w3id.org/nmdc/nmdc types: bytes: name: bytes description: An integer value that corresponds to a size in bytes from_schema: https://w3id.org/nmdc/nmdc see_also: - UO:0000233 base: int uri: xsd:long decimal degree: name: decimal degree description: A decimal degree expresses latitude or longitude as decimal fractions. from_schema: https://w3id.org/nmdc/nmdc see_also: - https://en.wikipedia.org/wiki/Decimal_degrees base: float uri: xsd:decimal language code: name: language code description: A language code conforming to ISO_639-1 from_schema: https://w3id.org/nmdc/nmdc see_also: - https://en.wikipedia.org/wiki/ISO_639-1 base: str uri: xsd:language unit: name: unit from_schema: https://w3id.org/nmdc/nmdc mappings: - qud:Unit - UO:0000000 base: str uri: xsd:string external_identifier: name: external_identifier description: A CURIE representing an external identifier from_schema: https://w3id.org/nmdc/nmdc see_also: - https://microbiomedata.github.io/nmdc-schema/identifiers.html typeof: uriorcurie uri: xsd:anyURI pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$ string: name: string description: A character string from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Text base: str uri: xsd:string integer: name: integer description: An integer from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Integer base: int uri: xsd:integer boolean: name: boolean description: A binary (true or false) value from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Boolean base: Bool uri: xsd:boolean repr: bool float: name: float description: A real number that conforms to the xsd:float specification from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Float base: float uri: xsd:float double: name: double description: A real number that conforms to the xsd:double specification from_schema: https://w3id.org/nmdc/nmdc close_mappings: - schema:Float base: float uri: xsd:double decimal: name: decimal description: A real number with arbitrary precision that conforms to the xsd:decimal specification from_schema: https://w3id.org/nmdc/nmdc broad_mappings: - schema:Number base: Decimal uri: xsd:decimal time: name: time description: A time object represents a (local) time of day, independent of any particular day notes: - URI is dateTime because OWL reasoners do not work with straight date or time from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Time base: XSDTime uri: xsd:dateTime repr: str date: name: date description: a date (year, month and day) in an idealized calendar notes: - URI is dateTime because OWL reasoners don't work with straight date or time from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:Date base: XSDDate uri: xsd:date repr: str datetime: name: datetime description: The combination of a date and time from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - schema:DateTime base: XSDDateTime uri: xsd:dateTime repr: str date_or_datetime: name: date_or_datetime description: Either a date or a datetime from_schema: https://w3id.org/nmdc/nmdc base: str uri: linkml:DateOrDatetime repr: str uriorcurie: name: uriorcurie description: a URI or a CURIE from_schema: https://w3id.org/nmdc/nmdc base: URIorCURIE uri: xsd:anyURI repr: str curie: name: curie conforms_to: https://www.w3.org/TR/curie/ description: a compact URI comments: - in RDF serializations this MUST be expanded to a URI - in non-RDF serializations MAY be serialized as the compact representation from_schema: https://w3id.org/nmdc/nmdc base: Curie uri: xsd:string repr: str uri: name: uri conforms_to: https://www.ietf.org/rfc/rfc3987.txt description: a complete 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 case it is translated directly to a node from_schema: https://w3id.org/nmdc/nmdc close_mappings: - schema:URL base: URI uri: xsd:anyURI repr: str ncname: name: ncname description: Prefix part of CURIE from_schema: https://w3id.org/nmdc/nmdc base: NCName uri: xsd:string repr: str objectidentifier: name: objectidentifier description: A URI or CURIE that represents an object in the model. comments: - Used for inheritence and type checking from_schema: https://w3id.org/nmdc/nmdc base: ElementIdentifier uri: shex:iri repr: str nodeidentifier: name: nodeidentifier description: A URI, CURIE or BNODE that represents a node in a model. from_schema: https://w3id.org/nmdc/nmdc base: NodeIdentifier uri: shex:nonLiteral repr: str enums: StatusEnum: name: StatusEnum from_schema: https://w3id.org/nmdc/nmdc permissible_values: pass: text: pass fail: text: fail ExtractionTargetEnum: name: ExtractionTargetEnum from_schema: https://w3id.org/nmdc/nmdc permissible_values: DNA: text: DNA RNA: text: RNA metabolite: text: metabolite protein: text: protein LibraryTypeEnum: name: LibraryTypeEnum from_schema: https://w3id.org/nmdc/nmdc permissible_values: DNA: text: DNA RNA: text: RNA JgiContTypeEnum: name: JgiContTypeEnum from_schema: https://w3id.org/nmdc/nmdc permissible_values: plate: text: plate tube: text: tube YesNoEnum: name: YesNoEnum description: replaces DnaDnaseEnum and DnaseRnaEnum from_schema: https://w3id.org/nmdc/nmdc permissible_values: 'no': text: 'no' 'yes': text: 'yes' BiosampleCategoryEnum: name: BiosampleCategoryEnum description: Funding-based, sample location-based, or experimental method-based defined categories notes: - Currently, these values can associated with biosamples via the biosample_categories slot - They might also be applicable to other classes - They are intended to enable metadata search and or filtering, for example in the NMDC data portal, https://data.microbiomedata.org/ from_schema: https://w3id.org/nmdc/nmdc aliases: - category tag permissible_values: LTER: text: LTER meaning: https://lternet.edu/ title: National Science Foundation's Long Term Ecological Research Network SIP: text: SIP SFA: text: SFA description: Science Focus Area projects funded through the Department of Energy Office of Science Biological and Environmental Research Program meaning: https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance title: Department of Energy Office of Science Biological and Environmental Research Program Laboratory Science Focus Areas FICUS: text: FICUS meaning: https://jgi.doe.gov/user-programs/program-info/ficus-overview title: Facilities Integrating Collaborations for User Science NEON: text: NEON meaning: https://www.neonscience.org title: National Science Foundation's National Ecological Observatory Network file type enum: name: file type enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: Metagenome Raw Reads: text: Metagenome Raw Reads annotations: file_name_pattern: tag: file_name_pattern value: ^\.fastq(\.gz)?$ Metagenome Raw Read 1: text: Metagenome Raw Read 1 description: Read 1 raw sequencing data, aka forward reads annotations: file_name_pattern: tag: file_name_pattern value: ^.+_R1\.fastq(\.gz)?$ examples: - value: BMI_H25VYBGXH_19S_31WellG1_R1.fastq.gz Metagenome Raw Read 2: text: Metagenome Raw Read 2 description: Read 2 raw sequencing data, aka reverse reads annotations: file_name_pattern: tag: file_name_pattern value: ^.+_R2\.fastq(\.gz)?$ examples: - value: BMI_H25VYBGXH_19S_31WellG1_R2.fastq.gz FT ICR-MS Analysis Results: text: FT ICR-MS Analysis Results description: FT ICR-MS-based molecular formula assignment results table GC-MS Metabolomics Results: text: GC-MS Metabolomics Results description: GC-MS-based metabolite assignment results table Metaproteomics Workflow Statistics: text: Metaproteomics Workflow Statistics description: Aggregate workflow statistics file Protein Report: text: Protein Report description: Filtered protein report file Peptide Report: text: Peptide Report description: Filtered peptide report file Unfiltered Metaproteomics Results: text: Unfiltered Metaproteomics Results description: MSGFjobs and MASIC output file Read Count and RPKM: text: Read Count and RPKM description: Annotation read count and RPKM per feature JSON QC non-rRNA R2: text: QC non-rRNA R2 description: QC removed rRNA reads (R2) fastq QC non-rRNA R1: text: QC non-rRNA R1 description: QC removed rRNA reads (R1) fastq Metagenome Bins: text: Metagenome Bins description: Metagenome bin contigs fasta Metagenome Bins Compression File: text: Metagenome Bins Compression File description: Compressed file containing all metagenome bins and associated files annotations: file_name_pattern: tag: file_name_pattern value: '[mag_wf_activity_id]_hqmq_bin.zip' Metagenome Bins Info File: text: Metagenome Bins Info File description: File containing version information on the binning workflow annotations: file_name_pattern: tag: file_name_pattern value: '[mag_wf_activity_id]_bin.info' CheckM Statistics: text: CheckM Statistics description: CheckM statistics report Read Based Analysis Info File: text: Read Based Analysis Info File description: File containing reads based analysis information annotations: file_name_pattern: tag: file_name_pattern value: profiler.info GTDBTK Bacterial Summary: text: GTDBTK Bacterial Summary description: GTDBTK bacterial summary GTDBTK Archaeal Summary: text: GTDBTK Archaeal Summary description: GTDBTK archaeal summary GOTTCHA2 Krona Plot: text: GOTTCHA2 Krona Plot description: GOTTCHA2 krona plot HTML file GOTTCHA2 Classification Report: text: GOTTCHA2 Classification Report description: GOTTCHA2 classification report file GOTTCHA2 Report Full: text: GOTTCHA2 Report Full description: GOTTCHA2 report file Kraken2 Krona Plot: text: Kraken2 Krona Plot description: Kraken2 krona plot HTML file Centrifuge Krona Plot: text: Centrifuge Krona Plot description: Centrifuge krona plot HTML file Centrifuge output report file: text: Centrifuge output report file description: Centrifuge output report file Kraken2 Classification Report: text: Kraken2 Classification Report description: Kraken2 output report file Kraken2 Taxonomic Classification: text: Kraken2 Taxonomic Classification description: Kraken2 output read classification file Centrifuge Classification Report: text: Centrifuge Classification Report description: Centrifuge output report file Centrifuge Taxonomic Classification: text: Centrifuge Taxonomic Classification description: Centrifuge output read classification file Structural Annotation GFF: text: Structural Annotation GFF description: GFF3 format file with structural annotations annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_structural_annotation.gff' Structural Annotation Stats Json: text: Structural Annotation Stats Json description: Structural annotations stats json annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_structural_annotation_stats.json' Functional Annotation GFF: text: Functional Annotation GFF description: GFF3 format file with functional annotations annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_functional_annotation.gff' Annotation Info File: text: Annotation Info File description: File containing annotation info annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_imgap.info' Annotation Amino Acid FASTA: text: Annotation Amino Acid FASTA description: FASTA amino acid file for annotated proteins annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_proteins.faa' Annotation Enzyme Commission: text: Annotation Enzyme Commission description: Tab delimited file for EC annotation annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_ec.tsv' Annotation KEGG Orthology: text: Annotation KEGG Orthology description: Tab delimited file for KO annotation annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_ko.tsv' Assembly Info File: text: Assembly Info File description: File containing assembly info annotations: file_name_pattern: tag: file_name_pattern value: README.txt Assembly Coverage BAM: text: Assembly Coverage BAM description: Sorted bam file of reads mapping back to the final assembly annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_pairedMapped.sam.gz' Assembly AGP: text: Assembly AGP description: An AGP format file that describes the assembly Assembly Scaffolds: text: Assembly Scaffolds description: Final assembly scaffolds fasta annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_assembly.contigs.fasta' Assembly Contigs: text: Assembly Contigs description: Final assembly contigs fasta annotations: file_name_pattern: tag: file_name_pattern value: assembly.contigs.fasta Assembly Coverage Stats: text: Assembly Coverage Stats description: Assembled contigs coverage information annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_pairedMapped_sorted.bam.cov' Contig Mapping File: text: Contig Mapping File description: Contig mappings between contigs and scaffolds annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_contig_names_mapping.tsv' Error Corrected Reads: text: Error Corrected Reads description: Error corrected reads fastq annotations: file_name_pattern: tag: file_name_pattern value: input.corr.fastq.gz Filtered Sequencing Reads: text: Filtered Sequencing Reads description: Reads QC result fastq (clean data) annotations: file_name_pattern: tag: file_name_pattern value: '/.+?(?=filter)/filter-METAGENOME.fastq.gz ' Read Filtering Info File: text: Read Filtering Info File description: File containing read filtering information annotations: file_name_pattern: tag: file_name_pattern value: '[rqc_wf_activity_id]_readsQC.info' QC Statistics Extended: text: QC Statistics Extended description: Extended report including methods and results for read filtering annotations: file_name_pattern: tag: file_name_pattern value: /.+?(?=filter)/filtered-report.txt QC Statistics: text: QC Statistics description: Reads QC summary statistics annotations: file_name_pattern: tag: file_name_pattern value: '[rqc_wf_activity_id]_filterStats2.txt' TIGRFam Annotation GFF: text: TIGRFam Annotation GFF description: GFF3 format file with TIGRfam annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_tigrfam.gff' CRT Annotation GFF: text: CRT Annotation GFF description: GFF3 format file with CRT annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_crt.gff' Genemark Annotation GFF: text: Genemark Annotation GFF description: GFF3 format file with Genemark annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_genemark.gff' Prodigal Annotation GFF: text: Prodigal Annotation GFF description: GFF3 format file with Prodigal annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_prodigal.gff' TRNA Annotation GFF: text: TRNA Annotation GFF description: GFF3 format file with TRNA annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_trna.gff' Misc Annotation GFF: text: Misc Annotation GFF description: GFF3 format file with Misc annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_rfam_misc_bind_misc_feature_regulatory.gff' RFAM Annotation GFF: text: RFAM Annotation GFF description: GFF3 format file with RFAM annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_rfam.gff' TMRNA Annotation GFF: text: TMRNA Annotation GFF description: GFF3 format file with TMRNA annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_rfam_ncrna_tmrna.gff' Crispr Terms: text: Crispr Terms description: Crispr Terms annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_crt.crisprs' Product Names: text: Product Names description: Product names file annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_product_names.tsv' Gene Phylogeny tsv: text: Gene Phylogeny tsv description: Gene Phylogeny tsv annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_gene_phylogeny.tsv' Scaffold Lineage tsv: text: Scaffold Lineage tsv description: phylogeny at the scaffold level annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_scaffold_lineage.tsv' Clusters of Orthologous Groups (COG) Annotation GFF: text: Clusters of Orthologous Groups (COG) Annotation GFF description: GFF3 format file with COGs annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_cog.gff' KO_EC Annotation GFF: text: KO_EC Annotation GFF description: GFF3 format file with KO_EC annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_ko_ec.gff' CATH FunFams (Functional Families) Annotation GFF: text: CATH FunFams (Functional Families) Annotation GFF description: GFF3 format file with CATH FunFams annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_cath_funfam.gff' SUPERFam Annotation GFF: text: SUPERFam Annotation GFF description: GFF3 format file with SUPERFam annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_supfam.gff' SMART Annotation GFF: text: SMART Annotation GFF description: GFF3 format file with SMART annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_smart.gff' Pfam Annotation GFF: text: Pfam Annotation GFF description: GFF3 format file with Pfam annotations: file_name_pattern: tag: file_name_pattern value: '[GOLD-AP]_pfam.gff' Annotation Statistics: text: Annotation Statistics description: Annotation statistics report Direct Infusion FT ICR-MS Raw Data: text: Direct Infusion FT ICR-MS Raw Data description: Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance mass spectrometry raw data acquired in broadband full scan mode Raw Compressed Metagenome Interleaved Paired-End Reads: text: Raw Compressed Metagenome Interleaved Paired-End Reads description: Raw sequencing reads from a metagenome that is in interleaved paired-end format and compressed using GNU zip format. credit enum: name: credit enum comments: - credit enums come from https://casrai.org/credit/ from_schema: https://w3id.org/nmdc/nmdc permissible_values: Conceptualization: text: Conceptualization description: Conceptualization Data curation: text: Data curation description: Data curation Formal Analysis: text: Formal Analysis description: Formal Analysis Funding acquisition: text: Funding acquisition description: Funding acquisition Investigation: text: Investigation description: Investigation Methodology: text: Methodology description: Methodology Project administration: text: Project administration description: Project administration Resources: text: Resources description: Resources Software: text: Software description: Software Supervision: text: Supervision description: Supervision Validation: text: Validation description: Validation Visualization: text: Visualization description: Visualization Writing original draft: text: Writing original draft description: Writing – original draft Writing review and editing: text: Writing review and editing description: Writing – review & editing Principal Investigator: text: Principal Investigator description: principal investigator role meaning: OBI:0000103 Submitter: text: Submitter description: the person(s) who enter study and biosample metadata into the NMDC submission portal meaning: EFO:0001741 processing_institution_enum: name: processing_institution_enum notes: - This will become the range of processing_institution.omics processing - use ROR meanings like https://ror.org/0168r3w48 for UCSD from_schema: https://w3id.org/nmdc/nmdc permissible_values: UCSD: text: UCSD meaning: https://ror.org/0168r3w48 title: University of California, San Diego JGI: text: JGI meaning: https://ror.org/04xm1d337 title: Joint Genome Institute EMSL: text: EMSL meaning: https://ror.org/04rc0xn13 title: Environmental Molecular Sciences Laboratory notes: - replaces Environmental Molecular Science Laboratory - replaces Environmental Molecular Sciences Lab Battelle: text: Battelle meaning: https://ror.org/01h5tnr73 title: Battelle Memorial Institute ANL: text: ANL meaning: https://ror.org/05gvnxz63 title: Argonne National Laboratory StudyCategoryEnum: name: StudyCategoryEnum from_schema: https://w3id.org/nmdc/nmdc permissible_values: research_study: text: research_study description: A detailed examination, analysis, or critical inspection of a hypothesis-driven experiment. exact_mappings: - SIO:001066 - NCIT:C63536 - ISA:Study close_mappings: - OBI:0000355 consortium: text: consortium description: A group formed to undertake a venture that is beyond the capabilities of the individual members. Each member of the consortium brings a high level of expertise in a specific area to ensure the successful completion of the project. comments: - A consortium has collections of data, those data do not come from a hypothesis-driven experiment. exact_mappings: - NCIT:C61538 ContainerTypeEnum: name: ContainerTypeEnum title: Container type enumeration from_schema: https://w3id.org/nmdc/nmdc permissible_values: screw_top_conical: text: screw_top_conical title: Screw top conical tube aliases: - falcon tube DeviceTypeEnum: name: DeviceTypeEnum title: Shaker type enumeration from_schema: https://w3id.org/nmdc/nmdc permissible_values: orbital_shaker: text: orbital_shaker title: Orbital shaker thermomixer: text: thermomixer title: Thermomixer SamplingMethodEnum: name: SamplingMethodEnum from_schema: https://w3id.org/nmdc/nmdc permissible_values: weighing: text: weighing title: Weighing SolventEnum: name: SolventEnum title: Solvent enumeration from_schema: https://w3id.org/nmdc/nmdc permissible_values: deionized_water: text: deionized_water title: Deionized water broad_mappings: - CHEBI:15377 methanol: text: methanol meaning: CHEBI:17790 title: Methanol chloroform: text: chloroform meaning: CHEBI:35255 title: Chloroform analysis_type_enum: name: analysis_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: metabolomics: text: metabolomics metagenomics: text: metagenomics metaproteomics: text: metaproteomics metatranscriptomics: text: metatranscriptomics natural organic matter: text: natural organic matter rna_sample_format_enum: name: rna_sample_format_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: 10 mM Tris-HCl: text: 10 mM Tris-HCl DNAStable: text: DNAStable Ethanol: text: Ethanol Low EDTA TE: text: Low EDTA TE MDA reaction buffer: text: MDA reaction buffer PBS: text: PBS Pellet: text: Pellet RNAStable: text: RNAStable TE: text: TE Water: text: Water Gentegra-DNA: text: Gentegra-DNA Gentegra-RNA: text: Gentegra-RNA dna_sample_format_enum: name: dna_sample_format_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: 10 mM Tris-HCl: text: 10 mM Tris-HCl DNAStable: text: DNAStable Ethanol: text: Ethanol Low EDTA TE: text: Low EDTA TE MDA reaction buffer: text: MDA reaction buffer PBS: text: PBS Pellet: text: Pellet RNAStable: text: RNAStable TE: text: TE Water: text: Water Gentegra-DNA: text: Gentegra-DNA Gentegra-RNA: text: Gentegra-RNA sample_type_enum: name: sample_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: soil: 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 permissible_values: dust: text: dust organic matter: text: organic matter particulate matter: text: particulate matter volatile organic compounds: text: volatile organic compounds biological contaminants: text: biological contaminants radon: text: radon nutrients: text: nutrients biocides: text: biocides 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 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 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 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 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 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 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 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 cur_land_use_enum: name: cur_land_use_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: badlands: text: badlands cities: text: cities conifers: text: conifers annotations: originally: tag: originally value: conifers (e.g. pine,spruce,fir,cypress) examples: - value: cypress - value: fir - value: pine - value: spruce crop trees: text: crop trees annotations: originally: tag: originally value: crop trees (nuts,fruit,christmas trees,nursery trees) examples: - value: christmas trees - value: fruit - value: nursery trees - value: nuts farmstead: text: farmstead gravel: text: gravel hardwoods: text: hardwoods annotations: originally: tag: originally value: hardwoods (e.g. oak,hickory,elm,aspen) examples: - value: aspen - value: elm - value: hickory - value: oak hayland: text: hayland horticultural plants: text: horticultural plants annotations: originally: tag: originally value: horticultural plants (e.g. tulips) examples: - value: tulips industrial areas: text: industrial areas intermixed hardwood and conifers: text: intermixed hardwood and conifers marshlands: text: marshlands annotations: originally: tag: originally value: marshlands (grass,sedges,rushes) examples: - value: grass - value: rushes - value: sedgees meadows: text: meadows annotations: originally: tag: originally value: meadows (grasses,alfalfa,fescue,bromegrass,timothy) examples: - value: alfalfa - value: bromegrass - value: fescue - value: grasses - value: timothy mines/quarries: text: mines/quarries mudflats: text: mudflats oil waste areas: text: oil waste areas pastureland: text: pastureland annotations: originally: tag: originally value: pastureland (grasslands used for livestock grazing) comments: - grasslands used for livestock grazing permanent snow or ice: text: permanent snow or ice rainforest: text: rainforest annotations: originally: tag: originally value: rainforest (evergreen forest receiving greater than 406 cm annual rainfall) comments: - evergreen forest receiving greater than 406 cm annual rainfall rangeland: text: rangeland roads/railroads: text: roads/railroads rock: text: rock row crops: text: row crops saline seeps: text: saline seeps salt flats: text: salt flats sand: text: sand shrub crops: text: shrub crops annotations: originally: tag: originally value: shrub crops (blueberries,nursery ornamentals,filberts) examples: - value: blueberries - value: filberts - value: nursery ornamentals shrub land: text: shrub land annotations: originally: tag: originally value: shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus) examples: - value: creosote bush - value: eucalyptus - value: mesquite - value: sage-brush - value: shrub oak small grains: text: small grains successional shrub land: text: successional shrub land annotations: originally: tag: originally value: successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries) examples: - value: blackberries - value: chokecherry - value: hazels - value: shrub dogwoods - value: sumacs - value: tree saplings swamp: text: swamp annotations: originally: tag: originally value: swamp (permanent or semi-permanent water body dominated by woody plants) comments: - permanent or semi-permanent water body dominated by woody plants tropical: text: tropical annotations: originally: tag: originally value: tropical (e.g. mangrove,palms) examples: - value: mangrove - value: palms tundra: text: tundra annotations: originally: tag: originally value: tundra (mosses,lichens) examples: - value: lichens - value: mosses vegetable crops: text: vegetable crops vine crops: text: vine crops annotations: originally: tag: originally value: vine crops (grapes) examples: - value: grapes hcr_geol_age_enum: name: hcr_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 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 plant_sex_enum: name: plant_sex_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 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 floor_finish_mat_enum: name: floor_finish_mat_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: tile: text: tile wood strip or parquet: text: wood strip or parquet carpet: text: carpet rug: text: rug laminate wood: text: laminate wood lineoleum: text: lineoleum vinyl composition tile: text: vinyl composition tile sheet vinyl: text: sheet vinyl stone: text: stone bamboo: text: bamboo cork: text: cork terrazo: text: terrazo concrete: text: concrete none: text: none sealed: text: sealed clear finish: text: clear finish paint: text: paint none or unfinished: text: none or unfinished 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 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 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 soil_horizon_enum: name: soil_horizon_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 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 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 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 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 from_schema: https://w3id.org/nmdc/nmdc permissible_values: Clastic: text: Clastic Carbonate: text: Carbonate Coal: text: Coal Biosilicieous: text: Biosilicieous other: text: other 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 surf_material_enum: name: surf_material_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 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 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 from_schema: https://w3id.org/nmdc/nmdc permissible_values: Acrisols: text: Acrisols Andosols: text: Andosols Arenosols: text: Arenosols Cambisols: text: Cambisols Chernozems: text: Chernozems Ferralsols: text: Ferralsols Fluvisols: text: Fluvisols Gleysols: text: Gleysols Greyzems: text: Greyzems Gypsisols: text: Gypsisols Histosols: text: Histosols Kastanozems: text: Kastanozems Lithosols: text: Lithosols Luvisols: text: Luvisols Nitosols: text: Nitosols Phaeozems: text: Phaeozems Planosols: text: Planosols Podzols: text: Podzols Podzoluvisols: text: Podzoluvisols Rankers: text: Rankers Regosols: text: Regosols Rendzinas: text: Rendzinas Solonchaks: text: Solonchaks Solonetz: text: Solonetz Vertisols: text: Vertisols Yermosols: text: Yermosols 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 wall_texture_enum: name: wall_texture_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 from_schema: https://w3id.org/nmdc/nmdc permissible_values: end: text: end mid: text: mid downtown: text: downtown drawings_enum: name: drawings_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 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 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 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 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 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 from_schema: https://w3id.org/nmdc/nmdc permissible_values: DF: text: DF RT: text: RT KB: text: KB MSL: text: MSL other: text: other ext_wall_orient_enum: name: ext_wall_orient_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: north: text: north south: text: south east: text: east west: text: west northeast: text: northeast southeast: text: southeast southwest: 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 from_schema: https://w3id.org/nmdc/nmdc permissible_values: north: text: north south: text: south east: text: east west: text: west northeast: text: northeast southeast: text: southeast southwest: text: southwest northwest: text: northwest window_cover_enum: name: window_cover_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 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 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 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 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 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 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 from_schema: https://w3id.org/nmdc/nmdc permissible_values: ATP: text: ATP MPN: text: MPN other: text: other vis_media_enum: name: vis_media_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 room_condt_enum: name: room_condt_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 visible signs of mold/mildew: text: visible signs of mold/mildew samp_collect_point_enum: name: samp_collect_point_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 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 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 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 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 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 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 door_type_wood_enum: name: door_type_wood_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: bettened and ledged: text: bettened and ledged battened: text: battened ledged and braced: text: ledged and braced ledged and framed: text: ledged and framed ledged, braced and frame: text: ledged, braced and frame framed and paneled: text: framed and paneled glashed or sash: text: glashed or sash flush: text: flush louvered: text: louvered wire gauged: text: wire gauged 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 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 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 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 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 shading_device_type_enum: name: shading_device_type_enum from_schema: https://w3id.org/nmdc/nmdc permissible_values: bahama shutters: text: bahama shutters exterior roll blind: text: exterior roll blind gambrel awning: text: gambrel awning hood awning: text: hood awning porchroller awning: text: porchroller awning sarasota shutters: text: sarasota shutters slatted aluminum: text: slatted aluminum solid aluminum awning: text: solid aluminum awning sun screen: text: sun screen tree: text: tree trellis: text: trellis venetian awning: text: venetian awning train_stat_loc_enum: name: train_stat_loc_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 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 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 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 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 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 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 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 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 slots: metagenome_annotation_id: name: metagenome_annotation_id from_schema: https://w3id.org/nmdc/nmdc range: WorkflowExecutionActivity gene_function_id: name: gene_function_id from_schema: https://w3id.org/nmdc/nmdc range: uriorcurie count: name: count from_schema: https://w3id.org/nmdc/nmdc range: integer functional_annotation_agg: name: functional_annotation_agg from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: FunctionalAnnotationAggMember inlined: true inlined_as_list: true neon_deims_sdr_link: name: neon_deims_sdr_link from_schema: https://w3id.org/nmdc/nmdc range: string neon_eco_type: name: neon_eco_type from_schema: https://w3id.org/nmdc/nmdc range: string neon_soil_type: name: neon_soil_type from_schema: https://w3id.org/nmdc/nmdc range: string ecosystem_path_id: name: ecosystem_path_id description: A unique id representing the GOLD classifiers associated with a sample. from_schema: https://w3id.org/nmdc/nmdc range: string habitat: name: habitat from_schema: https://w3id.org/nmdc/nmdc range: string location: name: location from_schema: https://w3id.org/nmdc/nmdc range: string community: name: community from_schema: https://w3id.org/nmdc/nmdc range: string ncbi_taxonomy_name: name: ncbi_taxonomy_name from_schema: https://w3id.org/nmdc/nmdc range: string ncbi_project_name: name: ncbi_project_name from_schema: https://w3id.org/nmdc/nmdc range: string sample_collection_site: name: sample_collection_site from_schema: https://w3id.org/nmdc/nmdc range: string sample_collection_year: name: sample_collection_year from_schema: https://w3id.org/nmdc/nmdc range: integer sample_collection_month: name: sample_collection_month from_schema: https://w3id.org/nmdc/nmdc status: name: status from_schema: https://w3id.org/nmdc/nmdc range: StatusEnum library_preparation_kit: name: library_preparation_kit from_schema: https://w3id.org/nmdc/nmdc range: string extraction_method: name: extraction_method from_schema: https://w3id.org/nmdc/nmdc extraction_target: name: extraction_target from_schema: https://w3id.org/nmdc/nmdc range: ExtractionTargetEnum quality_control_report: name: quality_control_report from_schema: https://w3id.org/nmdc/nmdc range: QualityControlReport pcr_cycles: name: pcr_cycles from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - OBI:0002475 range: integer input_mass: name: input_mass description: Total mass of sample used in activity. title: sample mass used from_schema: https://w3id.org/nmdc/nmdc aliases: - sample mass - sample weight exact_mappings: - MS:1000004 range: QuantityValue library_type: name: library_type title: library type examples: - value: DNA from_schema: https://w3id.org/nmdc/nmdc range: LibraryTypeEnum zinc: name: zinc annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: mg/kg (ppm) occurrence: tag: occurrence value: '1' description: Concentration of zinc in the sample title: zinc examples: - value: 2.5 mg/kg from_schema: https://w3id.org/nmdc/nmdc see_also: - https://www.ornl.gov/content/bio-scales-0 aliases: - zinc is_a: attribute range: QuantityValue manganese: name: manganese annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: mg/kg (ppm) occurrence: tag: occurrence value: '1' description: Concentration of manganese in the sample title: manganese examples: - value: 24.7 mg/kg from_schema: https://w3id.org/nmdc/nmdc see_also: - https://www.ornl.gov/content/bio-scales-0 aliases: - manganese is_a: attribute range: QuantityValue ammonium_nitrogen: name: ammonium_nitrogen annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: mg/kg occurrence: tag: occurrence value: '1' description: Concentration of ammonium nitrogen in the sample title: ammonium nitrogen examples: - value: 2.3 mg/kg from_schema: https://w3id.org/nmdc/nmdc see_also: - https://www.ornl.gov/content/bio-scales-0 aliases: - ammonium_nitrogen - NH4-N is_a: attribute range: QuantityValue nitrate_nitrogen: name: nitrate_nitrogen annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: mg/kg occurrence: tag: occurrence value: '1' description: Concentration of nitrate nitrogen in the sample title: nitrate_nitrogen comments: - often below some specified limit of detection examples: - value: 0.29 mg/kg from_schema: https://w3id.org/nmdc/nmdc see_also: - https://www.ornl.gov/content/bio-scales-0 aliases: - nitrate_nitrogen - NO3-N is_a: attribute range: QuantityValue nitrite_nitrogen: name: nitrite_nitrogen annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: mg/kg occurrence: tag: occurrence value: '1' description: Concentration of nitrite nitrogen in the sample title: nitrite_nitrogen examples: - value: 1.2 mg/kg from_schema: https://w3id.org/nmdc/nmdc see_also: - https://www.ornl.gov/content/bio-scales-0 aliases: - nitrite_nitrogen - NO2-N is_a: attribute range: QuantityValue lbc_thirty: name: lbc_thirty annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: ppm CaCO3/pH occurrence: tag: occurrence value: '1' description: lime buffer capacity, determined after 30 minute incubation title: lime buffer capacity (at 30 minutes) comments: - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit examples: - value: 543 mg/kg from_schema: https://w3id.org/nmdc/nmdc see_also: - https://www.ornl.gov/content/bio-scales-0 - https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF aliases: - lbc_thirty - lbc30 - lime buffer capacity (at 30 minutes) is_a: attribute range: QuantityValue lbceq: name: lbceq annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: ppm CaCO3/pH occurrence: tag: occurrence value: '1' description: lime buffer capacity, determined at equilibrium after 5 day incubation title: lime buffer capacity (after 5 day incubation) comments: - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit examples: - value: 1575 mg/kg from_schema: https://w3id.org/nmdc/nmdc see_also: - https://www.ornl.gov/content/bio-scales-0 aliases: - lbceq - lime buffer capacity (at 5-day equilibrium) is_a: attribute range: QuantityValue env_package: name: env_package description: MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported in_subset: - mixs extension from_schema: https://w3id.org/nmdc/nmdc aliases: - environmental package is_a: attribute range: TextValue embargoed: name: embargoed description: If true, the data are embargoed and not available for public access. todos: - make this required? - first apply to Biosample - try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata? - applying to a Study may nto be granular enough from_schema: https://w3id.org/nmdc/nmdc range: boolean recommended: true collected_from: name: collected_from description: The Site from which a Biosample was collected todos: - add an OBO slot_uri ? comments: - this illustrates implementing a Biosample relation with a (binary) slot from_schema: https://w3id.org/nmdc/nmdc domain: Biosample range: FieldResearchSite biosample_categories: name: biosample_categories title: Categories the biosample belongs to from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: BiosampleCategoryEnum date_created: name: date_created description: from database class from_schema: https://w3id.org/nmdc/nmdc etl_software_version: name: etl_software_version description: from database class from_schema: https://w3id.org/nmdc/nmdc related_identifiers: name: related_identifiers description: Identifiers assigned to a thing that is similar to that which is represented in NMDC. Related identifier are not an identical match and may have some variation. title: Related Identifiers from_schema: https://w3id.org/nmdc/nmdc notes: name: notes description: from study class from_schema: https://w3id.org/nmdc/nmdc canary: name: canary description: a slot that can be added and removed as evidence that schema changes have propagated to other systems from_schema: https://w3id.org/nmdc/nmdc ess_dive_datasets: name: ess_dive_datasets description: List of ESS-DIVE dataset DOIs from_schema: https://w3id.org/nmdc/nmdc multivalued: true has_credit_associations: name: has_credit_associations annotations: display_hint: tag: display_hint value: Other researchers associated with this study. description: 'This slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study' notes: - 'had just been "inlined: true"' from_schema: https://w3id.org/nmdc/nmdc domain: Study slot_uri: prov:qualifiedAssociation multivalued: true range: CreditAssociation inlined_as_list: true study_image: name: study_image description: Links a study to one or more images. from_schema: https://w3id.org/nmdc/nmdc domain: Study multivalued: true range: ImageValue inlined: true relevant_protocols: name: relevant_protocols from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: string funding_sources: name: funding_sources description: 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. comments: - Include only the name of the funding organization and the award or contract number. examples: - value: National Sciences Foundation Dimensions of Biodiversity (award no. 1342701) - value: U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract DE-AC05-00OR2275 from_schema: https://w3id.org/nmdc/nmdc close_mappings: - NCIT:C39409 multivalued: true range: string applied_role: name: applied_role deprecated: A credit association may have multiple roles. So, use the applied roles slot. from_schema: https://w3id.org/nmdc/nmdc domain: CreditAssociation slot_uri: prov:hadRole range: credit enum applied_roles: name: applied_roles annotations: display_hint: tag: display_hint value: 'Identify all CRediT roles associated with this contributor. CRediT Information: https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/' from_schema: https://w3id.org/nmdc/nmdc domain: CreditAssociation multivalued: true range: credit enum required: true applies_to_person: name: applies_to_person todos: - prov:agent takes an Agent object. Is a person value an Agent? Also try to relate to principal investigator slot? could include OBI:0000103 principal investigator role... do we need to define the OBI prefix? from_schema: https://w3id.org/nmdc/nmdc domain: CreditAssociation range: PersonValue required: true study_category: name: study_category description: The type of research initiative from_schema: https://w3id.org/nmdc/nmdc range: StudyCategoryEnum object_set: name: object_set description: Applies to a property that links a database object to a set of objects. This is necessary in a json document to provide context for a list, and to allow for a single json object that combines multiple object types from_schema: https://w3id.org/nmdc/nmdc mixin: true domain: Database multivalued: true inlined_as_list: true biosample_set: name: biosample_set description: This property links a database object to the set of samples within it. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: Biosample study_set: name: study_set description: This property links a database object to the set of studies within it. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: Study field_research_site_set: name: field_research_site_set from_schema: https://w3id.org/nmdc/nmdc domain: Database multivalued: true range: FieldResearchSite inlined_as_list: true collecting_biosamples_from_site_set: name: collecting_biosamples_from_site_set from_schema: https://w3id.org/nmdc/nmdc domain: Database multivalued: true range: CollectingBiosamplesFromSite inlined_as_list: true data_object_set: name: data_object_set description: This property links a database object to the set of data objects within it. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: DataObject genome_feature_set: name: genome_feature_set description: This property links a database object to the set of all features from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: GenomeFeature functional_annotation_set: name: functional_annotation_set description: This property links a database object to the set of all functional annotations from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: FunctionalAnnotation activity_set: name: activity_set description: This property links a database object to the set of workflow activities. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: WorkflowExecutionActivity mags_activity_set: name: mags_activity_set description: This property links a database object to the set of MAGs analysis activities. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: MagsAnalysisActivity metabolomics_analysis_activity_set: name: metabolomics_analysis_activity_set description: This property links a database object to the set of metabolomics analysis activities. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: MetabolomicsAnalysisActivity metaproteomics_analysis_activity_set: name: metaproteomics_analysis_activity_set description: This property links a database object to the set of metaproteomics analysis activities. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: MetaproteomicsAnalysisActivity metagenome_annotation_activity_set: name: metagenome_annotation_activity_set description: This property links a database object to the set of metagenome annotation activities. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: MetagenomeAnnotationActivity metagenome_assembly_set: name: metagenome_assembly_set description: This property links a database object to the set of metagenome assembly activities. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: MetagenomeAssembly metagenome_sequencing_activity_set: name: metagenome_sequencing_activity_set description: This property links a database object to the set of metagenome sequencing activities. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: MetagenomeSequencingActivity metatranscriptome_activity_set: name: metatranscriptome_activity_set description: This property links a database object to the set of metatranscriptome analysis activities. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: MetatranscriptomeActivity read_qc_analysis_activity_set: name: read_qc_analysis_activity_set description: This property links a database object to the set of read QC analysis activities. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: ReadQcAnalysisActivity read_based_taxonomy_analysis_activity_set: name: read_based_taxonomy_analysis_activity_set description: This property links a database object to the set of read based analysis activities. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: ReadBasedTaxonomyAnalysisActivity nom_analysis_activity_set: name: nom_analysis_activity_set description: This property links a database object to the set of natural organic matter (NOM) analysis activities. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: NomAnalysisActivity omics_processing_set: name: omics_processing_set description: This property links a database object to the set of omics processings within it. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: OmicsProcessing pooling_set: name: pooling_set from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: Pooling processed_sample_set: name: processed_sample_set description: This property links a database object to the set of processed samples within it. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: ProcessedSample extraction_set: name: extraction_set description: This property links a database object to the set of extractions within it. from_schema: https://w3id.org/nmdc/nmdc mixins: - object_set domain: Database multivalued: true range: Extraction library_preparation_set: name: library_preparation_set description: This property links a database object to the set of DNA extractions within it. from_schema: https://w3id.org/nmdc/nmdc aliases: - library_construction_set mixins: - object_set domain: Database multivalued: true range: LibraryPreparation omics_type: name: omics_type description: The type of omics data notes: - was the range string at one point? the values in MongoDB don't look like NMDC classes examples: - value: metatranscriptome - value: metagenome from_schema: https://w3id.org/nmdc/nmdc range: ControlledTermValue data_object_type: name: data_object_type description: The type of file represented by the data object. examples: - value: FT ICR-MS Analysis Results - value: GC-MS Metabolomics Results from_schema: https://w3id.org/nmdc/nmdc range: file type enum compression_type: name: compression_type description: If provided, specifies the compression type todos: - consider enum examples: - value: gzip from_schema: https://w3id.org/nmdc/nmdc range: string gold_path_field: name: gold_path_field description: This is a grouping for any of the gold path fields from_schema: https://w3id.org/nmdc/nmdc is_a: attribute abstract: true range: string ecosystem: name: ecosystem description: An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path. comments: - The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. from_schema: https://w3id.org/nmdc/nmdc see_also: - https://gold.jgi.doe.gov/help is_a: gold_path_field ecosystem_category: name: ecosystem_category description: Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path. comments: - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. from_schema: https://w3id.org/nmdc/nmdc see_also: - https://gold.jgi.doe.gov/help is_a: gold_path_field ecosystem_type: name: ecosystem_type description: Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path. comments: - The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. from_schema: https://w3id.org/nmdc/nmdc see_also: - https://gold.jgi.doe.gov/help is_a: gold_path_field ecosystem_subtype: name: ecosystem_subtype description: Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. comments: - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. from_schema: https://w3id.org/nmdc/nmdc see_also: - https://gold.jgi.doe.gov/help is_a: gold_path_field specific_ecosystem: name: specific_ecosystem description: Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path. comments: - Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. from_schema: https://w3id.org/nmdc/nmdc see_also: - https://gold.jgi.doe.gov/help is_a: gold_path_field principal_investigator: name: principal_investigator description: Principal Investigator who led the study and/or generated the dataset. from_schema: https://w3id.org/nmdc/nmdc aliases: - PI is_a: attribute range: PersonValue dois: name: dois description: A digital object identifier, which is intended to persistantly identify some resource on the web. todos: - the previous doi slot was an attribute, but attribute seems committed to biosamples - should we assert a parent term here? comments: - See especially the resourceTypeGeneral section of the DataCite pdf, on pp48-53 as of 2023-07-19 from_schema: https://w3id.org/nmdc/nmdc see_also: - https://schema.datacite.org/meta/kernel-4.4/doc/DataCite-MetadataKernel_v4.4.pdf - https://api.crossref.org/types aliases: - DOIs - digital object identifiers abstract: true multivalued: true range: uriorcurie pattern: ^doi:10.\d{2,9}/.*$ award_dois: name: award_dois description: One or more DOIs that links a study, or similar entiry, to information about the funding authority. examples: - value: doi:10.46936/10.25585/60000880 description: award_dois link to to an award document. Should not be used to link to datasets or publications. For example, doi:10.15485/1577267 is not an award doi, but a dataset doi. from_schema: https://w3id.org/nmdc/nmdc is_a: dois dataset_dois: name: dataset_dois description: One or more DOIs that links a study, or similar entity, to the generated data. examples: - value: doi:10.15485/1577267 description: dataset_dois link to data encoded in a defined structure (as defined by DataCite). Should not be used to link to publications or administrative information like funding requests or awards. from_schema: https://w3id.org/nmdc/nmdc is_a: dois publication_dois: name: publication_dois description: One or more DOIs that links a study, or similar entity, to a publication. examples: - value: doi:10.1126/science.1058040 description: publication_dois link to a prose document, preferably a peer-reviewed journal article. Should not be used to link to datasets or administrative information like funding requests or awards from_schema: https://w3id.org/nmdc/nmdc is_a: dois add_date: name: add_date description: The date on which the information was added to the database. from_schema: https://w3id.org/nmdc/nmdc range: string emsl_project_dois: name: emsl_project_dois description: One or more DOIs that links to an EMSL Research Campaign page. title: EMSL Project DOI todos: - Make as a subproperty of award_dois examples: - value: doi:10.46936/intm.proj.2021.6014 description: emsl_project_dois link to the document outlining the EMSL specific award for the project. Should not be used to link to datasets or publications. from_schema: https://w3id.org/nmdc/nmdc is_a: dois mixins: - emsl_identifiers mod_date: name: mod_date description: The last date on which the database information was modified. from_schema: https://w3id.org/nmdc/nmdc range: string sample_collection_day: name: sample_collection_day from_schema: https://w3id.org/nmdc/nmdc range: integer sample_collection_hour: name: sample_collection_hour from_schema: https://w3id.org/nmdc/nmdc range: integer sample_collection_minute: name: sample_collection_minute from_schema: https://w3id.org/nmdc/nmdc range: integer salinity_category: name: salinity_category description: 'Categorical description of the sample''s salinity. Examples: halophile, halotolerant, hypersaline, huryhaline' notes: - maps to gold:salinity from_schema: https://w3id.org/nmdc/nmdc see_also: - https://github.com/microbiomedata/nmdc-metadata/pull/297 range: string soluble_iron_micromol: name: soluble_iron_micromol from_schema: https://w3id.org/nmdc/nmdc range: string host_name: name: host_name from_schema: https://w3id.org/nmdc/nmdc range: string subsurface_depth: name: subsurface_depth from_schema: https://w3id.org/nmdc/nmdc range: QuantityValue proport_woa_temperature: name: proport_woa_temperature from_schema: https://w3id.org/nmdc/nmdc range: string biogas_temperature: name: biogas_temperature from_schema: https://w3id.org/nmdc/nmdc range: string soil_annual_season_temp: name: soil_annual_season_temp from_schema: https://w3id.org/nmdc/nmdc range: string biogas_retention_time: name: biogas_retention_time from_schema: https://w3id.org/nmdc/nmdc range: string processing_institution: name: processing_institution description: The organization that processed the sample. from_schema: https://w3id.org/nmdc/nmdc range: processing_institution_enum completion_date: name: completion_date from_schema: https://w3id.org/nmdc/nmdc range: string metagenome_assembly_parameter: name: metagenome_assembly_parameter from_schema: https://w3id.org/nmdc/nmdc abstract: true has_peptide_quantifications: name: has_peptide_quantifications from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: PeptideQuantification asm_score: name: asm_score description: A score for comparing metagenomic assembly quality from same sample. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float scaffolds: name: scaffolds description: Total sequence count of all scaffolds. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float scaf_logsum: name: scaf_logsum description: The sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float scaf_powsum: name: scaf_powsum description: Powersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25). from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float scaf_max: name: scaf_max description: Maximum scaffold length. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float scaf_bp: name: scaf_bp description: Total size in bp of all scaffolds. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float scaf_n50: name: scaf_n50 description: Given a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float scaf_n90: name: scaf_n90 description: Given a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float scaf_l50: name: scaf_l50 description: Given a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float scaf_l90: name: scaf_l90 description: The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float scaf_n_gt50k: name: scaf_n_gt50k description: Total sequence count of scaffolds greater than 50 KB. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float scaf_l_gt50k: name: scaf_l_gt50k description: Total size in bp of all scaffolds greater than 50 KB. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float scaf_pct_gt50k: name: scaf_pct_gt50k description: Total sequence size percentage of scaffolds greater than 50 KB. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float contigs: name: contigs description: The sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float contig_bp: name: contig_bp description: Total size in bp of all contigs. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float ctg_n50: name: ctg_n50 description: Given a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float ctg_l50: name: ctg_l50 description: Given a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float ctg_n90: name: ctg_n90 description: Given a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float ctg_l90: name: ctg_l90 description: The L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float ctg_logsum: name: ctg_logsum description: Maximum contig length. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float ctg_powsum: name: ctg_powsum description: Powersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25). from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float ctg_max: name: ctg_max description: Maximum contig length. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float gap_pct: name: gap_pct description: The gap size percentage of all scaffolds. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float gc_std: name: gc_std description: Standard deviation of GC content of all contigs. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float gc_avg: name: gc_avg description: Average of GC content of all contigs. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float num_input_reads: name: num_input_reads description: The sequence count number of input reads for assembly. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float num_aligned_reads: name: num_aligned_reads description: The sequence count number of input reads aligned to assembled contigs. from_schema: https://w3id.org/nmdc/nmdc is_a: metagenome_assembly_parameter range: float read_qc_analysis_statistic: name: read_qc_analysis_statistic from_schema: https://w3id.org/nmdc/nmdc abstract: true mags_list: name: mags_list from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: MagBin too_short_contig_num: name: too_short_contig_num from_schema: https://w3id.org/nmdc/nmdc range: integer binned_contig_num: name: binned_contig_num from_schema: https://w3id.org/nmdc/nmdc range: integer input_contig_num: name: input_contig_num from_schema: https://w3id.org/nmdc/nmdc range: integer unbinned_contig_num: name: unbinned_contig_num from_schema: https://w3id.org/nmdc/nmdc range: integer low_depth_contig_num: name: low_depth_contig_num from_schema: https://w3id.org/nmdc/nmdc range: integer input_read_count: name: input_read_count description: The sequence count number of input reads for QC analysis. from_schema: https://w3id.org/nmdc/nmdc is_a: read_qc_analysis_statistic range: float input_base_count: name: input_base_count description: The nucleotide base count number of input reads for QC analysis. from_schema: https://w3id.org/nmdc/nmdc is_a: read_qc_analysis_statistic range: float output_read_count: name: output_read_count description: After QC analysis sequence count number. from_schema: https://w3id.org/nmdc/nmdc is_a: read_qc_analysis_statistic range: float output_base_count: name: output_base_count description: After QC analysis nucleotide base count number. from_schema: https://w3id.org/nmdc/nmdc is_a: read_qc_analysis_statistic range: float output_read_bases: name: output_read_bases description: TODO from_schema: https://w3id.org/nmdc/nmdc range: float input_read_bases: name: input_read_bases description: 'TODO ' from_schema: https://w3id.org/nmdc/nmdc range: float has_calibration: name: has_calibration description: A reference to a file that holds calibration information. from_schema: https://w3id.org/nmdc/nmdc range: string has_metabolite_quantifications: name: has_metabolite_quantifications from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: MetaboliteQuantification version: name: version from_schema: https://w3id.org/nmdc/nmdc total_bases: name: total_bases todos: - this slot needs some basic textual annotations and constraints from_schema: https://w3id.org/nmdc/nmdc members_id: name: members_id todos: - this slot needs some basic textual annotations and constraints from_schema: https://w3id.org/nmdc/nmdc bin_name: name: bin_name from_schema: https://w3id.org/nmdc/nmdc range: string number_of_contig: name: number_of_contig from_schema: https://w3id.org/nmdc/nmdc range: integer completeness: name: completeness from_schema: https://w3id.org/nmdc/nmdc range: float contamination: name: contamination from_schema: https://w3id.org/nmdc/nmdc range: float gene_count: name: gene_count from_schema: https://w3id.org/nmdc/nmdc range: integer bin_quality: name: bin_quality from_schema: https://w3id.org/nmdc/nmdc range: string num_16s: name: num_16s from_schema: https://w3id.org/nmdc/nmdc range: integer num_5s: name: num_5s from_schema: https://w3id.org/nmdc/nmdc range: integer num_23s: name: num_23s from_schema: https://w3id.org/nmdc/nmdc range: integer num_t_rna: name: num_t_rna from_schema: https://w3id.org/nmdc/nmdc range: integer gtdbtk_domain: name: gtdbtk_domain from_schema: https://w3id.org/nmdc/nmdc range: string gtdbtk_phylum: name: gtdbtk_phylum from_schema: https://w3id.org/nmdc/nmdc range: string gtdbtk_class: name: gtdbtk_class from_schema: https://w3id.org/nmdc/nmdc range: string gtdbtk_order: name: gtdbtk_order from_schema: https://w3id.org/nmdc/nmdc range: string gtdbtk_family: name: gtdbtk_family from_schema: https://w3id.org/nmdc/nmdc range: string gtdbtk_genus: name: gtdbtk_genus from_schema: https://w3id.org/nmdc/nmdc range: string gtdbtk_species: name: gtdbtk_species from_schema: https://w3id.org/nmdc/nmdc range: string language: name: language description: Should use ISO 639-1 code e.g. "en", "fr" from_schema: https://w3id.org/nmdc/nmdc range: language code attribute: name: attribute description: 'A attribute of a biosample. Examples: depth, habitat, material. For NMDC, attributes SHOULD be mapped to terms within a MIxS template' from_schema: https://w3id.org/nmdc/nmdc aliases: - field - property - template field - key - characteristic abstract: true has_raw_value: name: has_raw_value description: The value that was specified for an annotation in raw form, i.e. a string. E.g. "2 cm" or "2-4 cm" from_schema: https://w3id.org/nmdc/nmdc domain: AttributeValue multivalued: false range: string has_unit: name: has_unit description: Links a QuantityValue to a unit from_schema: https://w3id.org/nmdc/nmdc aliases: - scale mappings: - qud:unit - schema:unitCode range: unit has_numeric_value: name: has_numeric_value description: Links a quantity value to a number from_schema: https://w3id.org/nmdc/nmdc mappings: - qud:quantityValue - schema:value multivalued: false range: float has_minimum_numeric_value: name: has_minimum_numeric_value description: The minimum value part, expressed as number, of the quantity value when the value covers a range. from_schema: https://w3id.org/nmdc/nmdc is_a: has_numeric_value has_maximum_numeric_value: name: has_maximum_numeric_value description: The maximum value part, expressed as number, of the quantity value when the value covers a range. from_schema: https://w3id.org/nmdc/nmdc is_a: has_numeric_value has_boolean_value: name: has_boolean_value description: Links a quantity value to a boolean from_schema: https://w3id.org/nmdc/nmdc multivalued: false range: boolean latitude: name: latitude description: latitude examples: - value: '-33.460524' from_schema: https://w3id.org/nmdc/nmdc mappings: - schema:latitude domain: GeolocationValue slot_uri: wgs84:lat range: decimal degree longitude: name: longitude description: longitude examples: - value: '150.168149' from_schema: https://w3id.org/nmdc/nmdc mappings: - schema:longitude domain: GeolocationValue slot_uri: wgs84:long range: decimal degree term: name: term description: pointer to an ontology class notes: - 'removed ''slot_uri: rdf:type''' from_schema: https://w3id.org/nmdc/nmdc domain: ControlledTermValue range: OntologyClass inlined: true orcid: name: orcid description: The ORCID of a person. from_schema: https://w3id.org/nmdc/nmdc domain: PersonValue range: string email: name: email description: An email address for an entity such as a person. This should be the primary email address used. from_schema: https://w3id.org/nmdc/nmdc slot_uri: schema:email range: string alternate_emails: name: alternate_emails description: One or more other email addresses for an entity. from_schema: https://w3id.org/nmdc/nmdc range: string profile_image_url: name: profile_image_url description: A url that points to an image of a person. from_schema: https://w3id.org/nmdc/nmdc domain: PersonValue range: string has_input: name: has_input description: An input to a process. from_schema: https://w3id.org/nmdc/nmdc aliases: - input domain: NamedThing multivalued: true range: NamedThing has_output: name: has_output description: An output biosample to a processing step from_schema: https://w3id.org/nmdc/nmdc aliases: - output domain: NamedThing multivalued: true range: NamedThing part_of: name: part_of description: Links a resource to another resource that either logically or physically includes it. from_schema: https://w3id.org/nmdc/nmdc aliases: - is part of domain: NamedThing slot_uri: dcterms:isPartOf multivalued: true range: NamedThing execution_resource: name: execution_resource examples: - value: NERSC-Cori from_schema: https://w3id.org/nmdc/nmdc is_a: attribute url: name: url notes: - See issue 207 - this clashes with the mixs field from_schema: https://w3id.org/nmdc/nmdc is_a: attribute range: string display_order: name: display_order description: When rendering information, this attribute to specify the order in which the information should be rendered. from_schema: https://w3id.org/nmdc/nmdc is_a: attribute git_url: name: git_url examples: - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1 from_schema: https://w3id.org/nmdc/nmdc is_a: attribute range: string file_size_bytes: name: file_size_bytes description: Size of the file in bytes from_schema: https://w3id.org/nmdc/nmdc is_a: attribute range: bytes md5_checksum: name: md5_checksum description: MD5 checksum of file (pre-compressed) from_schema: https://w3id.org/nmdc/nmdc is_a: attribute range: string keywords: name: keywords description: A list of keywords that used to associate the entity. Keywords SHOULD come from controlled vocabularies, including MESH, ENVO. from_schema: https://w3id.org/nmdc/nmdc mappings: - dcterms:subject multivalued: true range: string objective: name: objective description: The scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract. from_schema: https://w3id.org/nmdc/nmdc mappings: - SIO:000337 multivalued: false range: string websites: name: websites description: A list of websites that are associated with the entity. from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: string publications: name: publications description: A list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible. from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: string highest_similarity_score: name: highest_similarity_score todos: - Yuri to fill in description from_schema: https://w3id.org/nmdc/nmdc range: float metabolite_quantified: name: metabolite_quantified description: the specific metabolite identifier from_schema: https://w3id.org/nmdc/nmdc range: ChemicalEntity all_proteins: name: all_proteins description: the list of protein identifiers that are associated with the peptide sequence from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: GeneProduct best_protein: name: best_protein description: the specific protein identifier most correctly associated with the peptide sequence from_schema: https://w3id.org/nmdc/nmdc range: GeneProduct min_q_value: name: min_q_value description: smallest Q-Value associated with the peptide sequence as provided by MSGFPlus tool from_schema: https://w3id.org/nmdc/nmdc see_also: - OBI:0001442 range: float peptide_sequence: name: peptide_sequence from_schema: https://w3id.org/nmdc/nmdc range: string peptide_spectral_count: name: peptide_spectral_count description: sum of filter passing MS2 spectra associated with the peptide sequence within a given LC-MS/MS data file from_schema: https://w3id.org/nmdc/nmdc range: integer peptide_sum_masic_abundance: name: peptide_sum_masic_abundance description: combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the peptide sequence from a given LC-MS/MS data file using the MASIC tool from_schema: https://w3id.org/nmdc/nmdc range: integer chemical_formula: name: chemical_formula description: A generic grouping for molecular formulae and empirical formulae from_schema: https://w3id.org/nmdc/nmdc range: string inchi_key: name: inchi_key notes: - 'key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental testing. J Cheminform. 4:12' from_schema: https://w3id.org/nmdc/nmdc range: string inchi: name: inchi from_schema: https://w3id.org/nmdc/nmdc range: string peptide_sequence_count: name: peptide_sequence_count description: count of peptide sequences grouped to the best_protein from_schema: https://w3id.org/nmdc/nmdc range: integer protein_spectral_count: name: protein_spectral_count description: sum of filter passing MS2 spectra associated with the best protein within a given LC-MS/MS data file from_schema: https://w3id.org/nmdc/nmdc range: integer protein_sum_masic_abundance: name: protein_sum_masic_abundance description: combined MS1 extracted ion chromatograms derived from MS2 spectra associated with the best protein from a given LC-MS/MS data file using the MASIC tool from_schema: https://w3id.org/nmdc/nmdc range: integer smiles: name: smiles description: A string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol. from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: string started_at_time: name: started_at_time notes: - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/ It may not be complete, but it is good enough for now.' from_schema: https://w3id.org/nmdc/nmdc mappings: - prov:startedAtTime pattern: ^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$ ended_at_time: name: ended_at_time notes: - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/ It may not be complete, but it is good enough for now.' from_schema: https://w3id.org/nmdc/nmdc mappings: - prov:endedAtTime pattern: ^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$ was_informed_by: name: was_informed_by from_schema: https://w3id.org/nmdc/nmdc mappings: - prov:wasInformedBy range: Activity was_generated_by: name: was_generated_by from_schema: https://w3id.org/nmdc/nmdc mappings: - prov:wasGeneratedBy range: Activity used: name: used from_schema: https://w3id.org/nmdc/nmdc mappings: - prov:used domain: Activity id: name: id description: A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI notes: - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?' - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions - minting authority shoulders should probably be enumerated and checked in the pattern examples: - value: nmdc:mgmag-00-x012.1_7_c1 description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248 from_schema: https://w3id.org/nmdc/nmdc identifier: true range: uriorcurie required: true pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$ name: name: name description: A human readable label for an entity from_schema: https://w3id.org/nmdc/nmdc range: string description: name: description description: a human-readable description of a thing from_schema: https://w3id.org/nmdc/nmdc slot_uri: dcterms:description range: string type: name: type description: An optional string that specifies the type object. This is used to allow for searches for different kinds of objects. deprecated: Due to confusion about what values are used for this slot, it is best not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248. MAM removed designates_type and rdf:type slot uri 2022-11-30 examples: - value: nmdc:Biosample - value: nmdc:Study from_schema: https://w3id.org/nmdc/nmdc range: string title: name: title description: A name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study. from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - dcterms:title range: string alternative_titles: name: alternative_titles description: A list of alternative titles for the entity. The distinction between title and alternative titles is application-specific. from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - dcterms:alternative multivalued: true range: string alternative_names: name: alternative_names description: A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific. from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - dcterms:alternative - skos:altLabel multivalued: true range: string alternative_descriptions: name: alternative_descriptions description: A list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific. from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: string alternative_identifiers: name: alternative_identifiers description: A list of alternative identifiers for the entity. from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: uriorcurie pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$ start_date: name: start_date description: The date on which any process or activity was started todos: - add date string validation pattern comments: - We are using string representations of dates until all components of our ecosystem can handle ISO 8610 dates - The date should be formatted as YYYY-MM-DD from_schema: https://w3id.org/nmdc/nmdc range: string end_date: name: end_date description: The date on which any process or activity was ended todos: - add date string validation pattern comments: - We are using string representations of dates until all components of our ecosystem can handle ISO 8610 dates - The date should be formatted as YYYY-MM-DD from_schema: https://w3id.org/nmdc/nmdc range: string protocol_link: name: protocol_link from_schema: https://w3id.org/nmdc/nmdc range: Protocol nucleic_acid_concentration: name: nucleic_acid_concentration from_schema: https://w3id.org/nmdc/nmdc range: InstrumentValue biomaterial_purity: name: biomaterial_purity from_schema: https://w3id.org/nmdc/nmdc range: QuantityValue instrument_name: name: instrument_name description: The name of the instrument that was used for processing the sample. from_schema: https://w3id.org/nmdc/nmdc external_database_identifiers: name: external_database_identifiers description: Link to corresponding identifier in external database notes: - had tried ranges of external identifier and string comments: - The value of this field is always a registered CURIE from_schema: https://w3id.org/nmdc/nmdc close_mappings: - skos:closeMatch is_a: alternative_identifiers abstract: true multivalued: true range: external_identifier pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$ img_identifiers: name: img_identifiers description: A list of identifiers that relate the biosample to records in the IMG database. title: IMG Identifiers todos: - add is_a or mixin modeling, like other external_database_identifiers - what class would IMG records belong to?! Are they Studies, Biosamples, or something else? from_schema: https://w3id.org/nmdc/nmdc is_a: external_database_identifiers pattern: ^img\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\/\.]*$ igsn_identifiers: name: igsn_identifiers from_schema: https://w3id.org/nmdc/nmdc mixin: true gold_identifiers: name: gold_identifiers from_schema: https://w3id.org/nmdc/nmdc see_also: - https://gold.jgi.doe.gov/ mixin: true emsl_identifiers: name: emsl_identifiers from_schema: https://w3id.org/nmdc/nmdc mixin: true mgnify_identifiers: name: mgnify_identifiers from_schema: https://w3id.org/nmdc/nmdc see_also: - https://www.ebi.ac.uk/metagenomics/ mixin: true insdc_identifiers: name: insdc_identifiers description: Any identifier covered by the International Nucleotide Sequence Database Collaboration comments: - note that we deliberately abstract over which of the partner databases accepted the initial submission - 'the first letter of the accession indicates which partner accepted the initial submission: E for ENA, D for DDBJ, or S or N for NCBI.' from_schema: https://w3id.org/nmdc/nmdc see_also: - https://www.insdc.org/ - https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html aliases: - EBI identifiers - NCBI identifiers - DDBJ identifiers mixin: true massive_identifiers: name: massive_identifiers description: identifiers for entities according to MASSIVE from_schema: https://w3id.org/nmdc/nmdc mixin: true neon_identifiers: name: neon_identifiers description: identifiers for entities according to NEON from_schema: https://w3id.org/nmdc/nmdc mixin: true jgi_portal_identifiers: name: jgi_portal_identifiers description: identifiers for entities according to JGI Portal from_schema: https://w3id.org/nmdc/nmdc mixin: true gnps_identifiers: name: gnps_identifiers from_schema: https://w3id.org/nmdc/nmdc mixin: true study_identifiers: name: study_identifiers from_schema: https://w3id.org/nmdc/nmdc is_a: external_database_identifiers abstract: true jgi_portal_study_identifiers: name: jgi_portal_study_identifiers id_prefixes: - jgi.proposal description: 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. title: JGI Portal Study identifiers comments: - 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 examples: - value: jgi.proposal:507130 from_schema: https://w3id.org/nmdc/nmdc is_a: study_identifiers mixins: - jgi_portal_identifiers pattern: ^jgi.proposal:\d+$ neon_study_identifiers: name: neon_study_identifiers from_schema: https://w3id.org/nmdc/nmdc is_a: study_identifiers mixins: - neon_identifiers insdc_sra_ena_study_identifiers: name: insdc_sra_ena_study_identifiers description: identifiers for corresponding project in INSDC SRA / ENA examples: - value: https://bioregistry.io/insdc.sra:SRP121659 description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome from_schema: https://w3id.org/nmdc/nmdc see_also: - https://github.com/bioregistry/bioregistry/issues/109 - https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies - https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies aliases: - EBI ENA study identifiers - NCBI SRA identifiers - DDBJ SRA identifiers is_a: study_identifiers mixins: - insdc_identifiers pattern: ^insdc.sra:(E|D|S)RP[0-9]{6,}$ insdc_bioproject_identifiers: name: insdc_bioproject_identifiers description: identifiers for corresponding project in INSDC Bioproject comments: - these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?) one to one examples: - value: https://bioregistry.io/bioproject:PRJNA366857 description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome from_schema: https://w3id.org/nmdc/nmdc see_also: - https://www.ncbi.nlm.nih.gov/bioproject/ - https://www.ddbj.nig.ac.jp/bioproject/index-e.html aliases: - NCBI bioproject identifiers - DDBJ bioproject identifiers is_a: study_identifiers mixins: - insdc_identifiers pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$ gold_study_identifiers: name: gold_study_identifiers description: identifiers for corresponding project(s) in GOLD title: GOLD Study Identifiers comments: - uses the prefix GS (but possibly in a different case) examples: - value: https://bioregistry.io/gold:Gs0110115 from_schema: https://w3id.org/nmdc/nmdc see_also: - https://gold.jgi.doe.gov/studies is_a: study_identifiers mixins: - gold_identifiers pattern: ^gold:Gs[0-9]+$ mgnify_project_identifiers: name: mgnify_project_identifiers description: identifiers for corresponding project in MGnify examples: - value: https://bioregistry.io/mgnify.proj:MGYS00005757 from_schema: https://w3id.org/nmdc/nmdc is_a: study_identifiers mixins: - mgnify_identifiers pattern: ^mgnify.proj:[A-Z]+[0-9]+$ gnps_task_identifiers: name: gnps_task_identifiers description: identifiers that link a NMDC study to a web-based report about metabolomics analysis progress and results title: GNPS task identifiers comments: - 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 examples: - value: gnps.task:4b848c342a4f4abc871bdf8a09a60807 from_schema: https://w3id.org/nmdc/nmdc see_also: - https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysisActivity/ is_a: study_identifiers mixins: - gnps_identifiers pattern: ^gnps\.task:[a-f0-9]+$ massive_study_identifiers: name: massive_study_identifiers description: identifiers for corresponding study in MASSIVE todos: - prefix not defined yet examples: - value: MASSIVE:MSV000090886 description: MASSIVE id for MASSIVE's metabolomics analysis of Gb0305843, resolvable with prefix http://identifiers.org/massive/ from_schema: https://w3id.org/nmdc/nmdc see_also: - https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=83574f41458a4b259621d5c32a4d82f9 is_a: study_identifiers mixins: - massive_identifiers pattern: '^MASSIVE:' biosample_identifiers: name: biosample_identifiers from_schema: https://w3id.org/nmdc/nmdc is_a: external_database_identifiers abstract: true neon_biosample_identifiers: name: neon_biosample_identifiers from_schema: https://w3id.org/nmdc/nmdc is_a: biosample_identifiers mixins: - neon_identifiers gold_biosample_identifiers: name: gold_biosample_identifiers description: identifiers for corresponding sample in GOLD examples: - value: https://bioregistry.io/gold:Gb0312930 from_schema: https://w3id.org/nmdc/nmdc is_a: biosample_identifiers mixins: - gold_identifiers pattern: ^gold:Gb[0-9]+$ insdc_biosample_identifiers: name: insdc_biosample_identifiers description: identifiers for corresponding sample in INSDC examples: - value: https://bioregistry.io/biosample:SAMEA5989477 - value: https://bioregistry.io/biosample:SAMD00212331 description: I13_N_5-10 sample from Soil fungal diversity along elevational gradients from_schema: https://w3id.org/nmdc/nmdc see_also: - https://github.com/bioregistry/bioregistry/issues/108 - https://www.ebi.ac.uk/biosamples/ - https://www.ncbi.nlm.nih.gov/biosample - https://www.ddbj.nig.ac.jp/biosample/index-e.html aliases: - EBI biosample identifiers - NCBI biosample identifiers - DDBJ biosample identifiers is_a: biosample_identifiers mixins: - insdc_identifiers pattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$ insdc_secondary_sample_identifiers: name: insdc_secondary_sample_identifiers description: secondary identifiers for corresponding sample in INSDC comments: - ENA redirects these to primary IDs, e.g. https://www.ebi.ac.uk/ena/browser/view/DRS166340 -> SAMD00212331 - MGnify uses these as their primary sample IDs examples: - value: https://bioregistry.io/insdc.sra:DRS166340 description: I13_N_5-10 sample from Soil fungal diversity along elevational gradients from_schema: https://w3id.org/nmdc/nmdc is_a: biosample_identifiers mixins: - insdc_identifiers pattern: ^biosample:(E|D|S)RS[0-9]{6,}$ emsl_biosample_identifiers: name: emsl_biosample_identifiers description: A list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database. title: EMSL Biosample Identifiers todos: - removed "planned" once NEXUS is online - determine real expansion for emsl prefix from_schema: https://w3id.org/nmdc/nmdc is_a: biosample_identifiers mixins: - emsl_identifiers igsn_biosample_identifiers: name: igsn_biosample_identifiers description: A list of identifiers for the biosample from the IGSN database. title: IGSN Biosample Identifiers from_schema: https://w3id.org/nmdc/nmdc is_a: biosample_identifiers mixins: - igsn_identifiers omics_processing_identifiers: name: omics_processing_identifiers from_schema: https://w3id.org/nmdc/nmdc is_a: external_database_identifiers abstract: true gold_sequencing_project_identifiers: name: gold_sequencing_project_identifiers description: identifiers for corresponding sequencing project in GOLD examples: - value: https://bioregistry.io/gold:Gp0108335 from_schema: https://w3id.org/nmdc/nmdc is_a: omics_processing_identifiers mixins: - gold_identifiers pattern: ^gold:Gp[0-9]+$ insdc_experiment_identifiers: name: insdc_experiment_identifiers from_schema: https://w3id.org/nmdc/nmdc is_a: external_database_identifiers mixins: - insdc_identifiers pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$ analysis_identifiers: name: analysis_identifiers from_schema: https://w3id.org/nmdc/nmdc is_a: external_database_identifiers abstract: true gold_analysis_project_identifiers: name: gold_analysis_project_identifiers description: identifiers for corresponding analysis project in GOLD examples: - value: https://bioregistry.io/gold:Ga0526289 from_schema: https://w3id.org/nmdc/nmdc is_a: analysis_identifiers mixins: - gold_identifiers pattern: ^gold:Ga[0-9]+$ insdc_analysis_identifiers: name: insdc_analysis_identifiers comments: - in INSDC this is a run but it corresponds to a GOLD analysis examples: - value: https://www.ebi.ac.uk/metagenomics/runs/DRR218479 description: Illumina MiSeq paired end sequencing of SAMD00212331 - value: https://www.ebi.ac.uk/ena/browser/view/ERR436051 from_schema: https://w3id.org/nmdc/nmdc is_a: analysis_identifiers mixins: - insdc_identifiers pattern: ^insdc.sra:(E|D|S)RR[0-9]{6,}$ mgnify_analysis_identifiers: name: mgnify_analysis_identifiers notes: - 'removed pattern: "^mgnify:MGYA[0-9]+$" ## TODO https://github.com/bioregistry/bioregistry/issues/109' examples: - value: https://www.ebi.ac.uk/metagenomics/analyses/MGYA00002270 description: combined analyses (taxonomic, functional) of sample ERS438107 from_schema: https://w3id.org/nmdc/nmdc is_a: analysis_identifiers mixins: - mgnify_identifiers assembly_identifiers: name: assembly_identifiers from_schema: https://w3id.org/nmdc/nmdc abstract: true insdc_assembly_identifiers: name: insdc_assembly_identifiers from_schema: https://w3id.org/nmdc/nmdc is_a: assembly_identifiers mixins: - insdc_identifiers pattern: ^insdc.sra:[A-Z]+[0-9]+(\.[0-9]+)?$ dissolving_activity_set: name: dissolving_activity_set title: dissolving activity set from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: DissolvingActivity inlined_as_list: true material_sample_set: name: material_sample_set title: material sample set from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: MaterialSample inlined_as_list: true material_sampling_activity_set: name: material_sampling_activity_set title: material sampling activity set from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: MaterialSamplingActivity inlined_as_list: true reaction_activity_set: name: reaction_activity_set from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: ReactionActivity inlined_as_list: true dissolution_aided_by: name: dissolution_aided_by title: dissolution aided by from_schema: https://w3id.org/nmdc/nmdc aliases: - shaker range: LabDevice inlined: true dissolution_reagent: name: dissolution_reagent title: dissolution reagent from_schema: https://w3id.org/nmdc/nmdc aliases: - solvent range: SolventEnum dissolution_volume: name: dissolution_volume title: dissolution volume from_schema: https://w3id.org/nmdc/nmdc aliases: - volume range: QuantityValue inlined: true dissolved_in: name: dissolved_in title: dissolved in from_schema: https://w3id.org/nmdc/nmdc aliases: - container range: MaterialContainer inlined: true material_input: name: material_input title: material input from_schema: https://w3id.org/nmdc/nmdc range: MaterialSample material_output: name: material_output title: material output from_schema: https://w3id.org/nmdc/nmdc range: MaterialSample device_type: name: device_type title: device type from_schema: https://w3id.org/nmdc/nmdc aliases: - shaker type range: DeviceTypeEnum activity_speed: name: activity_speed title: activity speed from_schema: https://w3id.org/nmdc/nmdc aliases: - shake_speed range: QuantityValue inlined: true activity_temperature: name: activity_temperature todos: - constrain units from_schema: https://w3id.org/nmdc/nmdc range: QuantityValue inlined: true activity_time: name: activity_time title: activity time from_schema: https://w3id.org/nmdc/nmdc aliases: - shake_time range: QuantityValue inlined: true container_size: name: container_size title: container size from_schema: https://w3id.org/nmdc/nmdc range: QuantityValue inlined: true container_type: name: container_type title: container type from_schema: https://w3id.org/nmdc/nmdc range: ContainerTypeEnum amount_collected: name: amount_collected title: amount collected from_schema: https://w3id.org/nmdc/nmdc range: QuantityValue inlined: true collected_into: name: collected_into title: collected into from_schema: https://w3id.org/nmdc/nmdc range: MaterialContainer inlined: true sampling_method: name: sampling_method title: sampling method from_schema: https://w3id.org/nmdc/nmdc range: SamplingMethodEnum reaction_aided_by: name: reaction_aided_by title: reaction aided by from_schema: https://w3id.org/nmdc/nmdc aliases: - shaker range: LabDevice inlined: true reaction_temperature: name: reaction_temperature from_schema: https://w3id.org/nmdc/nmdc reaction_time: name: reaction_time from_schema: https://w3id.org/nmdc/nmdc range: QuantityValue inlined: true analysis_type: name: analysis_type description: Select all the data types associated or available for this biosample title: analysis/data type examples: - value: metagenomics; metabolomics; proteomics from_schema: https://w3id.org/nmdc/nmdc see_also: - MIxS:investigation_type rank: 3 multivalued: true slot_group: Sample ID range: analysis_type_enum recommended: true sample_link: name: sample_link description: A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample. title: sample linkage comments: - 'This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)' examples: - value: IGSN:DSJ0284 from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{text}:{text}' multivalued: true slot_group: Sample ID range: string recommended: true collection_date_inc: name: collection_date_inc description: Date the incubation was harvested/collected/ended. Only relevant for incubation samples. title: incubation collection date notes: - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only comments: - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. examples: - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc see_also: - MIxS:collection_date rank: 2 string_serialization: '{date, arbitrary precision}' slot_group: MIxS Inspired recommended: true collection_time: name: collection_time description: The time of sampling, either as an instance (single point) or interval. title: collection time, GMT notes: - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only comments: - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter' examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc see_also: - MIxS:collection_date rank: 1 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired recommended: true collection_time_inc: name: collection_time_inc description: Time the incubation was harvested/collected/ended. Only relevant for incubation samples. title: incubation collection time, GMT notes: - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only comments: - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter' examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc see_also: - MIxS:collection_date rank: 3 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired recommended: true experimental_factor_other: name: experimental_factor_other description: Other details about your sample that you feel can't be accurately represented in the available columns. title: experimental factor- other comments: - This slot accepts open-ended text about your sample. - We recommend using key:value pairs. - Provided pairs will be considered for inclusion as future slots/terms in this data collection template. 