--- id: https://w3id.org/biolink/biolink-model name: Biolink-Model description: Entity and association taxonomy and datamodel for life-sciences data license: https://creativecommons.org/publicdomain/zero/1.0/ # Version should be kept in sync with primary Git repository release tag version: 4.2.1 ## ------------ ## ## PREFIXES ## ------------ # CURIE namespaces (prefixes/base URI's) mappings of prefixes used in the body of the Biolink Model specification # are resolved using a specific precedence order, for use in the generation of the Biolink Model context.jsonld # mappings to namespaces. Any prefixes encountered in the Biolink Model but not resolved by the following # precedence sources, are anonymously declared by linkml as http://example.org/UNKNOWN/ rooted base URI's # which should ideally be repaired in one of the precedence lists. # # 1. The following 'prefixes:' delimited list has first precedence in resolution. # prefixes: AGRKB: 'https://www.alliancegenome.org/' apollo: 'https://github.com/GMOD/Apollo' AspGD: 'http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=' biolink: 'https://w3id.org/biolink/vocab/' bioschemas: 'https://bioschemas.org/' linkml: 'https://w3id.org/linkml/' CAID: 'http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=' # Placeholder: just points to GMOD Chado wiki CHADO: 'http://gmod.org/wiki/Chado/' # Placeholders: not sure how 'chembio'and CHEMBL.MECHANISM really resolve ChemBank: 'http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=' CHEMBL.MECHANISM: 'https://www.ebi.ac.uk/chembl/mechanism/inspect/' CID: 'http://pubchem.ncbi.nlm.nih.gov/compound/' CLINVAR: 'http://identifiers.org/clinvar' COAR_RESOURCE: 'http://purl.org/coar/resource_type/' COG: 'https://www.ncbi.nlm.nih.gov/research/cog-project/' ComplexPortal: 'https://www.ebi.ac.uk/complexportal/complex/' CPT: 'https://www.ama-assn.org/practice-management/cpt/' CTD.CHEMICAL: 'http://ctdbase.org/detail.go?type=chem&acc=' CTD.DISEASE: 'http://ctdbase.org/detail.go?type=disease&db=MESH&acc=' CTD.GENE: 'http://ctdbase.org/detail.go?type=gene&acc=' CTD: 'http://ctdbase.org/' DGIdb: 'https://www.dgidb.org/interaction_types' dcat: 'http://www.w3.org/ns/dcat#' dct: 'http://purl.org/dc/terms/' dcid: 'https://datacommons.org/browser/' doi: 'https://doi.org/' DOID-PROPERTY: 'http://purl.obolibrary.org/obo/doid#' DrugCentral: 'http://drugcentral.org/drugcard/' ECTO: 'http://purl.obolibrary.org/obo/ECTO_' EDAM-DATA: 'http://edamontology.org/data_' EDAM-FORMAT: 'http://edamontology.org/format_' EDAM-OPERATION: 'http://edamontology.org/operation_' EDAM-TOPIC: 'http://edamontology.org/topic_' EFO: 'http://www.ebi.ac.uk/efo/EFO_' ExO: 'http://purl.obolibrary.org/obo/ExO_' fabio: 'http://purl.org/spar/fabio/' foaf: 'http://xmlns.com/foaf/0.1/' foodb.compound: 'http://foodb.ca/compounds/' foodb.food: 'http://foodb.ca/foods/' FYECO: 'https://www.pombase.org/term/' FYPO: 'http://purl.obolibrary.org/obo/FYPO_' # Fission Yeast Phenotype Ontology gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#' GOREL: 'http://purl.obolibrary.org/obo/GOREL_' # GOP: Gene Ontology Property (not really a GO term but an associated metadatum) GOP: 'http://purl.obolibrary.org/obo/go#' gpi: 'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#' GSID: 'https://scholar.google.com/citations?user=' GTEx: 'https://www.gtexportal.org/home/gene/' GTOPDB: 'https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=' gtpo: 'https://rdf.guidetopharmacology.org/ns/gtpo#' HANCESTRO: 'http://www.ebi.ac.uk/ancestro/ancestro_' HCPCS: 