diff --git a/linkml-schema/bican_biolink.yaml b/linkml-schema/bican_biolink.yaml new file mode 100644 index 00000000..52fb6622 --- /dev/null +++ b/linkml-schema/bican_biolink.yaml @@ -0,0 +1,2056 @@ +name: Biolink-Model +description: Entity and association taxonomy and datamodel for life-sciences data +id: https://w3id.org/biolink/biolink-model +version: 4.2.0-rc.2 +imports: +- linkml:types +license: https://creativecommons.org/publicdomain/zero/1.0/ +prefixes: + AGRKB: + prefix_prefix: AGRKB + prefix_reference: https://www.alliancegenome.org/ + apollo: + prefix_prefix: apollo + prefix_reference: https://github.com/GMOD/Apollo + AspGD: + prefix_prefix: AspGD + prefix_reference: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid= + biolink: + prefix_prefix: biolink + prefix_reference: https://w3id.org/biolink/vocab/ + bioschemas: + prefix_prefix: bioschemas + prefix_reference: https://bioschemas.org/ + linkml: + prefix_prefix: linkml + prefix_reference: https://w3id.org/linkml/ + CAID: + prefix_prefix: CAID + prefix_reference: http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid= + CHADO: + prefix_prefix: CHADO + prefix_reference: http://gmod.org/wiki/Chado/ + ChemBank: + prefix_prefix: ChemBank + prefix_reference: http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid= + CHEMBL.MECHANISM: + prefix_prefix: CHEMBL.MECHANISM + prefix_reference: https://www.ebi.ac.uk/chembl/mechanism/inspect/ + CID: + prefix_prefix: CID + prefix_reference: http://pubchem.ncbi.nlm.nih.gov/compound/ + CLINVAR: + prefix_prefix: CLINVAR + prefix_reference: http://identifiers.org/clinvar + COAR_RESOURCE: + prefix_prefix: COAR_RESOURCE + prefix_reference: http://purl.org/coar/resource_type/ + COG: + prefix_prefix: COG + prefix_reference: https://www.ncbi.nlm.nih.gov/research/cog-project/ + ComplexPortal: + prefix_prefix: ComplexPortal + prefix_reference: https://www.ebi.ac.uk/complexportal/complex/ + CPT: + prefix_prefix: CPT + prefix_reference: https://www.ama-assn.org/practice-management/cpt/ + CTD.CHEMICAL: + prefix_prefix: CTD.CHEMICAL + prefix_reference: http://ctdbase.org/detail.go?type=chem&acc= + CTD.DISEASE: + prefix_prefix: CTD.DISEASE + prefix_reference: http://ctdbase.org/detail.go?type=disease&db=MESH&acc= + CTD.GENE: + prefix_prefix: CTD.GENE + prefix_reference: http://ctdbase.org/detail.go?type=gene&acc= + CTD: + prefix_prefix: CTD + prefix_reference: http://ctdbase.org/ + DGIdb: + prefix_prefix: DGIdb + prefix_reference: https://www.dgidb.org/interaction_types + dcat: + prefix_prefix: dcat + prefix_reference: http://www.w3.org/ns/dcat# + dct: + prefix_prefix: dct + prefix_reference: http://purl.org/dc/terms/ + dcid: + prefix_prefix: dcid + prefix_reference: https://datacommons.org/browser/ + doi: + prefix_prefix: doi + prefix_reference: https://doi.org/ + DOID-PROPERTY: + prefix_prefix: DOID-PROPERTY + prefix_reference: http://purl.obolibrary.org/obo/doid# + DrugCentral: + prefix_prefix: DrugCentral + prefix_reference: http://drugcentral.org/drugcard/ + ECTO: + prefix_prefix: ECTO + prefix_reference: http://purl.obolibrary.org/obo/ECTO_ + EDAM-DATA: + prefix_prefix: EDAM-DATA + prefix_reference: http://edamontology.org/data_ + EDAM-FORMAT: + prefix_prefix: EDAM-FORMAT + prefix_reference: http://edamontology.org/format_ + EDAM-OPERATION: + prefix_prefix: EDAM-OPERATION + prefix_reference: http://edamontology.org/operation_ + EDAM-TOPIC: + prefix_prefix: EDAM-TOPIC + prefix_reference: http://edamontology.org/topic_ + EFO: + prefix_prefix: EFO + prefix_reference: http://www.ebi.ac.uk/efo/EFO_ + ExO: + prefix_prefix: ExO + prefix_reference: http://purl.obolibrary.org/obo/ExO_ + fabio: + prefix_prefix: fabio + prefix_reference: http://purl.org/spar/fabio/ + foaf: + prefix_prefix: foaf + prefix_reference: http://xmlns.com/foaf/0.1/ + foodb.compound: + prefix_prefix: foodb.compound + prefix_reference: http://foodb.ca/compounds/ + foodb.food: + prefix_prefix: foodb.food + prefix_reference: http://foodb.ca/foods/ + FYECO: + prefix_prefix: FYECO + prefix_reference: https://www.pombase.org/term/ + FYPO: + prefix_prefix: FYPO + prefix_reference: http://purl.obolibrary.org/obo/FYPO_ + gff3: + prefix_prefix: gff3 + prefix_reference: https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md# + GOREL: + prefix_prefix: GOREL + prefix_reference: http://purl.obolibrary.org/obo/GOREL_ + GOP: + prefix_prefix: GOP + prefix_reference: http://purl.obolibrary.org/obo/go# + gpi: + prefix_prefix: gpi + prefix_reference: https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md# + GSID: + prefix_prefix: GSID + prefix_reference: https://scholar.google.com/citations?user= + GTEx: + prefix_prefix: GTEx + prefix_reference: https://www.gtexportal.org/home/gene/ + GTOPDB: + prefix_prefix: GTOPDB + prefix_reference: https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId= + gtpo: + prefix_prefix: gtpo + prefix_reference: https://rdf.guidetopharmacology.org/ns/gtpo# + HANCESTRO: + prefix_prefix: HANCESTRO + prefix_reference: http://www.ebi.ac.uk/ancestro/ancestro_ + HCPCS: + prefix_prefix: HCPCS + prefix_reference: http://purl.bioontology.org/ontology/HCPCS/ + HsapDv: + prefix_prefix: HsapDv + prefix_reference: http://purl.obolibrary.org/obo/HsapDv_ + ICD10: + prefix_prefix: ICD10 + prefix_reference: https://icd.codes/icd9cm/ + ICD9: + prefix_prefix: ICD9 + prefix_reference: http://translator.ncats.nih.gov/ICD9_ + interpro: + prefix_prefix: interpro + prefix_reference: https://www.ebi.ac.uk/interpro/entry/ + INO: + prefix_prefix: INO + prefix_reference: http://purl.obolibrary.org/obo/INO_ + isbn: + prefix_prefix: isbn + prefix_reference: https://www.isbn-international.org/identifier/ + isni: + prefix_prefix: isni + prefix_reference: https://isni.org/isni/ + issn: + prefix_prefix: issn + prefix_reference: https://portal.issn.org/resource/ISSN/ + ncats.drug: + prefix_prefix: ncats.drug + prefix_reference: https://drugs.ncats.io/drug/ + KEGG.BRITE: + prefix_prefix: KEGG.BRITE + prefix_reference: 'https://bioregistry.io/kegg.brite:' + KEGG: + prefix_prefix: KEGG + prefix_reference: http://www.kegg.jp/entry/ + KEGG.GENES: + prefix_prefix: KEGG.GENES + prefix_reference: 'https://bioregistry.io/kegg.genes:bsu:' + KEGG.PATHWAY: + prefix_prefix: KEGG.PATHWAY + prefix_reference: 'https://bioregistry.io/kegg.pathway:' + KEGG.RCLASS: + prefix_prefix: KEGG.RCLASS + prefix_reference: 'https://www.genome.jp/dbget-bin/www_bget?rc:' + LOINC: + prefix_prefix: LOINC + prefix_reference: http://loinc.org/rdf/ + MAXO: + prefix_prefix: MAXO + prefix_reference: http://purl.obolibrary.org/obo/MAXO_ + medgen: + prefix_prefix: medgen + prefix_reference: https://www.ncbi.nlm.nih.gov/medgen/ + metacyc.reaction: + prefix_prefix: metacyc.reaction + prefix_reference: 'http://identifiers.org/metacyc.reaction:' + METANETX.REACTION: + prefix_prefix: METANETX.REACTION + prefix_reference: https://www.metanetx.org/equa_info/ + MESH: + prefix_prefix: MESH + prefix_reference: http://id.nlm.nih.gov/mesh/ + MI: + prefix_prefix: MI + prefix_reference: http://purl.obolibrary.org/obo/MI_ + mirbase: + prefix_prefix: mirbase + prefix_reference: http://identifiers.org/mirbase + mmmp.biomaps: + prefix_prefix: mmmp.biomaps + prefix_reference: 'https://bioregistry.io/mmmp.biomaps:' + MmusDv: + prefix_prefix: MmusDv + prefix_reference: http://purl.obolibrary.org/obo/MMUSDV_ + MSigDB: + prefix_prefix: MSigDB + prefix_reference: https://www.gsea-msigdb.org/gsea/msigdb/ + NBO-PROPERTY: + prefix_prefix: NBO-PROPERTY + prefix_reference: http://purl.obolibrary.org/obo/nbo# + ncats.bioplanet: + prefix_prefix: ncats.bioplanet + prefix_reference: https://tripod.nih.gov/bioplanet/detail.jsp?pid= + NCBIGene: + prefix_prefix: NCBIGene + prefix_reference: http://identifiers.org/ncbigene/ + NCIT-OBO: + prefix_prefix: NCIT-OBO + prefix_reference: http://purl.obolibrary.org/obo/ncit# + NDDF: + prefix_prefix: NDDF + prefix_reference: http://purl.bioontology.org/ontology/NDDF/ + NLMID: + prefix_prefix: NLMID + prefix_reference: https://www.ncbi.nlm.nih.gov/nlmcatalog/?term= + OBAN: + prefix_prefix: OBAN + prefix_reference: http://purl.org/oban/ + OMIM.PS: + prefix_prefix: OMIM.PS + prefix_reference: https://www.omim.org/phenotypicSeries/ + ORCID: + prefix_prefix: ORCID + prefix_reference: https://orcid.org/ + orphanet: + prefix_prefix: orphanet + prefix_reference: http://www.orpha.net/ORDO/Orphanet_ + os: + prefix_prefix: os + prefix_reference: https://github.com/cmungall/owlstar/blob/master/owlstar.ttl + PANTHER.FAMILY: + prefix_prefix: PANTHER.FAMILY + prefix_reference: http://www.pantherdb.org/panther/family.do?clsAccession= + PathWhiz: + prefix_prefix: PathWhiz + prefix_reference: http://smpdb.ca/pathways/# + pav: + prefix_prefix: pav + prefix_reference: http://purl.org/pav/ + PHARMGKB.CHEMICAL: + prefix_prefix: PHARMGKB.CHEMICAL + prefix_reference: https://www.pharmgkb.org/chemical/ + PHARMGKB.DISEASE: + prefix_prefix: PHARMGKB.DISEASE + prefix_reference: https://www.pharmgkb.org/disease/ + PHARMGKB.GENE: + prefix_prefix: PHARMGKB.GENE + prefix_reference: https://www.pharmgkb.org/gene/ + PHARMGKB.PATHWAYS: + prefix_prefix: PHARMGKB.PATHWAYS + prefix_reference: https://www.pharmgkb.org/pathway/ + PHARMGKB.VARIANT: + prefix_prefix: PHARMGKB.VARIANT + prefix_reference: https://www.pharmgkb.org/variant/ + PHAROS: + prefix_prefix: PHAROS + prefix_reference: http://pharos.nih.gov + PomBase: + prefix_prefix: PomBase + prefix_reference: https://www.pombase.org/gene/ + prov: + prefix_prefix: prov + prefix_reference: http://www.w3.org/ns/prov# + qud: + prefix_prefix: qud + prefix_reference: http://qudt.org/1.1/schema/qudt# + REPODB: + prefix_prefix: REPODB + prefix_reference: http://apps.chiragjpgroup.org/repoDB/ + ResearchID: + prefix_prefix: ResearchID + prefix_reference: https://publons.com/researcher/ + RO: + prefix_prefix: RO + prefix_reference: http://purl.obolibrary.org/obo/RO_ + RXNORM: + prefix_prefix: RXNORM + prefix_reference: http://purl.bioontology.org/ontology/RXNORM/ + RXCUI: + prefix_prefix: RXCUI + prefix_reference: https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm= + schema: + prefix_prefix: schema + prefix_reference: http://schema.org/ + ScopusID: + prefix_prefix: ScopusID + prefix_reference: https://www.scopus.com/authid/detail.uri?authorId= + SEED.REACTION: + prefix_prefix: SEED.REACTION + prefix_reference: https://modelseed.org/biochem/reactions/ + SEMMEDDB: + prefix_prefix: SEMMEDDB + prefix_reference: https://skr3.nlm.nih.gov/SemMedDB + SIO: + prefix_prefix: SIO + prefix_reference: http://semanticscience.org/resource/SIO_ + SNOMEDCT: + prefix_prefix: SNOMEDCT + prefix_reference: http://snomed.info/id/ + SPDI: + prefix_prefix: SPDI + prefix_reference: https://api.ncbi.nlm.nih.gov/variation/v0/spdi/ + UBERGRAPH: + prefix_prefix: UBERGRAPH + prefix_reference: http://translator.renci.org/ubergraph-axioms.ofn# + UBERON_CORE: + prefix_prefix: UBERON_CORE + prefix_reference: http://purl.obolibrary.org/obo/uberon/core# + UBERON_NONAMESPACE: + prefix_prefix: UBERON_NONAMESPACE + prefix_reference: http://purl.obolibrary.org/obo/core# + STY: + prefix_prefix: STY + prefix_reference: http://purl.bioontology.org/ontology/STY/ + UMLSSG: + prefix_prefix: UMLSSG + prefix_reference: https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt + UniProtKB: + prefix_prefix: UniProtKB + prefix_reference: http://purl.uniprot.org/uniprot/ + UNIPROT.ISOFORM: + prefix_prefix: UNIPROT.ISOFORM + prefix_reference: http://purl.uniprot.org/isoforms/ + VANDF: + prefix_prefix: VANDF + prefix_reference: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/ + UO-PROPERTY: + prefix_prefix: UO-PROPERTY + prefix_reference: http://purl.obolibrary.org/obo/uo# + VMC: + prefix_prefix: VMC + prefix_reference: https://github.com/ga4gh/vr-spec/ + WBls: + prefix_prefix: WBls + prefix_reference: http://purl.obolibrary.org/obo/WBls_ + WBbt: + prefix_prefix: WBbt + prefix_reference: http://purl.obolibrary.org/obo/WBbt_ + WBVocab: + prefix_prefix: WBVocab + prefix_reference: http://bio2rdf.org/wormbase_vocabulary + WIKIDATA: + prefix_prefix: WIKIDATA + prefix_reference: https://www.wikidata.org/entity/ + WIKIDATA_PROPERTY: + prefix_prefix: WIKIDATA_PROPERTY + prefix_reference: https://www.wikidata.org/prop/ + wgs: + prefix_prefix: wgs + prefix_reference: http://www.w3.org/2003/01/geo/wgs84_pos + XPO: + prefix_prefix: XPO + prefix_reference: http://purl.obolibrary.org/obo/XPO_ + Xenbase: + prefix_prefix: Xenbase + prefix_reference: http://www.xenbase.org/gene/showgene.do?method=display&geneId= + PMC: + prefix_prefix: PMC + prefix_reference: http://europepmc.org/articles/PMC +emit_prefixes: +- rdf +- rdfs +- xsd +- skos +- oboInOwl +- BIOGRID +- SO +default_curi_maps: +- obo_context +- idot_context +- monarch_context +- semweb_context +default_prefix: biolink +default_range: string +subsets: + model_organism_database: + name: model_organism_database + definition_uri: https://w3id.org/biolink/vocab/ModelOrganismDatabase + description: Subset that is relevant for a typical Model Organism Database (MOD) + from_schema: https://w3id.org/biolink/biolink-model + translator_minimal: + name: translator_minimal + definition_uri: https://w3id.org/biolink/vocab/TranslatorMinimal + description: Minimum subset of translator work + from_schema: https://w3id.org/biolink/biolink-model + samples: + name: samples + definition_uri: https://w3id.org/biolink/vocab/Samples + description: Sample/biosample datamodel + from_schema: https://w3id.org/biolink/biolink-model + testing: + name: testing + definition_uri: https://w3id.org/biolink/vocab/Testing + description: TBD + from_schema: https://w3id.org/biolink/biolink-model +types: + chemical formula value: + name: chemical formula value + definition_uri: https://w3id.org/biolink/vocab/ChemicalFormulaValue + description: A chemical formula + notes: + - Should be implemented as a stronger type + from_schema: https://w3id.org/biolink/biolink-model + base: str + uri: xsd:string + iri type: + name: iri type + definition_uri: https://w3id.org/biolink/vocab/IriType + description: An IRI + from_schema: https://w3id.org/biolink/biolink-model + typeof: uriorcurie + base: URIorCURIE + uri: xsd:anyURI + repr: str + label type: + name: label type + definition_uri: https://w3id.org/biolink/vocab/LabelType + description: A string that provides a human-readable name for an entity + from_schema: https://w3id.org/biolink/biolink-model + typeof: string + base: str + uri: xsd:string + predicate type: + name: predicate type + definition_uri: https://w3id.org/biolink/vocab/PredicateType + description: A CURIE from the biolink related_to hierarchy. For example, biolink:related_to, + biolink:causes, biolink:treats. + from_schema: https://w3id.org/biolink/biolink-model + typeof: uriorcurie + base: URIorCURIE + uri: xsd:anyURI + repr: str + narrative text: + name: narrative text + definition_uri: https://w3id.org/biolink/vocab/NarrativeText + description: A string that provides a human-readable description of something + from_schema: https://w3id.org/biolink/biolink-model + typeof: string + base: str + uri: xsd:string + symbol type: + name: symbol type + definition_uri: https://w3id.org/biolink/vocab/SymbolType + from_schema: https://w3id.org/biolink/biolink-model + typeof: string + base: str + uri: xsd:string + frequency value: + name: frequency value + definition_uri: https://w3id.org/biolink/vocab/FrequencyValue + from_schema: https://w3id.org/biolink/biolink-model + typeof: string + base: str + uri: UO:0000105 + percentage frequency value: + name: percentage frequency value + definition_uri: https://w3id.org/biolink/vocab/PercentageFrequencyValue + from_schema: https://w3id.org/biolink/biolink-model + typeof: double + base: float + uri: UO:0000187 + quotient: + name: quotient + definition_uri: https://w3id.org/biolink/vocab/Quotient + from_schema: https://w3id.org/biolink/biolink-model + aliases: + - ratio + typeof: double + base: float + uri: UO:0010006 + unit: + name: unit + id_prefixes: + - UO + definition_uri: https://w3id.org/biolink/vocab/Unit + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - qud:Unit + typeof: string + base: str + uri: UO:0000000 + time type: + name: time type + definition_uri: https://w3id.org/biolink/vocab/TimeType + from_schema: https://w3id.org/biolink/biolink-model + typeof: time + base: XSDTime + uri: xsd:time + repr: str + biological sequence: + name: biological sequence + definition_uri: https://w3id.org/biolink/vocab/BiologicalSequence + from_schema: https://w3id.org/biolink/biolink-model + typeof: string + base: str + uri: xsd:string + string: + name: string + definition_uri: https://w3id.org/linkml/String + description: A character string + notes: + - In RDF serializations, a slot with range of string is treated as a literal or + type xsd:string. If you are authoring schemas in LinkML YAML, the type is + referenced with the lower case "string". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + exact_mappings: + - schema:Text + base: str + uri: xsd:string + integer: + name: integer + definition_uri: https://w3id.org/linkml/Integer + description: An integer + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "integer". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + exact_mappings: + - schema:Integer + base: int + uri: xsd:integer + boolean: + name: boolean + definition_uri: https://w3id.org/linkml/Boolean + description: A binary (true or false) value + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "boolean". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + exact_mappings: + - schema:Boolean + base: Bool + uri: xsd:boolean + repr: bool + float: + name: float + definition_uri: https://w3id.org/linkml/Float + description: A real number that conforms to the xsd:float specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "float". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + exact_mappings: + - schema:Float + base: float + uri: xsd:float + double: + name: double + definition_uri: https://w3id.org/linkml/Double + description: A real number that conforms to the xsd:double specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "double". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + close_mappings: + - schema:Float + base: float + uri: xsd:double + decimal: + name: decimal + definition_uri: https://w3id.org/linkml/Decimal + description: A real number with arbitrary precision that conforms to the xsd:decimal + specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "decimal". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + broad_mappings: + - schema:Number + base: Decimal + uri: xsd:decimal + time: + name: time + definition_uri: https://w3id.org/linkml/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 + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "time". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + exact_mappings: + - schema:Time + base: XSDTime + uri: xsd:time + repr: str + date: + name: date + definition_uri: https://w3id.org/linkml/Date + description: a date (year, month and day) in an idealized calendar + notes: + - URI is dateTime because OWL reasoners don't work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + exact_mappings: + - schema:Date + base: XSDDate + uri: xsd:date + repr: str + datetime: + name: datetime + definition_uri: https://w3id.org/linkml/Datetime + description: The combination of a date and time + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "datetime". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + exact_mappings: + - schema:DateTime + base: XSDDateTime + uri: xsd:dateTime + repr: str + date_or_datetime: + name: date_or_datetime + definition_uri: https://w3id.org/linkml/DateOrDatetime + description: Either a date or a datetime + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date_or_datetime". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + base: str + uri: linkml:DateOrDatetime + repr: str + uriorcurie: + name: uriorcurie + definition_uri: https://w3id.org/linkml/Uriorcurie + description: a URI or a CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uriorcurie". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + base: URIorCURIE + uri: xsd:anyURI + repr: str + curie: + name: curie + definition_uri: https://w3id.org/linkml/Curie + conforms_to: https://www.w3.org/TR/curie/ + description: a compact URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "curie". + comments: + - in RDF serializations this MUST be expanded to a URI + - in non-RDF serializations MAY be serialized as the compact representation + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + base: Curie + uri: xsd:string + repr: str + uri: + name: uri + definition_uri: https://w3id.org/linkml/Uri + conforms_to: https://www.ietf.org/rfc/rfc3987.txt + description: a complete URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uri". + comments: + - in RDF serializations a slot with range of uri is treated as a literal or type + xsd:anyURI unless it is an identifier or a reference to an identifier, in which + case it is translated directly to a node + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + close_mappings: + - schema:URL + base: URI + uri: xsd:anyURI + repr: str + ncname: + name: ncname + definition_uri: https://w3id.org/linkml/Ncname + description: Prefix part of CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "ncname". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + base: NCName + uri: xsd:string + repr: str + objectidentifier: + name: objectidentifier + definition_uri: https://w3id.org/linkml/Objectidentifier + description: A URI or CURIE that represents an object in the model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "objectidentifier". + comments: + - Used for inheritance and type checking + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + base: ElementIdentifier + uri: shex:iri + repr: str + nodeidentifier: + name: nodeidentifier + definition_uri: https://w3id.org/linkml/Nodeidentifier + description: A URI, CURIE or BNODE that represents a node in a model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "nodeidentifier". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + base: NodeIdentifier + uri: shex:nonLiteral + repr: str + jsonpointer: + name: jsonpointer + definition_uri: https://w3id.org/linkml/Jsonpointer + conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 + description: A string encoding a JSON Pointer. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to a valid object within the current + instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpointer". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + base: str + uri: xsd:string + repr: str + jsonpath: + name: jsonpath + definition_uri: https://w3id.org/linkml/Jsonpath + conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html + description: A string encoding a JSON Path. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to zero or more valid objects within + the current instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpath". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + base: str + uri: xsd:string + repr: str + sparqlpath: + name: sparqlpath + definition_uri: https://w3id.org/linkml/Sparqlpath + conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths + description: A string encoding a SPARQL Property Path. The value of the string + MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects + within the current instance document when encoded as RDF. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "sparqlpath". + from_schema: https://w3id.org/linkml/types + imported_from: linkml:types + base: str + uri: xsd:string + repr: str +slots: + has attribute: + name: has attribute + definition_uri: https://w3id.org/biolink/vocab/has_attribute + description: connects any entity to an attribute + in_subset: + - samples + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - SIO:000008 + close_mappings: + - OBI:0001927 + narrow_mappings: + - OBAN:association_has_subject_property + - OBAN:association_has_object_property + - CPT:has_possibly_included_panel_element + - DRUGBANK:category + - EFO:is_executed_in + - HANCESTRO:0301 + - LOINC:has_action_guidance + - LOINC:has_adjustment + - LOINC:has_aggregation_view + - LOINC:has_approach_guidance + - LOINC:has_divisor + - LOINC:has_exam + - LOINC:has_method + - LOINC:has_modality_subtype + - LOINC:has_object_guidance + - LOINC:has_scale + - LOINC:has_suffix + - LOINC:has_time_aspect + - LOINC:has_time_modifier + - LOINC:has_timing_of + - NCIT:R88 + - NCIT:eo_disease_has_property_or_attribute + - NCIT:has_data_element + - NCIT:has_pharmaceutical_administration_method + - NCIT:has_pharmaceutical_basic_dose_form + - NCIT:has_pharmaceutical_intended_site + - NCIT:has_pharmaceutical_release_characteristics + - NCIT:has_pharmaceutical_state_of_matter + - NCIT:has_pharmaceutical_transformation + - NCIT:is_qualified_by + - NCIT:qualifier_applies_to + - NCIT:role_has_domain + - NCIT:role_has_range + - INO:0000154 + - HANCESTRO:0308 + - OMIM:has_inheritance_type + - orphanet:C016 + - orphanet:C017 + - RO:0000053 + - RO:0000086 + - RO:0000087 + - SNOMED:has_access + - SNOMED:has_clinical_course + - SNOMED:has_count_of_base_of_active_ingredient + - SNOMED:has_dose_form_administration_method + - SNOMED:has_dose_form_release_characteristic + - SNOMED:has_dose_form_transformation + - SNOMED:has_finding_context + - SNOMED:has_finding_informer + - SNOMED:has_inherent_attribute + - SNOMED:has_intent + - SNOMED:has_interpretation + - SNOMED:has_laterality + - SNOMED:has_measurement_method + - SNOMED:has_method + - SNOMED:has_priority + - SNOMED:has_procedure_context + - SNOMED:has_process_duration + - SNOMED:has_property + - SNOMED:has_revision_status + - SNOMED:has_scale_type + - SNOMED:has_severity + - SNOMED:has_specimen + - SNOMED:has_state_of_matter + - SNOMED:has_subject_relationship_context + - SNOMED:has_surgical_approach + - SNOMED:has_technique + - SNOMED:has_temporal_context + - SNOMED:has_time_aspect + - SNOMED:has_units + - UMLS:has_structural_class + - UMLS:has_supported_concept_property + - UMLS:has_supported_concept_relationship + - UMLS:may_be_qualified_by + domain: entity + slot_uri: biolink:has_attribute + multivalued: true + owner: entity + domain_of: + - entity + range: attribute + has attribute type: + name: has attribute type + definition_uri: https://w3id.org/biolink/vocab/has_attribute_type + description: connects an attribute to a class that describes it + in_subset: + - samples + from_schema: https://w3id.org/biolink/biolink-model + narrow_mappings: + - LOINC:has_modality_type + - LOINC:has_view_type + domain: attribute + slot_uri: biolink:has_attribute_type + multivalued: false + owner: attribute + domain_of: + - attribute + range: ontology class + required: true + has qualitative value: + name: has qualitative value + definition_uri: https://w3id.org/biolink/vocab/has_qualitative_value + description: connects an attribute to a value + in_subset: + - samples + from_schema: https://w3id.org/biolink/biolink-model + domain: attribute + slot_uri: biolink:has_qualitative_value + multivalued: false + owner: attribute + domain_of: + - attribute + range: named thing + has quantitative value: + name: has quantitative value + definition_uri: https://w3id.org/biolink/vocab/has_quantitative_value + description: connects an attribute to a value + in_subset: + - samples + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - qud:quantityValue + narrow_mappings: + - SNOMED:has_concentration_strength_numerator_value + - SNOMED:has_presentation_strength_denominator_value + - SNOMED:has_presentation_strength_numerator_value + domain: attribute + slot_uri: biolink:has_quantitative_value + multivalued: true + owner: attribute + domain_of: + - attribute + range: quantity value + inlined: true + has numeric value: + name: has numeric value + definition_uri: https://w3id.org/biolink/vocab/has_numeric_value + description: connects a quantity value to a number + in_subset: + - samples + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - qud:quantityValue + domain: quantity value + slot_uri: biolink:has_numeric_value + multivalued: false + owner: quantity value + domain_of: + - quantity value + range: double + has unit: + name: has unit + definition_uri: https://w3id.org/biolink/vocab/has_unit + description: connects a quantity value to a unit + in_subset: + - samples + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - qud:unit + - IAO:0000039 + close_mappings: + - EFO:0001697 + - UO-PROPERTY:is_unit_of + narrow_mappings: + - SNOMED:has_concentration_strength_denominator_unit + - SNOMED:has_concentration_strength_numerator_unit + - SNOMED:has_presentation_strength_denominator_unit + - SNOMED:has_presentation_strength_numerator_unit + - SNOMED:has_unit_of_presentation + domain: quantity value + slot_uri: biolink:has_unit + multivalued: false + owner: quantity value + domain_of: + - quantity value + range: unit + node property: + name: node property + definition_uri: https://w3id.org/biolink/vocab/node_property + description: A grouping for any property that holds between a node and a value + from_schema: https://w3id.org/biolink/biolink-model + domain: named thing + slot_uri: biolink:node_property + owner: node property + range: string + id: + name: id + definition_uri: https://w3id.org/biolink/vocab/id + description: A unique identifier for an entity. Must be either a CURIE shorthand + for a URI or a complete URI + in_subset: + - translator_minimal + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - AGRKB:primaryId + - gff3:ID + - gpi:DB_Object_ID + domain: entity + slot_uri: biolink:id + identifier: true + owner: entity + domain_of: + - ontology class + - entity + range: string + required: true + iri: + name: iri + definition_uri: https://w3id.org/biolink/vocab/iri + description: An IRI for an entity. This is determined by the id using expansion + rules. + in_subset: + - translator_minimal + - samples + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - WIKIDATA_PROPERTY:P854 + slot_uri: biolink:iri + owner: entity + domain_of: + - attribute + - entity + range: iri type + type: + name: type + definition_uri: https://w3id.org/biolink/vocab/type + from_schema: https://w3id.org/biolink/biolink-model + mappings: + - rdf:type + exact_mappings: + - gff3:type + - gpi:DB_Object_Type + domain: entity + slot_uri: rdf:type + multivalued: true + owner: entity + domain_of: + - entity + range: string + category: + name: category + definition_uri: https://w3id.org/biolink/vocab/category + description: Name of the high level ontology class in which this entity is categorized. + Corresponds to the label for the biolink entity type class. In a neo4j database + this MAY correspond to the neo4j label tag. In an RDF database it should be + a biolink model class URI. This field is multi-valued. It should include values + for ancestors of the biolink class; for example, a protein such as Shh would + have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. + In an RDF database, nodes will typically have an rdf:type triples. This can + be to the most specific biolink class, or potentially to a class more specific + than something in biolink. For example, a sequence feature `f` may have a rdf:type + assertion to a SO class such as TF_binding_site, which is more specific than + anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, + biolink:NamedThing} + in_subset: + - translator_minimal + from_schema: https://w3id.org/biolink/biolink-model + is_a: type + domain: entity + slot_uri: biolink:category + multivalued: true + designates_type: true + owner: entity + domain_of: + - entity + is_class_field: true + range: uriorcurie + name: + name: name + definition_uri: https://w3id.org/biolink/vocab/name + description: A human-readable name for an attribute or entity. + in_subset: + - translator_minimal + - samples + from_schema: https://w3id.org/biolink/biolink-model + aliases: + - label + - display name + - title + mappings: + - rdfs:label + exact_mappings: + - gff3:Name + - gpi:DB_Object_Name + narrow_mappings: + - dct:title + - WIKIDATA_PROPERTY:P1476 + domain: entity + slot_uri: rdfs:label + owner: macromolecular machine mixin + domain_of: + - attribute + - entity + - macromolecular machine mixin + range: label type + symbol: + name: symbol + definition_uri: https://w3id.org/biolink/vocab/symbol + description: Symbol for a particular thing + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - AGRKB:symbol + - gpi:DB_Object_Symbol + is_a: node property + domain: named thing + slot_uri: biolink:symbol + owner: symbol + domain_of: + - gene + range: string + synonym: + name: synonym + definition_uri: https://w3id.org/biolink/vocab/synonym + description: Alternate human-readable names for a thing + in_subset: + - translator_minimal + from_schema: https://w3id.org/biolink/biolink-model + aliases: + - alias + narrow_mappings: + - skos:altLabel + - gff3:Alias + - AGRKB:synonyms + - gpi:DB_Object_Synonyms + - HANCESTRO:0330 + - IAO:0000136 + - RXNORM:has_tradename + is_a: node property + domain: named thing + slot_uri: biolink:synonym + multivalued: true + owner: named thing + domain_of: + - named thing + range: label type + deprecated: + name: deprecated + definition_uri: https://w3id.org/biolink/vocab/deprecated + description: A boolean flag indicating that an entity is no longer considered + current or valid. + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - oboInOwl:ObsoleteClass + slot_uri: biolink:deprecated + owner: entity + domain_of: + - entity + range: boolean + xref: + name: xref + definition_uri: https://w3id.org/biolink/vocab/xref + description: A database cross reference or alternative identifier for a NamedThing + or edge between two NamedThings. This property should point to a database record + or webpage that supports the existence of the edge, or gives more detail about + the edge. This property can be used on a node or edge to provide multiple URIs + or CURIE cross references. + in_subset: + - translator_minimal + from_schema: https://w3id.org/biolink/biolink-model + aliases: + - dbxref + - Dbxref + - DbXref + - record_url + - source_record_urls + narrow_mappings: + - gff3:Dbxref + - gpi:DB_Xrefs + domain: named thing + slot_uri: biolink:xref + multivalued: true + owner: gene + domain_of: + - named thing + - gene + range: uriorcurie + full name: + name: full name + definition_uri: https://w3id.org/biolink/vocab/full_name + description: a long-form human readable name for a thing + from_schema: https://w3id.org/biolink/biolink-model + is_a: node property + domain: named thing + slot_uri: biolink:full_name + owner: named thing + domain_of: + - named thing + range: label type + description: + name: description + definition_uri: https://w3id.org/biolink/vocab/description + description: a human-readable description of an entity + in_subset: + - translator_minimal + from_schema: https://w3id.org/biolink/biolink-model + aliases: + - definition + mappings: + - dct:description + exact_mappings: + - IAO:0000115 + - skos:definitions + narrow_mappings: + - gff3:Description + slot_uri: dct:description + owner: entity + domain_of: + - entity + range: narrative text + has taxonomic rank: + name: has taxonomic rank + definition_uri: https://w3id.org/biolink/vocab/has_taxonomic_rank + from_schema: https://w3id.org/biolink/biolink-model + mappings: + - WIKIDATA:P105 + is_a: node property + domain: named thing + slot_uri: biolink:has_taxonomic_rank + multivalued: false + owner: organism taxon + domain_of: + - organism taxon + range: taxonomic rank + has biological sequence: + name: has biological sequence + definition_uri: https://w3id.org/biolink/vocab/has_biological_sequence + description: connects a genomic feature to its sequence + from_schema: https://w3id.org/biolink/biolink-model + is_a: node property + domain: named thing + slot_uri: biolink:has_biological_sequence + owner: genomic entity + domain_of: + - genomic entity + range: biological sequence + related to: + name: related to + definition_uri: https://w3id.org/biolink/vocab/related_to + annotations: + canonical_predicate: + tag: canonical_predicate + value: true + description: A relationship that is asserted between two named things + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - UMLS:related_to + narrow_mappings: + - SEMMEDDB:compared_with + - SEMMEDDB:higher_than + - SEMMEDDB:lower_than + - BFO:0000054 + - UBERON_CORE:protects + - GOREL:0002005 + - GOREL:0012006 + - BTO:related_to + - CHEBI:is_conjugate_acid_of + - CHEBI:is_conjugate_base_of + - CPT:has_add_on_code + - CPT:mapped_to + - EFO:0006351 + - FMA:connected_to + - FMA:continuous_with + - FMA:homonym_of + - FMA:related_developmental_entity_of + - RO:0002093 + - RO:0002092 + - RO:0002084 + - HCPCS:mapped_to + - HMDB:disease + - HMDB:has_protein_association + - IAO:0000136 + - LOINC:has_answer + - LOINC:has_challenge + - LOINC:has_evaluation + - LOINC:mapped_to + - LOINC:mth_has_expanded_form + - MESH:RO + - MESH:has_mapping_qualifier + - MESH:mapped_to + - MONDO:disease_shares_features_of + - NCIT:disease_may_have_associated_disease + - NCIT:human_disease_maps_to_eo_disease + - NCIT:is_abnormal_cell_of_disease + - NCIT:is_related_to_endogenous_product + - UBERON_NONAMESPACE:connected_to + - UBERON_NONAMESPACE:innervated_by + - NBO-PROPERTY:is_about + - RO:0000053 + - PATO:reciprocal_of + - RO:0000052 + - RO:0002001 + - RO:0002002 + - RO:0002003 + - RO:0002008 + - RO:0002134 + - RO:0002150 + - RO:0002159 + - RO:0002176 + - RO:0002177 + - RO:0002178 + - RO:0002179 + - RO:0002314 + - RO:0002322 + - RO:0002328 + - RO:0002332 + - RO:0002338 + - RO:0002339 + - RO:0002341 + - RO:0002342 + - RO:0002344 + - RO:0002348 + - RO:0002349 + - RO:0002356 + - RO:0002371 + - RO:0002372 + - RO:0002373 + - RO:0002374 + - RO:0002385 + - RO:0002387 + - RO:0002451 + - RO:0002494 + - RO:0002495 + - RO:0002568 + - RO:0002573 + - RO:0004026 + - RO:0004027 + - RO:0009001 + - RO:0009004 + - RXNORM:has_form + - RXNORM:reformulated_to + - SNOMED:has_associated_morphology + - SNOMED:has_associated_procedure + - SNOMED:has_direct_morphology + - SNOMED:has_disposition + - SNOMED:has_indirect_morphology + - SNOMED:has_modification + - SNOMED:has_procedure_morphology + - SNOMED:has_specimen_source_morphology + - SNOMED:inheres_in + - SNOMED:is_interpreted_by + - SNOMED:relative_to_part_of + - UBERON:synapsed_by + - UMLS:RO + - UMLS:RQ + - UMLS:class_code_classified_by + - UMLS:exhibited_by + - UMLS:has_context_binding + - UMLS:has_form + - UMLS:has_mapping_qualifier + - UMLS:larger_than + - UMLS:mapped_to + - UMLS:owning_section_of + broad_mappings: + - owl:topObjectProperty + domain: named thing + slot_uri: biolink:related_to + multivalued: true + inherited: true + owner: related to + symmetric: true + range: named thing + related to at instance level: + name: related to at instance level + definition_uri: https://w3id.org/biolink/vocab/related_to_at_instance_level + annotations: + canonical_predicate: + tag: canonical_predicate + value: true + description: Represents a relationship held between two instances of a data classes. Much + like an assertion component, in an ABox, these represent facts associated with + the conceptual model. + from_schema: https://w3id.org/biolink/biolink-model + is_a: related to + domain: named thing + slot_uri: biolink:related_to_at_instance_level + multivalued: true + inherited: true + owner: related to at instance level + symmetric: true + range: named thing + in taxon: + name: in taxon + definition_uri: https://w3id.org/biolink/vocab/in_taxon + annotations: + canonical_predicate: + tag: canonical_predicate + value: true + description: connects an entity to its taxonomic classification. Only certain + kinds of entities can be taxonomically classified; see 'thing with taxon' + in_subset: + - translator_minimal + from_schema: https://w3id.org/biolink/biolink-model + aliases: + - instance of + - is organism source of gene product + - organism has gene + - gene found in organism + - gene product has organism source + exact_mappings: + - RO:0002162 + - WIKIDATA_PROPERTY:P703 + narrow_mappings: + - RO:0002160 + is_a: related to at instance level + domain: thing with taxon + slot_uri: biolink:in_taxon + multivalued: true + inherited: true + owner: thing with taxon + domain_of: + - thing with taxon + range: organism taxon + in taxon label: + name: in taxon label + definition_uri: https://w3id.org/biolink/vocab/in_taxon_label + annotations: + denormalized: + tag: denormalized + value: true + description: The human readable scientific name for the taxon of the entity. + in_subset: + - translator_minimal + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - WIKIDATA_PROPERTY:P225 + is_a: node property + domain: thing with taxon + slot_uri: biolink:in_taxon_label + owner: thing with taxon + domain_of: + - thing with taxon + range: label type + provided by: + name: provided by + definition_uri: https://w3id.org/biolink/vocab/provided_by + description: The value in this node property represents the knowledge provider + that created or assembled the node and all of its attributes. Used internally + to represent how a particular node made its way into a knowledge provider or + graph. + from_schema: https://w3id.org/biolink/biolink-model + is_a: node property + domain: named thing + slot_uri: biolink:provided_by + multivalued: true + owner: named thing + domain_of: + - named thing + range: string + attribute_name: + name: attribute_name + definition_uri: https://w3id.org/biolink/vocab/name + description: The human-readable 'attribute name' can be set to a string which + reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence + annotation or it can default to the name associated with the 'has attribute + type' slot ontology term. + in_subset: + - translator_minimal + - samples + from_schema: https://w3id.org/biolink/biolink-model + aliases: + - label + - display name + - title + mappings: + - rdfs:label + exact_mappings: + - gff3:Name + - gpi:DB_Object_Name + narrow_mappings: + - dct:title + - WIKIDATA_PROPERTY:P1476 + is_a: name + domain: attribute + slot_uri: rdfs:label + alias: name + owner: attribute + domain_of: + - attribute + is_usage_slot: true + usage_slot_name: name + range: label type +classes: + ontology class: + name: ontology class + id_prefixes: + - MESH + - UMLS + - KEGG.BRITE + definition_uri: https://w3id.org/biolink/vocab/OntologyClass + description: a concept or class in an ontology, vocabulary or thesaurus. Note + that nodes in a biolink compatible KG can be considered both instances of biolink + classes, and OWL classes in their own right. In general you should not need + to use this class directly. Instead, use the appropriate biolink class. For + example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess + as the type. + comments: + - This is modeled as a mixin. 