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 recommended: true filter_method: name: filter_method description: Type of filter used or how the sample was filtered title: filter method comments: - describe the filter or provide a catalog number and manufacturer examples: - 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 recommended: true isotope_exposure: name: isotope_exposure description: List isotope exposure or addition applied to your sample. title: isotope exposure/addition todos: - Can we make the H218O correctly super and subscripted? comments: - This is required when your experimental design includes the use of isotopically labeled compounds examples: - 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 recommended: true micro_biomass_c_meth: name: micro_biomass_c_meth description: Reference or method used in determining microbial biomass carbon title: microbial biomass carbon method todos: - How should we separate values? | or ;? lets be consistent comments: - required if "microbial_biomass_c" is provided examples: - 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 recommended: true micro_biomass_n_meth: name: micro_biomass_n_meth description: Reference or method used in determining microbial biomass nitrogen title: microbial biomass nitrogen method comments: - required if "microbial_biomass_n" is provided examples: - 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 microbial_biomass_c: name: microbial_biomass_c description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. title: microbial biomass carbon comments: - If you provide this, correction factors used for conversion to the final units and method are required 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 microbial_biomass_n: name: microbial_biomass_n description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. title: microbial biomass nitrogen comments: - If you provide this, correction factors used for conversion to the final units and method are required 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 non_microb_biomass: name: non_microb_biomass description: Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ; title: non-microbial biomass 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 non_microb_biomass_method: name: non_microb_biomass_method description: Reference or method used in determining biomass title: non-microbial biomass method comments: - required if "non-microbial biomass" is provided 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 org_nitro_method: name: org_nitro_method description: Method used for obtaining organic nitrogen title: organic nitrogen method comments: - required if "org_nitro" is provided 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 other_treatment: name: other_treatment description: Other treatments applied to your samples that are not applicable to the provided fields title: other treatments comments: - 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 recommended: true start_date_inc: name: start_date_inc description: Date the incubation was started. Only relevant for incubation samples. title: incubation start date notes: - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only comments: - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. examples: - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc see_also: - MIxS:collection_date rank: 4 string_serialization: '{date, arbitrary precision}' slot_group: MIxS Inspired recommended: true start_time_inc: name: start_time_inc description: Time the incubation was started. Only relevant for incubation samples. title: incubation start time, GMT notes: - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only comments: - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter' examples: - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc see_also: - MIxS:collection_date rank: 5 string_serialization: '{time, seconds optional}' slot_group: MIxS Inspired recommended: true dnase_rna: name: dnase_rna title: DNase treated comments: - Note DNase treatment is required for all RNA samples. examples: - value: 'no' from_schema: https://w3id.org/nmdc/nmdc rank: 13 slot_group: JGI-Metatranscriptomics range: YesNoEnum recommended: true proposal_rna: name: proposal_rna title: RNA proposal ID comments: - Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. examples: - value: '504000' from_schema: https://w3id.org/nmdc/nmdc rank: 19 string_serialization: '{text}' slot_group: JGI-Metatranscriptomics recommended: true rna_absorb1: name: rna_absorb1 description: 260/280 measurement of RNA sample purity title: RNA absorbance 260/280 comments: - Recommended value is between 1 and 3. examples: - value: '2.02' from_schema: https://w3id.org/nmdc/nmdc rank: 7 is_a: biomaterial_purity string_serialization: '{float}' slot_group: JGI-Metatranscriptomics range: float recommended: true rna_absorb2: name: rna_absorb2 description: 260/230 measurement of RNA sample purity title: RNA absorbance 260/230 comments: - Recommended value is between 1 and 3. examples: - value: '2.02' from_schema: https://w3id.org/nmdc/nmdc rank: 8 is_a: biomaterial_purity string_serialization: '{float}' slot_group: JGI-Metatranscriptomics range: float recommended: true rna_collect_site: name: rna_collect_site description: Provide information on the site your RNA sample was collected from title: RNA collection site examples: - value: untreated pond water from_schema: https://w3id.org/nmdc/nmdc rank: 15 string_serialization: '{text}' slot_group: JGI-Metatranscriptomics recommended: true rna_concentration: name: rna_concentration title: RNA concentration in ng/ul comments: - Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000. examples: - value: '100' from_schema: https://w3id.org/nmdc/nmdc see_also: - nmdc:nucleic_acid_concentration rank: 5 string_serialization: '{float}' slot_group: JGI-Metatranscriptomics range: float recommended: true minimum_value: 0 maximum_value: 1000 rna_cont_type: name: rna_cont_type description: Tube or plate (96-well) title: RNA container type examples: - value: plate from_schema: https://w3id.org/nmdc/nmdc rank: 10 slot_group: JGI-Metatranscriptomics range: JgiContTypeEnum recommended: true rna_cont_well: name: rna_cont_well title: RNA plate position comments: - Required when 'plate' is selected for container type. - Leave blank if the sample will be shipped in a tube. - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation. - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8). examples: - value: B2 from_schema: https://w3id.org/nmdc/nmdc rank: 11 string_serialization: '{96 well plate pos}' slot_group: JGI-Metatranscriptomics recommended: true pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$ rna_container_id: name: rna_container_id title: RNA container label comments: - Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label. examples: - value: Pond_MT_041618 from_schema: https://w3id.org/nmdc/nmdc rank: 9 string_serialization: '{text < 20 characters}' slot_group: JGI-Metatranscriptomics recommended: true rna_isolate_meth: name: rna_isolate_meth description: Describe the method/protocol/kit used to extract DNA/RNA. title: RNA isolation method examples: - value: phenol/chloroform extraction from_schema: https://w3id.org/nmdc/nmdc rank: 16 string_serialization: '{text}' slot_group: JGI-Metatranscriptomics recommended: true rna_organisms: name: rna_organisms description: List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture. title: RNA expected organisms examples: - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%) from_schema: https://w3id.org/nmdc/nmdc rank: 14 string_serialization: '{text}' slot_group: JGI-Metatranscriptomics recommended: true rna_project_contact: name: rna_project_contact title: RNA seq project contact comments: - Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. examples: - value: John Jones from_schema: https://w3id.org/nmdc/nmdc rank: 18 string_serialization: '{text}' slot_group: JGI-Metatranscriptomics recommended: true rna_samp_id: name: rna_samp_id title: RNA sample ID comments: - Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. examples: - value: '187654' from_schema: https://w3id.org/nmdc/nmdc rank: 3 string_serialization: '{text}' slot_group: JGI-Metatranscriptomics recommended: true rna_sample_format: name: rna_sample_format description: Solution in which the RNA sample has been suspended title: RNA sample format examples: - value: Water from_schema: https://w3id.org/nmdc/nmdc rank: 12 slot_group: JGI-Metatranscriptomics range: rna_sample_format_enum recommended: true rna_sample_name: name: rna_sample_name description: Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only. title: RNA sample name examples: - value: JGI_pond_041618 from_schema: https://w3id.org/nmdc/nmdc rank: 4 string_serialization: '{text}' slot_group: JGI-Metatranscriptomics recommended: true minimum_value: 0 maximum_value: 2000 rna_seq_project: name: rna_seq_project title: RNA seq project ID comments: - Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. examples: - value: '1191234' from_schema: https://w3id.org/nmdc/nmdc rank: 1 string_serialization: '{text}' slot_group: JGI-Metatranscriptomics recommended: true rna_seq_project_pi: name: rna_seq_project_pi title: RNA seq project PI comments: - Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. examples: - value: Jane Johnson from_schema: https://w3id.org/nmdc/nmdc rank: 17 string_serialization: '{text}' slot_group: JGI-Metatranscriptomics recommended: true rna_seq_project_name: name: rna_seq_project_name title: RNA seq project name comments: - Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. examples: - value: JGI Pond metatranscriptomics from_schema: https://w3id.org/nmdc/nmdc rank: 2 string_serialization: '{text}' slot_group: JGI-Metatranscriptomics recommended: true rna_volume: name: rna_volume title: RNA volume in ul comments: - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager examples: - value: '25' from_schema: https://w3id.org/nmdc/nmdc rank: 6 string_serialization: '{float}' slot_group: JGI-Metatranscriptomics range: float recommended: true minimum_value: 0 maximum_value: 1000 dna_absorb1: name: dna_absorb1 description: 260/280 measurement of DNA sample purity title: DNA absorbance 260/280 comments: - Recommended value is between 1 and 3. examples: - value: '2.02' from_schema: https://w3id.org/nmdc/nmdc rank: 7 is_a: biomaterial_purity string_serialization: '{float}' slot_group: JGI-Metagenomics range: float recommended: true dna_absorb2: name: dna_absorb2 description: 260/230 measurement of DNA sample purity title: DNA absorbance 260/230 comments: - Recommended value is between 1 and 3. examples: - value: '2.02' from_schema: https://w3id.org/nmdc/nmdc rank: 8 is_a: biomaterial_purity string_serialization: '{float}' slot_group: JGI-Metagenomics range: float recommended: true dna_collect_site: name: dna_collect_site description: Provide information on the site your DNA sample was collected from title: DNA collection site examples: - value: untreated pond water from_schema: https://w3id.org/nmdc/nmdc rank: 15 string_serialization: '{text}' slot_group: JGI-Metagenomics recommended: true dna_concentration: name: dna_concentration title: DNA concentration in ng/ul comments: - Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000. examples: - value: '100' from_schema: https://w3id.org/nmdc/nmdc see_also: - nmdc:nucleic_acid_concentration rank: 5 string_serialization: '{float}' slot_group: JGI-Metagenomics range: float recommended: true minimum_value: 0 maximum_value: 2000 dna_cont_type: name: dna_cont_type description: Tube or plate (96-well) title: DNA container type examples: - value: plate from_schema: https://w3id.org/nmdc/nmdc rank: 10 slot_group: JGI-Metagenomics range: JgiContTypeEnum recommended: true dna_cont_well: name: dna_cont_well title: DNA plate position comments: - Required when 'plate' is selected for container type. - Leave blank if the sample will be shipped in a tube. - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation. - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8). examples: - value: B2 from_schema: https://w3id.org/nmdc/nmdc rank: 11 string_serialization: '{96 well plate pos}' slot_group: JGI-Metagenomics recommended: true pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$ dna_container_id: name: dna_container_id title: DNA container label comments: - Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label. examples: - value: Pond_MT_041618 from_schema: https://w3id.org/nmdc/nmdc rank: 9 string_serialization: '{text < 20 characters}' slot_group: JGI-Metagenomics recommended: true dna_dnase: name: dna_dnase title: DNase treatment DNA comments: - Note DNase treatment is required for all RNA samples. examples: - value: 'no' from_schema: https://w3id.org/nmdc/nmdc rank: 13 slot_group: JGI-Metagenomics range: YesNoEnum recommended: true dna_isolate_meth: name: dna_isolate_meth description: Describe the method/protocol/kit used to extract DNA/RNA. title: DNA isolation method examples: - value: phenol/chloroform extraction from_schema: https://w3id.org/nmdc/nmdc rank: 16 string_serialization: '{text}' slot_group: JGI-Metagenomics recommended: true dna_organisms: name: dna_organisms description: List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture. title: DNA expected organisms examples: - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%) from_schema: https://w3id.org/nmdc/nmdc rank: 14 string_serialization: '{text}' slot_group: JGI-Metagenomics recommended: true dna_project_contact: name: dna_project_contact title: DNA seq project contact comments: - Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. examples: - value: John Jones from_schema: https://w3id.org/nmdc/nmdc rank: 18 string_serialization: '{text}' slot_group: JGI-Metagenomics recommended: true dna_samp_id: name: dna_samp_id title: DNA sample ID todos: - Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled? comments: - Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. examples: - value: '187654' from_schema: https://w3id.org/nmdc/nmdc rank: 3 string_serialization: '{text}' slot_group: JGI-Metagenomics recommended: true dna_sample_format: name: dna_sample_format description: Solution in which the DNA sample has been suspended title: DNA sample format examples: - value: Water from_schema: https://w3id.org/nmdc/nmdc rank: 12 slot_group: JGI-Metagenomics range: dna_sample_format_enum recommended: true dna_sample_name: name: dna_sample_name description: Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only. title: DNA sample name examples: - value: JGI_pond_041618 from_schema: https://w3id.org/nmdc/nmdc rank: 4 string_serialization: '{text}' slot_group: JGI-Metagenomics recommended: true dna_seq_project: name: dna_seq_project title: DNA seq project ID comments: - Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. examples: - value: '1191234' from_schema: https://w3id.org/nmdc/nmdc rank: 1 string_serialization: '{text}' slot_group: JGI-Metagenomics recommended: true dna_seq_project_pi: name: dna_seq_project_pi title: DNA seq project PI comments: - Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. examples: - value: Jane Johnson from_schema: https://w3id.org/nmdc/nmdc rank: 17 string_serialization: '{text}' slot_group: JGI-Metagenomics recommended: true dna_seq_project_name: name: dna_seq_project_name title: DNA seq project name comments: - Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. examples: - value: JGI Pond metagenomics from_schema: https://w3id.org/nmdc/nmdc rank: 2 string_serialization: '{text}' slot_group: JGI-Metagenomics recommended: true dna_volume: name: dna_volume title: DNA volume in ul comments: - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager examples: - value: '25' from_schema: https://w3id.org/nmdc/nmdc rank: 6 string_serialization: '{float}' slot_group: JGI-Metagenomics range: float recommended: true minimum_value: 0 maximum_value: 1000 proposal_dna: name: proposal_dna title: DNA proposal ID comments: - Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. examples: - value: '504000' from_schema: https://w3id.org/nmdc/nmdc rank: 19 string_serialization: '{text}' slot_group: JGI-Metagenomics recommended: true emsl_store_temp: name: emsl_store_temp description: The temperature at which the sample should be stored upon delivery to EMSL title: EMSL sample storage temperature, deg. C todos: - add 'see_alsos' with link to NEXUS info comments: - Enter a temperature in celsius. Numeric portion only. examples: - value: '-80' from_schema: https://w3id.org/nmdc/nmdc rank: 4 string_serialization: '{float}' slot_group: EMSL recommended: true project_id: name: project_id description: Proposal IDs or names associated with dataset title: project ID from_schema: https://w3id.org/nmdc/nmdc rank: 1 string_serialization: '{text}' slot_group: EMSL recommended: true replicate_number: name: replicate_number description: If sending biological replicates, indicate the rep number here. title: replicate number comments: - This will guide staff in ensuring your samples are blocked & randomized correctly from_schema: https://w3id.org/nmdc/nmdc rank: 6 string_serialization: '{integer}' slot_group: EMSL recommended: true sample_shipped: name: sample_shipped description: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL. title: sample shipped amount comments: - This field is only required when completing metadata for samples being submitted to EMSL for analyses. examples: - value: 15 g - value: 100 uL - value: 5 mL from_schema: https://w3id.org/nmdc/nmdc rank: 3 string_serialization: '{float} {unit}' slot_group: EMSL recommended: true sample_type: name: sample_type description: Type of sample being submitted title: sample type comments: - This can vary from 'environmental package' if the sample is an extraction. examples: - value: water extracted soil from_schema: https://w3id.org/nmdc/nmdc rank: 2 slot_group: EMSL range: sample_type_enum recommended: true technical_reps: name: technical_reps description: If sending technical replicates of the same sample, indicate the replicate count. title: number technical replicate comments: - This field is only required when completing metadata for samples being submitted to EMSL for analyses. examples: - value: '2' from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{integer}' slot_group: EMSL recommended: true abs_air_humidity: name: abs_air_humidity annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: gram per gram, kilogram per kilogram, kilogram, pound occurrence: tag: occurrence value: '1' description: Actual mass of water vapor - mh20 - present in the air water vapor mixture title: absolute air humidity examples: - value: 9 gram per gram from_schema: https://w3id.org/nmdc/nmdc aliases: - absolute air humidity is_a: core field slot_uri: MIXS:0000122 multivalued: false range: QuantityValue add_recov_method: name: add_recov_method annotations: expected_value: tag: expected_value value: enumeration;timestamp occurrence: tag: occurrence value: '1' description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If "other" is specified, please propose entry in "additional info" field title: secondary and tertiary recovery methods and start date examples: - value: Polymer Addition;2018-06-21T14:30Z from_schema: https://w3id.org/nmdc/nmdc aliases: - secondary and tertiary recovery methods and start date is_a: core field slot_uri: MIXS:0001009 multivalued: false range: TextValue additional_info: name: additional_info annotations: expected_value: tag: expected_value value: text occurrence: tag: occurrence value: '1' description: Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary title: additional info examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - additional info is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000300 multivalued: false range: TextValue address: name: address annotations: expected_value: tag: expected_value value: value occurrence: tag: occurrence value: '1' description: The street name and building number where the sampling occurred. title: address examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - address is_a: core field string_serialization: '{integer}{text}' slot_uri: MIXS:0000218 multivalued: false range: TextValue adj_room: name: adj_room annotations: expected_value: tag: expected_value value: room name;room number occurrence: tag: occurrence value: '1' description: List of rooms (room number, room name) immediately adjacent to the sampling room title: adjacent rooms examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - adjacent rooms is_a: core field string_serialization: '{text};{integer}' slot_uri: MIXS:0000219 multivalued: false range: TextValue aero_struc: name: aero_struc annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together title: aerospace structure examples: - value: plane from_schema: https://w3id.org/nmdc/nmdc aliases: - aerospace structure is_a: core field string_serialization: '[plane|glider]' slot_uri: MIXS:0000773 multivalued: false range: TextValue agrochem_addition: name: agrochem_addition annotations: expected_value: tag: expected_value value: agrochemical name;agrochemical amount;timestamp preferred_unit: tag: preferred_unit value: gram, mole per liter, milligram per liter occurrence: tag: occurrence value: m description: Addition of fertilizers, pesticides, etc. - amount and time of applications title: history/agrochemical additions examples: - value: roundup;5 milligram per liter;2018-06-21 from_schema: https://w3id.org/nmdc/nmdc aliases: - history/agrochemical additions is_a: core field string_serialization: '{text};{float} {unit};{timestamp}' slot_uri: MIXS:0000639 multivalued: true range: TextValue air_PM_concen: name: air_PM_concen annotations: expected_value: tag: expected_value value: particulate matter name;measurement value preferred_unit: tag: preferred_unit value: micrograms per cubic meter occurrence: tag: occurrence value: m description: 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 title: air particulate matter concentration examples: - value: PM2.5;10 microgram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - air particulate matter concentration is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000108 multivalued: true range: TextValue air_temp: name: air_temp annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: degree Celsius occurrence: tag: occurrence value: '1' description: Temperature of the air at the time of sampling title: air temperature examples: - value: 20 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - air temperature is_a: core field slot_uri: MIXS:0000124 multivalued: false range: QuantityValue air_temp_regm: name: air_temp_regm annotations: expected_value: tag: expected_value value: temperature value;treatment interval and duration preferred_unit: tag: preferred_unit value: meter occurrence: tag: occurrence value: m description: Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens title: air temperature regimen examples: - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - air temperature regimen is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000551 multivalued: true range: TextValue al_sat: name: al_sat annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: percentage occurrence: tag: occurrence value: '1' description: Aluminum saturation (esp. For tropical soils) title: extreme_unusual_properties/Al saturation examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - extreme_unusual_properties/Al saturation is_a: core field slot_uri: MIXS:0000607 multivalued: false range: QuantityValue al_sat_meth: name: al_sat_meth annotations: expected_value: tag: expected_value value: PMID,DOI or URL occurrence: tag: occurrence value: '1' description: Reference or method used in determining Al saturation title: extreme_unusual_properties/Al saturation method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - extreme_unusual_properties/Al saturation method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000324 multivalued: false range: TextValue alkalinity: name: alkalinity annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milliequivalent per liter, milligram per liter occurrence: tag: occurrence value: '1' description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate title: alkalinity examples: - value: 50 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - alkalinity is_a: core field slot_uri: MIXS:0000421 multivalued: false range: QuantityValue alkalinity_method: name: alkalinity_method annotations: expected_value: tag: expected_value value: description of method occurrence: tag: occurrence value: '1' description: Method used for alkalinity measurement title: alkalinity method examples: - value: titration from_schema: https://w3id.org/nmdc/nmdc aliases: - alkalinity method is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000298 multivalued: false range: TextValue alkyl_diethers: name: alkyl_diethers annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: mole per liter occurrence: tag: occurrence value: '1' description: Concentration of alkyl diethers title: alkyl diethers examples: - value: 0.005 mole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - alkyl diethers is_a: core field slot_uri: MIXS:0000490 multivalued: false range: QuantityValue alt: name: alt annotations: expected_value: tag: expected_value value: measurement value description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air title: altitude examples: - value: 100 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - altitude is_a: environment field slot_uri: MIXS:0000094 multivalued: false range: QuantityValue aminopept_act: name: aminopept_act annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: mole per liter per hour occurrence: tag: occurrence value: '1' description: Measurement of aminopeptidase activity title: aminopeptidase activity examples: - value: 0.269 mole per liter per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - aminopeptidase activity is_a: core field slot_uri: MIXS:0000172 multivalued: false range: QuantityValue ammonium: name: ammonium annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter, milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of ammonium in the sample title: ammonium examples: - value: 1.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - ammonium is_a: core field slot_uri: MIXS:0000427 multivalued: false range: QuantityValue amount_light: name: amount_light annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: lux, lumens per square meter occurrence: tag: occurrence value: '1' description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area title: amount of light examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - amount of light is_a: core field slot_uri: MIXS:0000140 multivalued: false range: QuantityValue ances_data: name: ances_data annotations: expected_value: tag: expected_value value: free text occurrence: tag: occurrence value: '1' description: Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) title: ancestral data examples: - value: A/3*B from_schema: https://w3id.org/nmdc/nmdc aliases: - ancestral data is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000247 multivalued: false range: TextValue annual_precpt: name: annual_precpt annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: millimeter occurrence: tag: occurrence value: '1' description: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. title: mean annual precipitation examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - mean annual precipitation is_a: core field slot_uri: MIXS:0000644 multivalued: false range: QuantityValue annual_temp: name: annual_temp annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: degree Celsius occurrence: tag: occurrence value: '1' description: Mean annual temperature title: mean annual temperature examples: - value: 12.5 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - mean annual temperature is_a: core field slot_uri: MIXS:0000642 multivalued: false range: QuantityValue antibiotic_regm: name: antibiotic_regm annotations: expected_value: tag: expected_value value: antibiotic name;antibiotic amount;treatment interval and duration preferred_unit: tag: preferred_unit value: milligram occurrence: tag: occurrence value: m description: Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens title: antibiotic regimen examples: - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - antibiotic regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000553 multivalued: true range: TextValue api: name: api annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: degrees API occurrence: tag: occurrence value: '1' description: 'API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API)' title: API gravity examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - API gravity is_a: core field slot_uri: MIXS:0000157 multivalued: false range: QuantityValue arch_struc: name: arch_struc annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: An architectural structure is a human-made, free-standing, immobile outdoor construction title: architectural structure examples: - value: shed from_schema: https://w3id.org/nmdc/nmdc aliases: - architectural structure is_a: core field slot_uri: MIXS:0000774 multivalued: false range: arch_struc_enum aromatics_pc: name: aromatics_pc annotations: expected_value: tag: expected_value value: name;measurement value preferred_unit: tag: preferred_unit value: percent occurrence: tag: occurrence value: '1' description: 'Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' title: aromatics wt% examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - aromatics wt% is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000133 multivalued: false range: TextValue asphaltenes_pc: name: asphaltenes_pc annotations: expected_value: tag: expected_value value: name;measurement value preferred_unit: tag: preferred_unit value: percent occurrence: tag: occurrence value: '1' description: 'Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' title: asphaltenes wt% examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - asphaltenes wt% is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000135 multivalued: false range: TextValue atmospheric_data: name: atmospheric_data annotations: expected_value: tag: expected_value value: atmospheric data name;measurement value occurrence: tag: occurrence value: m description: Measurement of atmospheric data; can include multiple data title: atmospheric data examples: - value: wind speed;9 knots from_schema: https://w3id.org/nmdc/nmdc aliases: - atmospheric data is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0001097 multivalued: true range: TextValue avg_dew_point: name: avg_dew_point annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: degree Celsius occurrence: tag: occurrence value: '1' description: The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day title: average dew point examples: - value: 25.5 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - average dew point is_a: core field slot_uri: MIXS:0000141 multivalued: false range: QuantityValue avg_occup: name: avg_occup annotations: expected_value: tag: expected_value value: value occurrence: tag: occurrence value: '1' description: Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room. title: average daily occupancy examples: - value: '2' from_schema: https://w3id.org/nmdc/nmdc aliases: - average daily occupancy is_a: core field slot_uri: MIXS:0000775 multivalued: false range: TextValue avg_temp: name: avg_temp annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: degree Celsius occurrence: tag: occurrence value: '1' description: The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day title: average temperature examples: - value: 12.5 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - average temperature is_a: core field slot_uri: MIXS:0000142 multivalued: false range: QuantityValue bac_prod: name: bac_prod annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per cubic meter per day occurrence: tag: occurrence value: '1' description: Bacterial production in the water column measured by isotope uptake title: bacterial production examples: - value: 5 milligram per cubic meter per day from_schema: https://w3id.org/nmdc/nmdc aliases: - bacterial production is_a: core field slot_uri: MIXS:0000683 multivalued: false range: QuantityValue bac_resp: name: bac_resp annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per cubic meter per day, micromole oxygen per liter per hour occurrence: tag: occurrence value: '1' description: Measurement of bacterial respiration in the water column title: bacterial respiration examples: - value: 300 micromole oxygen per liter per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - bacterial respiration is_a: core field slot_uri: MIXS:0000684 multivalued: false range: QuantityValue bacteria_carb_prod: name: bacteria_carb_prod annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: nanogram per hour occurrence: tag: occurrence value: '1' description: Measurement of bacterial carbon production title: bacterial carbon production examples: - value: 2.53 microgram per liter per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - bacterial carbon production is_a: core field slot_uri: MIXS:0000173 multivalued: false range: QuantityValue barometric_press: name: barometric_press annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: millibar occurrence: tag: occurrence value: '1' description: Force per unit area exerted against a surface by the weight of air above that surface title: barometric pressure examples: - value: 5 millibar from_schema: https://w3id.org/nmdc/nmdc aliases: - barometric pressure is_a: core field slot_uri: MIXS:0000096 multivalued: false range: QuantityValue basin: name: basin annotations: expected_value: tag: expected_value value: name occurrence: tag: occurrence value: '1' description: Name of the basin (e.g. Campos) title: basin name examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - basin name is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000290 multivalued: false range: TextValue bathroom_count: name: bathroom_count annotations: expected_value: tag: expected_value value: value occurrence: tag: occurrence value: '1' description: The number of bathrooms in the building title: bathroom count examples: - value: '1' from_schema: https://w3id.org/nmdc/nmdc aliases: - bathroom count is_a: core field slot_uri: MIXS:0000776 multivalued: false range: TextValue bedroom_count: name: bedroom_count annotations: expected_value: tag: expected_value value: value occurrence: tag: occurrence value: '1' description: The number of bedrooms in the building title: bedroom count examples: - value: '2' from_schema: https://w3id.org/nmdc/nmdc aliases: - bedroom count is_a: core field slot_uri: MIXS:0000777 multivalued: false range: TextValue benzene: name: benzene annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of benzene in the sample title: benzene examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - benzene is_a: core field slot_uri: MIXS:0000153 multivalued: false range: QuantityValue biochem_oxygen_dem: name: biochem_oxygen_dem annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period title: biochemical oxygen demand examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - biochemical oxygen demand is_a: core field slot_uri: MIXS:0000653 multivalued: false range: QuantityValue biocide: name: biocide annotations: expected_value: tag: expected_value value: name;name;timestamp occurrence: tag: occurrence value: '1' description: List of biocides (commercial name of product and supplier) and date of administration title: biocide administration examples: - value: ALPHA 1427;Baker Hughes;2008-01-23 from_schema: https://w3id.org/nmdc/nmdc aliases: - biocide administration is_a: core field string_serialization: '{text};{text};{timestamp}' slot_uri: MIXS:0001011 multivalued: false range: TextValue biocide_admin_method: name: biocide_admin_method annotations: expected_value: tag: expected_value value: measurement value;frequency;duration;duration preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) title: biocide administration method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - biocide administration method is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}' slot_uri: MIXS:0000456 multivalued: false range: TextValue biol_stat: name: biol_stat annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The level of genome modification. title: biological status examples: - value: natural from_schema: https://w3id.org/nmdc/nmdc aliases: - biological status is_a: core field slot_uri: MIXS:0000858 multivalued: false range: biol_stat_enum biomass: name: biomass annotations: expected_value: tag: expected_value value: biomass type;measurement value preferred_unit: tag: preferred_unit value: ton, kilogram, gram occurrence: tag: occurrence value: m description: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements title: biomass examples: - value: total;20 gram from_schema: https://w3id.org/nmdc/nmdc aliases: - biomass is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000174 multivalued: true range: TextValue biotic_regm: name: biotic_regm annotations: expected_value: tag: expected_value value: free text occurrence: tag: occurrence value: '1' description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. title: biotic regimen examples: - value: sample inoculated with Rhizobium spp. Culture from_schema: https://w3id.org/nmdc/nmdc aliases: - biotic regimen is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001038 multivalued: false range: TextValue biotic_relationship: name: biotic_relationship annotations: expected_value: tag: expected_value value: enumeration description: Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object title: observed biotic relationship examples: - value: free living from_schema: https://w3id.org/nmdc/nmdc aliases: - observed biotic relationship is_a: nucleic acid sequence source field slot_uri: MIXS:0000028 multivalued: false range: biotic_relationship_enum bishomohopanol: name: bishomohopanol annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter, microgram per gram occurrence: tag: occurrence value: '1' description: Concentration of bishomohopanol title: bishomohopanol examples: - value: 14 microgram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - bishomohopanol is_a: core field slot_uri: MIXS:0000175 multivalued: false range: QuantityValue blood_press_diast: name: blood_press_diast annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: millimeter mercury occurrence: tag: occurrence value: '1' description: Resting diastolic blood pressure, measured as mm mercury title: host blood pressure diastolic examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - host blood pressure diastolic is_a: core field slot_uri: MIXS:0000258 multivalued: false range: QuantityValue blood_press_syst: name: blood_press_syst annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: millimeter mercury occurrence: tag: occurrence value: '1' description: Resting systolic blood pressure, measured as mm mercury title: host blood pressure systolic examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - host blood pressure systolic is_a: core field slot_uri: MIXS:0000259 multivalued: false range: QuantityValue bromide: name: bromide annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: parts per million occurrence: tag: occurrence value: '1' description: Concentration of bromide title: bromide examples: - value: 0.05 parts per million from_schema: https://w3id.org/nmdc/nmdc aliases: - bromide is_a: core field slot_uri: MIXS:0000176 multivalued: false range: QuantityValue build_docs: name: build_docs annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The building design, construction and operation documents title: design, construction, and operation documents examples: - value: maintenance plans from_schema: https://w3id.org/nmdc/nmdc aliases: - design, construction, and operation documents is_a: core field slot_uri: MIXS:0000787 multivalued: false range: build_docs_enum build_occup_type: name: build_occup_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: m description: The primary function for which a building or discrete part of a building is intended to be used title: building occupancy type examples: - value: market from_schema: https://w3id.org/nmdc/nmdc aliases: - building occupancy type is_a: core field slot_uri: MIXS:0000761 multivalued: true range: build_occup_type_enum building_setting: name: building_setting annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: A location (geography) where a building is set title: building setting examples: - value: rural from_schema: https://w3id.org/nmdc/nmdc aliases: - building setting is_a: core field slot_uri: MIXS:0000768 multivalued: false range: building_setting_enum built_struc_age: name: built_struc_age annotations: expected_value: tag: expected_value value: value preferred_unit: tag: preferred_unit value: year occurrence: tag: occurrence value: '1' description: The age of the built structure since construction title: built structure age examples: - value: '15' from_schema: https://w3id.org/nmdc/nmdc aliases: - built structure age is_a: core field slot_uri: MIXS:0000145 multivalued: false range: QuantityValue built_struc_set: name: built_struc_set annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The characterization of the location of the built structure as high or low human density title: built structure setting examples: - value: rural from_schema: https://w3id.org/nmdc/nmdc aliases: - built structure setting is_a: core field string_serialization: '[urban|rural]' slot_uri: MIXS:0000778 multivalued: false range: TextValue built_struc_type: name: built_struc_type annotations: expected_value: tag: expected_value value: free text occurrence: tag: occurrence value: '1' description: A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads title: built structure type examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - built structure type is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000721 multivalued: false range: TextValue calcium: name: calcium annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter, micromole per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of calcium in the sample title: calcium examples: - value: 0.2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - calcium is_a: core field slot_uri: MIXS:0000432 multivalued: false range: QuantityValue carb_dioxide: name: carb_dioxide annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter, parts per million occurrence: tag: occurrence value: '1' description: Carbon dioxide (gas) amount or concentration at the time of sampling title: carbon dioxide examples: - value: 410 parts per million from_schema: https://w3id.org/nmdc/nmdc aliases: - carbon dioxide is_a: core field slot_uri: MIXS:0000097 multivalued: false range: QuantityValue carb_monoxide: name: carb_monoxide annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter, parts per million occurrence: tag: occurrence value: '1' description: Carbon monoxide (gas) amount or concentration at the time of sampling title: carbon monoxide examples: - value: 0.1 parts per million from_schema: https://w3id.org/nmdc/nmdc aliases: - carbon monoxide is_a: core field slot_uri: MIXS:0000098 multivalued: false range: QuantityValue carb_nitro_ratio: name: carb_nitro_ratio annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: Ratio of amount or concentrations of carbon to nitrogen title: carbon/nitrogen ratio examples: - value: '0.417361111' from_schema: https://w3id.org/nmdc/nmdc aliases: - carbon/nitrogen ratio is_a: core field slot_uri: MIXS:0000310 multivalued: false range: QuantityValue ceil_area: name: ceil_area annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: square meter occurrence: tag: occurrence value: '1' description: The area of the ceiling space within the room title: ceiling area examples: - value: 25 square meter from_schema: https://w3id.org/nmdc/nmdc aliases: - ceiling area is_a: core field slot_uri: MIXS:0000148 multivalued: false range: QuantityValue ceil_cond: name: ceil_cond annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas title: ceiling condition examples: - value: damaged from_schema: https://w3id.org/nmdc/nmdc aliases: - ceiling condition is_a: core field slot_uri: MIXS:0000779 multivalued: false range: ceil_cond_enum ceil_finish_mat: name: ceil_finish_mat annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The type of material used to finish a ceiling title: ceiling finish material examples: - value: stucco from_schema: https://w3id.org/nmdc/nmdc aliases: - ceiling finish material is_a: core field slot_uri: MIXS:0000780 multivalued: false range: ceil_finish_mat_enum ceil_struc: name: ceil_struc annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The construction format of the ceiling title: ceiling structure examples: - value: concrete from_schema: https://w3id.org/nmdc/nmdc aliases: - ceiling structure is_a: core field string_serialization: '[wood frame|concrete]' slot_uri: MIXS:0000782 multivalued: false range: TextValue ceil_texture: name: ceil_texture annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The feel, appearance, or consistency of a ceiling surface title: ceiling texture examples: - value: popcorn from_schema: https://w3id.org/nmdc/nmdc aliases: - ceiling texture is_a: core field slot_uri: MIXS:0000783 multivalued: false range: ceil_texture_enum ceil_thermal_mass: name: ceil_thermal_mass annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: joule per degree Celsius occurrence: tag: occurrence value: '1' description: The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow title: ceiling thermal mass examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - ceiling thermal mass is_a: core field slot_uri: MIXS:0000143 multivalued: false range: QuantityValue ceil_type: name: ceil_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The type of ceiling according to the ceiling's appearance or construction title: ceiling type examples: - value: coffered from_schema: https://w3id.org/nmdc/nmdc aliases: - ceiling type is_a: core field slot_uri: MIXS:0000784 multivalued: false range: ceil_type_enum ceil_water_mold: name: ceil_water_mold annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Signs of the presence of mold or mildew on the ceiling title: ceiling signs of water/mold examples: - value: presence of mold visible from_schema: https://w3id.org/nmdc/nmdc aliases: - ceiling signs of water/mold is_a: core field string_serialization: '[presence of mold visible|no presence of mold visible]' slot_uri: MIXS:0000781 multivalued: false range: TextValue chem_administration: name: chem_administration annotations: expected_value: tag: expected_value value: CHEBI;timestamp occurrence: tag: occurrence value: m description: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi title: chemical administration examples: - value: agar [CHEBI:2509];2018-05-11T20:00Z from_schema: https://w3id.org/nmdc/nmdc aliases: - chemical administration is_a: core field string_serialization: '{termLabel} {[termID]};{timestamp}' slot_uri: MIXS:0000751 multivalued: true range: ControlledTermValue chem_mutagen: name: chem_mutagen annotations: expected_value: tag: expected_value value: mutagen name;mutagen amount;treatment interval and duration preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: m description: Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens title: chemical mutagen examples: - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - chemical mutagen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000555 multivalued: true range: TextValue chem_oxygen_dem: name: chem_oxygen_dem annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite title: chemical oxygen demand examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - chemical oxygen demand is_a: core field slot_uri: MIXS:0000656 multivalued: false range: QuantityValue chem_treat_method: name: chem_treat_method annotations: expected_value: tag: expected_value value: measurement value;frequency;duration;duration preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) title: chemical treatment method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - chemical treatment method is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}' slot_uri: MIXS:0000457 multivalued: false range: string chem_treatment: name: chem_treatment annotations: expected_value: tag: expected_value value: name;name;timestamp occurrence: tag: occurrence value: '1' description: List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included title: chemical treatment examples: - value: ACCENT 1125;DOW;2010-11-17 from_schema: https://w3id.org/nmdc/nmdc aliases: - chemical treatment is_a: core field string_serialization: '{text};{text};{timestamp}' slot_uri: MIXS:0001012 multivalued: false range: TextValue chimera_check: name: chimera_check annotations: expected_value: tag: expected_value value: name and version of software, parameters used description: Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences. title: chimera check software examples: - value: uchime;v4.1;default parameters from_schema: https://w3id.org/nmdc/nmdc aliases: - chimera check software is_a: sequencing field string_serialization: '{software};{version};{parameters}' slot_uri: MIXS:0000052 multivalued: false range: TextValue chloride: name: chloride annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of chloride in the sample title: chloride examples: - value: 5000 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - chloride is_a: core field slot_uri: MIXS:0000429 multivalued: false range: QuantityValue chlorophyll: name: chlorophyll annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per cubic meter, microgram per liter occurrence: tag: occurrence value: '1' description: Concentration of chlorophyll title: chlorophyll examples: - value: 5 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - chlorophyll is_a: core field slot_uri: MIXS:0000177 multivalued: false range: QuantityValue climate_environment: name: climate_environment annotations: expected_value: tag: expected_value value: climate name;treatment interval and duration occurrence: tag: occurrence value: m description: Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates title: climate environment examples: - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - climate environment is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001040 multivalued: true range: TextValue collection_date: name: collection_date annotations: expected_value: tag: expected_value value: date and time description: 'The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant' title: collection date examples: - value: 2018-05-11T10:00:00+01:00; 2018-05-11 from_schema: https://w3id.org/nmdc/nmdc aliases: - collection date is_a: environment field slot_uri: MIXS:0000011 multivalued: false range: TimestampValue conduc: name: conduc annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milliSiemens per centimeter occurrence: tag: occurrence value: '1' description: Electrical conductivity of water title: conductivity examples: - value: 10 milliSiemens per centimeter from_schema: https://w3id.org/nmdc/nmdc aliases: - conductivity is_a: core field slot_uri: MIXS:0000692 multivalued: false range: QuantityValue cool_syst_id: name: cool_syst_id annotations: expected_value: tag: expected_value value: unique identifier occurrence: tag: occurrence value: '1' description: The cooling system identifier title: cooling system identifier examples: - value: '12345' from_schema: https://w3id.org/nmdc/nmdc aliases: - cooling system identifier is_a: core field slot_uri: MIXS:0000785 multivalued: false range: TextValue crop_rotation: name: crop_rotation annotations: expected_value: tag: expected_value value: crop rotation status;schedule occurrence: tag: occurrence value: '1' description: Whether or not crop is rotated, and if yes, rotation schedule title: history/crop rotation examples: - value: yes;R2/2017-01-01/2018-12-31/P6M from_schema: https://w3id.org/nmdc/nmdc aliases: - history/crop rotation is_a: core field string_serialization: '{boolean};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000318 multivalued: false range: TextValue cult_root_med: name: cult_root_med annotations: expected_value: tag: expected_value value: name, PMID,DOI or url occurrence: tag: occurrence value: '1' description: Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors. title: culture rooting medium examples: - value: http://himedialabs.com/TD/PT158.pdf from_schema: https://w3id.org/nmdc/nmdc aliases: - culture rooting medium is_a: core field string_serialization: '{text}|{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001041 multivalued: false range: TextValue cur_land_use: name: cur_land_use annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Present state of sample site title: current land use examples: - value: conifers from_schema: https://w3id.org/nmdc/nmdc aliases: - current land use is_a: core field slot_uri: MIXS:0001080 multivalued: false range: cur_land_use_enum cur_vegetation: name: cur_vegetation annotations: expected_value: tag: expected_value value: current vegetation type occurrence: tag: occurrence value: '1' description: Vegetation classification from one or more standard classification systems, or agricultural crop title: current vegetation examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - current vegetation is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000312 multivalued: false range: TextValue cur_vegetation_meth: name: cur_vegetation_meth annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Reference or method used in vegetation classification title: current vegetation method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - current vegetation method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000314 multivalued: false range: TextValue date_last_rain: name: date_last_rain annotations: expected_value: tag: expected_value value: timestamp occurrence: tag: occurrence value: '1' description: The date of the last time it rained title: date last rain examples: - value: 2018-05-11:T14:30Z from_schema: https://w3id.org/nmdc/nmdc aliases: - date last rain is_a: core field slot_uri: MIXS:0000786 multivalued: false range: TimestampValue density: name: density annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: gram per cubic meter, gram per cubic centimeter occurrence: tag: occurrence value: '1' description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) title: density examples: - value: 1000 kilogram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - density is_a: core field slot_uri: MIXS:0000435 multivalued: false range: QuantityValue depos_env: name: depos_env annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If "other" is specified, please propose entry in "additional info" field title: depositional environment examples: - value: Continental - Alluvial from_schema: https://w3id.org/nmdc/nmdc aliases: - depositional environment is_a: core field slot_uri: MIXS:0000992 multivalued: false range: depos_env_enum depth: name: depth annotations: expected_value: tag: expected_value value: measurement value description: The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples. title: depth examples: - value: 10 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - depth is_a: environment field slot_uri: MIXS:0000018 multivalued: false range: QuantityValue dew_point: name: dew_point annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: degree Celsius occurrence: tag: occurrence value: '1' description: The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. title: dew point examples: - value: 22 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - dew point is_a: core field slot_uri: MIXS:0000129 multivalued: false range: QuantityValue diether_lipids: name: diether_lipids annotations: expected_value: tag: expected_value value: diether lipid name;measurement value preferred_unit: tag: preferred_unit value: nanogram per liter occurrence: tag: occurrence value: m description: Concentration of diether lipids; can include multiple types of diether lipids title: diether lipids examples: - value: 0.2 nanogram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - diether lipids is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000178 multivalued: true range: TextValue diss_carb_dioxide: name: diss_carb_dioxide annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter, milligram per liter occurrence: tag: occurrence value: '1' description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample title: dissolved carbon dioxide examples: - value: 5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - dissolved carbon dioxide is_a: core field slot_uri: MIXS:0000436 multivalued: false range: QuantityValue diss_hydrogen: name: diss_hydrogen annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter occurrence: tag: occurrence value: '1' description: Concentration of dissolved hydrogen title: dissolved hydrogen examples: - value: 0.3 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - dissolved hydrogen is_a: core field slot_uri: MIXS:0000179 multivalued: false range: QuantityValue diss_inorg_carb: name: diss_inorg_carb annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter, milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter title: dissolved inorganic carbon examples: - value: 2059 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - dissolved inorganic carbon is_a: core field slot_uri: MIXS:0000434 multivalued: false range: QuantityValue diss_inorg_nitro: name: diss_inorg_nitro annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter, micromole per liter occurrence: tag: occurrence value: '1' description: Concentration of dissolved inorganic nitrogen title: dissolved inorganic nitrogen examples: - value: 761 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - dissolved inorganic nitrogen is_a: core field slot_uri: MIXS:0000698 multivalued: false range: QuantityValue diss_inorg_phosp: name: diss_inorg_phosp annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter, milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of dissolved inorganic phosphorus in the sample title: dissolved inorganic phosphorus examples: - value: 56.5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - dissolved inorganic phosphorus is_a: core field slot_uri: MIXS:0000106 multivalued: false range: QuantityValue diss_iron: name: diss_iron annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: Concentration of dissolved iron in the sample title: dissolved iron examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - dissolved iron is_a: core field slot_uri: MIXS:0000139 multivalued: false range: QuantityValue diss_org_carb: name: diss_org_carb annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter, milligram per liter occurrence: tag: occurrence value: '1' description: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid title: dissolved organic carbon examples: - value: 197 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - dissolved organic carbon is_a: core field slot_uri: MIXS:0000433 multivalued: false range: QuantityValue diss_org_nitro: name: diss_org_nitro annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter, milligram per liter occurrence: tag: occurrence value: '1' description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 title: dissolved organic nitrogen examples: - value: 0.05 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - dissolved organic nitrogen is_a: core field slot_uri: MIXS:0000162 multivalued: false range: QuantityValue diss_oxygen: name: diss_oxygen annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per kilogram, milligram per liter occurrence: tag: occurrence value: '1' description: Concentration of dissolved oxygen title: dissolved oxygen examples: - value: 175 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - dissolved oxygen is_a: core field slot_uri: MIXS:0000119 multivalued: false range: QuantityValue diss_oxygen_fluid: name: diss_oxygen_fluid annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per kilogram, milligram per liter occurrence: tag: occurrence value: '1' description: Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). title: dissolved oxygen in fluids examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - dissolved oxygen in fluids is_a: core field slot_uri: MIXS:0000438 multivalued: false range: QuantityValue door_comp_type: name: door_comp_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The composite type of the door title: door type, composite examples: - value: revolving from_schema: https://w3id.org/nmdc/nmdc aliases: - door type, composite is_a: core field slot_uri: MIXS:0000795 multivalued: false range: door_comp_type_enum door_cond: name: door_cond annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The phsical condition of the door title: door condition examples: - value: new from_schema: https://w3id.org/nmdc/nmdc aliases: - door condition is_a: core field slot_uri: MIXS:0000788 multivalued: false range: door_cond_enum door_direct: name: door_direct annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The direction the door opens title: door direction of opening examples: - value: inward from_schema: https://w3id.org/nmdc/nmdc aliases: - door direction of opening is_a: core field slot_uri: MIXS:0000789 multivalued: false range: door_direct_enum door_loc: name: door_loc annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The relative location of the door in the room title: door location examples: - value: north from_schema: https://w3id.org/nmdc/nmdc aliases: - door location is_a: core field slot_uri: MIXS:0000790 multivalued: false range: door_loc_enum door_mat: name: door_mat annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The material the door is composed of title: door material examples: - value: wood from_schema: https://w3id.org/nmdc/nmdc aliases: - door material is_a: core field slot_uri: MIXS:0000791 multivalued: false range: door_mat_enum door_move: name: door_move annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The type of movement of the door title: door movement examples: - value: swinging from_schema: https://w3id.org/nmdc/nmdc aliases: - door movement is_a: core field slot_uri: MIXS:0000792 multivalued: false range: door_move_enum door_size: name: door_size annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: square meter occurrence: tag: occurrence value: '1' description: The size of the door title: door area or size examples: - value: 2.5 square meter from_schema: https://w3id.org/nmdc/nmdc aliases: - door area or size is_a: core field slot_uri: MIXS:0000158 multivalued: false range: QuantityValue door_type: name: door_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The type of door material title: door type examples: - value: wooden from_schema: https://w3id.org/nmdc/nmdc aliases: - door type is_a: core field slot_uri: MIXS:0000794 multivalued: false range: door_type_enum door_type_metal: name: door_type_metal annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The type of metal door title: door type, metal examples: - value: hollow from_schema: https://w3id.org/nmdc/nmdc aliases: - door type, metal is_a: core field slot_uri: MIXS:0000796 multivalued: false range: door_type_metal_enum door_type_wood: name: door_type_wood annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The type of wood door title: door type, wood examples: - value: battened from_schema: https://w3id.org/nmdc/nmdc aliases: - door type, wood is_a: core field slot_uri: MIXS:0000797 multivalued: false range: door_type_wood_enum door_water_mold: name: door_water_mold annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Signs of the presence of mold or mildew on a door title: door signs of water/mold examples: - value: presence of mold visible from_schema: https://w3id.org/nmdc/nmdc aliases: - door signs of water/mold is_a: core field string_serialization: '[presence of mold visible|no presence of mold visible]' slot_uri: MIXS:0000793 multivalued: false range: TextValue down_par: name: down_par annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microEinstein per square meter per second, microEinstein per square centimeter per second occurrence: tag: occurrence value: '1' description: Visible waveband radiance and irradiance measurements in the water column title: downward PAR examples: - value: 28.71 microEinstein per square meter per second from_schema: https://w3id.org/nmdc/nmdc aliases: - downward PAR is_a: core field slot_uri: MIXS:0000703 multivalued: false range: QuantityValue drainage_class: name: drainage_class annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Drainage classification from a standard system such as the USDA system title: drainage classification examples: - value: well from_schema: https://w3id.org/nmdc/nmdc aliases: - drainage classification is_a: core field slot_uri: MIXS:0001085 multivalued: false range: drainage_class_enum drawings: name: drawings annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents title: drawings examples: - value: sketch from_schema: https://w3id.org/nmdc/nmdc aliases: - drawings is_a: core field slot_uri: MIXS:0000798 multivalued: false range: drawings_enum efficiency_percent: name: efficiency_percent annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter occurrence: tag: occurrence value: '1' description: Percentage of volatile solids removed from the anaerobic digestor title: efficiency percent examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - efficiency percent is_a: core field slot_uri: MIXS:0000657 multivalued: false range: QuantityValue elev: name: elev annotations: expected_value: tag: expected_value value: measurement value description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit. title: elevation examples: - value: 100 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - elevation is_a: environment field slot_uri: MIXS:0000093 multivalued: false range: QuantityValue elevator: name: elevator annotations: expected_value: tag: expected_value value: value occurrence: tag: occurrence value: '1' description: The number of elevators within the built structure title: elevator count examples: - value: '2' from_schema: https://w3id.org/nmdc/nmdc aliases: - elevator count is_a: core field slot_uri: MIXS:0000799 multivalued: false range: TextValue emulsions: name: emulsions annotations: expected_value: tag: expected_value value: emulsion name;measurement value preferred_unit: tag: preferred_unit value: gram per liter occurrence: tag: occurrence value: m description: Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types title: emulsions examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - emulsions is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000660 multivalued: true range: TextValue env_broad_scale: name: env_broad_scale annotations: expected_value: tag: expected_value value: The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes. description: 'Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS' title: broad-scale environmental context examples: - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean from_schema: https://w3id.org/nmdc/nmdc aliases: - broad-scale environmental context is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000012 multivalued: false range: ControlledIdentifiedTermValue env_local_scale: name: env_local_scale annotations: expected_value: tag: expected_value value: Environmental entities having causal influences upon the entity at time of sampling. description: 'Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.' title: local environmental context examples: - value: 'litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336].' from_schema: https://w3id.org/nmdc/nmdc aliases: - local environmental context is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000013 multivalued: false range: ControlledIdentifiedTermValue env_medium: name: env_medium annotations: expected_value: tag: expected_value value: The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. description: 'Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).' title: environmental medium examples: - value: 'soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]' from_schema: https://w3id.org/nmdc/nmdc aliases: - environmental medium is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000014 multivalued: false range: ControlledIdentifiedTermValue escalator: name: escalator annotations: expected_value: tag: expected_value value: value occurrence: tag: occurrence value: '1' description: The number of escalators within the built structure title: escalator count examples: - value: '4' from_schema: https://w3id.org/nmdc/nmdc aliases: - escalator count is_a: core field slot_uri: MIXS:0000800 multivalued: false range: TextValue ethylbenzene: name: ethylbenzene annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of ethylbenzene in the sample title: ethylbenzene examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - ethylbenzene is_a: core field slot_uri: MIXS:0000155 multivalued: false range: QuantityValue exp_duct: name: exp_duct annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: square meter occurrence: tag: occurrence value: '1' description: The amount of exposed ductwork in the room title: exposed ductwork examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - exposed ductwork is_a: core field slot_uri: MIXS:0000144 multivalued: false range: QuantityValue exp_pipe: name: exp_pipe annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: The number of exposed pipes in the room title: exposed pipes examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - exposed pipes is_a: core field slot_uri: MIXS:0000220 multivalued: false range: QuantityValue experimental_factor: name: experimental_factor annotations: expected_value: tag: expected_value value: text or EFO and/or OBI description: Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI title: experimental factor examples: - value: time series design [EFO:EFO_0001779] from_schema: https://w3id.org/nmdc/nmdc aliases: - experimental factor is_a: investigation field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000008 multivalued: false range: ControlledTermValue ext_door: name: ext_door annotations: expected_value: tag: expected_value value: value occurrence: tag: occurrence value: '1' description: The number of exterior doors in the built structure title: exterior door count examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - exterior door count is_a: core field slot_uri: MIXS:0000170 multivalued: false range: TextValue ext_wall_orient: name: ext_wall_orient annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The orientation of the exterior wall title: orientations of exterior wall examples: - value: northwest from_schema: https://w3id.org/nmdc/nmdc aliases: - orientations of exterior wall is_a: core field slot_uri: MIXS:0000817 multivalued: false range: ext_wall_orient_enum ext_window_orient: name: ext_window_orient annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The compass direction the exterior window of the room is facing title: orientations of exterior window examples: - value: southwest from_schema: https://w3id.org/nmdc/nmdc aliases: - orientations of exterior window is_a: core field slot_uri: MIXS:0000818 multivalued: false range: ext_window_orient_enum extreme_event: name: extreme_event annotations: expected_value: tag: expected_value value: date occurrence: tag: occurrence value: '1' description: Unusual physical events that may have affected microbial populations title: history/extreme events examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - history/extreme events is_a: core field slot_uri: MIXS:0000320 multivalued: false range: TimestampValue fao_class: name: fao_class annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups title: soil_taxonomic/FAO classification examples: - value: Luvisols from_schema: https://w3id.org/nmdc/nmdc aliases: - soil_taxonomic/FAO classification is_a: core field slot_uri: MIXS:0001083 multivalued: false range: fao_class_enum fertilizer_regm: name: fertilizer_regm annotations: expected_value: tag: expected_value value: fertilizer name;fertilizer amount;treatment interval and duration preferred_unit: tag: preferred_unit value: gram, mole per liter, milligram per liter occurrence: tag: occurrence value: m description: Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens title: fertilizer regimen examples: - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - fertilizer regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000556 multivalued: true range: TextValue field: name: field annotations: expected_value: tag: expected_value value: name occurrence: tag: occurrence value: '1' description: Name of the hydrocarbon field (e.g. Albacora) title: field name examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - field name is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000291 multivalued: false range: TextValue filter_type: name: filter_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: m description: A device which removes solid particulates or airborne molecular contaminants title: filter type examples: - value: HEPA from_schema: https://w3id.org/nmdc/nmdc aliases: - filter type is_a: core field slot_uri: MIXS:0000765 multivalued: true range: filter_type_enum fire: name: fire annotations: expected_value: tag: expected_value value: date occurrence: tag: occurrence value: '1' description: Historical and/or physical evidence of fire title: history/fire examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - history/fire is_a: core field slot_uri: MIXS:0001086 multivalued: false range: TimestampValue fireplace_type: name: fireplace_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: A firebox with chimney title: fireplace type examples: - value: wood burning from_schema: https://w3id.org/nmdc/nmdc aliases: - fireplace type is_a: core field string_serialization: '[gas burning|wood burning]' slot_uri: MIXS:0000802 multivalued: false range: TextValue flooding: name: flooding annotations: expected_value: tag: expected_value value: date occurrence: tag: occurrence value: '1' description: Historical and/or physical evidence of flooding title: history/flooding examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - history/flooding is_a: core field slot_uri: MIXS:0000319 multivalued: false range: TimestampValue floor_age: name: floor_age annotations: expected_value: tag: expected_value value: value preferred_unit: tag: preferred_unit value: years, weeks, days occurrence: tag: occurrence value: '1' description: The time period since installment of the carpet or flooring title: floor age examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - floor age is_a: core field slot_uri: MIXS:0000164 multivalued: false range: QuantityValue floor_area: name: floor_area annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: square meter occurrence: tag: occurrence value: '1' description: The area of the floor space within the room title: floor area examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - floor area is_a: core field slot_uri: MIXS:0000165 multivalued: false range: QuantityValue floor_cond: name: floor_cond annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas title: floor condition examples: - value: new from_schema: https://w3id.org/nmdc/nmdc aliases: - floor condition is_a: core field slot_uri: MIXS:0000803 multivalued: false range: floor_cond_enum floor_count: name: floor_count annotations: expected_value: tag: expected_value value: value occurrence: tag: occurrence value: '1' description: The number of floors in the building, including basements and mechanical penthouse title: floor count examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - floor count is_a: core field slot_uri: MIXS:0000225 multivalued: false range: TextValue floor_finish_mat: name: floor_finish_mat annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The floor covering type; the finished surface that is walked on title: floor finish material examples: - value: carpet from_schema: https://w3id.org/nmdc/nmdc aliases: - floor finish material is_a: core field slot_uri: MIXS:0000804 multivalued: false range: floor_finish_mat_enum floor_struc: name: floor_struc annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Refers to the structural elements and subfloor upon which the finish flooring is installed title: floor structure examples: - value: concrete from_schema: https://w3id.org/nmdc/nmdc aliases: - floor structure is_a: core field slot_uri: MIXS:0000806 multivalued: false range: floor_struc_enum floor_thermal_mass: name: floor_thermal_mass annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: joule per degree Celsius occurrence: tag: occurrence value: '1' description: The ability of the floor to provide inertia against temperature fluctuations title: floor thermal mass examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - floor thermal mass is_a: core field slot_uri: MIXS:0000166 multivalued: false range: QuantityValue floor_water_mold: name: floor_water_mold annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Signs of the presence of mold or mildew in a room title: floor signs of water/mold examples: - value: ceiling discoloration from_schema: https://w3id.org/nmdc/nmdc aliases: - floor signs of water/mold is_a: core field slot_uri: MIXS:0000805 multivalued: false range: floor_water_mold_enum fluor: name: fluor annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram chlorophyll a per cubic meter, volts occurrence: tag: occurrence value: '1' description: Raw or converted fluorescence of water title: fluorescence examples: - value: 2.5 volts from_schema: https://w3id.org/nmdc/nmdc aliases: - fluorescence is_a: core field slot_uri: MIXS:0000704 multivalued: false range: QuantityValue freq_clean: name: freq_clean annotations: expected_value: tag: expected_value value: enumeration or {text} occurrence: tag: occurrence value: '1' description: The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually. title: frequency of cleaning examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - frequency of cleaning is_a: core field slot_uri: MIXS:0000226 multivalued: false range: QuantityValue freq_cook: name: freq_cook annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: The number of times a meal is cooked per week title: frequency of cooking examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - frequency of cooking is_a: core field slot_uri: MIXS:0000227 multivalued: false range: QuantityValue fungicide_regm: name: fungicide_regm annotations: expected_value: tag: expected_value value: fungicide name;fungicide amount;treatment interval and duration preferred_unit: tag: preferred_unit value: gram, mole per liter, milligram per liter occurrence: tag: occurrence value: m description: Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens title: fungicide regimen examples: - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - fungicide regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000557 multivalued: true range: TextValue furniture: name: furniture annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The types of furniture present in the sampled room title: furniture examples: - value: chair from_schema: https://w3id.org/nmdc/nmdc aliases: - furniture is_a: core field slot_uri: MIXS:0000807 multivalued: false range: furniture_enum gaseous_environment: name: gaseous_environment annotations: expected_value: tag: expected_value value: gaseous compound name;gaseous compound amount;treatment interval and duration preferred_unit: tag: preferred_unit value: micromole per liter occurrence: tag: occurrence value: m description: Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens title: gaseous environment examples: - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - gaseous environment is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000558 multivalued: true range: TextValue gaseous_substances: name: gaseous_substances annotations: expected_value: tag: expected_value value: gaseous substance name;measurement value preferred_unit: tag: preferred_unit value: micromole per liter occurrence: tag: occurrence value: m description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances title: gaseous substances examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - gaseous substances is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000661 multivalued: true range: TextValue gender_restroom: name: gender_restroom annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The gender type of the restroom title: gender of restroom examples: - value: male from_schema: https://w3id.org/nmdc/nmdc aliases: - gender of restroom is_a: core field slot_uri: MIXS:0000808 multivalued: false range: gender_restroom_enum genetic_mod: name: genetic_mod annotations: expected_value: tag: expected_value value: PMID,DOI,url or free text occurrence: tag: occurrence value: '1' description: Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection title: genetic modification examples: - value: aox1A transgenic from_schema: https://w3id.org/nmdc/nmdc aliases: - genetic modification is_a: core field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0000859 multivalued: false range: TextValue geo_loc_name: name: geo_loc_name annotations: expected_value: tag: expected_value value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location name' description: The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ) title: geographic location (country and/or sea,region) examples: - value: 'USA: Maryland, Bethesda' from_schema: https://w3id.org/nmdc/nmdc aliases: - geographic location (country and/or sea,region) is_a: environment field string_serialization: '{term}: {term}, {text}' slot_uri: MIXS:0000010 multivalued: false range: TextValue glucosidase_act: name: glucosidase_act annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: mol per liter per hour occurrence: tag: occurrence value: '1' description: Measurement of glucosidase activity title: glucosidase activity examples: - value: 5 mol per liter per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - glucosidase activity is_a: core field slot_uri: MIXS:0000137 multivalued: false range: QuantityValue gravidity: name: gravidity annotations: expected_value: tag: expected_value value: gravidity status;timestamp occurrence: tag: occurrence value: '1' description: Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used title: gravidity examples: - value: yes;due date:2018-05-11 from_schema: https://w3id.org/nmdc/nmdc aliases: - gravidity is_a: core field string_serialization: '{boolean};{timestamp}' slot_uri: MIXS:0000875 multivalued: false range: TextValue gravity: name: gravity annotations: expected_value: tag: expected_value value: gravity factor value;treatment interval and duration preferred_unit: tag: preferred_unit value: meter per square second, g occurrence: tag: occurrence value: m description: Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments title: gravity examples: - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - gravity is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000559 multivalued: true range: TextValue growth_facil: name: growth_facil annotations: expected_value: tag: expected_value value: free text or CO occurrence: tag: occurrence value: '1' description: 'Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research' title: growth facility examples: - value: Growth chamber [CO_715:0000189] from_schema: https://w3id.org/nmdc/nmdc aliases: - growth facility is_a: core field string_serialization: '{text}|{termLabel} {[termID]}' slot_uri: MIXS:0001043 multivalued: false range: ControlledTermValue growth_habit: name: growth_habit annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Characteristic shape, appearance or growth form of a plant species title: growth habit examples: - value: spreading from_schema: https://w3id.org/nmdc/nmdc aliases: - growth habit is_a: core field slot_uri: MIXS:0001044 multivalued: false range: growth_habit_enum growth_hormone_regm: name: growth_hormone_regm annotations: expected_value: tag: expected_value value: growth hormone name;growth hormone amount;treatment interval and duration preferred_unit: tag: preferred_unit value: gram, mole per liter, milligram per liter occurrence: tag: occurrence value: m description: Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens title: growth hormone regimen examples: - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - growth hormone regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000560 multivalued: true range: TextValue hall_count: name: hall_count annotations: expected_value: tag: expected_value value: value occurrence: tag: occurrence value: '1' description: The total count of hallways and cooridors in the built structure title: hallway/corridor count examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - hallway/corridor count is_a: core field slot_uri: MIXS:0000228 multivalued: false range: TextValue handidness: name: handidness annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The handidness of the individual sampled title: handidness examples: - value: right handedness from_schema: https://w3id.org/nmdc/nmdc aliases: - handidness is_a: core field slot_uri: MIXS:0000809 multivalued: false range: handidness_enum hc_produced: name: hc_produced annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If "other" is specified, please propose entry in "additional info" field title: hydrocarbon type produced examples: - value: Gas from_schema: https://w3id.org/nmdc/nmdc aliases: - hydrocarbon type produced is_a: core field slot_uri: MIXS:0000989 multivalued: false range: hc_produced_enum hcr: name: hcr annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Main Hydrocarbon Resource type. The term "Hydrocarbon Resource" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If "other" is specified, please propose entry in "additional info" field title: hydrocarbon resource type examples: - value: Oil Sand from_schema: https://w3id.org/nmdc/nmdc aliases: - hydrocarbon resource type is_a: core field slot_uri: MIXS:0000988 multivalued: false range: hcr_enum hcr_fw_salinity: name: hcr_fw_salinity annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS title: formation water salinity examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - formation water salinity is_a: core field slot_uri: MIXS:0000406 multivalued: false range: QuantityValue hcr_geol_age: name: hcr_geol_age annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field' title: hydrocarbon resource geological age examples: - value: Silurian from_schema: https://w3id.org/nmdc/nmdc aliases: - hydrocarbon resource geological age is_a: core field slot_uri: MIXS:0000993 multivalued: false range: hcr_geol_age_enum hcr_pressure: name: hcr_pressure annotations: expected_value: tag: expected_value value: measurement value range preferred_unit: tag: preferred_unit value: atmosphere, kilopascal occurrence: tag: occurrence value: '1' description: Original pressure of the hydrocarbon resource title: hydrocarbon resource original pressure examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - hydrocarbon resource original pressure is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000395 multivalued: false range: TextValue hcr_temp: name: hcr_temp annotations: expected_value: tag: expected_value value: measurement value range preferred_unit: tag: preferred_unit value: degree Celsius occurrence: tag: occurrence value: '1' description: Original temperature of the hydrocarbon resource title: hydrocarbon resource original temperature examples: - value: 150-295 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - hydrocarbon resource original temperature is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000393 multivalued: false range: TextValue heat_cool_type: name: heat_cool_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: m description: Methods of conditioning or heating a room or building title: heating and cooling system type examples: - value: heat pump from_schema: https://w3id.org/nmdc/nmdc aliases: - heating and cooling system type is_a: core field slot_uri: MIXS:0000766 multivalued: true range: heat_cool_type_enum heat_deliv_loc: name: heat_deliv_loc annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The location of heat delivery within the room title: heating delivery locations examples: - value: north from_schema: https://w3id.org/nmdc/nmdc aliases: - heating delivery locations is_a: core field slot_uri: MIXS:0000810 multivalued: false range: heat_deliv_loc_enum heat_sys_deliv_meth: name: heat_sys_deliv_meth annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The method by which the heat is delivered through the system title: heating system delivery method examples: - value: radiant from_schema: https://w3id.org/nmdc/nmdc aliases: - heating system delivery method is_a: core field string_serialization: '[conductive|radiant]' slot_uri: MIXS:0000812 multivalued: false range: string heat_system_id: name: heat_system_id annotations: expected_value: tag: expected_value value: unique identifier occurrence: tag: occurrence value: '1' description: The heating system identifier title: heating system identifier examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - heating system identifier is_a: core field slot_uri: MIXS:0000833 multivalued: false range: TextValue heavy_metals: name: heavy_metals annotations: expected_value: tag: expected_value value: heavy metal name;measurement value unit preferred_unit: tag: preferred_unit value: microgram per gram occurrence: tag: occurrence value: m description: Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field. title: extreme_unusual_properties/heavy metals examples: - value: mercury;0.09 micrograms per gram from_schema: https://w3id.org/nmdc/nmdc aliases: - extreme_unusual_properties/heavy metals is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000652 multivalued: true range: TextValue heavy_metals_meth: name: heavy_metals_meth annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Reference or method used in determining heavy metals title: extreme_unusual_properties/heavy metals method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - extreme_unusual_properties/heavy metals method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000343 multivalued: false range: TextValue height_carper_fiber: name: height_carper_fiber annotations: expected_value: tag: expected_value value: value preferred_unit: tag: preferred_unit value: centimeter occurrence: tag: occurrence value: '1' description: The average carpet fiber height in the indoor environment title: height carpet fiber mat examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - height carpet fiber mat is_a: core field slot_uri: MIXS:0000167 multivalued: false range: QuantityValue herbicide_regm: name: herbicide_regm annotations: expected_value: tag: expected_value value: herbicide name;herbicide amount;treatment interval and duration preferred_unit: tag: preferred_unit value: gram, mole per liter, milligram per liter occurrence: tag: occurrence value: m description: Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens title: herbicide regimen examples: - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - herbicide regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000561 multivalued: true range: TextValue horizon_meth: name: horizon_meth annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Reference or method used in determining the horizon title: soil horizon method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - soil horizon method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000321 multivalued: false range: TextValue host_age: name: host_age annotations: expected_value: tag: expected_value value: value preferred_unit: tag: preferred_unit value: year, day, hour occurrence: tag: occurrence value: '1' description: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees title: host age examples: - value: 10 days from_schema: https://w3id.org/nmdc/nmdc aliases: - host age is_a: core field slot_uri: MIXS:0000255 multivalued: false range: QuantityValue host_body_habitat: name: host_body_habitat annotations: expected_value: tag: expected_value value: free text occurrence: tag: occurrence value: '1' description: Original body habitat where the sample was obtained from title: host body habitat examples: - value: nasopharynx from_schema: https://w3id.org/nmdc/nmdc aliases: - host body habitat is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000866 multivalued: false range: TextValue host_body_product: name: host_body_product annotations: expected_value: tag: expected_value value: FMA or UBERON occurrence: tag: occurrence value: '1' description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon title: host body product examples: - value: Portion of mucus [fma66938] from_schema: https://w3id.org/nmdc/nmdc aliases: - host body product is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000888 multivalued: false range: ControlledTermValue