'http://purl.bioontology.org/ontology/HCPCS/' HsapDv: 'http://purl.obolibrary.org/obo/HsapDv_' ICD10: 'https://icd.codes/icd9cm/' ICD9: 'http://translator.ncats.nih.gov/ICD9_' interpro: 'https://www.ebi.ac.uk/interpro/entry/' INO: 'http://purl.obolibrary.org/obo/INO_' isbn: 'https://www.isbn-international.org/identifier/' # note: a resolvable base URI not available from isbn-international isni: 'https://isni.org/isni/' issn: 'https://portal.issn.org/resource/ISSN/' ncats.drug: 'https://drugs.ncats.io/drug/' KEGG.BRITE: 'https://bioregistry.io/kegg.brite:' KEGG: 'http://www.kegg.jp/entry/' KEGG.GENES: 'https://bioregistry.io/kegg.genes:bsu:' KEGG.PATHWAY: 'https://bioregistry.io/kegg.pathway:' KEGG.RCLASS: 'https://www.genome.jp/dbget-bin/www_bget?rc:' LOINC: 'http://loinc.org/rdf/' MAXO: 'http://purl.obolibrary.org/obo/MAXO_' medgen: 'https://www.ncbi.nlm.nih.gov/medgen/' metacyc.reaction: 'http://identifiers.org/metacyc.reaction:' METANETX.REACTION: 'https://www.metanetx.org/equa_info/' MESH: 'http://id.nlm.nih.gov/mesh/' MI: 'http://purl.obolibrary.org/obo/MI_' mirbase: 'http://identifiers.org/mirbase' mmmp.biomaps: 'https://bioregistry.io/mmmp.biomaps:' MmusDv: 'http://purl.obolibrary.org/obo/MMUSDV_' MSigDB: 'https://www.gsea-msigdb.org/gsea/msigdb/' NBO-PROPERTY: 'http://purl.obolibrary.org/obo/nbo#' ncats.bioplanet: 'https://tripod.nih.gov/bioplanet/detail.jsp?pid=' NCBIGene: 'http://identifiers.org/ncbigene/' NCIT-OBO: 'http://purl.obolibrary.org/obo/ncit#' NDDF: 'http://purl.bioontology.org/ontology/NDDF/' NLMID: 'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term=' OBAN: 'http://purl.org/oban/' OMIM.PS: 'https://www.omim.org/phenotypicSeries/' ORCID: 'https://orcid.org/' orphanet: 'http://www.orpha.net/ORDO/Orphanet_' os: 'https://github.com/cmungall/owlstar/blob/master/owlstar.ttl' PANTHER.FAMILY: 'http://www.pantherdb.org/panther/family.do?clsAccession=' PathWhiz: 'http://smpdb.ca/pathways/#' # See also https://smpdb.ca/pathwhiz/ pav: 'http://purl.org/pav/' PHARMGKB.CHEMICAL: 'https://www.pharmgkb.org/chemical/' PHARMGKB.DISEASE: 'https://www.pharmgkb.org/disease/' PHARMGKB.GENE: 'https://www.pharmgkb.org/gene/' PHARMGKB.PATHWAYS: 'https://www.pharmgkb.org/pathway/' PHARMGKB.VARIANT: 'https://www.pharmgkb.org/variant/' PHAROS: 'http://pharos.nih.gov' PomBase: 'https://www.pombase.org/gene/' prov: 'http://www.w3.org/ns/prov#' qud: 'http://qudt.org/1.1/schema/qudt#' REPODB: 'http://apps.chiragjpgroup.org/repoDB/' ResearchID: 'https://publons.com/researcher/' RO: 'http://purl.obolibrary.org/obo/RO_' RXNORM: 'http://purl.bioontology.org/ontology/RXNORM/' RXCUI: 'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=' schema: 'http://schema.org/' ScopusID: 'https://www.scopus.com/authid/detail.uri?authorId=' SEED.REACTION: 'https://modelseed.org/biochem/reactions/' SEMMEDDB: 'https://skr3.nlm.nih.gov/SemMedDB' SIO: 'http://semanticscience.org/resource/SIO_' SNOMEDCT: 'http://snomed.info/id/' SPDI: 'https://api.ncbi.nlm.nih.gov/variation/v0/spdi/' UBERGRAPH: 'http://translator.renci.org/ubergraph-axioms.ofn#' UBERON_CORE: 'http://purl.obolibrary.org/obo/uberon/core#' UBERON_NONAMESPACE: 'http://purl.obolibrary.org/obo/core#' STY: 'http://purl.bioontology.org/ontology/STY/' UMLSSG: 'https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt' UniProtKB: 'http://purl.uniprot.org/uniprot/' UNIPROT.ISOFORM: 'http://purl.uniprot.org/isoforms/' VANDF: 'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/' UO-PROPERTY: 'http://purl.obolibrary.org/obo/uo#' VMC: 'https://github.com/ga4gh/vr-spec/' WBls: 