'ontology class' should not be the primary type + of a node in the KG. Instead you should use an informative bioloink category, + such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI + or CHEMBL), etc + - Note that formally this is a metaclass. Instances of this class are instances + in the graph, but can be the object of 'type' edges. For example, if we had + a node in the graph representing a specific brain of a specific patient (e.g + brain001), this could have a category of bl:Sample, and by typed more specifically + with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity + examples: + - value: UBERON:0000955 + description: the class 'brain' from the Uberon anatomy ontology + from_schema: https://w3id.org/biolink/biolink-model + see_also: + - https://github.com/biolink/biolink-model/issues/486 + exact_mappings: + - owl:Class + - schema:Class + mixin: true + slots: + - id + class_uri: biolink:OntologyClass + annotation: + name: annotation + definition_uri: https://w3id.org/biolink/vocab/Annotation + description: Biolink Model root class for entity annotations. + from_schema: https://w3id.org/biolink/biolink-model + abstract: true + class_uri: biolink:Annotation + quantity value: + name: quantity value + definition_uri: https://w3id.org/biolink/vocab/QuantityValue + description: A value of an attribute that is quantitative and measurable, expressed + as a combination of a unit and a numeric value + from_schema: https://w3id.org/biolink/biolink-model + is_a: annotation + slots: + - has unit + - has numeric value + class_uri: biolink:QuantityValue + attribute: + name: attribute + id_prefixes: + - EDAM-DATA + - EDAM-FORMAT + - EDAM-OPERATION + - EDAM-TOPIC + definition_uri: https://w3id.org/biolink/vocab/Attribute + description: A property or characteristic of an entity. For example, an apple + may have properties such as color, shape, age, crispiness. An environmental + sample may have attributes such as depth, lat, long, material. + in_subset: + - samples + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - SIO:000614 + is_a: named thing + mixins: + - ontology class + slots: + - id + - category + - type + - description + - has attribute + - deprecated + - provided by + - xref + - full name + - synonym + - attribute_name + - has attribute type + - has quantitative value + - has qualitative value + - iri + slot_usage: + name: + name: name + description: The human-readable 'attribute name' can be set to a string which + reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence + annotation or it can default to the name associated with the 'has attribute + type' slot ontology term. + class_uri: biolink:Attribute + entity: + name: entity + definition_uri: https://w3id.org/biolink/vocab/Entity + description: Root Biolink Model class for all things and informational relationships, + real or imagined. + from_schema: https://w3id.org/biolink/biolink-model + abstract: true + slots: + - id + - iri + - category + - type + - name + - description + - has attribute + - deprecated + class_uri: biolink:Entity + named thing: + name: named thing + definition_uri: https://w3id.org/biolink/vocab/NamedThing + description: a databased entity or concept/class + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - BFO:0000001 + - WIKIDATA:Q35120 + - UMLSSG:OBJC + - STY:T071 + - dcid:Thing + is_a: entity + slots: + - id + - iri + - category + - type + - name + - description + - has attribute + - deprecated + - provided by + - xref + - full name + - synonym + class_uri: biolink:NamedThing + taxonomic rank: + name: taxonomic rank + id_prefixes: + - TAXRANK + definition_uri: https://w3id.org/biolink/vocab/TaxonomicRank + description: 'A descriptor for the rank within a taxonomic classification. Example + instance: TAXRANK:0000017 (kingdom)' + from_schema: https://w3id.org/biolink/biolink-model + mappings: + - WIKIDATA:Q427626 + is_a: ontology class + slots: + - id + class_uri: biolink:TaxonomicRank + organism taxon: + name: organism taxon + id_prefixes: + - NCBITaxon + - MESH + - UMLS + definition_uri: https://w3id.org/biolink/vocab/OrganismTaxon + description: 'A classification of a set of organisms. Example instances: NCBITaxon:9606 + (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains + or subspecies.' + in_subset: + - model_organism_database + from_schema: https://w3id.org/biolink/biolink-model + aliases: + - taxon + - taxonomic classification + exact_mappings: + - WIKIDATA:Q16521 + - STY:T001 + - bioschemas:Taxon + narrow_mappings: + - dcid:BiologicalSpecies + is_a: named thing + values_from: + - NCBITaxon + slots: + - id + - iri + - category + - type + - name + - description + - has attribute + - deprecated + - provided by + - xref + - full name + - synonym + - has taxonomic rank + class_uri: biolink:OrganismTaxon + physical essence or occurrent: + name: physical essence or occurrent + definition_uri: https://w3id.org/biolink/vocab/PhysicalEssenceOrOccurrent + description: Either a physical or processual entity. + from_schema: https://w3id.org/biolink/biolink-model + mixin: true + class_uri: biolink:PhysicalEssenceOrOccurrent + physical essence: + name: physical essence + definition_uri: https://w3id.org/biolink/vocab/PhysicalEssence + description: Semantic mixin concept. Pertains to entities that have physical + properties such as mass, volume, or charge. + from_schema: https://w3id.org/biolink/biolink-model + is_a: physical essence or occurrent + mixin: true + class_uri: biolink:PhysicalEssence + physical entity: + name: physical entity + definition_uri: https://w3id.org/biolink/vocab/PhysicalEntity + description: An entity that has material reality (a.k.a. physical essence). + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - STY:T072 + narrow_mappings: + - STY:T073 + is_a: named thing + mixins: + - physical essence + slots: + - id + - iri + - category + - type + - name + - description + - has attribute + - deprecated + - provided by + - xref + - full name + - synonym + class_uri: biolink:PhysicalEntity + occurrent: + name: occurrent + definition_uri: https://w3id.org/biolink/vocab/Occurrent + description: A processual entity. + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - BFO:0000003 + is_a: physical essence or occurrent + mixin: true + class_uri: biolink:Occurrent + activity and behavior: + name: activity and behavior + definition_uri: https://w3id.org/biolink/vocab/ActivityAndBehavior + description: Activity or behavior of any independent integral living, organization + or mechanical actor in the world + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - UMLSSG:ACTI + is_a: occurrent + mixin: true + class_uri: biolink:ActivityAndBehavior + activity: + name: activity + definition_uri: https://w3id.org/biolink/vocab/Activity + description: An activity is something that occurs over a period of time and acts + upon or with entities; it may include