host_body_site: name: host_body_site annotations: expected_value: tag: expected_value value: FMA or UBERON occurrence: tag: occurrence value: '1' description: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON title: host body site examples: - value: gill [UBERON:0002535] from_schema: https://w3id.org/nmdc/nmdc aliases: - host body site is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000867 multivalued: false range: ControlledTermValue host_body_temp: name: host_body_temp annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: degree Celsius occurrence: tag: occurrence value: '1' description: Core body temperature of the host when sample was collected title: host body temperature examples: - value: 15 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - host body temperature is_a: core field slot_uri: MIXS:0000274 multivalued: false range: QuantityValue host_color: name: host_color annotations: expected_value: tag: expected_value value: color occurrence: tag: occurrence value: '1' description: The color of host title: host color examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - host color is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000260 multivalued: false range: TextValue host_common_name: name: host_common_name annotations: expected_value: tag: expected_value value: common name occurrence: tag: occurrence value: '1' description: Common name of the host. title: host common name examples: - value: human from_schema: https://w3id.org/nmdc/nmdc aliases: - host common name is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000248 multivalued: false range: TextValue host_diet: name: host_diet annotations: expected_value: tag: expected_value value: diet type occurrence: tag: occurrence value: m description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types title: host diet examples: - value: herbivore from_schema: https://w3id.org/nmdc/nmdc aliases: - host diet is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000869 multivalued: true range: TextValue host_dry_mass: name: host_dry_mass annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: kilogram, gram occurrence: tag: occurrence value: '1' description: Measurement of dry mass title: host dry mass examples: - value: 500 gram from_schema: https://w3id.org/nmdc/nmdc aliases: - host dry mass is_a: core field slot_uri: MIXS:0000257 multivalued: false range: QuantityValue host_family_relation: name: host_family_relation annotations: expected_value: tag: expected_value value: relationship type;arbitrary identifier occurrence: tag: occurrence value: m description: Familial relationships to other hosts in the same study; can include multiple relationships title: host family relationship examples: - value: offspring;Mussel25 from_schema: https://w3id.org/nmdc/nmdc aliases: - host family relationship is_a: core field string_serialization: '{text};{text}' slot_uri: MIXS:0000872 multivalued: true range: string host_genotype: name: host_genotype annotations: expected_value: tag: expected_value value: genotype occurrence: tag: occurrence value: '1' description: Observed genotype title: host genotype examples: - value: C57BL/6 from_schema: https://w3id.org/nmdc/nmdc aliases: - host genotype is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000365 multivalued: false range: TextValue host_growth_cond: name: host_growth_cond annotations: expected_value: tag: expected_value value: PMID,DOI,url or free text occurrence: tag: occurrence value: '1' description: Literature reference giving growth conditions of the host title: host growth conditions examples: - value: https://academic.oup.com/icesjms/article/68/2/349/617247 from_schema: https://w3id.org/nmdc/nmdc aliases: - host growth conditions is_a: core field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0000871 multivalued: false range: TextValue host_height: name: host_height annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: centimeter, millimeter, meter occurrence: tag: occurrence value: '1' description: The height of subject title: host height examples: - value: 0.1 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - host height is_a: core field slot_uri: MIXS:0000264 multivalued: false range: QuantityValue host_last_meal: name: host_last_meal annotations: expected_value: tag: expected_value value: content;duration occurrence: tag: occurrence value: m description: Content of last meal and time since feeding; can include multiple values title: host last meal examples: - value: corn feed;P2H from_schema: https://w3id.org/nmdc/nmdc aliases: - host last meal is_a: core field string_serialization: '{text};{duration}' slot_uri: MIXS:0000870 multivalued: true range: TextValue host_length: name: host_length annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: centimeter, millimeter, meter occurrence: tag: occurrence value: '1' description: The length of subject title: host length examples: - value: 1 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - host length is_a: core field slot_uri: MIXS:0000256 multivalued: false range: QuantityValue host_life_stage: name: host_life_stage annotations: expected_value: tag: expected_value value: stage occurrence: tag: occurrence value: '1' description: Description of life stage of host title: host life stage examples: - value: adult from_schema: https://w3id.org/nmdc/nmdc aliases: - host life stage is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000251 multivalued: false range: TextValue host_phenotype: name: host_phenotype annotations: expected_value: tag: expected_value value: PATO or HP occurrence: tag: occurrence value: '1' description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP title: host phenotype examples: - value: elongated [PATO:0001154] from_schema: https://w3id.org/nmdc/nmdc aliases: - host phenotype is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000874 multivalued: false range: ControlledTermValue host_sex: name: host_sex annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Gender or physical sex of the host. title: host sex examples: - value: non-binary from_schema: https://w3id.org/nmdc/nmdc aliases: - host sex is_a: core field slot_uri: MIXS:0000811 multivalued: false range: host_sex_enum host_shape: name: host_shape annotations: expected_value: tag: expected_value value: shape occurrence: tag: occurrence value: '1' description: Morphological shape of host title: host shape examples: - value: round from_schema: https://w3id.org/nmdc/nmdc aliases: - host shape is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000261 multivalued: false range: TextValue host_subject_id: name: host_subject_id annotations: expected_value: tag: expected_value value: unique identifier occurrence: tag: occurrence value: '1' description: A unique identifier by which each subject can be referred to, de-identified. title: host subject id examples: - value: MPI123 from_schema: https://w3id.org/nmdc/nmdc aliases: - host subject id is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000861 multivalued: false range: TextValue host_subspecf_genlin: name: host_subspecf_genlin annotations: expected_value: tag: expected_value value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar. occurrence: tag: occurrence value: m description: Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123. title: host subspecific genetic lineage examples: - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious' from_schema: https://w3id.org/nmdc/nmdc aliases: - host subspecific genetic lineage is_a: core field string_serialization: '{rank name}:{text}' slot_uri: MIXS:0001318 multivalued: true range: string host_substrate: name: host_substrate annotations: expected_value: tag: expected_value value: substrate name occurrence: tag: occurrence value: '1' description: The growth substrate of the host. title: host substrate examples: - value: rock from_schema: https://w3id.org/nmdc/nmdc aliases: - host substrate is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000252 multivalued: false range: TextValue host_symbiont: name: host_symbiont annotations: expected_value: tag: expected_value value: species name or common name occurrence: tag: occurrence value: m description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. title: observed host symbionts examples: - value: flukeworms from_schema: https://w3id.org/nmdc/nmdc aliases: - observed host symbionts is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001298 multivalued: true range: string host_taxid: name: host_taxid annotations: expected_value: tag: expected_value value: NCBI taxon identifier occurrence: tag: occurrence value: '1' description: NCBI taxon id of the host, e.g. 9606 title: host taxid comments: - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value from_schema: https://w3id.org/nmdc/nmdc aliases: - host taxid is_a: core field slot_uri: MIXS:0000250 multivalued: false range: ControlledIdentifiedTermValue host_tot_mass: name: host_tot_mass annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: kilogram, gram occurrence: tag: occurrence value: '1' description: Total mass of the host at collection, the unit depends on host title: host total mass examples: - value: 2500 gram from_schema: https://w3id.org/nmdc/nmdc aliases: - host total mass is_a: core field slot_uri: MIXS:0000263 multivalued: false range: QuantityValue host_wet_mass: name: host_wet_mass annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: kilogram, gram occurrence: tag: occurrence value: '1' description: Measurement of wet mass title: host wet mass examples: - value: 1500 gram from_schema: https://w3id.org/nmdc/nmdc aliases: - host wet mass is_a: core field slot_uri: MIXS:0000567 multivalued: false range: QuantityValue humidity: name: humidity annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: gram per cubic meter occurrence: tag: occurrence value: '1' description: Amount of water vapour in the air, at the time of sampling title: humidity examples: - value: 25 gram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - humidity is_a: core field slot_uri: MIXS:0000100 multivalued: false range: QuantityValue humidity_regm: name: humidity_regm annotations: expected_value: tag: expected_value value: humidity value;treatment interval and duration preferred_unit: tag: preferred_unit value: gram per cubic meter occurrence: tag: occurrence value: m description: Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens title: humidity regimen examples: - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - humidity regimen is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000568 multivalued: true range: TextValue indoor_space: name: indoor_space annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used title: indoor space examples: - value: foyer from_schema: https://w3id.org/nmdc/nmdc aliases: - indoor space is_a: core field slot_uri: MIXS:0000763 multivalued: false range: indoor_space_enum indoor_surf: name: indoor_surf annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Type of indoor surface title: indoor surface examples: - value: wall from_schema: https://w3id.org/nmdc/nmdc aliases: - indoor surface is_a: core field slot_uri: MIXS:0000764 multivalued: false range: indoor_surf_enum indust_eff_percent: name: indust_eff_percent annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: percentage occurrence: tag: occurrence value: '1' description: Percentage of industrial effluents received by wastewater treatment plant title: industrial effluent percent examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - industrial effluent percent is_a: core field slot_uri: MIXS:0000662 multivalued: false range: QuantityValue inorg_particles: name: inorg_particles annotations: expected_value: tag: expected_value value: inorganic particle name;measurement value preferred_unit: tag: preferred_unit value: mole per liter, milligram per liter occurrence: tag: occurrence value: m description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles title: inorganic particles examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - inorganic particles is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000664 multivalued: true range: TextValue inside_lux: name: inside_lux annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: kilowatt per square metre occurrence: tag: occurrence value: '1' description: The recorded value at sampling time (power density) title: inside lux light examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - inside lux light is_a: core field slot_uri: MIXS:0000168 multivalued: false range: QuantityValue int_wall_cond: name: int_wall_cond annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas title: interior wall condition examples: - value: damaged from_schema: https://w3id.org/nmdc/nmdc aliases: - interior wall condition is_a: core field slot_uri: MIXS:0000813 multivalued: false range: int_wall_cond_enum iw_bt_date_well: name: iw_bt_date_well annotations: expected_value: tag: expected_value value: timestamp occurrence: tag: occurrence value: '1' description: Injection water breakthrough date per well following a secondary and/or tertiary recovery title: injection water breakthrough date of specific well examples: - value: '2018-05-11' from_schema: https://w3id.org/nmdc/nmdc aliases: - injection water breakthrough date of specific well is_a: core field slot_uri: MIXS:0001010 multivalued: false range: TimestampValue iwf: name: iwf annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: percent occurrence: tag: occurrence value: '1' description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) title: injection water fraction examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - injection water fraction is_a: core field slot_uri: MIXS:0000455 multivalued: false range: QuantityValue last_clean: name: last_clean annotations: expected_value: tag: expected_value value: timestamp occurrence: tag: occurrence value: '1' description: The last time the floor was cleaned (swept, mopped, vacuumed) title: last time swept/mopped/vacuumed examples: - value: 2018-05-11:T14:30Z from_schema: https://w3id.org/nmdc/nmdc aliases: - last time swept/mopped/vacuumed is_a: core field slot_uri: MIXS:0000814 multivalued: false range: TimestampValue lat_lon: name: lat_lon annotations: expected_value: tag: expected_value value: decimal degrees, limit to 8 decimal points description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system title: geographic location (latitude and longitude) examples: - value: 50.586825 6.408977 from_schema: https://w3id.org/nmdc/nmdc aliases: - geographic location (latitude and longitude) is_a: environment field string_serialization: '{float} {float}' slot_uri: MIXS:0000009 multivalued: false range: GeolocationValue light_intensity: name: light_intensity annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: lux occurrence: tag: occurrence value: '1' description: Measurement of light intensity title: light intensity examples: - value: 0.3 lux from_schema: https://w3id.org/nmdc/nmdc aliases: - light intensity is_a: core field slot_uri: MIXS:0000706 multivalued: false range: QuantityValue light_regm: name: light_regm annotations: expected_value: tag: expected_value value: exposure type;light intensity;light quality preferred_unit: tag: preferred_unit value: lux; micrometer, nanometer, angstrom occurrence: tag: occurrence value: '1' description: Information about treatment(s) involving exposure to light, including both light intensity and quality. title: light regimen examples: - value: incandescant light;10 lux;450 nanometer from_schema: https://w3id.org/nmdc/nmdc aliases: - light regimen is_a: core field string_serialization: '{text};{float} {unit};{float} {unit}' slot_uri: MIXS:0000569 multivalued: false range: TextValue light_type: name: light_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: m description: Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light title: light type examples: - value: desk lamp from_schema: https://w3id.org/nmdc/nmdc aliases: - light type is_a: core field slot_uri: MIXS:0000769 multivalued: true range: light_type_enum link_addit_analys: name: link_addit_analys annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Link to additional analysis results performed on the sample title: links to additional analysis examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - links to additional analysis is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000340 multivalued: false range: TextValue link_class_info: name: link_class_info annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Link to digitized soil maps or other soil classification information title: link to classification information examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - link to classification information is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000329 multivalued: false range: TextValue link_climate_info: name: link_climate_info annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Link to climate resource title: link to climate information examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - link to climate information is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000328 multivalued: false range: TextValue lithology: name: lithology annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If "other" is specified, please propose entry in "additional info" field' title: lithology examples: - value: Volcanic from_schema: https://w3id.org/nmdc/nmdc aliases: - lithology is_a: core field slot_uri: MIXS:0000990 multivalued: false range: lithology_enum local_class: name: local_class annotations: expected_value: tag: expected_value value: local classification name occurrence: tag: occurrence value: '1' description: Soil classification based on local soil classification system title: soil_taxonomic/local classification examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - soil_taxonomic/local classification is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000330 multivalued: false range: TextValue local_class_meth: name: local_class_meth annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Reference or method used in determining the local soil classification title: soil_taxonomic/local classification method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - soil_taxonomic/local classification method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000331 multivalued: false range: TextValue magnesium: name: magnesium annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: mole per liter, milligram per liter, parts per million, micromole per kilogram occurrence: tag: occurrence value: '1' description: Concentration of magnesium in the sample title: magnesium examples: - value: 52.8 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - magnesium is_a: core field slot_uri: MIXS:0000431 multivalued: false range: QuantityValue max_occup: name: max_occup annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: The maximum amount of people allowed in the indoor environment title: maximum occupancy examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - maximum occupancy is_a: core field slot_uri: MIXS:0000229 multivalued: false range: QuantityValue mean_frict_vel: name: mean_frict_vel annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: meter per second occurrence: tag: occurrence value: '1' description: Measurement of mean friction velocity title: mean friction velocity examples: - value: 0.5 meter per second from_schema: https://w3id.org/nmdc/nmdc aliases: - mean friction velocity is_a: core field slot_uri: MIXS:0000498 multivalued: false range: QuantityValue mean_peak_frict_vel: name: mean_peak_frict_vel annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: meter per second occurrence: tag: occurrence value: '1' description: Measurement of mean peak friction velocity title: mean peak friction velocity examples: - value: 1 meter per second from_schema: https://w3id.org/nmdc/nmdc aliases: - mean peak friction velocity is_a: core field slot_uri: MIXS:0000502 multivalued: false range: QuantityValue mech_struc: name: mech_struc annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: 'mechanical structure: a moving structure' title: mechanical structure examples: - value: elevator from_schema: https://w3id.org/nmdc/nmdc aliases: - mechanical structure is_a: core field slot_uri: MIXS:0000815 multivalued: false range: mech_struc_enum mechanical_damage: name: mechanical_damage annotations: expected_value: tag: expected_value value: damage type;body site occurrence: tag: occurrence value: m description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites title: mechanical damage examples: - value: pruning;bark from_schema: https://w3id.org/nmdc/nmdc aliases: - mechanical damage is_a: core field string_serialization: '{text};{text}' slot_uri: MIXS:0001052 multivalued: true range: TextValue methane: name: methane annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter, parts per billion, parts per million occurrence: tag: occurrence value: '1' description: Methane (gas) amount or concentration at the time of sampling title: methane examples: - value: 1800 parts per billion from_schema: https://w3id.org/nmdc/nmdc aliases: - methane is_a: core field slot_uri: MIXS:0000101 multivalued: false range: QuantityValue micro_biomass_meth: name: micro_biomass_meth annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Reference or method used in determining microbial biomass title: microbial biomass method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - microbial biomass method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000339 multivalued: false range: string microbial_biomass: name: microbial_biomass annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: ton, kilogram, gram per kilogram soil occurrence: tag: occurrence value: '1' description: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units title: microbial biomass examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - microbial biomass is_a: core field slot_uri: MIXS:0000650 multivalued: false range: QuantityValue mineral_nutr_regm: name: mineral_nutr_regm annotations: expected_value: tag: expected_value value: mineral nutrient name;mineral nutrient amount;treatment interval and duration preferred_unit: tag: preferred_unit value: gram, mole per liter, milligram per liter occurrence: tag: occurrence value: m description: Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens title: mineral nutrient regimen examples: - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - mineral nutrient regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000570 multivalued: true range: TextValue misc_param: name: misc_param annotations: expected_value: tag: expected_value value: parameter name;measurement value occurrence: tag: occurrence value: m description: Any other measurement performed or parameter collected, that is not listed here title: miscellaneous parameter examples: - value: Bicarbonate ion concentration;2075 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - miscellaneous parameter is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000752 multivalued: true range: TextValue n_alkanes: name: n_alkanes annotations: expected_value: tag: expected_value value: n-alkane name;measurement value preferred_unit: tag: preferred_unit value: micromole per liter occurrence: tag: occurrence value: m description: Concentration of n-alkanes; can include multiple n-alkanes title: n-alkanes examples: - value: n-hexadecane;100 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - n-alkanes is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000503 multivalued: true range: TextValue nitrate: name: nitrate annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter, milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of nitrate in the sample title: nitrate examples: - value: 65 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - nitrate is_a: core field slot_uri: MIXS:0000425 multivalued: false range: QuantityValue nitrite: name: nitrite annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter, milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of nitrite in the sample title: nitrite examples: - value: 0.5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - nitrite is_a: core field slot_uri: MIXS:0000426 multivalued: false range: QuantityValue nitro: name: nitro annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter occurrence: tag: occurrence value: '1' description: Concentration of nitrogen (total) title: nitrogen examples: - value: 4.2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - nitrogen is_a: core field slot_uri: MIXS:0000504 multivalued: false range: QuantityValue non_min_nutr_regm: name: non_min_nutr_regm annotations: expected_value: tag: expected_value value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration preferred_unit: tag: preferred_unit value: gram, mole per liter, milligram per liter occurrence: tag: occurrence value: m description: Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens title: non-mineral nutrient regimen examples: - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - non-mineral nutrient regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000571 multivalued: true range: string nucl_acid_amp: name: nucl_acid_amp annotations: expected_value: tag: expected_value value: PMID, DOI or URL description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids title: nucleic acid amplification examples: - value: https://phylogenomics.me/protocols/16s-pcr-protocol/ from_schema: https://w3id.org/nmdc/nmdc aliases: - nucleic acid amplification is_a: sequencing field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000038 multivalued: false range: TextValue nucl_acid_ext: name: nucl_acid_ext annotations: expected_value: tag: expected_value value: PMID, DOI or URL description: A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample title: nucleic acid extraction examples: - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf from_schema: https://w3id.org/nmdc/nmdc aliases: - nucleic acid extraction is_a: sequencing field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000037 multivalued: false range: TextValue number_pets: name: number_pets annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: The number of pets residing in the sampled space title: number of pets examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - number of pets is_a: core field slot_uri: MIXS:0000231 multivalued: false range: QuantityValue number_plants: name: number_plants annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: The number of plant(s) in the sampling space title: number of houseplants examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - number of houseplants is_a: core field slot_uri: MIXS:0000230 multivalued: false range: QuantityValue number_resident: name: number_resident annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: The number of individuals currently occupying in the sampling location title: number of residents examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - number of residents is_a: core field slot_uri: MIXS:0000232 multivalued: false range: QuantityValue occup_density_samp: name: occup_density_samp annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: Average number of occupants at time of sampling per square footage title: occupant density at sampling examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - occupant density at sampling is_a: core field slot_uri: MIXS:0000217 multivalued: false range: QuantityValue occup_document: name: occup_document annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The type of documentation of occupancy title: occupancy documentation examples: - value: estimate from_schema: https://w3id.org/nmdc/nmdc aliases: - occupancy documentation is_a: core field slot_uri: MIXS:0000816 multivalued: false range: occup_document_enum occup_samp: name: occup_samp annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: Number of occupants present at time of sample within the given space title: occupancy at sampling examples: - value: '10' from_schema: https://w3id.org/nmdc/nmdc aliases: - occupancy at sampling is_a: core field slot_uri: MIXS:0000772 multivalued: false range: QuantityValue org_carb: name: org_carb annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter occurrence: tag: occurrence value: '1' description: Concentration of organic carbon title: organic carbon examples: - value: 1.5 microgram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - organic carbon is_a: core field slot_uri: MIXS:0000508 multivalued: false range: QuantityValue org_count_qpcr_info: name: org_count_qpcr_info annotations: expected_value: tag: expected_value value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles preferred_unit: tag: preferred_unit value: number of cells per gram (or ml or cm^2) occurrence: tag: occurrence value: '1' description: 'If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)' title: organism count qPCR information examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - organism count qPCR information is_a: core field string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles' slot_uri: MIXS:0000099 multivalued: false range: string org_matter: name: org_matter annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter occurrence: tag: occurrence value: '1' description: Concentration of organic matter title: organic matter examples: - value: 1.75 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - organic matter is_a: core field slot_uri: MIXS:0000204 multivalued: false range: QuantityValue org_nitro: name: org_nitro annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter occurrence: tag: occurrence value: '1' description: Concentration of organic nitrogen title: organic nitrogen examples: - value: 4 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - organic nitrogen is_a: core field slot_uri: MIXS:0000205 multivalued: false range: QuantityValue org_particles: name: org_particles annotations: expected_value: tag: expected_value value: particle name;measurement value preferred_unit: tag: preferred_unit value: gram per liter occurrence: tag: occurrence value: m description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. title: organic particles examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - organic particles is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000665 multivalued: true range: TextValue organism_count: name: organism_count annotations: expected_value: tag: expected_value value: organism name;measurement value;enumeration preferred_unit: tag: preferred_unit value: number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter occurrence: tag: occurrence value: m description: 'Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)' title: organism count examples: - value: total prokaryotes;3.5e7 cells per milliliter;qPCR from_schema: https://w3id.org/nmdc/nmdc aliases: - organism count is_a: core field slot_uri: MIXS:0000103 multivalued: true range: QuantityValue owc_tvdss: name: owc_tvdss annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: meter occurrence: tag: occurrence value: '1' description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) title: oil water contact depth examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - oil water contact depth is_a: core field slot_uri: MIXS:0000405 multivalued: false range: QuantityValue oxy_stat_samp: name: oxy_stat_samp annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Oxygenation status of sample title: oxygenation status of sample examples: - value: aerobic from_schema: https://w3id.org/nmdc/nmdc aliases: - oxygenation status of sample is_a: core field slot_uri: MIXS:0000753 multivalued: false range: oxy_stat_samp_enum oxygen: name: oxygen annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Oxygen (gas) amount or concentration at the time of sampling title: oxygen examples: - value: 600 parts per million from_schema: https://w3id.org/nmdc/nmdc aliases: - oxygen is_a: core field slot_uri: MIXS:0000104 multivalued: false range: QuantityValue part_org_carb: name: part_org_carb annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter occurrence: tag: occurrence value: '1' description: Concentration of particulate organic carbon title: particulate organic carbon examples: - value: 1.92 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - particulate organic carbon is_a: core field slot_uri: MIXS:0000515 multivalued: false range: QuantityValue part_org_nitro: name: part_org_nitro annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter, micromole per liter occurrence: tag: occurrence value: '1' description: Concentration of particulate organic nitrogen title: particulate organic nitrogen examples: - value: 0.3 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - particulate organic nitrogen is_a: core field slot_uri: MIXS:0000719 multivalued: false range: QuantityValue particle_class: name: particle_class annotations: expected_value: tag: expected_value value: particle name;measurement value preferred_unit: tag: preferred_unit value: micrometer occurrence: tag: occurrence value: m description: Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values title: particle classification examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - particle classification is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000206 multivalued: true range: TextValue pcr_cond: name: pcr_cond annotations: expected_value: tag: expected_value value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles description: Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' title: pcr conditions examples: - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35 from_schema: https://w3id.org/nmdc/nmdc aliases: - pcr conditions is_a: sequencing field string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles slot_uri: MIXS:0000049 multivalued: false range: TextValue pcr_primers: name: pcr_primers annotations: expected_value: tag: expected_value value: 'FWD: forward primer sequence;REV:reverse primer sequence' description: PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters title: pcr primers examples: - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT from_schema: https://w3id.org/nmdc/nmdc aliases: - pcr primers is_a: sequencing field string_serialization: FWD:{dna};REV:{dna} slot_uri: MIXS:0000046 multivalued: false range: TextValue permeability: name: permeability annotations: expected_value: tag: expected_value value: measurement value range preferred_unit: tag: preferred_unit value: mD occurrence: tag: occurrence value: '1' description: 'Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))' title: permeability examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - permeability is_a: core field string_serialization: '{integer} - {integer} {unit}' slot_uri: MIXS:0000404 multivalued: false range: TextValue perturbation: name: perturbation annotations: expected_value: tag: expected_value value: perturbation type name;perturbation interval and duration occurrence: tag: occurrence value: m description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types title: perturbation examples: - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - perturbation is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000754 multivalued: true range: TextValue pesticide_regm: name: pesticide_regm annotations: expected_value: tag: expected_value value: pesticide name;pesticide amount;treatment interval and duration preferred_unit: tag: preferred_unit value: gram, mole per liter, milligram per liter occurrence: tag: occurrence value: m description: Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens title: pesticide regimen examples: - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - pesticide regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000573 multivalued: true range: TextValue petroleum_hydrocarb: name: petroleum_hydrocarb annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter occurrence: tag: occurrence value: '1' description: Concentration of petroleum hydrocarbon title: petroleum hydrocarbon examples: - value: 0.05 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - petroleum hydrocarbon is_a: core field slot_uri: MIXS:0000516 multivalued: false range: QuantityValue ph: name: ph annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid title: pH examples: - value: '7.2' from_schema: https://w3id.org/nmdc/nmdc aliases: - pH is_a: core field slot_uri: MIXS:0001001 multivalued: false range: double ph_meth: name: ph_meth annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Reference or method used in determining ph title: pH method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - pH method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001106 multivalued: false range: TextValue ph_regm: name: ph_regm annotations: expected_value: tag: expected_value value: measurement value;treatment interval and duration occurrence: tag: occurrence value: m description: Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen title: pH regimen examples: - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - pH regimen is_a: core field string_serialization: '{float};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001056 multivalued: true range: TextValue phaeopigments: name: phaeopigments annotations: expected_value: tag: expected_value value: phaeopigment name;measurement value preferred_unit: tag: preferred_unit value: milligram per cubic meter occurrence: tag: occurrence value: m description: Concentration of phaeopigments; can include multiple phaeopigments title: phaeopigments examples: - value: 2.5 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - phaeopigments is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000180 multivalued: true range: TextValue phosphate: name: phosphate annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter occurrence: tag: occurrence value: '1' description: Concentration of phosphate title: phosphate examples: - value: 0.7 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - phosphate is_a: core field slot_uri: MIXS:0000505 multivalued: false range: QuantityValue phosplipid_fatt_acid: name: phosplipid_fatt_acid annotations: expected_value: tag: expected_value value: phospholipid fatty acid name;measurement value preferred_unit: tag: preferred_unit value: mole per gram, mole per liter occurrence: tag: occurrence value: m description: Concentration of phospholipid fatty acids; can include multiple values title: phospholipid fatty acid examples: - value: 2.98 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - phospholipid fatty acid is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000181 multivalued: true range: TextValue photon_flux: name: photon_flux annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: number of photons per second per unit area occurrence: tag: occurrence value: '1' description: Measurement of photon flux title: photon flux examples: - value: 3.926 micromole photons per second per square meter from_schema: https://w3id.org/nmdc/nmdc aliases: - photon flux is_a: core field slot_uri: MIXS:0000725 multivalued: false range: QuantityValue plant_growth_med: name: plant_growth_med annotations: expected_value: tag: expected_value value: EO or enumeration occurrence: tag: occurrence value: '1' description: Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary title: plant growth medium examples: - value: hydroponic plant culture media [EO:0007067] from_schema: https://w3id.org/nmdc/nmdc aliases: - plant growth medium is_a: core field slot_uri: MIXS:0001057 multivalued: false range: ControlledTermValue plant_product: name: plant_product annotations: expected_value: tag: expected_value value: product name occurrence: tag: occurrence value: '1' description: Substance produced by the plant, where the sample was obtained from title: plant product examples: - value: xylem sap [PO:0025539] from_schema: https://w3id.org/nmdc/nmdc aliases: - plant product is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001058 multivalued: false range: TextValue plant_sex: name: plant_sex annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. title: plant sex examples: - value: Hermaphroditic from_schema: https://w3id.org/nmdc/nmdc aliases: - plant sex is_a: core field slot_uri: MIXS:0001059 multivalued: false range: plant_sex_enum plant_struc: name: plant_struc annotations: expected_value: tag: expected_value value: PO occurrence: tag: occurrence value: '1' description: Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here. title: plant structure examples: - value: epidermis [PO:0005679] from_schema: https://w3id.org/nmdc/nmdc aliases: - plant structure is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0001060 multivalued: false range: ControlledTermValue pollutants: name: pollutants annotations: expected_value: tag: expected_value value: pollutant name;measurement value preferred_unit: tag: preferred_unit value: gram, mole per liter, milligram per liter, microgram per cubic meter occurrence: tag: occurrence value: m description: Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant title: pollutants examples: - value: lead;0.15 microgram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - pollutants is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000107 multivalued: true range: TextValue pool_dna_extracts: name: pool_dna_extracts annotations: expected_value: tag: expected_value value: pooling status;number of pooled extracts occurrence: tag: occurrence value: '1' description: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given title: pooling of DNA extracts (if done) examples: - value: yes;5 from_schema: https://w3id.org/nmdc/nmdc aliases: - pooling of DNA extracts (if done) is_a: core field string_serialization: '{boolean};{integer}' slot_uri: MIXS:0000325 multivalued: false range: TextValue porosity: name: porosity annotations: expected_value: tag: expected_value value: measurement value or range preferred_unit: tag: preferred_unit value: percentage occurrence: tag: occurrence value: '1' description: Porosity of deposited sediment is volume of voids divided by the total volume of sample title: porosity examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - porosity is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000211 multivalued: false range: TextValue potassium: name: potassium annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of potassium in the sample title: potassium examples: - value: 463 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - potassium is_a: core field slot_uri: MIXS:0000430 multivalued: false range: QuantityValue pour_point: name: pour_point annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: degree Celsius occurrence: tag: occurrence value: '1' description: 'Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)' title: pour point examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - pour point is_a: core field slot_uri: MIXS:0000127 multivalued: false range: QuantityValue pre_treatment: name: pre_treatment annotations: expected_value: tag: expected_value value: pre-treatment type occurrence: tag: occurrence value: '1' description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater title: pre-treatment examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - pre-treatment is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000348 multivalued: false range: TextValue pres_animal_insect: name: pres_animal_insect annotations: expected_value: tag: expected_value value: enumeration;count occurrence: tag: occurrence value: '1' description: The type and number of animals or insects present in the sampling space. title: presence of pets, animals, or insects examples: - value: cat;5 from_schema: https://w3id.org/nmdc/nmdc aliases: - presence of pets, animals, or insects is_a: core field slot_uri: MIXS:0000819 multivalued: false range: string pattern: ^(cat|dog|rodent|snake|other);\d+$ pressure: name: pressure annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: atmosphere occurrence: tag: occurrence value: '1' description: Pressure to which the sample is subject to, in atmospheres title: pressure examples: - value: 50 atmosphere from_schema: https://w3id.org/nmdc/nmdc aliases: - pressure is_a: core field slot_uri: MIXS:0000412 multivalued: false range: QuantityValue prev_land_use_meth: name: prev_land_use_meth annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Reference or method used in determining previous land use and dates title: history/previous land use method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - history/previous land use method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000316 multivalued: false range: string previous_land_use: name: previous_land_use annotations: expected_value: tag: expected_value value: land use name;date occurrence: tag: occurrence value: '1' description: Previous land use and dates title: history/previous land use examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - history/previous land use is_a: core field string_serialization: '{text};{timestamp}' slot_uri: MIXS:0000315 multivalued: false range: TextValue primary_prod: name: primary_prod annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per cubic meter per day, gram per square meter per day occurrence: tag: occurrence value: '1' description: Measurement of primary production, generally measured as isotope uptake title: primary production examples: - value: 100 milligram per cubic meter per day from_schema: https://w3id.org/nmdc/nmdc aliases: - primary production is_a: core field slot_uri: MIXS:0000728 multivalued: false range: QuantityValue primary_treatment: name: primary_treatment annotations: expected_value: tag: expected_value value: primary treatment type occurrence: tag: occurrence value: '1' description: The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed title: primary treatment examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - primary treatment is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000349 multivalued: false range: TextValue prod_rate: name: prod_rate annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: cubic meter per day occurrence: tag: occurrence value: '1' description: Oil and/or gas production rates per well (e.g. 524 m3 / day) title: production rate examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - production rate is_a: core field slot_uri: MIXS:0000452 multivalued: false range: QuantityValue prod_start_date: name: prod_start_date annotations: expected_value: tag: expected_value value: timestamp occurrence: tag: occurrence value: '1' description: Date of field's first production title: production