'http://purl.obolibrary.org/obo/WBls_' WBbt: 'http://purl.obolibrary.org/obo/WBbt_' WBVocab: 'http://bio2rdf.org/wormbase_vocabulary' WIKIDATA: 'https://www.wikidata.org/entity/' # Wikidata Entity WIKIDATA_PROPERTY: 'https://www.wikidata.org/prop/' wgs: 'http://www.w3.org/2003/01/geo/wgs84_pos' XPO: 'http://purl.obolibrary.org/obo/XPO_' # Xenopus Phenotype Ontology Xenbase: 'http://www.xenbase.org/gene/showgene.do?method=display&geneId=' PMC: 'http://europepmc.org/articles/PMC' default_prefix: biolink default_range: string default_curi_maps: - obo_context - idot_context - monarch_context - semweb_context emit_prefixes: - rdf - rdfs - xsd - skos - oboInOwl - BIOGRID - SO ## ------------ ## SUBSETS ## ------------ subsets: model_organism_database: description: >- Subset that is relevant for a typical Model Organism Database (MOD) translator_minimal: description: >- Minimum subset of translator work samples: description: >- Sample/biosample datamodel testing: description: >- TBD ## ------------ ## TYPES ## ------------ imports: - linkml:types types: chemical formula value: uri: xsd:string base: str description: A chemical formula notes: - Should be implemented as a stronger type iri type: typeof: uriorcurie description: >- An IRI label type: typeof: string description: >- A string that provides a human-readable name for an entity predicate type: typeof: uriorcurie description: >- A CURIE from the biolink related_to hierarchy. For example, biolink:related_to, biolink:causes, biolink:treats. narrative text: typeof: string description: >- A string that provides a human-readable description of something symbol type: typeof: string frequency value: typeof: string uri: UO:0000105 percentage frequency value: typeof: double uri: UO:0000187 quotient: aliases: ['ratio'] typeof: double uri: UO:0010006 unit: typeof: string uri: UO:0000000 id_prefixes: - UO exact_mappings: - qud:Unit time type: typeof: time biological sequence: typeof: string ## ------------ ## SLOTS ## ------------ slots: has attribute: description: >- connects any entity to an attribute domain: entity range: attribute multivalued: true in_subset: - samples close_mappings: # RTX term meaning 'specifies value of' tagged as inverse of 'biolink:has attribute' - OBI:0001927 exact_mappings: - SIO:000008 narrow_mappings: # if 'has attribute' annotates a NamedThing as subject or # object of an association, these OBAN mappings may apply - OBAN:association_has_subject_property - OBAN:association_has_object_property - CPT:has_possibly_included_panel_element - DRUGBANK:category # RTX contributed terms. Could perhaps review for more semantically precise mappings? - 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 # disease is stage - 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 # RTX tagged a few RO terms as 'biolink:related_to' but semantics suggest a better mapping here - 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 has attribute type: description: >- connects an attribute to a class that describes it domain: attribute range: ontology class multivalued: false required: true in_subset: - samples narrow_mappings: - LOINC:has_modality_type - LOINC:has_view_type # TRAPI Attribute schema alignment: # value: NamedThing.name # value_type: NamedThing.category # value_type_name: quantity_value.NamedThing.name has qualitative value: description: >- connects an attribute to a value domain: attribute range: named thing multivalued: false in_subset: - samples # TRAPI Attribute schema alignment: # value: quantity_value.has_numeric_value[double] - may be a