consuming, processing, transforming, modifying, + relocating, using, or generating entities. + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - prov:Activity + - NCIT:C43431 + - STY:T052 + narrow_mappings: + - STY:T056 + - STY:T057 + - STY:T064 + - STY:T066 + - STY:T062 + - STY:T065 + - STY:T058 + is_a: named thing + mixins: + - activity and behavior + slots: + - id + - iri + - category + - type + - name + - description + - has attribute + - deprecated + - provided by + - xref + - full name + - synonym + class_uri: biolink:Activity + procedure: + name: procedure + id_prefixes: + - CPT + definition_uri: https://w3id.org/biolink/vocab/Procedure + description: A series of actions conducted in a certain order or manner + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - UMLSSG:PROC + - dcid:MedicalProcedure + narrow_mappings: + - STY:T059 + - STY:T060 + - STY:T061 + - STY:T063 + is_a: named thing + mixins: + - activity and behavior + slots: + - id + - iri + - category + - type + - name + - description + - has attribute + - deprecated + - provided by + - xref + - full name + - synonym + class_uri: biolink:Procedure + subject of investigation: + name: subject of investigation + definition_uri: https://w3id.org/biolink/vocab/SubjectOfInvestigation + description: An entity that has the role of being studied in an investigation, + study, or experiment + from_schema: https://w3id.org/biolink/biolink-model + mixin: true + class_uri: biolink:SubjectOfInvestigation + material sample: + name: material sample + id_prefixes: + - BIOSAMPLE + - GOLD.META + definition_uri: https://w3id.org/biolink/vocab/MaterialSample + description: A sample is a limited quantity of something (e.g. an individual or + set of individuals from a population, or a portion of a substance) to be used + for testing, analysis, inspection, investigation, demonstration, or trial use. + [SIO] + from_schema: https://w3id.org/biolink/biolink-model + aliases: + - biospecimen + - sample + - biosample + - physical sample + exact_mappings: + - OBI:0000747 + - SIO:001050 + is_a: physical entity + mixins: + - subject of investigation + slots: + - id + - iri + - category + - type + - name + - description + - has attribute + - deprecated + - provided by + - xref + - full name + - synonym + class_uri: biolink:MaterialSample + thing with taxon: + name: thing with taxon + definition_uri: https://w3id.org/biolink/vocab/ThingWithTaxon + description: A mixin that can be used on any entity that can be taxonomically + classified. This includes individual organisms; genes, their products and other + molecular entities; body parts; biological processes + from_schema: https://w3id.org/biolink/biolink-model + mixin: true + slots: + - in taxon + - in taxon label + class_uri: biolink:ThingWithTaxon + biological entity: + name: biological entity + definition_uri: https://w3id.org/biolink/vocab/BiologicalEntity + from_schema: https://w3id.org/biolink/biolink-model + aliases: + - bioentity + narrow_mappings: + - WIKIDATA:Q28845870 + - STY:T050 + - SIO:010046 + - STY:T129 + is_a: named thing + abstract: true + mixins: + - thing with taxon + slots: + - id + - iri + - category + - type + - name + - description + - has attribute + - deprecated + - provided by + - xref + - full name + - synonym + - in taxon + - in taxon label + class_uri: biolink:BiologicalEntity + genomic entity: + name: genomic entity + definition_uri: https://w3id.org/biolink/vocab/GenomicEntity + in_subset: + - translator_minimal + from_schema: https://w3id.org/biolink/biolink-model + narrow_mappings: + - STY:T028 + - GENO:0000897 + mixin: true + slots: + - has biological sequence + class_uri: biolink:GenomicEntity + chemical entity or gene or gene product: + name: chemical entity or gene or gene product + definition_uri: https://w3id.org/biolink/vocab/ChemicalEntityOrGeneOrGeneProduct + description: A union of chemical entities and children, and gene or gene product. + This mixin is helpful to use when searching across chemical entities that must + include genes and their children as chemical entities. + from_schema: https://w3id.org/biolink/biolink-model + mixin: true + class_uri: biolink:ChemicalEntityOrGeneOrGeneProduct + macromolecular machine mixin: + name: macromolecular machine mixin + definition_uri: https://w3id.org/biolink/vocab/MacromolecularMachineMixin + description: A union of gene locus, gene product, and macromolecular complex. + These are the basic units of function in a cell. They either carry out individual + biological activities, or they encode molecules which do this. + from_schema: https://w3id.org/biolink/biolink-model + mixin: true + slots: + - name + class_uri: biolink:MacromolecularMachineMixin + gene or gene product: + name: gene or gene product + id_prefixes: + - CHEMBL.TARGET + - IUPHAR.FAMILY + definition_uri: https://w3id.org/biolink/vocab/GeneOrGeneProduct + description: A union of gene loci or gene products. Frequently an identifier for + one will be used as proxy for another + from_schema: https://w3id.org/biolink/biolink-model + is_a: macromolecular machine mixin + mixin: true + slots: + - name + class_uri: biolink:GeneOrGeneProduct + gene: + name: gene + id_prefixes: + - NCBIGene + - ENSEMBL + - HGNC + - MGI + - ZFIN + - dictyBase + - WB + - WormBase + - FB + - RGD + - SGD + - PomBase + - OMIM + - KEGG.GENES + - UMLS + - Xenbase + - AspGD + - PHARMGKB.GENE + definition_uri: https://w3id.org/biolink/vocab/Gene + description: A region (or regions) that includes all of the sequence elements + necessary to encode a functional transcript. A gene locus may include regulatory + regions, transcribed regions and/or other functional sequence regions. + in_subset: + - translator_minimal + - model_organism_database + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - SO:0000704 + - SIO:010035 + - WIKIDATA:Q7187 + - dcid:Gene + narrow_mappings: + - bioschemas:gene + broad_mappings: + - NCIT:C45822 + is_a: biological entity + mixins: + - gene or gene product + - genomic entity + - chemical entity or gene or gene product + - physical essence + - ontology class + slots: + - id + - iri + - category + - type + - name + - description + - has attribute + - deprecated + - provided by + - full name + - synonym + - in taxon + - in taxon label + - symbol + - xref + - has biological sequence + class_uri: biolink:Gene + genome: + name: genome + definition_uri: https://w3id.org/biolink/vocab/Genome + description: A genome is the sum of genetic material within a cell or virion. + in_subset: + - model_organism_database + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - SO:0001026 + - SIO:000984 + - WIKIDATA:Q7020 + close_mappings: + - dcid:GenomeAssemblyUnit + is_a: biological entity + mixins: + - genomic entity + - physical essence + - ontology class + slots: + - id + - iri + - category + - type + - name + - description + - has attribute + - deprecated + - provided by + - xref + - full name + - synonym + - in taxon + - in taxon label + - has biological sequence + class_uri: biolink:Genome +metamodel_version: 1.7.0 +source_file_size: 42695 +generation_date: '2024-03-20T11:42:00' +