start date examples: - value: '2018-05-11' from_schema: https://w3id.org/nmdc/nmdc aliases: - production start date is_a: core field slot_uri: MIXS:0001008 multivalued: false range: TimestampValue profile_position: name: profile_position annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas title: profile position examples: - value: summit from_schema: https://w3id.org/nmdc/nmdc aliases: - profile position is_a: core field slot_uri: MIXS:0001084 multivalued: false range: profile_position_enum quad_pos: name: quad_pos annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The quadrant position of the sampling room within the building title: quadrant position examples: - value: West side from_schema: https://w3id.org/nmdc/nmdc aliases: - quadrant position is_a: core field slot_uri: MIXS:0000820 multivalued: false range: quad_pos_enum radiation_regm: name: radiation_regm annotations: expected_value: tag: expected_value value: radiation type name;radiation amount;treatment interval and duration preferred_unit: tag: preferred_unit value: rad, gray occurrence: tag: occurrence value: m description: Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens title: radiation regimen examples: - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - radiation regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000575 multivalued: true range: TextValue rainfall_regm: name: rainfall_regm annotations: expected_value: tag: expected_value value: measurement value;treatment interval and duration preferred_unit: tag: preferred_unit value: millimeter occurrence: tag: occurrence value: m description: Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens title: rainfall regimen examples: - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - rainfall regimen is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000576 multivalued: true range: TextValue reactor_type: name: reactor_type annotations: expected_value: tag: expected_value value: reactor type name occurrence: tag: occurrence value: '1' description: Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage title: reactor type examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - reactor type is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000350 multivalued: false range: TextValue redox_potential: name: redox_potential annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: millivolt occurrence: tag: occurrence value: '1' description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential title: redox potential examples: - value: 300 millivolt from_schema: https://w3id.org/nmdc/nmdc aliases: - redox potential is_a: core field slot_uri: MIXS:0000182 multivalued: false range: QuantityValue rel_air_humidity: name: rel_air_humidity annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: percentage occurrence: tag: occurrence value: '1' description: Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air title: relative air humidity examples: - value: 80% from_schema: https://w3id.org/nmdc/nmdc aliases: - relative air humidity is_a: core field slot_uri: MIXS:0000121 multivalued: false range: QuantityValue rel_humidity_out: name: rel_humidity_out annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: gram of air, kilogram of air occurrence: tag: occurrence value: '1' description: The recorded outside relative humidity value at the time of sampling title: outside relative humidity examples: - value: 12 per kilogram of air from_schema: https://w3id.org/nmdc/nmdc aliases: - outside relative humidity is_a: core field slot_uri: MIXS:0000188 multivalued: false range: QuantityValue rel_samp_loc: name: rel_samp_loc annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The sampling location within the train car title: relative sampling location examples: - value: center of car from_schema: https://w3id.org/nmdc/nmdc aliases: - relative sampling location is_a: core field slot_uri: MIXS:0000821 multivalued: false range: rel_samp_loc_enum reservoir: name: reservoir annotations: expected_value: tag: expected_value value: name occurrence: tag: occurrence value: '1' description: Name of the reservoir (e.g. Carapebus) title: reservoir name examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - reservoir name is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000303 multivalued: false range: TextValue resins_pc: name: resins_pc annotations: expected_value: tag: expected_value value: name;measurement value preferred_unit: tag: preferred_unit value: percent occurrence: tag: occurrence value: '1' description: 'Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' title: resins wt% examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - resins wt% is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000134 multivalued: false range: TextValue room_air_exch_rate: name: room_air_exch_rate annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: liter per hour occurrence: tag: occurrence value: '1' description: The rate at which outside air replaces indoor air in a given space title: room air exchange rate examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - room air exchange rate is_a: core field slot_uri: MIXS:0000169 multivalued: false range: QuantityValue room_architec_elem: name: room_architec_elem annotations: expected_value: tag: expected_value value: free text occurrence: tag: occurrence value: '1' description: The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure title: room architectural elements examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - room architectural elements is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000233 multivalued: false range: string room_condt: name: room_condt annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The condition of the room at the time of sampling title: room condition examples: - value: new from_schema: https://w3id.org/nmdc/nmdc aliases: - room condition is_a: core field slot_uri: MIXS:0000822 multivalued: false range: room_condt_enum room_connected: name: room_connected annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: List of rooms connected to the sampling room by a doorway title: rooms connected by a doorway examples: - value: office from_schema: https://w3id.org/nmdc/nmdc aliases: - rooms connected by a doorway is_a: core field slot_uri: MIXS:0000826 multivalued: false range: room_connected_enum room_count: name: room_count annotations: expected_value: tag: expected_value value: value occurrence: tag: occurrence value: '1' description: The total count of rooms in the built structure including all room types title: room count examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - room count is_a: core field slot_uri: MIXS:0000234 multivalued: false range: TextValue room_dim: name: room_dim annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: meter occurrence: tag: occurrence value: '1' description: The length, width and height of sampling room title: room dimensions examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - room dimensions is_a: core field string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}' slot_uri: MIXS:0000192 multivalued: false range: TextValue room_door_dist: name: room_door_dist annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: meter occurrence: tag: occurrence value: '1' description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms title: room door distance examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - room door distance is_a: core field string_serialization: '{integer} {unit}' slot_uri: MIXS:0000193 multivalued: false range: TextValue room_door_share: name: room_door_share annotations: expected_value: tag: expected_value value: room name;room number occurrence: tag: occurrence value: '1' description: List of room(s) (room number, room name) sharing a door with the sampling room title: rooms that share a door with sampling room examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - rooms that share a door with sampling room is_a: core field string_serialization: '{text};{integer}' slot_uri: MIXS:0000242 multivalued: false range: TextValue room_hallway: name: room_hallway annotations: expected_value: tag: expected_value value: room name;room number occurrence: tag: occurrence value: '1' description: List of room(s) (room number, room name) located in the same hallway as sampling room title: rooms that are on the same hallway examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - rooms that are on the same hallway is_a: core field string_serialization: '{text};{integer}' slot_uri: MIXS:0000238 multivalued: false range: TextValue room_loc: name: room_loc annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The position of the room within the building title: room location in building examples: - value: interior room from_schema: https://w3id.org/nmdc/nmdc aliases: - room location in building is_a: core field slot_uri: MIXS:0000823 multivalued: false range: room_loc_enum room_moist_dam_hist: name: room_moist_dam_hist annotations: expected_value: tag: expected_value value: value occurrence: tag: occurrence value: '1' description: The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed title: room moisture damage or mold history examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - room moisture damage or mold history is_a: core field slot_uri: MIXS:0000235 multivalued: false range: integer room_net_area: name: room_net_area annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: square feet, square meter occurrence: tag: occurrence value: '1' description: The net floor area of sampling room. Net area excludes wall thicknesses title: room net area examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - room net area is_a: core field string_serialization: '{integer} {unit}' slot_uri: MIXS:0000194 multivalued: false range: TextValue room_occup: name: room_occup annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: Count of room occupancy at time of sampling title: room occupancy examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - room occupancy is_a: core field slot_uri: MIXS:0000236 multivalued: false range: QuantityValue room_samp_pos: name: room_samp_pos annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The horizontal sampling position in the room relative to architectural elements title: room sampling position examples: - value: south corner from_schema: https://w3id.org/nmdc/nmdc aliases: - room sampling position is_a: core field slot_uri: MIXS:0000824 multivalued: false range: room_samp_pos_enum room_type: name: room_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure title: room type examples: - value: bathroom from_schema: https://w3id.org/nmdc/nmdc aliases: - room type is_a: core field slot_uri: MIXS:0000825 multivalued: false range: room_type_enum room_vol: name: room_vol annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: cubic feet, cubic meter occurrence: tag: occurrence value: '1' description: Volume of sampling room title: room volume examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - room volume is_a: core field string_serialization: '{integer} {unit}' slot_uri: MIXS:0000195 multivalued: false range: TextValue room_wall_share: name: room_wall_share annotations: expected_value: tag: expected_value value: room name;room number occurrence: tag: occurrence value: '1' description: List of room(s) (room number, room name) sharing a wall with the sampling room title: rooms that share a wall with sampling room examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - rooms that share a wall with sampling room is_a: core field string_serialization: '{text};{integer}' slot_uri: MIXS:0000243 multivalued: false range: TextValue room_window_count: name: room_window_count annotations: expected_value: tag: expected_value value: value occurrence: tag: occurrence value: '1' description: Number of windows in the room title: room window count examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - room window count is_a: core field slot_uri: MIXS:0000237 multivalued: false range: integer root_cond: name: root_cond annotations: expected_value: tag: expected_value value: PMID,DOI,url or free text occurrence: tag: occurrence value: '1' description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. title: rooting conditions examples: - value: http://himedialabs.com/TD/PT158.pdf from_schema: https://w3id.org/nmdc/nmdc aliases: - rooting conditions is_a: core field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001061 multivalued: false range: TextValue root_med_carbon: name: root_med_carbon annotations: expected_value: tag: expected_value value: carbon source name;measurement value preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: Source of organic carbon in the culture rooting medium; e.g. sucrose. title: rooting medium carbon examples: - value: sucrose from_schema: https://w3id.org/nmdc/nmdc aliases: - rooting medium carbon is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000577 multivalued: false range: TextValue root_med_macronutr: name: root_med_macronutr annotations: expected_value: tag: expected_value value: macronutrient name;measurement value preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). title: rooting medium macronutrients examples: - value: KH2PO4;170¬†milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - rooting medium macronutrients is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000578 multivalued: false range: TextValue root_med_micronutr: name: root_med_micronutr annotations: expected_value: tag: expected_value value: micronutrient name;measurement value preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L). title: rooting medium micronutrients examples: - value: H3BO3;6.2¬†milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - rooting medium micronutrients is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000579 multivalued: false range: TextValue root_med_ph: name: root_med_ph annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: pH measurement of the culture rooting medium; e.g. 5.5. title: rooting medium pH examples: - value: '7.5' from_schema: https://w3id.org/nmdc/nmdc aliases: - rooting medium pH is_a: core field slot_uri: MIXS:0001062 multivalued: false range: QuantityValue root_med_regl: name: root_med_regl annotations: expected_value: tag: expected_value value: regulator name;measurement value preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. title: rooting medium regulators examples: - value: abscisic acid;0.75 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - rooting medium regulators is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000581 multivalued: false range: TextValue root_med_solid: name: root_med_solid annotations: expected_value: tag: expected_value value: name occurrence: tag: occurrence value: '1' description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. title: rooting medium solidifier examples: - value: agar from_schema: https://w3id.org/nmdc/nmdc aliases: - rooting medium solidifier is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001063 multivalued: false range: TextValue root_med_suppl: name: root_med_suppl annotations: expected_value: tag: expected_value value: supplement name;measurement value preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). title: rooting medium organic supplements examples: - value: nicotinic acid;0.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - rooting medium organic supplements is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000580 multivalued: false range: TextValue salinity: name: salinity annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: practical salinity unit, percentage occurrence: tag: occurrence value: '1' description: The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater. title: salinity examples: - value: 25 practical salinity unit from_schema: https://w3id.org/nmdc/nmdc aliases: - salinity is_a: core field slot_uri: MIXS:0000183 multivalued: false range: QuantityValue salinity_meth: name: salinity_meth annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Reference or method used in determining salinity title: salinity method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - salinity method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000341 multivalued: false range: TextValue salt_regm: name: salt_regm annotations: expected_value: tag: expected_value value: salt name;salt amount;treatment interval and duration preferred_unit: tag: preferred_unit value: gram, microgram, mole per liter, gram per liter occurrence: tag: occurrence value: m description: Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens title: salt regimen examples: - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - salt regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000582 multivalued: true range: TextValue samp_capt_status: name: samp_capt_status annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Reason for the sample title: sample capture status examples: - value: farm sample from_schema: https://w3id.org/nmdc/nmdc aliases: - sample capture status is_a: core field slot_uri: MIXS:0000860 multivalued: false range: samp_capt_status_enum samp_collec_device: name: samp_collec_device annotations: expected_value: tag: expected_value value: device name description: 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). title: sample collection device examples: - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] from_schema: https://w3id.org/nmdc/nmdc aliases: - sample collection device is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000002 multivalued: false range: string samp_collec_method: name: samp_collec_method annotations: expected_value: tag: expected_value value: PMID,DOI,url , or text description: The method employed for collecting the sample. title: sample collection method examples: - value: swabbing from_schema: https://w3id.org/nmdc/nmdc aliases: - sample collection method is_a: nucleic acid sequence source field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001225 multivalued: false range: string samp_collect_point: name: samp_collect_point annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If "other" is specified, please propose entry in "additional info" field title: sample collection point examples: - value: well from_schema: https://w3id.org/nmdc/nmdc aliases: - sample collection point is_a: core field slot_uri: MIXS:0001015 multivalued: false range: samp_collect_point_enum samp_dis_stage: name: samp_dis_stage annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. title: sample disease stage examples: - value: infection from_schema: https://w3id.org/nmdc/nmdc aliases: - sample disease stage is_a: core field slot_uri: MIXS:0000249 multivalued: false range: samp_dis_stage_enum samp_floor: name: samp_floor annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The floor of the building, where the sampling room is located title: sampling floor examples: - value: 4th floor from_schema: https://w3id.org/nmdc/nmdc aliases: - sampling floor is_a: core field slot_uri: MIXS:0000828 multivalued: false range: samp_floor_enum samp_loc_corr_rate: name: samp_loc_corr_rate annotations: expected_value: tag: expected_value value: measurement value range preferred_unit: tag: preferred_unit value: millimeter per year occurrence: tag: occurrence value: '1' description: Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays title: corrosion rate at sample location examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - corrosion rate at sample location is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000136 multivalued: false range: TextValue samp_mat_process: name: samp_mat_process annotations: expected_value: tag: expected_value value: text description: A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed. title: sample material processing examples: - value: filtering of seawater, storing samples in ethanol from_schema: https://w3id.org/nmdc/nmdc aliases: - sample material processing is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000016 multivalued: false range: ControlledTermValue samp_md: name: samp_md annotations: expected_value: tag: expected_value value: measurement value;enumeration preferred_unit: tag: preferred_unit value: meter occurrence: tag: occurrence value: '1' description: In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If "other" is specified, please propose entry in "additional info" field title: sample measured depth examples: - value: 1534 meter;MSL from_schema: https://w3id.org/nmdc/nmdc aliases: - sample measured depth is_a: core field slot_uri: MIXS:0000413 multivalued: false range: QuantityValue samp_name: name: samp_name annotations: expected_value: tag: expected_value value: text description: A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name. title: sample name examples: - value: ISDsoil1 from_schema: https://w3id.org/nmdc/nmdc aliases: - sample name is_a: investigation field string_serialization: '{text}' slot_uri: MIXS:0001107 multivalued: false range: string samp_preserv: name: samp_preserv annotations: expected_value: tag: expected_value value: name;measurement value preferred_unit: tag: preferred_unit value: milliliter occurrence: tag: occurrence value: '1' description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) title: preservative added to sample examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - preservative added to sample is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000463 multivalued: false range: TextValue samp_room_id: name: samp_room_id annotations: expected_value: tag: expected_value value: value occurrence: tag: occurrence value: '1' description: Sampling room number. This ID should be consistent with the designations on the building floor plans title: sampling room ID or name examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - sampling room ID or name is_a: core field slot_uri: MIXS:0000244 multivalued: false range: TextValue samp_size: name: samp_size annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: millliter, gram, milligram, liter description: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. title: amount or size of sample collected examples: - value: 5 liter from_schema: https://w3id.org/nmdc/nmdc aliases: - amount or size of sample collected is_a: nucleic acid sequence source field slot_uri: MIXS:0000001 multivalued: false range: QuantityValue samp_sort_meth: name: samp_sort_meth annotations: expected_value: tag: expected_value value: description of method occurrence: tag: occurrence value: m description: Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor. title: sample size sorting method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - sample size sorting method is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000216 multivalued: true range: TextValue samp_store_dur: name: samp_store_dur annotations: expected_value: tag: expected_value value: duration occurrence: tag: occurrence value: '1' description: Duration for which the sample was stored title: sample storage duration examples: - value: P1Y6M from_schema: https://w3id.org/nmdc/nmdc aliases: - sample storage duration is_a: core field string_serialization: '{duration}' slot_uri: MIXS:0000116 multivalued: false range: TextValue samp_store_loc: name: samp_store_loc annotations: expected_value: tag: expected_value value: location name occurrence: tag: occurrence value: '1' description: Location at which sample was stored, usually name of a specific freezer/room title: sample storage location examples: - value: Freezer no:5 from_schema: https://w3id.org/nmdc/nmdc aliases: - sample storage location is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000755 multivalued: false range: TextValue samp_store_temp: name: samp_store_temp annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: degree Celsius occurrence: tag: occurrence value: '1' description: Temperature at which sample was stored, e.g. -80 degree Celsius title: sample storage temperature examples: - value: -80 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - sample storage temperature is_a: core field slot_uri: MIXS:0000110 multivalued: false range: QuantityValue samp_subtype: name: samp_subtype annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Name of sample sub-type. For example if "sample type" is "Produced Water" then subtype could be "Oil Phase" or "Water Phase". If "other" is specified, please propose entry in "additional info" field title: sample subtype examples: - value: biofilm from_schema: https://w3id.org/nmdc/nmdc aliases: - sample subtype is_a: core field slot_uri: MIXS:0000999 multivalued: false range: samp_subtype_enum samp_taxon_id: name: samp_taxon_id annotations: expected_value: tag: expected_value value: Taxonomy ID description: 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. title: Taxonomy ID of DNA sample comments: - coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value from_schema: https://w3id.org/nmdc/nmdc aliases: - Taxonomy ID of DNA sample is_a: investigation field slot_uri: MIXS:0001320 multivalued: false range: ControlledIdentifiedTermValue samp_time_out: name: samp_time_out annotations: expected_value: tag: expected_value value: time preferred_unit: tag: preferred_unit value: hour occurrence: tag: occurrence value: '1' description: The recent and long term history of outside sampling title: sampling time outside examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - sampling time outside is_a: core field slot_uri: MIXS:0000196 multivalued: false range: TextValue samp_transport_cond: name: samp_transport_cond annotations: expected_value: tag: expected_value value: measurement value;measurement value preferred_unit: tag: preferred_unit value: days;degree Celsius occurrence: tag: occurrence value: '1' description: Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) title: sample transport conditions examples: - value: 5 days;-20 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - sample transport conditions is_a: core field string_serialization: '{float} {unit};{float} {unit}' slot_uri: MIXS:0000410 multivalued: false range: TextValue samp_tvdss: name: samp_tvdss annotations: expected_value: tag: expected_value value: measurement value or measurement value range preferred_unit: tag: preferred_unit value: meter occurrence: tag: occurrence value: '1' description: Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m title: sample true vertical depth subsea examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - sample true vertical depth subsea is_a: core field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000409 multivalued: false range: TextValue samp_type: name: samp_type annotations: expected_value: tag: expected_value value: GENEPIO:0001246 occurrence: tag: occurrence value: '1' description: The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246). title: sample type examples: - value: built environment sample [GENEPIO:0001248] from_schema: https://w3id.org/nmdc/nmdc aliases: - sample type is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000998 multivalued: false range: TextValue samp_vol_we_dna_ext: name: samp_vol_we_dna_ext annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: millliter, gram, milligram, square centimeter description: 'Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001).' title: sample volume or weight for DNA extraction examples: - value: 1500 milliliter from_schema: https://w3id.org/nmdc/nmdc aliases: - sample volume or weight for DNA extraction is_a: nucleic acid sequence source field slot_uri: MIXS:0000111 multivalued: false range: QuantityValue samp_weather: name: samp_weather annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The weather on the sampling day title: sampling day weather examples: - value: foggy from_schema: https://w3id.org/nmdc/nmdc aliases: - sampling day weather is_a: core field slot_uri: MIXS:0000827 multivalued: false range: samp_weather_enum samp_well_name: name: samp_well_name annotations: expected_value: tag: expected_value value: name occurrence: tag: occurrence value: '1' description: Name of the well (e.g. BXA1123) where sample was taken title: sample well name examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - sample well name is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000296 multivalued: false range: TextValue saturates_pc: name: saturates_pc annotations: expected_value: tag: expected_value value: name;measurement value preferred_unit: tag: preferred_unit value: percent occurrence: tag: occurrence value: '1' description: 'Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)' title: saturates wt% examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - saturates wt% is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000131 multivalued: false range: TextValue season: name: season annotations: expected_value: tag: expected_value value: NCIT:C94729 occurrence: tag: occurrence value: '1' description: The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729). title: season examples: - value: autumn [NCIT:C94733] from_schema: https://w3id.org/nmdc/nmdc aliases: - season is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000829 multivalued: false range: TextValue season_environment: name: season_environment annotations: expected_value: tag: expected_value value: seasonal environment name;treatment interval and duration occurrence: tag: occurrence value: m description: Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment title: seasonal environment examples: - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - seasonal environment is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001068 multivalued: true range: TextValue season_precpt: name: season_precpt annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: millimeter occurrence: tag: occurrence value: '1' description: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. title: mean seasonal precipitation examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - mean seasonal precipitation is_a: core field slot_uri: MIXS:0000645 multivalued: false range: QuantityValue season_temp: name: season_temp annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: degree Celsius occurrence: tag: occurrence value: '1' description: Mean seasonal temperature title: mean seasonal temperature examples: - value: 18 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - mean seasonal temperature is_a: core field slot_uri: MIXS:0000643 multivalued: false range: QuantityValue season_use: name: season_use annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The seasons the space is occupied title: seasonal use examples: - value: Winter from_schema: https://w3id.org/nmdc/nmdc aliases: - seasonal use is_a: core field slot_uri: MIXS:0000830 multivalued: false range: season_use_enum secondary_treatment: name: secondary_treatment annotations: expected_value: tag: expected_value value: secondary treatment type occurrence: tag: occurrence value: '1' description: The process for substantially degrading the biological content of the sewage title: secondary treatment examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - secondary treatment is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000351 multivalued: false range: TextValue sediment_type: name: sediment_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Information about the sediment type based on major constituents title: sediment type examples: - value: biogenous from_schema: https://w3id.org/nmdc/nmdc aliases: - sediment type is_a: core field slot_uri: MIXS:0001078 multivalued: false range: sediment_type_enum seq_meth: name: seq_meth annotations: expected_value: tag: expected_value value: Text or OBI description: Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103). title: sequencing method examples: - value: 454 Genome Sequencer FLX [OBI:0000702] from_schema: https://w3id.org/nmdc/nmdc aliases: - sequencing method is_a: sequencing field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000050 multivalued: false range: TextValue seq_quality_check: name: seq_quality_check annotations: expected_value: tag: expected_value value: none or manually edited description: Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA title: sequence quality check examples: - value: none from_schema: https://w3id.org/nmdc/nmdc aliases: - sequence quality check is_a: sequencing field string_serialization: '[none|manually edited]' slot_uri: MIXS:0000051 multivalued: false range: TextValue sewage_type: name: sewage_type annotations: expected_value: tag: expected_value value: sewage type name occurrence: tag: occurrence value: '1' description: Type of wastewater treatment plant as municipial or industrial title: sewage type examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - sewage type is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000215 multivalued: false range: TextValue shad_dev_water_mold: name: shad_dev_water_mold annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Signs of the presence of mold or mildew on the shading device title: shading device signs of water/mold examples: - value: no presence of mold visible from_schema: https://w3id.org/nmdc/nmdc aliases: - shading device signs of water/mold is_a: core field string_serialization: '[presence of mold visible|no presence of mold visible]' slot_uri: MIXS:0000834 multivalued: false range: string shading_device_cond: name: shading_device_cond annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The physical condition of the shading device at the time of sampling title: shading device condition examples: - value: new from_schema: https://w3id.org/nmdc/nmdc aliases: - shading device condition is_a: core field slot_uri: MIXS:0000831 multivalued: false range: shading_device_cond_enum shading_device_loc: name: shading_device_loc annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The location of the shading device in relation to the built structure title: shading device location examples: - value: exterior from_schema: https://w3id.org/nmdc/nmdc aliases: - shading device location is_a: core field string_serialization: '[exterior|interior]' slot_uri: MIXS:0000832 multivalued: false range: TextValue shading_device_mat: name: shading_device_mat annotations: expected_value: tag: expected_value value: material name occurrence: tag: occurrence value: '1' description: The material the shading device is composed of title: shading device material examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - shading device material is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000245 multivalued: false range: TextValue shading_device_type: name: shading_device_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The type of shading device title: shading device type examples: - value: slatted aluminum awning from_schema: https://w3id.org/nmdc/nmdc aliases: - shading device type is_a: core field slot_uri: MIXS:0000835 multivalued: false range: shading_device_type_enum sieving: name: sieving annotations: expected_value: tag: expected_value value: design name and/or size;amount occurrence: tag: occurrence value: '1' description: Collection design of pooled samples and/or sieve size and amount of sample sieved title: composite design/sieving examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - composite design/sieving is_a: core field string_serialization: '{{text}|{float} {unit}};{float} {unit}' slot_uri: MIXS:0000322 multivalued: false range: TextValue silicate: name: silicate annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter occurrence: tag: occurrence value: '1' description: Concentration of silicate title: silicate examples: - value: 0.05 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - silicate is_a: core field slot_uri: MIXS:0000184 multivalued: false range: QuantityValue size_frac: name: size_frac annotations: expected_value: tag: expected_value value: filter size value range description: Filtering pore size used in sample preparation title: size fraction selected examples: - value: 0-0.22 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - size fraction selected is_a: nucleic acid sequence source field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000017 multivalued: false range: TextValue size_frac_low: name: size_frac_low annotations: expected_value: tag: expected_value value: value preferred_unit: tag: preferred_unit value: micrometer occurrence: tag: occurrence value: '1' description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample title: size-fraction lower threshold examples: - value: 0.2 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - size-fraction lower threshold is_a: core field slot_uri: MIXS:0000735 multivalued: false range: QuantityValue size_frac_up: name: size_frac_up annotations: expected_value: tag: expected_value value: value preferred_unit: tag: preferred_unit value: micrometer occurrence: tag: occurrence value: '1' description: Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample title: size-fraction upper threshold examples: - value: 20 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - size-fraction upper threshold is_a: core field slot_uri: MIXS:0000736 multivalued: false range: QuantityValue slope_aspect: name: slope_aspect annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: degree occurrence: tag: occurrence value: '1' description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. title: slope aspect examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - slope aspect is_a: core field slot_uri: MIXS:0000647 multivalued: false range: QuantityValue slope_gradient: name: slope_gradient annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: percentage occurrence: tag: occurrence value: '1' description: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer title: slope gradient examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - slope gradient is_a: core field slot_uri: MIXS:0000646 multivalued: false range: QuantityValue sludge_retent_time: name: sludge_retent_time annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: hours occurrence: tag: occurrence value: '1' description: The time activated sludge remains in reactor title: sludge retention time examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - sludge retention time is_a: core field slot_uri: MIXS:0000669 multivalued: false range: QuantityValue sodium: name: sodium annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Sodium concentration in the sample title: sodium examples: - value: 10.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - sodium is_a: core field slot_uri: MIXS:0000428 multivalued: false range: QuantityValue soil_horizon: name: soil_horizon annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: 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 title: soil horizon examples: - value: A horizon from_schema: https://w3id.org/nmdc/nmdc aliases: - soil horizon is_a: core field slot_uri: MIXS:0001082 multivalued: false range: soil_horizon_enum soil_text_measure: name: soil_text_measure annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: 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. title: soil texture measurement examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - soil texture measurement is_a: core field slot_uri: MIXS:0000335 multivalued: false range: QuantityValue soil_texture_meth: name: soil_texture_meth annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Reference or method used in determining soil texture title: soil texture method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - soil texture method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000336 multivalued: false range: string soil_type: name: soil_type annotations: expected_value: tag: expected_value value: ENVO_00001998 occurrence: tag: occurrence value: '1' description: Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes. title: soil type examples: - value: plinthosol [ENVO:00002250] from_schema: https://w3id.org/nmdc/nmdc aliases: - soil type is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000332 multivalued: false range: TextValue soil_type_meth: name: soil_type_meth annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Reference or method used in determining soil series name or other lower-level classification title: soil type method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - soil type method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000334 multivalued: false range: TextValue solar_irradiance: name: solar_irradiance annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: kilowatts per square meter per day, ergs per square centimeter per second occurrence: tag: occurrence value: '1' description: The amount of solar energy that arrives at a specific area of a surface during a specific time interval title: solar irradiance examples: - value: 1.36 kilowatts per square meter per day from_schema: https://w3id.org/nmdc/nmdc aliases: - solar irradiance is_a: core field slot_uri: MIXS:0000112 multivalued: false range: QuantityValue soluble_inorg_mat: name: soluble_inorg_mat annotations: expected_value: tag: expected_value value: soluble inorganic material name;measurement value preferred_unit: tag: preferred_unit value: gram, microgram, mole per liter, gram per liter, parts per million occurrence: tag: occurrence value: m description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. title: soluble inorganic material examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - soluble inorganic material is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000672 multivalued: true range: TextValue soluble_org_mat: name: soluble_org_mat annotations: expected_value: tag: expected_value value: soluble organic material name;measurement value preferred_unit: tag: preferred_unit value: gram, microgram, mole per liter, gram per liter, parts per million occurrence: tag: occurrence value: m description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. title: soluble organic material examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - soluble organic material is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000673 multivalued: true range: TextValue soluble_react_phosp: name: soluble_react_phosp annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter, milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of soluble reactive phosphorus title: soluble reactive phosphorus examples: - value: 0.1 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - soluble reactive phosphorus is_a: core field slot_uri: MIXS:0000738 multivalued: false range: QuantityValue source_mat_id: name: source_mat_id annotations: expected_value: tag: expected_value value: 'for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer' description: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2). title: source material identifiers examples: - value: MPI012345 from_schema: https://w3id.org/nmdc/nmdc aliases: - source material identifiers is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000026 multivalued: false range: TextValue space_typ_state: name: space_typ_state annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Customary or normal state of the space title: space typical state examples: - value: typically occupied from_schema: https://w3id.org/nmdc/nmdc aliases: - space typical state is_a: core field string_serialization: '[typically occupied|typically unoccupied]' slot_uri: MIXS:0000770 multivalued: false range: TextValue specific: name: specific annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: 'The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents' title: specifications examples: - value: construction from_schema: https://w3id.org/nmdc/nmdc aliases: - specifications is_a: core field slot_uri: MIXS:0000836 multivalued: false range: specific_enum specific_humidity: name: specific_humidity annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: gram of air, kilogram of air occurrence: tag: occurrence value: '1' description: The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound. title: specific humidity examples: - value: 15 per kilogram of air from_schema: https://w3id.org/nmdc/nmdc aliases: - specific humidity is_a: core field slot_uri: MIXS:0000214 multivalued: false range: QuantityValue sr_dep_env: name: sr_dep_env annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field title: source rock depositional environment examples: - value: Marine from_schema: https://w3id.org/nmdc/nmdc aliases: - source rock depositional environment is_a: core field slot_uri: MIXS:0000996 multivalued: false range: sr_dep_env_enum sr_geol_age: name: sr_geol_age annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If "other" is specified, please propose entry in "additional info" field' title: source rock geological age examples: - value: Silurian from_schema: https://w3id.org/nmdc/nmdc aliases: - source rock geological age is_a: core field slot_uri: MIXS:0000997 multivalued: false range: sr_geol_age_enum sr_kerog_type: name: sr_kerog_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If "other" is specified, please propose entry in "additional info" field' title: source rock kerogen type examples: - value: Type IV from_schema: https://w3id.org/nmdc/nmdc aliases: - source rock kerogen type is_a: core field slot_uri: MIXS:0000994 multivalued: false range: sr_kerog_type_enum sr_lithology: name: sr_lithology annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If "other" is specified, please propose entry in "additional info" field title: source rock lithology examples: - value: Coal from_schema: https://w3id.org/nmdc/nmdc aliases: - source rock lithology is_a: core field slot_uri: MIXS:0000995 multivalued: false range: sr_lithology_enum standing_water_regm: name: standing_water_regm annotations: expected_value: tag: expected_value value: standing water type;treatment interval and duration occurrence: tag: occurrence value: m description: Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens title: standing water regimen examples: - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - standing water regimen is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001069 multivalued: true range: TextValue store_cond: name: store_cond annotations: expected_value: tag: expected_value value: storage condition type;duration occurrence: tag: occurrence value: '1' description: Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other). title: storage conditions examples: - value: -20 degree Celsius freezer;P2Y10D from_schema: https://w3id.org/nmdc/nmdc aliases: - storage conditions is_a: core field string_serialization: '{text};{duration}' slot_uri: MIXS:0000327 multivalued: false range: TextValue substructure_type: name: substructure_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: m description: The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level title: substructure type examples: - value: basement from_schema: https://w3id.org/nmdc/nmdc aliases: - substructure type is_a: core field slot_uri: MIXS:0000767 multivalued: true range: substructure_type_enum sulfate: name: sulfate annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter, milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of sulfate in the sample title: sulfate examples: - value: 5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - sulfate is_a: core field slot_uri: MIXS:0000423 multivalued: false range: QuantityValue sulfate_fw: name: sulfate_fw annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: Original sulfate concentration in the hydrocarbon resource title: sulfate in formation water examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - sulfate in formation water is_a: core field slot_uri: MIXS:0000407 multivalued: false range: QuantityValue sulfide: name: sulfide annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter, milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of sulfide in the sample title: sulfide examples: - value: 2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - sulfide is_a: core field slot_uri: MIXS:0000424 multivalued: false range: QuantityValue surf_air_cont: name: surf_air_cont annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: m description: Contaminant identified on surface title: surface-air contaminant examples: - value: radon from_schema: https://w3id.org/nmdc/nmdc aliases: - surface-air contaminant is_a: core field slot_uri: MIXS:0000759 multivalued: true range: surf_air_cont_enum surf_humidity: name: surf_humidity annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: percentage occurrence: tag: occurrence value: '1' description: 'Surfaces: water activity as a function of air and material moisture' title: surface humidity examples: - value: 10% from_schema: https://w3id.org/nmdc/nmdc aliases: - surface humidity is_a: core field slot_uri: MIXS:0000123 multivalued: false range: QuantityValue surf_material: name: surf_material annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Surface materials at the point of sampling title: surface material examples: - value: wood from_schema: https://w3id.org/nmdc/nmdc aliases: - surface material is_a: core field slot_uri: MIXS:0000758 multivalued: false range: surf_material_enum surf_moisture: name: surf_moisture annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: parts per million, gram per cubic meter, gram per square meter occurrence: tag: occurrence value: '1' description: Water held on a surface title: surface moisture examples: - value: 0.01 gram per square meter from_schema: https://w3id.org/nmdc/nmdc aliases: - surface moisture is_a: core field slot_uri: MIXS:0000128 multivalued: false range: QuantityValue surf_moisture_ph: name: surf_moisture_ph annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: ph measurement of surface title: surface moisture pH examples: - value: '7' from_schema: https://w3id.org/nmdc/nmdc aliases: - surface moisture pH is_a: core field slot_uri: MIXS:0000760 multivalued: false range: double surf_temp: name: surf_temp annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: degree Celsius occurrence: tag: occurrence value: '1' description: Temperature of the surface at the time of sampling title: surface temperature examples: - value: 15 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - surface temperature is_a: core field slot_uri: MIXS:0000125 multivalued: false range: QuantityValue suspend_part_matter: name: suspend_part_matter annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: Concentration of suspended particulate matter title: suspended particulate matter examples: - value: 0.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - suspended particulate matter is_a: core field slot_uri: MIXS:0000741 multivalued: false range: QuantityValue suspend_solids: name: suspend_solids annotations: expected_value: tag: expected_value value: suspended solid name;measurement value preferred_unit: tag: preferred_unit value: gram, microgram, milligram per liter, mole per liter, gram per liter, part per million occurrence: tag: occurrence value: m description: Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances title: suspended solids examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - suspended solids is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000150 multivalued: true range: TextValue tan: name: tan annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: 'Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)' title: total acid number examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - total acid number is_a: core field slot_uri: MIXS:0000120 multivalued: false range: QuantityValue target_gene: name: target_gene annotations: expected_value: tag: expected_value value: gene name description: Targeted gene or locus name for marker gene studies title: target gene examples: - value: 16S rRNA, 18S rRNA, nif, amoA, rpo from_schema: https://w3id.org/nmdc/nmdc aliases: - target gene is_a: sequencing field string_serialization: '{text}' slot_uri: MIXS:0000044 multivalued: false range: TextValue target_subfragment: name: target_subfragment annotations: expected_value: tag: expected_value value: gene fragment name description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA title: target subfragment examples: - value: V6, V9, ITS from_schema: https://w3id.org/nmdc/nmdc aliases: - target subfragment is_a: sequencing field string_serialization: '{text}' slot_uri: MIXS:0000045 multivalued: false range: TextValue temp: name: temp annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: degree Celsius description: Temperature of the sample at the time of sampling. title: temperature examples: - value: 25 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - temperature is_a: environment field slot_uri: MIXS:0000113 multivalued: false range: QuantityValue temp_out: name: temp_out annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: degree Celsius occurrence: tag: occurrence value: '1' description: The recorded temperature value at sampling time outside title: temperature outside house examples: - value: 5 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - temperature outside house is_a: core field slot_uri: MIXS:0000197 multivalued: false range: QuantityValue tertiary_treatment: name: tertiary_treatment annotations: expected_value: tag: expected_value value: tertiary treatment type occurrence: tag: occurrence value: '1' description: The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment title: tertiary treatment examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - tertiary treatment is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000352 multivalued: false range: TextValue tidal_stage: name: tidal_stage annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Stage of tide title: tidal stage examples: - value: high tide from_schema: https://w3id.org/nmdc/nmdc aliases: - tidal stage is_a: core field slot_uri: MIXS:0000750 multivalued: false range: tidal_stage_enum tillage: name: tillage annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: m description: Note method(s) used for tilling title: history/tillage examples: - value: chisel from_schema: https://w3id.org/nmdc/nmdc aliases: - history/tillage is_a: core field slot_uri: MIXS:0001081 multivalued: true range: tillage_enum tiss_cult_growth_med: name: tiss_cult_growth_med annotations: expected_value: tag: expected_value value: PMID,DOI,url or free text occurrence: tag: occurrence value: '1' description: Description of plant tissue culture growth media used title: tissue culture growth media examples: - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf from_schema: https://w3id.org/nmdc/nmdc aliases: - tissue culture growth media is_a: core field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001070 multivalued: false range: TextValue toluene: name: toluene annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of toluene in the sample title: toluene examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - toluene is_a: core field slot_uri: MIXS:0000154 multivalued: false range: QuantityValue tot_carb: name: tot_carb annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter occurrence: tag: occurrence value: '1' description: Total carbon content title: total carbon examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - total carbon is_a: core field slot_uri: MIXS:0000525 multivalued: false range: QuantityValue tot_depth_water_col: name: tot_depth_water_col annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: meter occurrence: tag: occurrence value: '1' description: Measurement of total depth of water column title: total depth of water column examples: - value: 500 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - total depth of water column is_a: core field slot_uri: MIXS:0000634 multivalued: false range: QuantityValue tot_diss_nitro: name: tot_diss_nitro annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter occurrence: tag: occurrence value: '1' description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen' title: total dissolved nitrogen examples: - value: 40 microgram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - total dissolved nitrogen is_a: core field slot_uri: MIXS:0000744 multivalued: false range: QuantityValue tot_inorg_nitro: name: tot_inorg_nitro annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter occurrence: tag: occurrence value: '1' description: Total inorganic nitrogen content title: total inorganic nitrogen examples: - value: 40 microgram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - total inorganic nitrogen is_a: core field slot_uri: MIXS:0000745 multivalued: false range: QuantityValue tot_iron: name: tot_iron annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter, milligram per kilogram occurrence: tag: occurrence value: '1' description: Concentration of total iron in the sample title: total iron examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - total iron is_a: core field slot_uri: MIXS:0000105 multivalued: false range: QuantityValue tot_nitro: name: tot_nitro annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter, micromole per liter, milligram per liter occurrence: tag: occurrence value: '1' description: 'Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen' title: total nitrogen concentration examples: - value: 50 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - total nitrogen concentration is_a: core field slot_uri: MIXS:0000102 multivalued: false range: QuantityValue tot_nitro_cont_meth: name: tot_nitro_cont_meth annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Reference or method used in determining the total nitrogen title: total nitrogen content method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - total nitrogen content method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000338 multivalued: false range: string tot_nitro_content: name: tot_nitro_content annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter, micromole per liter, milligram per liter occurrence: tag: occurrence value: '1' description: Total nitrogen content of the sample title: total nitrogen content examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - total nitrogen content is_a: core field slot_uri: MIXS:0000530 multivalued: false range: QuantityValue tot_org_c_meth: name: tot_org_c_meth annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Reference or method used in determining total organic carbon title: total organic carbon method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - total organic carbon method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000337 multivalued: false range: TextValue tot_org_carb: name: tot_org_carb annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: gram Carbon per kilogram sample material occurrence: tag: occurrence value: '1' description: 'Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content' title: total organic carbon examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - total organic carbon is_a: core field slot_uri: MIXS:0000533 multivalued: false range: QuantityValue tot_part_carb: name: tot_part_carb annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter, micromole per liter occurrence: tag: occurrence value: '1' description: Total particulate carbon content title: total particulate carbon examples: - value: 35 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - total particulate carbon is_a: core field slot_uri: MIXS:0000747 multivalued: false range: QuantityValue tot_phosp: name: tot_phosp annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: micromole per liter, milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: 'Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus' title: total phosphorus examples: - value: 0.03 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - total phosphorus is_a: core field slot_uri: MIXS:0000117 multivalued: false range: QuantityValue tot_phosphate: name: tot_phosphate annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: microgram per liter, micromole per liter occurrence: tag: occurrence value: '1' description: Total amount or concentration of phosphate title: total phosphate examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - total phosphate is_a: core field slot_uri: MIXS:0000689 multivalued: false range: QuantityValue tot_sulfur: name: tot_sulfur annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of total sulfur in the sample title: total sulfur examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - total sulfur is_a: core field slot_uri: MIXS:0000419 multivalued: false range: QuantityValue train_line: name: train_line annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The subway line name title: train line examples: - value: red from_schema: https://w3id.org/nmdc/nmdc aliases: - train line is_a: core field slot_uri: MIXS:0000837 multivalued: false range: train_line_enum train_stat_loc: name: train_stat_loc annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The train station collection location title: train station collection location examples: - value: forest hills from_schema: https://w3id.org/nmdc/nmdc aliases: - train station collection location is_a: core field slot_uri: MIXS:0000838 multivalued: false range: train_stat_loc_enum train_stop_loc: name: train_stop_loc annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The train stop collection location title: train stop collection location examples: - value: end from_schema: https://w3id.org/nmdc/nmdc aliases: - train stop collection location is_a: core field slot_uri: MIXS:0000839 multivalued: false range: train_stop_loc_enum turbidity: name: turbidity annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: formazin turbidity unit, formazin nephelometric units occurrence: tag: occurrence value: '1' description: Measure of the amount of cloudiness or haziness in water caused by individual particles title: turbidity examples: - value: 0.3 nephelometric turbidity units from_schema: https://w3id.org/nmdc/nmdc aliases: - turbidity is_a: core field slot_uri: MIXS:0000191 multivalued: false range: QuantityValue tvdss_of_hcr_press: name: tvdss_of_hcr_press annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: meter occurrence: tag: occurrence value: '1' description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). title: depth (TVDSS) of hydrocarbon resource pressure examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - depth (TVDSS) of hydrocarbon resource pressure is_a: core field slot_uri: MIXS:0000397 multivalued: false range: QuantityValue tvdss_of_hcr_temp: name: tvdss_of_hcr_temp annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: meter occurrence: tag: occurrence value: '1' description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). title: depth (TVDSS) of hydrocarbon resource temperature examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - depth (TVDSS) of hydrocarbon resource temperature is_a: core field slot_uri: MIXS:0000394 multivalued: false range: QuantityValue typ_occup_density: name: typ_occup_density annotations: expected_value: tag: expected_value value: measurement value occurrence: tag: occurrence value: '1' description: Customary or normal density of occupants title: typical occupant density examples: - value: '25' from_schema: https://w3id.org/nmdc/nmdc aliases: - typical occupant density is_a: core field slot_uri: MIXS:0000771 multivalued: false range: double ventilation_rate: name: ventilation_rate annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: cubic meter per minute, liters per second occurrence: tag: occurrence value: '1' description: Ventilation rate of the system in the sampled premises title: ventilation rate examples: - value: 750 cubic meter per minute from_schema: https://w3id.org/nmdc/nmdc aliases: - ventilation rate is_a: core field slot_uri: MIXS:0000114 multivalued: false range: QuantityValue ventilation_type: name: ventilation_type annotations: expected_value: tag: expected_value value: ventilation type name occurrence: tag: occurrence value: '1' description: Ventilation system used in the sampled premises title: ventilation type examples: - value: Operable windows from_schema: https://w3id.org/nmdc/nmdc aliases: - ventilation type is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000756 multivalued: false range: TextValue vfa: name: vfa annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of Volatile Fatty Acids in the sample title: volatile fatty acids examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - volatile fatty acids is_a: core field slot_uri: MIXS:0000152 multivalued: false range: QuantityValue vfa_fw: name: vfa_fw annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter occurrence: tag: occurrence value: '1' description: Original volatile fatty acid concentration in the hydrocarbon resource title: vfa in formation water examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - vfa in formation water is_a: core field slot_uri: MIXS:0000408 multivalued: false range: QuantityValue vis_media: name: vis_media annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The building visual media title: visual media examples: - value: 3D scans from_schema: https://w3id.org/nmdc/nmdc aliases: - visual media is_a: core field slot_uri: MIXS:0000840 multivalued: false range: vis_media_enum viscosity: name: viscosity annotations: expected_value: tag: expected_value value: measurement value;measurement value preferred_unit: tag: preferred_unit value: cP at degree Celsius occurrence: tag: occurrence value: '1' description: A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) title: viscosity examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - viscosity is_a: core field string_serialization: '{float} {unit};{float} {unit}' slot_uri: MIXS:0000126 multivalued: false range: TextValue volatile_org_comp: name: volatile_org_comp annotations: expected_value: tag: expected_value value: volatile organic compound name;measurement value preferred_unit: tag: preferred_unit value: microgram per cubic meter, parts per million, nanogram per liter occurrence: tag: occurrence value: m description: Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound title: volatile organic compounds examples: - value: formaldehyde;500 nanogram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - volatile organic compounds is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000115 multivalued: true range: TextValue wall_area: name: wall_area annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: square meter occurrence: tag: occurrence value: '1' description: The total area of the sampled room's walls title: wall area examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - wall area is_a: core field slot_uri: MIXS:0000198 multivalued: false range: QuantityValue wall_const_type: name: wall_const_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. title: wall construction type examples: - value: fire resistive from_schema: https://w3id.org/nmdc/nmdc aliases: - wall construction type is_a: core field slot_uri: MIXS:0000841 multivalued: false range: wall_const_type_enum wall_finish_mat: name: wall_finish_mat annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The material utilized to finish the outer most layer of the wall title: wall finish material examples: - value: wood from_schema: https://w3id.org/nmdc/nmdc aliases: - wall finish material is_a: core field slot_uri: MIXS:0000842 multivalued: false range: wall_finish_mat_enum wall_height: name: wall_height annotations: expected_value: tag: expected_value value: value preferred_unit: tag: preferred_unit value: centimeter occurrence: tag: occurrence value: '1' description: The average height of the walls in the sampled room title: wall height examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - wall height is_a: core field slot_uri: MIXS:0000221 multivalued: false range: QuantityValue wall_loc: name: wall_loc annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The relative location of the wall within the room title: wall location examples: - value: north from_schema: https://w3id.org/nmdc/nmdc aliases: - wall location is_a: core field slot_uri: MIXS:0000843 multivalued: false range: wall_loc_enum wall_surf_treatment: name: wall_surf_treatment annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The surface treatment of interior wall title: wall surface treatment examples: - value: paneling from_schema: https://w3id.org/nmdc/nmdc aliases: - wall surface treatment is_a: core field slot_uri: MIXS:0000845 multivalued: false range: wall_surf_treatment_enum wall_texture: name: wall_texture annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The feel, appearance, or consistency of a wall surface title: wall texture examples: - value: popcorn from_schema: https://w3id.org/nmdc/nmdc aliases: - wall texture is_a: core field slot_uri: MIXS:0000846 multivalued: false range: wall_texture_enum wall_thermal_mass: name: wall_thermal_mass annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: joule per degree Celsius occurrence: tag: occurrence value: '1' description: The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint title: wall thermal mass examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - wall thermal mass is_a: core field slot_uri: MIXS:0000222 multivalued: false range: QuantityValue wall_water_mold: name: wall_water_mold annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Signs of the presence of mold or mildew on a wall title: wall signs of water/mold examples: - value: no presence of mold visible from_schema: https://w3id.org/nmdc/nmdc aliases: - wall signs of water/mold is_a: core field string_serialization: '[presence of mold visible|no presence of mold visible]' slot_uri: MIXS:0000844 multivalued: false range: TextValue wastewater_type: name: wastewater_type annotations: expected_value: tag: expected_value value: wastewater type name occurrence: tag: occurrence value: '1' description: The origin of wastewater such as human waste, rainfall, storm drains, etc. title: wastewater type examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - wastewater type is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000353 multivalued: false range: TextValue water_cont_soil_meth: name: water_cont_soil_meth annotations: expected_value: tag: expected_value value: PMID,DOI or url occurrence: tag: occurrence value: '1' description: Reference or method used in determining the water content of soil title: water content method examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - water content method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000323 multivalued: false range: string water_content: name: water_content annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: gram per gram or cubic centimeter per cubic centimeter occurrence: tag: occurrence value: '1' description: Water content measurement title: water content examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - water content is_a: core field slot_uri: MIXS:0000185 multivalued: false range: QuantityValue water_current: name: water_current annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: cubic meter per second, knots occurrence: tag: occurrence value: '1' description: Measurement of magnitude and direction of flow within a fluid title: water current examples: - value: 10 cubic meter per second from_schema: https://w3id.org/nmdc/nmdc aliases: - water current is_a: core field slot_uri: MIXS:0000203 multivalued: false range: QuantityValue water_cut: name: water_cut annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: percent occurrence: tag: occurrence value: '1' description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams title: water cut examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - water cut is_a: core field slot_uri: MIXS:0000454 multivalued: false range: QuantityValue water_feat_size: name: water_feat_size annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: square meter occurrence: tag: occurrence value: '1' description: The size of the water feature title: water feature size examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - water feature size is_a: core field slot_uri: MIXS:0000223 multivalued: false range: QuantityValue water_feat_type: name: water_feat_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The type of water feature present within the building being sampled title: water feature type examples: - value: stream from_schema: https://w3id.org/nmdc/nmdc aliases: - water feature type is_a: core field slot_uri: MIXS:0000847 multivalued: false range: water_feat_type_enum water_prod_rate: name: water_prod_rate annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: cubic meter per day occurrence: tag: occurrence value: '1' description: Water production rates per well (e.g. 987 m3 / day) title: water production rate examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - water production rate is_a: core field slot_uri: MIXS:0000453 multivalued: false range: QuantityValue water_temp_regm: name: water_temp_regm annotations: expected_value: tag: expected_value value: measurement value;treatment interval and duration preferred_unit: tag: preferred_unit value: degree Celsius occurrence: tag: occurrence value: m description: Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens title: water temperature regimen examples: - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - water temperature regimen is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000590 multivalued: true range: TextValue watering_regm: name: watering_regm annotations: expected_value: tag: expected_value value: measurement value;treatment interval and duration preferred_unit: tag: preferred_unit value: milliliter, liter occurrence: tag: occurrence value: m description: Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens title: watering regimen examples: - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - watering regimen is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000591 multivalued: true range: TextValue weekday: name: weekday annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The day of the week when sampling occurred title: weekday examples: - value: Sunday from_schema: https://w3id.org/nmdc/nmdc aliases: - weekday is_a: core field slot_uri: MIXS:0000848 multivalued: false range: weekday_enum win: name: win annotations: expected_value: tag: expected_value value: text occurrence: tag: occurrence value: '1' description: 'A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)' title: well identification number examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - well identification number is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000297 multivalued: false range: TextValue wind_direction: name: wind_direction annotations: expected_value: tag: expected_value value: wind direction name occurrence: tag: occurrence value: '1' description: Wind direction is the direction from which a wind originates title: wind direction examples: - value: Northwest from_schema: https://w3id.org/nmdc/nmdc aliases: - wind direction is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000757 multivalued: false range: TextValue wind_speed: name: wind_speed annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: meter per second, kilometer per hour occurrence: tag: occurrence value: '1' description: Speed of wind measured at the time of sampling title: wind speed examples: - value: 21 kilometer per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - wind speed is_a: core field slot_uri: MIXS:0000118 multivalued: false range: QuantityValue window_cond: name: window_cond annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The physical condition of the window at the time of sampling title: window condition examples: - value: rupture from_schema: https://w3id.org/nmdc/nmdc aliases: - window condition is_a: core field slot_uri: MIXS:0000849 multivalued: false range: window_cond_enum window_cover: name: window_cover annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The type of window covering title: window covering examples: - value: curtains from_schema: https://w3id.org/nmdc/nmdc aliases: - window covering is_a: core field slot_uri: MIXS:0000850 multivalued: false range: window_cover_enum window_horiz_pos: name: window_horiz_pos annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The horizontal position of the window on the wall title: window horizontal position examples: - value: middle from_schema: https://w3id.org/nmdc/nmdc aliases: - window horizontal position is_a: core field slot_uri: MIXS:0000851 multivalued: false range: window_horiz_pos_enum window_loc: name: window_loc annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The relative location of the window within the room title: window location examples: - value: west from_schema: https://w3id.org/nmdc/nmdc aliases: - window location is_a: core field slot_uri: MIXS:0000852 multivalued: false range: window_loc_enum window_mat: name: window_mat annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The type of material used to finish a window title: window material examples: - value: wood from_schema: https://w3id.org/nmdc/nmdc aliases: - window material is_a: core field slot_uri: MIXS:0000853 multivalued: false range: window_mat_enum window_open_freq: name: window_open_freq annotations: expected_value: tag: expected_value value: value occurrence: tag: occurrence value: '1' description: The number of times windows are opened per week title: window open frequency examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - window open frequency is_a: core field slot_uri: MIXS:0000246 multivalued: false range: TextValue window_size: name: window_size annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: inch, meter occurrence: tag: occurrence value: '1' description: The window's length and width title: window area/size examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - window area/size is_a: core field string_serialization: '{float} {unit} x {float} {unit}' slot_uri: MIXS:0000224 multivalued: false range: TextValue window_status: name: window_status annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Defines whether the windows were open or closed during environmental testing title: window status examples: - value: open from_schema: https://w3id.org/nmdc/nmdc aliases: - window status is_a: core field string_serialization: '[closed|open]' slot_uri: MIXS:0000855 multivalued: false range: TextValue window_type: name: window_type annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The type of windows title: window type examples: - value: fixed window from_schema: https://w3id.org/nmdc/nmdc aliases: - window type is_a: core field slot_uri: MIXS:0000856 multivalued: false range: window_type_enum window_vert_pos: name: window_vert_pos annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: The vertical position of the window on the wall title: window vertical position examples: - value: middle from_schema: https://w3id.org/nmdc/nmdc aliases: - window vertical position is_a: core field slot_uri: MIXS:0000857 multivalued: false range: window_vert_pos_enum window_water_mold: name: window_water_mold annotations: expected_value: tag: expected_value value: enumeration occurrence: tag: occurrence value: '1' description: Signs of the presence of mold or mildew on the window. title: window signs of water/mold examples: - value: no presence of mold visible from_schema: https://w3id.org/nmdc/nmdc aliases: - window signs of water/mold is_a: core field string_serialization: '[presence of mold visible|no presence of mold visible]' slot_uri: MIXS:0000854 multivalued: false range: TextValue xylene: name: xylene annotations: expected_value: tag: expected_value value: measurement value preferred_unit: tag: preferred_unit value: milligram per liter, parts per million occurrence: tag: occurrence value: '1' description: Concentration of xylene in the sample title: xylene examples: - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - xylene is_a: core field 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 from_schema: https://w3id.org/nmdc/nmdc abstract: true 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 from_schema: https://w3id.org/nmdc/nmdc abstract: true has numeric value: name: has numeric value from_schema: https://w3id.org/nmdc/nmdc owner: QuantityValue range: double environment field: name: environment field description: field describing environmental aspect of a sample 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 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 from_schema: https://w3id.org/nmdc/nmdc range: ChemicalEntity stoichiometry: name: stoichiometry description: from reaction participant class from_schema: https://w3id.org/nmdc/nmdc range: integer subject: name: subject from_schema: https://w3id.org/nmdc/nmdc range: GeneProduct has_function: name: has_function notes: - the range for has_function was asserted as functional_annotation_term/FunctionalAnnotationTerm, - but is actually taking string arguments in MongoDB, - and those are frequently fulltext, not CURIEs. MAM 2021-06-23 from_schema: https://w3id.org/nmdc/nmdc range: string pattern: ^(KEGG_PATHWAY:\w{2,4}\d{5}|KEGG.REACTION:R\d+|RHEA:\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\d{1,2}(\.\d{0,3}){0,3}|GO:\d{7}|MetaNetX:(MNXR\d+|EMPTY)|SEED:\w+|KEGG\.ORTHOLOGY:K\d+|EGGNOG:\w+|PFAM:PF\d{5}|TIGRFAM:TIGR\d+|SUPFAM:\w+|CATH:[1-6]\.[0-9]+\.[0-9]+\.[0-9]+|PANTHER.FAMILY:PTHR\d{5}(\:SF\d{1,3})?)$ has_participants: name: has_participants from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - RO:0000057 abstract: true gff_coordinate: name: gff_coordinate description: A positive 1-based integer coordinate indicating start or end comments: - For features that cross the origin of a circular feature (e.g. most bacterial genomes, plasmids, and some viral genomes), the requirement for start to be less than or equal to end is satisfied by making end = the position of the end + the length of the landmark feature. from_schema: https://w3id.org/nmdc/nmdc range: integer minimum_value: 1 seqid: name: seqid description: The ID of the landmark used to establish the coordinate system for the current feature. todos: - change range from string to object from_schema: https://w3id.org/nmdc/nmdc range: string strand: name: strand description: The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand). todos: - set the range to an enum? from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - biolink:strand direction: name: direction description: One of l->r, r->l, bidirectional, neutral from_schema: https://w3id.org/nmdc/nmdc encodes: name: encodes description: The gene product encoded by this feature. Typically this is used for a CDS feature or gene feature which will encode a protein. It can also be used by a nc transcript ot gene feature that encoded a ncRNA from_schema: https://w3id.org/nmdc/nmdc range: GeneProduct end: name: end description: The end of the feature in positive 1-based integer coordinates comments: - '- "constraint: end > start" - "For features that cross the origin of a circular feature, end = the position of the end + the length of the landmark feature."' from_schema: https://w3id.org/nmdc/nmdc close_mappings: - biolink:end_interbase_coordinate is_a: gff_coordinate feature_type: name: feature_type description: 'TODO: Yuri to write' from_schema: https://w3id.org/nmdc/nmdc has_part: name: has_part description: A pathway can be broken down to a series of reaction step from_schema: https://w3id.org/nmdc/nmdc multivalued: true range: Reaction is_balanced: name: is_balanced from_schema: https://w3id.org/nmdc/nmdc range: boolean is_diastereoselective: name: is_diastereoselective from_schema: https://w3id.org/nmdc/nmdc range: boolean is_fully_characterized: name: is_fully_characterized description: False if includes R-groups from_schema: https://w3id.org/nmdc/nmdc range: boolean is_stereo: name: is_stereo from_schema: https://w3id.org/nmdc/nmdc range: boolean is_transport: name: is_transport from_schema: https://w3id.org/nmdc/nmdc range: boolean left_participants: name: left_participants from_schema: https://w3id.org/nmdc/nmdc is_a: has_participants multivalued: true range: ReactionParticipant phase: name: phase description: The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2. from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - biolink:phase range: integer minimum_value: 0 maximum_value: 2 right_participants: name: right_participants from_schema: https://w3id.org/nmdc/nmdc is_a: has_participants multivalued: true range: ReactionParticipant smarts_string: name: smarts_string from_schema: https://w3id.org/nmdc/nmdc range: string start: name: start description: The start of the feature in positive 1-based integer coordinates from_schema: https://w3id.org/nmdc/nmdc close_mappings: - biolink:start_interbase_coordinate is_a: gff_coordinate classes: FunctionalAnnotationAggMember: name: FunctionalAnnotationAggMember from_schema: https://w3id.org/nmdc/nmdc slots: - metagenome_annotation_id - gene_function_id - count Database: name: Database description: An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest from_schema: https://w3id.org/nmdc/nmdc aliases: - NMDC metadata object slots: - functional_annotation_agg - library_preparation_set - processed_sample_set - extraction_set - activity_set - biosample_set - data_object_set - dissolving_activity_set - functional_annotation_set - genome_feature_set - mags_activity_set - material_sample_set - material_sampling_activity_set - metabolomics_analysis_activity_set - metagenome_annotation_activity_set - metagenome_assembly_set - metagenome_sequencing_activity_set - metaproteomics_analysis_activity_set - metatranscriptome_activity_set - nom_analysis_activity_set - omics_processing_set - reaction_activity_set - read_qc_analysis_activity_set - read_based_taxonomy_analysis_activity_set - study_set - field_research_site_set - collecting_biosamples_from_site_set - date_created - etl_software_version - metatranscriptome_activity_set - pooling_set - extraction_set slot_usage: date_created: name: date_created todos: - description etl_software_version: name: etl_software_version todos: - description metatranscriptome_activity_set: name: metatranscriptome_activity_set todos: - description tree_root: true Pooling: name: Pooling description: physical combination of several instances of like material. from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - OBI:0600016 is_a: BiosampleProcessing slot_usage: has_input: name: has_input minimum_cardinality: 2 has_output: name: has_output minimum_cardinality: 1 maximum_cardinality: 1 id: name: id required: true pattern: ^(nmdc):poolp-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$ structured_pattern: syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true Extraction: name: Extraction description: A material separation in which a desired component of an input material is separated from the remainder. from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - OBI:0302884 is_a: BiosampleProcessing slots: - extraction_method - extraction_target - processing_institution - protocol_link - quality_control_report - input_mass slot_usage: has_input: name: has_input required: true has_output: name: has_output required: true id: name: id required: true pattern: ^(nmdc):extrp-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$ structured_pattern: syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true Protocol: name: Protocol from_schema: https://w3id.org/nmdc/nmdc slots: - url - name QualityControlReport: name: QualityControlReport from_schema: https://w3id.org/nmdc/nmdc slots: - status - name LibraryPreparation: name: LibraryPreparation comments: - OBI:0000711 specifies a DNA input (but not ONLY a DNA input) from_schema: https://w3id.org/nmdc/nmdc aliases: - LibraryConstruction close_mappings: - OBI:0000711 is_a: BiosampleProcessing slots: - library_preparation_kit - library_type - pcr_cycles - processing_institution slot_usage: has_input: name: has_input required: true has_output: name: has_output required: true id: name: id required: true pattern: ^(nmdc):libprp-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$ structured_pattern: syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true FieldResearchSite: name: FieldResearchSite description: A site, outside of a laboratory, from which biosamples may be collected. title: Field Research Site comments: - Provides grouping of biosamples at level that's more specific than belonging to the same study - be very clear that this could be part of a larger site - In Bioscales, one might say that rhizosphere soil and bulk soil from around the same plant were obtained at the same site. In this case, the site would correspond to one tree. - might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833 from_schema: https://w3id.org/nmdc/nmdc aliases: - research plot is_a: Site slots: - cur_vegetation - elev - geo_loc_name - habitat - lat_lon - local_class - part_of - soil_type slot_usage: id: name: id required: true pattern: ^(nmdc):frsite-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$ structured_pattern: syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true CollectingBiosamplesFromSite: name: CollectingBiosamplesFromSite title: Collecting Biosamples From Site comments: - this illustrates implementing a Biosample relation with a process class from_schema: https://w3id.org/nmdc/nmdc close_mappings: - OBI:0000744 is_a: PlannedProcess slot_usage: has_input: name: has_input range: Site required: true has_output: name: has_output range: Biosample required: true id: name: id required: true pattern: ^(nmdc):clsite-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$ structured_pattern: syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true DataObject: name: DataObject description: An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects. notes: - removed previous id_prefixes value of GOLD, since we are now using pattern-based id validation comments: - removed id_prefixes value of GOLD, since we are now using pattern-based id validation in_subset: - data object subset from_schema: https://w3id.org/nmdc/nmdc is_a: NamedThing slots: - file_size_bytes - md5_checksum - data_object_type - compression_type - was_generated_by - url - type slot_usage: name: name: name required: true description: name: description required: true id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true Biosample: name: Biosample description: Biological source material which can be characterized by an experiment. alt_descriptions: embl.ena: source: embl.ena description: A sample contains information about the sequenced source material. Samples are associated with checklists, which define the fields used to annotate the samples. Samples are always associated with a taxon. todos: - could add GOLD and EBI's biosample definitions to the alt_descriptions? notes: - removed previous id_prefixes value of GOLD, since we are now using pattern-based id validation in_subset: - sample subset from_schema: https://w3id.org/nmdc/nmdc aliases: - sample - material sample - specimen - biospecimen exact_mappings: - OBI:0000747 - NCIT:C43412 - http://purl.obolibrary.org/obo/FBcv_0003024 is_a: MaterialEntity slots: - neon_biosample_identifiers - host_taxid - embargoed - collected_from - type - img_identifiers - samp_name - biosample_categories - type - part_of - id - alternative_identifiers - gold_biosample_identifiers - insdc_biosample_identifiers - emsl_biosample_identifiers - igsn_biosample_identifiers - abs_air_humidity - add_recov_method - additional_info - address - adj_room - aero_struc - agrochem_addition - air_PM_concen - air_temp - air_temp_regm - al_sat - al_sat_meth - alkalinity - alkalinity_method - alkyl_diethers - alt - aminopept_act - ammonium - ammonium_nitrogen - amount_light - ances_data - annual_precpt - annual_temp - antibiotic_regm - api - arch_struc - aromatics_pc - asphaltenes_pc - atmospheric_data - avg_dew_point - avg_occup - avg_temp - bac_prod - bac_resp - bacteria_carb_prod - barometric_press - basin - bathroom_count - bedroom_count - benzene - biochem_oxygen_dem - biocide - biocide_admin_method - biol_stat - biomass - biotic_regm - biotic_relationship - bishomohopanol - blood_press_diast - blood_press_syst - bromide - build_docs - build_occup_type - building_setting - built_struc_age - built_struc_set - built_struc_type - calcium - carb_dioxide - carb_monoxide - carb_nitro_ratio - ceil_area - ceil_cond - ceil_finish_mat - ceil_struc - ceil_texture - ceil_thermal_mass - ceil_type - ceil_water_mold - chem_administration - chem_mutagen - chem_oxygen_dem - chem_treat_method - chem_treatment - chimera_check - chloride - chlorophyll - climate_environment - collection_date - conduc - cool_syst_id - core field - crop_rotation - cult_root_med - cur_land_use - cur_vegetation - cur_vegetation_meth - date_last_rain - density - depos_env - depth - dew_point - diether_lipids - diss_carb_dioxide - diss_hydrogen - diss_inorg_carb - diss_inorg_nitro - diss_inorg_phosp - diss_iron - diss_org_carb - diss_org_nitro - diss_oxygen - diss_oxygen_fluid - dna_cont_well - door_comp_type - door_cond - door_direct - door_loc - door_mat - door_move - door_size - door_type - door_type_metal - door_type_wood - door_water_mold - down_par - drainage_class - drawings - ecosystem - ecosystem_category - ecosystem_subtype - ecosystem_type - efficiency_percent - elev - elevator - emulsions - env_broad_scale - env_local_scale - env_medium - env_package - environment field - escalator - ethylbenzene - exp_duct - exp_pipe - experimental_factor - ext_door - ext_wall_orient - ext_window_orient - extreme_event - fao_class - fertilizer_regm - field - filter_type - fire - fireplace_type - flooding - floor_age - floor_area - floor_cond - floor_count - floor_finish_mat - floor_struc - floor_thermal_mass - floor_water_mold - fluor - freq_clean - freq_cook - fungicide_regm - furniture - gaseous_environment - gaseous_substances - gender_restroom - genetic_mod - geo_loc_name - glucosidase_act - gravidity - gravity - growth_facil - growth_habit - growth_hormone_regm - hall_count - handidness - has numeric value - has raw value - has unit - hc_produced - hcr - hcr_fw_salinity - hcr_geol_age - hcr_pressure - hcr_temp - heat_cool_type - heat_deliv_loc - heat_sys_deliv_meth - heat_system_id - heavy_metals - heavy_metals_meth - height_carper_fiber - herbicide_regm - horizon_meth - host_age - host_body_habitat - host_body_product - host_body_site - host_body_temp - host_color - host_common_name - host_diet - host_dry_mass - host_family_relation - host_genotype - host_growth_cond - host_height - host_last_meal - host_length - host_life_stage - host_phenotype - host_sex - host_shape - host_subject_id - host_subspecf_genlin - host_substrate - host_symbiont - host_taxid - host_tot_mass - host_wet_mass - humidity - humidity_regm - indoor_space - indoor_surf - indust_eff_percent - inorg_particles - inside_lux - int_wall_cond - investigation field - iw_bt_date_well - iwf - last_clean - lat_lon - lbc_thirty - lbceq - light_intensity - light_regm - light_type - link_addit_analys - link_class_info - link_climate_info - lithology - local_class - local_class_meth - magnesium - manganese - max_occup - mean_frict_vel - mean_peak_frict_vel - mech_struc - mechanical_damage - methane - micro_biomass_meth - microbial_biomass - mineral_nutr_regm - misc_param - n_alkanes - nitrate - nitrate_nitrogen - nitrite - nitrite_nitrogen - nitro - non_min_nutr_regm - nucl_acid_amp - nucl_acid_ext - nucleic acid sequence source field - number_pets - number_plants - number_resident - occup_density_samp - occup_document - occup_samp - org_carb - org_count_qpcr_info - org_matter - org_nitro - org_particles - organism_count - owc_tvdss - oxy_stat_samp - oxygen - part_org_carb - part_org_nitro - particle_class - pcr_cond - pcr_primers - permeability - perturbation - pesticide_regm - petroleum_hydrocarb - ph - ph_meth - ph_regm - phaeopigments - phosphate - phosplipid_fatt_acid - photon_flux - plant_growth_med - plant_product - plant_sex - plant_struc - pollutants - pool_dna_extracts - porosity - potassium - pour_point - pre_treatment - pres_animal_insect - pressure - prev_land_use_meth - previous_land_use - primary_prod - primary_treatment - prod_rate - prod_start_date - profile_position - quad_pos - radiation_regm - rainfall_regm - reactor_type - redox_potential - rel_air_humidity - rel_humidity_out - rel_samp_loc - reservoir - resins_pc - room_air_exch_rate - room_architec_elem - room_condt - room_connected - room_count - room_dim - room_door_dist - room_door_share - room_hallway - room_loc - room_moist_dam_hist - room_net_area - room_occup - room_samp_pos - room_type - room_vol - room_wall_share - room_window_count - root_cond - root_med_carbon - root_med_macronutr - root_med_micronutr - root_med_ph - root_med_regl - root_med_solid - root_med_suppl - salinity - salinity_meth - salt_regm - samp_capt_status - samp_collec_device - samp_collec_method - samp_collect_point - samp_dis_stage - samp_floor - samp_loc_corr_rate - samp_mat_process - samp_md - samp_name - samp_preserv - samp_room_id - samp_size - samp_sort_meth - samp_store_dur - samp_store_loc - samp_store_temp - samp_subtype - samp_taxon_id - samp_time_out - samp_transport_cond - samp_tvdss - samp_type - samp_vol_we_dna_ext - samp_weather - samp_well_name - saturates_pc - season - season_environment - season_precpt - season_temp - season_use - secondary_treatment - sediment_type - seq_meth - seq_quality_check - sequencing field - sewage_type - shad_dev_water_mold - shading_device_cond - shading_device_loc - shading_device_mat - shading_device_type - sieving - silicate - size_frac - size_frac_low - size_frac_up - slope_aspect - slope_gradient - sludge_retent_time - sodium - soil_horizon - soil_text_measure - soil_texture_meth - soil_type - soil_type_meth - solar_irradiance - soluble_inorg_mat - soluble_org_mat - soluble_react_phosp - source_mat_id - space_typ_state - specific - specific_ecosystem - specific_humidity - sr_dep_env - sr_geol_age - sr_kerog_type - sr_lithology - standing_water_regm - store_cond - substructure_type - sulfate - sulfate_fw - sulfide - surf_air_cont - surf_humidity - surf_material - surf_moisture - surf_moisture_ph - surf_temp - suspend_part_matter - suspend_solids - tan - target_gene - target_subfragment - temp - temp_out - tertiary_treatment - tidal_stage - tillage - tiss_cult_growth_med - toluene - tot_carb - tot_depth_water_col - tot_diss_nitro - tot_inorg_nitro - tot_iron - tot_nitro - tot_nitro_cont_meth - tot_nitro_content - tot_org_c_meth - tot_org_carb - tot_part_carb - tot_phosp - tot_phosphate - tot_sulfur - train_line - train_stat_loc - train_stop_loc - turbidity - tvdss_of_hcr_press - tvdss_of_hcr_temp - typ_occup_density - ventilation_rate - ventilation_type - vfa - vfa_fw - vis_media - viscosity - volatile_org_comp - wall_area - wall_const_type - wall_finish_mat - wall_height - wall_loc - wall_surf_treatment - wall_texture - wall_thermal_mass - wall_water_mold - wastewater_type - water_cont_soil_meth - water_content - water_current - water_cut - water_feat_size - water_feat_type - water_prod_rate - water_temp_regm - watering_regm - weekday - win - wind_direction - wind_speed - window_cond - window_cover - window_horiz_pos - window_loc - window_mat - window_open_freq - window_size - window_status - window_type - window_vert_pos - window_water_mold - xylene - zinc - ecosystem - ecosystem_category - ecosystem_type - ecosystem_subtype - specific_ecosystem - add_date - community - habitat - host_name - location - mod_date - ncbi_taxonomy_name - proport_woa_temperature - salinity_category - sample_collection_site - soluble_iron_micromol - subsurface_depth - air_temp_regm - biotic_regm - biotic_relationship - climate_environment - experimental_factor - gaseous_environment - growth_facil - humidity_regm - light_regm - phosphate - samp_collec_method - samp_size - source_mat_id - watering_regm - dna_absorb1 - dna_absorb2 - dna_collect_site - dna_concentration - dna_cont_type - dna_cont_well - dna_container_id - dna_dnase - dna_isolate_meth - dna_organisms - dna_project_contact - dna_samp_id - dna_sample_format - dna_sample_name - dna_seq_project - dna_seq_project_pi - dna_seq_project_name - dna_volume - proposal_dna - dnase_rna - proposal_rna - rna_absorb1 - rna_absorb2 - rna_collect_site - rna_concentration - rna_cont_type - rna_cont_well - rna_container_id - rna_isolate_meth - rna_organisms - rna_project_contact - rna_samp_id - rna_sample_format - rna_sample_name - rna_seq_project - rna_seq_project_pi - rna_seq_project_name - rna_volume - collection_date_inc - collection_time - collection_time_inc - experimental_factor_other - filter_method - isotope_exposure - micro_biomass_c_meth - micro_biomass_n_meth - microbial_biomass_c - microbial_biomass_n - non_microb_biomass - non_microb_biomass_method - org_nitro_method - other_treatment - start_date_inc - start_time_inc - project_id - replicate_number - sample_shipped - sample_type - technical_reps - analysis_type - sample_link - zinc - manganese - ammonium_nitrogen - nitrate_nitrogen - nitrite_nitrogen - lbc_thirty - lbceq slot_usage: elev: name: elev title: elevation, meters comments: - All elevations must be reported in meters. Provide the numerical portion only. - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates. examples: - value: '100' range: float oxy_stat_samp: name: oxy_stat_samp range: oxy_stat_samp_enum id: name: id description: An NMDC assigned unique identifier for a biosample submitted to NMDC. required: true pattern: .* structured_pattern: syntax: .* interpolated: true gold_biosample_identifiers: name: gold_biosample_identifiers annotations: display_hint: tag: display_hint value: Provide the GOLD biosample IDs associated with this biosample. description: Unique identifier for a biosample submitted to GOLD that matches the NMDC submitted biosample comments: - This is the ID provided by GOLD that starts with 'GB' range: uriorcurie alternative_identifiers: name: alternative_identifiers description: Unique identifier for a biosample submitted to additional resources. 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? env_broad_scale: name: env_broad_scale required: true env_local_scale: name: env_local_scale required: true env_medium: name: env_medium required: true part_of: name: part_of range: Study required: true fire: name: fire annotations: expected_value: tag: expected_value value: date string todos: - is "to" acceptable? Is there a better way to request that be written? - This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot comments: - Provide the date the fire occurred. If extended burning occurred provide the date range. examples: - value: '1871-10-10' - value: 1871-10-01 to 1871-10-31 range: string 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]))?)?)?$ flooding: name: flooding annotations: expected_value: tag: expected_value value: date string todos: - is "to" acceptable? Is there a better way to request that be written? - What about if the "day" isn't known? Is this ok? - This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot comments: - Provide the date the flood occurred. If extended flooding occurred provide the date range. examples: - value: '1927-04-15' - value: 1927-04 to 1927-05 range: string extreme_event: name: extreme_event annotations: expected_value: tag: expected_value value: date, string todos: - This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot examples: - value: 1980-05-18, volcanic eruption range: string slope_aspect: name: slope_aspect description: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees). - This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. todos: - This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot comments: - Aspect is the orientation of slope, measured clockwise in degrees from 0 to 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270 is west-facing. examples: - value: '35' slope_gradient: name: slope_gradient todos: - Slope is a percent. How does the validation work? Check to correct examples examples: - value: 10% - value: 10 % - value: '0.10' al_sat: name: al_sat description: The relative abundance of aluminum in the sample title: aluminum saturation/ extreme unusual properties todos: - This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate? - I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement. comments: - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like all cations, aluminum held by the cation exchange complex is in equilibrium with aluminum in the soil solution. examples: - value: 27% al_sat_meth: name: al_sat_meth description: Reference or method used in determining Aluminum saturation title: aluminum saturation method/ extreme unusual properties todos: - This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot - I think it's weird the way GSC writes the title. I recommend this change. Thoughts? comments: - Required when aluminum saturation is provided. examples: - value: https://doi.org/10.1371/journal.pone.0176357 annual_precpt: name: annual_precpt todos: - This is no longer matching the listed IRI from GSC, added example. When NMDC has its own slots, map this to the MIxS slot examples: - value: 8.94 inch cur_vegetation: name: cur_vegetation description: Vegetation classification from one or more standard classification systems, or agricultural crop todos: - This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot - Recommend changing this from text value to some king of ontology? comments: - Values provided here can be specific species of vegetation or vegetation regions - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region examples: - value: deciduous forest - value: forest - value: Bauhinia variegata cur_vegetation_meth: name: cur_vegetation_meth todos: - This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find out how they accomplish this if provided. comments: - Required when current vegetation is provided. examples: - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x heavy_metals: name: heavy_metals description: Heavy metals present in the sample and their concentrations. title: heavy metals/ extreme unusual properties todos: - This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate? - I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement. notes: - Changed to multi-valued. In MIxS, you add another column to denote multiple heavy metals. We don't have that ability in the submission portal. comments: - For multiple heavy metals and concentrations, separate by ; examples: - value: mercury 0.09 micrograms per gram - value: mercury 0.09 ug/g; chromium 0.03 ug/g heavy_metals_meth: name: heavy_metals_meth title: heavy metals method/ extreme unusual properties todos: - This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot comments: - Required when heavy metals are provided - If different methods are used for multiple metals, indicate the metal and method. Separate metals by ; examples: - value: https://doi.org/10.3390/ijms9040434 - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8 multivalued: true season_precpt: name: season_precpt title: average seasonal precipitation todos: - This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot - check validation & examples. always mm? so value only? Or value + unit notes: - mean and average are the same thing, but it seems like bad practice to not be consistent. Changed mean to average comments: - Seasons are defined as spring (March, April, May), summer (June, July, August), autumn (September, October, November) and winter (December, January, February). examples: - value: 0.4 inch - value: 10.16 mm water_cont_soil_meth: name: water_cont_soil_meth todos: - Why is it soil water content method in the name but not the title? Is this slot used in other samples? - Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few). - Should this be multi valued? How to we manage and validate this? comments: - Required if providing water content examples: - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503 - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm water_content: name: water_content annotations: expected_value: tag: expected_value value: string preferred_unit: tag: preferred_unit value: gram per gram or cubic centimeter per cubic centimeter todos: - value in preferred unit is too limiting. need to change this - check and correct validation so examples are accepted - This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot - how to manage multiple water content methods? examples: - value: 0.75 g water/g dry soil - value: 75% water holding capacity - value: 1.1 g fresh weight/ dry weight - value: 10% water filled pore space multivalued: true range: string ph_meth: name: ph_meth comments: - This can include a link to the instrument used or a citation for the method. examples: - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB - value: https://doi.org/10.2136/sssabookser5.3.c16 tot_carb: name: tot_carb todos: - is this inorganic and organic? both? could use some clarification. - ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format examples: - value: 1 ug/L tot_nitro_cont_meth: name: tot_nitro_cont_meth examples: - value: https://doi.org/10.2134/agronmonogr9.2.c32 - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo tot_nitro_content: name: tot_nitro_content examples: - value: 5 mg N/ L tot_org_c_meth: name: tot_org_c_meth examples: - value: https://doi.org/10.1080/07352680902776556 tot_org_carb: name: tot_org_carb todos: - check description. How are they different? examples: - value: 5 mg N/ L salinity_meth: name: salinity_meth examples: - value: https://doi.org/10.1007/978-1-61779-986-0_28 sieving: name: sieving todos: - check validation and examples comments: - Describe how samples were composited or sieved. - Use 'sample link' to indicate which samples were combined. examples: - value: combined 2 cores | 4mm sieved - value: 4 mm sieved and homogenized - value: 50 g | 5 cores | 2 mm sieved climate_environment: name: climate_environment todos: - description says "can include multiple climates" but multivalued is set to false - add examples, i need to see some examples to add correctly formatted example. gaseous_environment: name: gaseous_environment todos: - would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value - did I do this right? keep the example that's provided and add another? so as to not override examples: - value: CO2; 500ppm above ambient; constant - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M watering_regm: name: watering_regm examples: - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M - value: 75% water holding capacity; constant source_mat_id: name: source_mat_id description: A globally unique identifier assigned to the biological sample. title: source material identifier todos: - Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID. comments: - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/). examples: - value: IGSN:AU1243 - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002 unique_keys: samp_name_unique_key: unique_key_name: samp_name_unique_key unique_key_slots: - samp_name notes: - 'id is already required to be unique because it is the identifier in Biosample''s parent class, NamedThing. Remember, notes like this could be exposed to end users. CJM suggested YAML # comment' rules: - preconditions: slot_conditions: dna_cont_well: name: dna_cont_well pattern: .+ postconditions: slot_conditions: dna_cont_type: name: dna_cont_type equals_string: plate description: DNA samples shipped to JGI for metagenomic analysis in tubes can't have any value for their plate position. title: dna_well_requires_plate - preconditions: slot_conditions: dna_cont_type: name: dna_cont_type equals_string: plate postconditions: slot_conditions: dna_cont_well: name: dna_cont_well pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$ description: DNA samples in plates must have a plate position that matches the regex. Note the requirement for an empty string in the tube case. Waiting for value_present validation to be added to runtime title: dna_plate_requires_well - preconditions: slot_conditions: rna_cont_well: name: rna_cont_well pattern: .+ postconditions: slot_conditions: rna_cont_type: name: rna_cont_type equals_string: plate description: RNA samples shipped to JGI for metagenomic analysis in tubes can't have any value for their plate position. title: rna_well_requires_plate - preconditions: slot_conditions: rna_cont_type: name: rna_cont_type equals_string: plate postconditions: slot_conditions: rna_cont_well: name: rna_cont_well pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$ description: RNA samples in plates must have a plate position that matches the regex. Note the requirement for an empty string in the tube case. Waiting for value_present validation to be added to runtime title: rna_plate_requires_well Study: name: Study description: A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects. alt_descriptions: embl.ena: source: embl.ena description: A study (project) groups together data submitted to the archive and controls its release date. A study accession is typically used when citing data submitted to ENA todos: - determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor - project_name is redundant with name, so excluding it notes: - sample GOLD link https://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 - GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers, but no longer for the Study.id comments: - The Study class can include both consortia and research studies. in_subset: - sample subset from_schema: https://w3id.org/nmdc/nmdc aliases: - proposal - research proposal - research study - investigation - project - umbrella project - research inititative exact_mappings: - OBI:0000066 - SIO:000747 - NCIT:C41198 - ISA:Investigation broad_mappings: - prov:Activity is_a: NamedThing slots: - emsl_project_dois - neon_study_identifiers - jgi_portal_study_identifiers - id - alternative_identifiers - gnps_task_identifiers - alternative_descriptions - alternative_names - alternative_titles - description - award_dois - dataset_dois - publication_dois - ecosystem - ecosystem_category - ecosystem_subtype - ecosystem_type - ess_dive_datasets - funding_sources - gold_study_identifiers - has_credit_associations - study_category - insdc_bioproject_identifiers - massive_study_identifiers - mgnify_project_identifiers - notes - objective - part_of - principal_investigator - publications - related_identifiers - relevant_protocols - specific_ecosystem - study_image - title - type - websites slot_usage: id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true name: name: name annotations: display_hint: tag: display_hint value: Provide a name for the study your samples will belong with. websites: name: websites annotations: display_hint: tag: display_hint value: Link to the Principal Investigator's research lab webpage or the study webpage associated with this collection of samples. Multiple links can be provided. description: name: description annotations: display_hint: tag: display_hint value: Provide a brief description of your study. description: A brief, link-free summary of a Study comments: - Include links in other Study slots, such as websites or dois. notes: name: notes annotations: display_hint: tag: display_hint value: Add any additional notes or comments about this study. alternative_identifiers: name: alternative_identifiers description: Unique identifier for a study submitted to additional resources. Matches that which has been submitted to NMDC alternative_names: name: alternative_names annotations: display_hint: tag: display_hint value: Project, study, or sample set names the are also associated with this submission or other names / identifiers for this study. related_identifiers: name: related_identifiers description: Unique identifier for a study submitted to additional resources. Similar, but not necessarily identical to that which has been submitted to NMDC insdc_bioproject_identifiers: name: insdc_bioproject_identifiers annotations: display_hint: tag: display_hint value: Provide the NCBI BioProject Accession Number associated with the listed NCBI BioProject Title. description: Unique identifier for a bioproject submitted to INSDC that relates to the NMDC submitted study. part_of: name: part_of description: Links a study or consortium to a parent study or consortium. comments: - Value is the id of the parent study or consortium. range: Study BiosampleProcessing: name: BiosampleProcessing description: 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. from_schema: https://w3id.org/nmdc/nmdc aliases: - material processing broad_mappings: - OBI:0000094 is_a: PlannedProcess slots: - has_input slot_usage: id: name: id required: true pattern: ^(nmdc):bsmprc-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$ structured_pattern: syntax: '{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true has_input: name: has_input range: Biosample OmicsProcessing: name: OmicsProcessing description: The methods and processes used to generate omics data from a biosample or organism. alt_descriptions: embl.ena: source: embl.ena description: An experiment contains information about a sequencing experiment including library and instrument details. comments: - The ID prefix for objects coming from GOLD will be gold:Gp in_subset: - sample subset from_schema: https://w3id.org/nmdc/nmdc aliases: - omics assay - sequencing project - experiment broad_mappings: - OBI:0000070 - ISA:Assay is_a: PlannedProcess slots: - add_date - chimera_check - gold_sequencing_project_identifiers - has_input - has_output - insdc_experiment_identifiers - instrument_name - mod_date - ncbi_project_name - nucl_acid_amp - nucl_acid_ext - omics_type - part_of - pcr_cond - pcr_primers - principal_investigator - processing_institution - samp_vol_we_dna_ext - seq_meth - seq_quality_check - target_gene - target_subfragment - type slot_usage: id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true has_input: name: has_input required: true CreditAssociation: name: CreditAssociation description: This class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0 from_schema: https://w3id.org/nmdc/nmdc aliases: - study role - credit table - associated researchers slots: - applies_to_person - applied_role - applied_roles - type class_uri: prov:Association WorkflowExecutionActivity: name: WorkflowExecutionActivity description: Represents an instance of an execution of a particular workflow alt_descriptions: embl.ena: source: embl.ena description: An analysis contains secondary analysis results derived from sequence reads (e.g. a genome assembly) comments: - Each instance of this (and all other) activities is a distinct run with start and stop times, potentially with different inputs and outputs in_subset: - workflow subset from_schema: https://w3id.org/nmdc/nmdc aliases: - analysis is_a: Activity slots: - execution_resource - git_url - has_input - has_output - part_of - type - version slot_usage: started_at_time: name: started_at_time required: true ended_at_time: name: ended_at_time required: true git_url: name: git_url required: true has_input: name: has_input required: true has_output: name: has_output required: true execution_resource: name: execution_resource required: true type: name: type required: true id: name: id required: true pattern: ^(nmdc):wf-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$ structured_pattern: syntax: '{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true MetagenomeAssembly: name: MetagenomeAssembly description: A workflow execution activity that converts sequencing reads into an assembled metagenome. comments: - instances of this class may use a de novo assembly strategy in most or all cases relevant to NMDC in_subset: - workflow subset from_schema: https://w3id.org/nmdc/nmdc is_a: WorkflowExecutionActivity slots: - type - asm_score - scaffolds - scaf_logsum - scaf_powsum - scaf_max - scaf_bp - scaf_n50 - scaf_n90 - scaf_l50 - scaf_l90 - scaf_n_gt50k - scaf_l_gt50k - scaf_pct_gt50k - contigs - contig_bp - ctg_n50 - ctg_l50 - ctg_n90 - ctg_l90 - ctg_logsum - ctg_powsum - ctg_max - gap_pct - gc_std - gc_avg - num_input_reads - num_aligned_reads - insdc_assembly_identifiers slot_usage: id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true MetatranscriptomeAssembly: name: MetatranscriptomeAssembly in_subset: - workflow subset from_schema: https://w3id.org/nmdc/nmdc is_a: WorkflowExecutionActivity slots: - asm_score - scaffolds - scaf_logsum - scaf_powsum - scaf_max - scaf_bp - scaf_n50 - scaf_n90 - scaf_l50 - scaf_l90 - scaf_n_gt50k - scaf_l_gt50k - scaf_pct_gt50k - contigs - contig_bp - ctg_n50 - ctg_l50 - ctg_n90 - ctg_l90 - ctg_logsum - ctg_powsum - ctg_max - gap_pct - gc_std - gc_avg - num_input_reads - num_aligned_reads - insdc_assembly_identifiers slot_usage: id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true MetagenomeAnnotationActivity: name: MetagenomeAnnotationActivity description: A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs in_subset: - workflow subset from_schema: https://w3id.org/nmdc/nmdc is_a: WorkflowExecutionActivity slots: - type - gold_analysis_project_identifiers slot_usage: id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true MetatranscriptomeAnnotationActivity: name: MetatranscriptomeAnnotationActivity in_subset: - workflow subset from_schema: https://w3id.org/nmdc/nmdc is_a: WorkflowExecutionActivity slots: - type - gold_analysis_project_identifiers slot_usage: id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true MetatranscriptomeActivity: name: MetatranscriptomeActivity description: A metatranscriptome activity that e.g. pools assembly and annotation activity. in_subset: - workflow subset from_schema: https://w3id.org/nmdc/nmdc is_a: WorkflowExecutionActivity slots: - type slot_usage: id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true MagsAnalysisActivity: name: MagsAnalysisActivity description: A workflow execution activity that uses computational binning tools to group assembled contigs into genomes title: Metagenome-Assembled Genome analysis activity in_subset: - workflow subset from_schema: https://w3id.org/nmdc/nmdc is_a: WorkflowExecutionActivity slots: - type - input_contig_num - binned_contig_num - too_short_contig_num - low_depth_contig_num - unbinned_contig_num - mags_list slot_usage: id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true MetagenomeSequencingActivity: name: MetagenomeSequencingActivity description: Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data. title: Metagenome sequencing activity in_subset: - workflow subset from_schema: https://w3id.org/nmdc/nmdc is_a: WorkflowExecutionActivity slot_usage: id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true ReadQcAnalysisActivity: name: ReadQcAnalysisActivity description: A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal title: Read quality control analysis activity in_subset: - workflow subset from_schema: https://w3id.org/nmdc/nmdc is_a: WorkflowExecutionActivity slots: - type - input_read_count - input_base_count - output_read_count - output_base_count - input_read_bases - output_read_bases - version slot_usage: id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true ReadBasedTaxonomyAnalysisActivity: name: ReadBasedTaxonomyAnalysisActivity description: A workflow execution activity that performs taxonomy classification using sequencing reads title: Read based analysis activity in_subset: - workflow subset from_schema: https://w3id.org/nmdc/nmdc is_a: WorkflowExecutionActivity slots: - type slot_usage: id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true MetabolomicsAnalysisActivity: name: MetabolomicsAnalysisActivity in_subset: - workflow subset from_schema: https://w3id.org/nmdc/nmdc is_a: WorkflowExecutionActivity slots: - has_calibration - has_metabolite_quantifications slot_usage: id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true MetaproteomicsAnalysisActivity: name: MetaproteomicsAnalysisActivity in_subset: - workflow subset from_schema: https://w3id.org/nmdc/nmdc is_a: WorkflowExecutionActivity slots: - has_peptide_quantifications slot_usage: used: name: used description: The instrument used to collect the data used in the analysis range: Instrument id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true NomAnalysisActivity: name: NomAnalysisActivity in_subset: - workflow subset from_schema: https://w3id.org/nmdc/nmdc is_a: WorkflowExecutionActivity slots: - has_calibration slot_usage: used: name: used description: The instrument used to collect the data used in the analysis range: string id: name: id required: true pattern: .* structured_pattern: syntax: .* interpolated: true NamedThing: name: NamedThing description: a databased entity or concept/class from_schema: https://w3id.org/nmdc/nmdc abstract: true slots: - id - name - description - alternative_identifiers MaterialEntity: name: MaterialEntity title: Material Entity from_schema: https://w3id.org/nmdc/nmdc aliases: - Material - Physical entity is_a: NamedThing abstract: true ProcessedSample: name: ProcessedSample title: Processed Sample from_schema: https://w3id.org/nmdc/nmdc is_a: MaterialEntity slots: - biomaterial_purity - dna_absorb1 - dna_concentration - external_database_identifiers - nucleic_acid_concentration slot_usage: id: name: id required: true pattern: ^(nmdc):procsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$ structured_pattern: syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true AnalyticalSample: name: AnalyticalSample title: Analytical Sample from_schema: https://w3id.org/nmdc/nmdc is_a: MaterialEntity slot_usage: id: name: id required: true pattern: ^(nmdc):ansm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$ structured_pattern: syntax: '{id_nmdc_prefix}:ansm-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true Site: name: Site title: Site comments: - BCO sample collection site ? from_schema: https://w3id.org/nmdc/nmdc is_a: MaterialEntity abstract: true slot_usage: id: name: id required: true pattern: ^(nmdc):site-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$ structured_pattern: syntax: '{id_nmdc_prefix}:site-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true PlannedProcess: name: PlannedProcess title: Planned Process from_schema: https://w3id.org/nmdc/nmdc is_a: NamedThing abstract: true slots: - end_date - has_input - has_output - protocol_link - start_date class_uri: OBI:0000011 OntologyClass: name: OntologyClass notes: - The identifiers for terms from external ontologies can't have their ids constrained to the nmdc namespace from_schema: https://w3id.org/nmdc/nmdc is_a: NamedThing slot_usage: id: name: id pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$ EnvironmentalMaterialTerm: name: EnvironmentalMaterialTerm from_schema: https://w3id.org/nmdc/nmdc is_a: OntologyClass AttributeValue: name: AttributeValue description: The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value from_schema: https://w3id.org/nmdc/nmdc slots: - has_raw_value - was_generated_by slot_usage: type: name: type description: An optional string that specified the type of object. InstrumentValue: name: InstrumentValue from_schema: https://w3id.org/nmdc/nmdc is_a: AttributeValue slots: - has_unit - has_numeric_value - instrument_name QuantityValue: name: QuantityValue description: A simple quantity, e.g. 2cm from_schema: https://w3id.org/nmdc/nmdc mappings: - schema:QuantityValue is_a: AttributeValue slots: - has_maximum_numeric_value - has_minimum_numeric_value - has_numeric_value - has_raw_value - has_unit slot_usage: has_raw_value: name: has_raw_value description: Unnormalized atomic string representation, should in syntax {number} {unit} has_unit: name: has_unit description: The unit of the quantity has_numeric_value: name: has_numeric_value description: The number part of the quantity range: double ImageValue: name: ImageValue description: An attribute value representing an image. from_schema: https://w3id.org/nmdc/nmdc is_a: AttributeValue slots: - url - description - display_order PersonValue: name: PersonValue description: An attribute value representing a person todos: - add additional fields e.g for institution - deprecate "has_raw_value" in favor of "name" from_schema: https://w3id.org/nmdc/nmdc is_a: AttributeValue slots: - email - name - orcid - profile_image_url - websites slot_usage: orcid: name: orcid annotations: display_hint: tag: display_hint value: Open Researcher and Contributor ID for this person. See https://orcid.org email: name: email annotations: display_hint: tag: display_hint value: Email address for this person. has_raw_value: name: has_raw_value description: The full name of the Investigator in format FIRST LAST. notes: - May eventually be deprecated in favor of "name". name: name: name annotations: display_hint: tag: display_hint value: First name, middle initial, and last name of this person. description: The full name of the Investigator. It should follow the format FIRST [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional. MagBin: name: MagBin from_schema: https://w3id.org/nmdc/nmdc slots: - bin_name - bin_quality - completeness - contamination - gene_count - gtdbtk_class - gtdbtk_domain - gtdbtk_family - gtdbtk_genus - gtdbtk_order - gtdbtk_phylum - gtdbtk_species - members_id - num_16s - num_23s - num_5s - num_t_rna - number_of_contig - total_bases - type Instrument: name: Instrument description: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI]. from_schema: https://w3id.org/nmdc/nmdc aliases: - device exact_mappings: - OBI:0000485 is_a: NamedThing slot_usage: id: name: id required: true pattern: ^(nmdc):inst-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$ structured_pattern: syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true MetaboliteQuantification: name: MetaboliteQuantification description: This is used to link a metabolomics analysis workflow to a specific metabolite from_schema: https://w3id.org/nmdc/nmdc slots: - alternative_identifiers - highest_similarity_score - metabolite_quantified PeptideQuantification: name: PeptideQuantification description: This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information from_schema: https://w3id.org/nmdc/nmdc slots: - all_proteins - best_protein - min_q_value - peptide_sequence - peptide_spectral_count - peptide_sum_masic_abundance ProteinQuantification: name: ProteinQuantification description: This is used to link a metaproteomics analysis workflow to a specific protein from_schema: https://w3id.org/nmdc/nmdc slots: - all_proteins - best_protein - peptide_sequence_count - protein_spectral_count - protein_sum_masic_abundance slot_usage: best_protein: name: best_protein description: the specific protein identifier most correctly grouped to its associated peptide sequences all_proteins: name: all_proteins description: the grouped list of protein identifiers associated with the peptide sequences that were grouped to a best protein ChemicalEntity: name: ChemicalEntity id_prefixes: - cas - CHEBI - CHEMBL.COMPOUND - DRUGBANK - HMDB - KEGG.COMPOUND - MESH - PUBCHEM.COMPOUND description: An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states comments: - As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode to this class. from_schema: https://w3id.org/nmdc/nmdc see_also: - https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html aliases: - metabolite - chemical substance - chemical compound - chemical exact_mappings: - biolink:ChemicalSubstance is_a: OntologyClass slots: - chemical_formula - inchi - inchi_key - smiles GeneProduct: name: GeneProduct id_prefixes: - PR - UniProtKB - gtpo description: A molecule encoded by a gene that has an evolved function notes: - we may include a more general gene product class in future to allow for ncRNA annotation from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - biolink:GeneProduct is_a: NamedThing TextValue: name: TextValue description: A basic string value from_schema: https://w3id.org/nmdc/nmdc is_a: AttributeValue slots: - language UrlValue: name: UrlValue description: A value that is a string that conforms to URL syntax from_schema: https://w3id.org/nmdc/nmdc is_a: AttributeValue TimestampValue: name: TimestampValue description: A value that is a timestamp. The range should be ISO-8601 notes: - 'removed the following slots: year, month, day' from_schema: https://w3id.org/nmdc/nmdc is_a: AttributeValue IntegerValue: name: IntegerValue description: A value that is an integer from_schema: https://w3id.org/nmdc/nmdc is_a: AttributeValue slots: - has_numeric_value BooleanValue: name: BooleanValue description: A value that is a boolean from_schema: https://w3id.org/nmdc/nmdc is_a: AttributeValue slots: - has_boolean_value ControlledTermValue: name: ControlledTermValue description: A controlled term or class from an ontology todos: - add fields for ontology, branch from_schema: https://w3id.org/nmdc/nmdc is_a: AttributeValue slots: - term ControlledIdentifiedTermValue: name: ControlledIdentifiedTermValue description: A controlled term or class from an ontology, requiring the presence of term with an id notes: - To be used for slots like env_broad_scale from_schema: https://w3id.org/nmdc/nmdc is_a: ControlledTermValue slot_usage: term: name: term required: true GeolocationValue: name: GeolocationValue description: A normalized value for a location on the earth's surface notes: - 'what did ''to_str: {latitude} {longitude}'' mean?' from_schema: https://w3id.org/nmdc/nmdc mappings: - schema:GeoCoordinates is_a: AttributeValue slots: - latitude - longitude slot_usage: has_raw_value: name: has_raw_value description: The raw value for a geolocation should follow {latitude} {longitude} latitude: name: latitude required: true longitude: name: longitude required: true Activity: name: Activity description: a provence-generating activity notes: - removed was_associated_with because we are trying to avoid instantiating id-less Agents from_schema: https://w3id.org/nmdc/nmdc mappings: - prov:Activity slots: - id - name - started_at_time - ended_at_time - was_informed_by - used slot_usage: id: name: id required: true pattern: ^(nmdc):act-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$ structured_pattern: syntax: '{id_nmdc_prefix}:act-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true DissolvingActivity: name: DissolvingActivity title: Dissolving activity from_schema: https://w3id.org/nmdc/nmdc aliases: - dissolution-activity slots: - dissolution_aided_by - dissolution_reagent - dissolution_volume - dissolved_in - material_input - material_output slot_usage: material_input: name: material_input examples: - value: somextract:6 material_output: name: material_output examples: - value: somextract:7 class_uri: CHMO:0002773 LabDevice: name: LabDevice title: Lab device from_schema: https://w3id.org/nmdc/nmdc slots: - device_type - activity_speed - activity_temperature - activity_time MaterialContainer: name: MaterialContainer title: Material container from_schema: https://w3id.org/nmdc/nmdc slots: - container_size - container_type MaterialSample: name: MaterialSample title: Material sample from_schema: https://w3id.org/nmdc/nmdc aliases: - Material entity is_a: NamedThing slot_usage: id: name: id required: true pattern: ^(nmdc):matsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})(\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\.-]+)?$ structured_pattern: syntax: '{id_nmdc_prefix}:matsm-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true MaterialSamplingActivity: name: MaterialSamplingActivity title: Material sampling activity from_schema: https://w3id.org/nmdc/nmdc aliases: - weighing-activity slots: - amount_collected - collected_into - material_output - sampling_method slot_usage: amount_collected: name: amount_collected aliases: - weighing-activity.weight collected_into: name: collected_into aliases: - weighing-activity.contanier material_output: name: material_output examples: - value: somextract:6 aliases: - weighing-activity.id class_uri: OBI:0000744 ReactionActivity: name: ReactionActivity title: Reaction activity from_schema: https://w3id.org/nmdc/nmdc aliases: - reaction-activity slots: - material_input - material_output - reaction_aided_by - reaction_temperature - reaction_time slot_usage: reaction_time: name: reaction_time todos: - constrain units - align with activity_time GenomeFeature: name: GenomeFeature description: A feature localized to an interval along a genome comments: - corresponds to an entry in GFF3 from_schema: https://w3id.org/nmdc/nmdc see_also: - https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md slots: - encodes - end - feature_type - phase - seqid - start - strand - type slot_usage: seqid: name: seqid required: true type: name: type description: A type from the sequence ontology range: OntologyClass start: name: start required: true end: name: end required: true FunctionalAnnotationTerm: name: FunctionalAnnotationTerm description: Abstract grouping class for any term/descriptor that can be applied to a functional unit of a genome (protein, ncRNA, complex). todos: - decide if this should be used for product naming from_schema: https://w3id.org/nmdc/nmdc aliases: - function - FunctionalAnnotation is_a: OntologyClass abstract: true Pathway: name: Pathway id_prefixes: - KEGG_PATHWAY - COG description: A pathway is a sequence of steps/reactions carried out by an organism or community of organisms from_schema: https://w3id.org/nmdc/nmdc aliases: - biological process - metabolic pathway - signaling pathway exact_mappings: - biolink:Pathway is_a: FunctionalAnnotationTerm slots: - has_part Reaction: name: Reaction id_prefixes: - KEGG.REACTION - RHEA - MetaCyc - EC - GO - MetaNetX - SEED - RetroRules description: An individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - biolink:MolecularActivity is_a: FunctionalAnnotationTerm slots: - direction - is_balanced - is_diastereoselective - is_fully_characterized - is_stereo - is_transport - left_participants - right_participants - smarts_string ReactionParticipant: name: ReactionParticipant description: Instances of this link a reaction to a chemical entity participant from_schema: https://w3id.org/nmdc/nmdc slots: - chemical - stoichiometry OrthologyGroup: name: OrthologyGroup id_prefixes: - CATH - EGGNOG - KEGG.ORTHOLOGY - PANTHER.FAMILY - PFAM - SUPFAM - TIGRFAM description: A set of genes or gene products in which all members are orthologous notes: - KEGG.ORTHOLOGY prefix is used for KO numbers from_schema: https://w3id.org/nmdc/nmdc exact_mappings: - biolink:GeneFamily is_a: FunctionalAnnotationTerm FunctionalAnnotation: name: FunctionalAnnotation description: An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods notes: - move id slot usage patterns to has_function slot usage? from_schema: https://w3id.org/nmdc/nmdc see_also: - https://img.jgi.doe.gov/docs/functional-annotation.pdf - https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl narrow_mappings: - biolink:GeneToGoTermAssociation slots: - has_function - subject - was_generated_by slot_usage: has_function: name: has_function notes: - this slot had been called id - Still missing patterns for COG and RetroRules. - These patterns aren't tied to the listed prefixes. A discussion about that possibility had been started, including the question of whether these lists are intended to be open examples or closed type: name: type description: TODO range: OntologyClass was_generated_by: name: was_generated_by description: provenance for the annotation. notes: - To be consistent with the rest of the NMDC schema we use the PROV annotation model, rather than GPAD range: MetagenomeAnnotationActivity source_file: nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml settings: id_nmdc_prefix: setting_key: id_nmdc_prefix setting_value: ^(nmdc) id_shoulder: setting_key: id_shoulder setting_value: ([0-9][a-z]{0,6}[0-9]) id_blade: setting_key: id_blade setting_value: ([A-Za-z0-9]{1,}) id_version: setting_key: id_version setting_value: (\.[A-Za-z0-9]{1,})* id_locus: setting_key: id_locus setting_value: (_[A-Za-z0-9_\.-]+)?$