vector? # value_type: quantity_value.has_unit.unit.uri # value_type_name: quantity_value.has_unit.unit.name[string] has quantitative value: description: >- connects an attribute to a value domain: attribute range: quantity value multivalued: true exact_mappings: - qud:quantityValue narrow_mappings: - SNOMED:has_concentration_strength_numerator_value - SNOMED:has_presentation_strength_denominator_value - SNOMED:has_presentation_strength_numerator_value in_subset: - samples has numeric value: description: >- connects a quantity value to a number domain: quantity value range: double multivalued: false exact_mappings: - qud:quantityValue in_subset: - samples has unit: description: >- connects a quantity value to a unit domain: quantity value range: unit multivalued: false close_mappings: # These RTX contributed terms mean "is unit of" which is the semantic inverse of this biolink:has_unit term - EFO:0001697 - UO-PROPERTY:is_unit_of exact_mappings: - qud:unit - IAO:0000039 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 in_subset: - samples base coordinate: is_a: sequence localization attribute aliases: ['one-based', 'fully-closed'] description: >- A position in the base coordinate system. Base coordinates start at position 1 instead of position 0. range: integer ## -------------------- ## NODE PROPERTY SLOTS ## -------------------- node property: description: >- A grouping for any property that holds between a node and a value domain: named thing id: identifier: true domain: entity description: >- A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI in_subset: - translator_minimal required: true exact_mappings: - AGRKB:primaryId - gff3:ID - gpi:DB_Object_ID iri: description: >- An IRI for an entity. This is determined by the id using expansion rules. range: iri type in_subset: - translator_minimal - samples exact_mappings: - WIKIDATA_PROPERTY:P854 type: slot_uri: rdf:type domain: entity exact_mappings: - gff3:type - gpi:DB_Object_Type multivalued: true category: is_a: type domain: entity range: uriorcurie designates_type: true 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} is_class_field: true multivalued: true in_subset: - translator_minimal publication type: slot_uri: dct:type description: >- Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass. values_from: # Not sure which takes precedence, if any... - dctypes - fabio - MESH_PUB - COAR_RESOURCE - WIKIDATA multivalued: true name: aliases: ['label', 'display name', 'title'] description: >- A human-readable name for an attribute or entity. domain: entity range: label type in_subset: - translator_minimal - samples slot_uri: rdfs:label exact_mappings: - gff3:Name - gpi:DB_Object_Name narrow_mappings: - dct:title - WIKIDATA_PROPERTY:P1476 stoichiometry: description: >- the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers. is_a: association slot range: integer reaction direction: description: >- the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.) is_a: association slot range: ReactionDirectionEnum narrow_mappings: - NCIT:C42677 reaction balanced: is_a: association slot range: boolean reaction side: description: >- the side of a reaction being modeled (ie: left or right) is_a: association slot range: ReactionSideEnum symbol: is_a: node property domain: named thing description: >- Symbol for a particular thing exact_mappings: - AGRKB:symbol - gpi:DB_Object_Symbol synonym: is_a: node property aliases: ['alias'] domain: named thing range: label type description: >- Alternate human-readable names for a thing multivalued: true in_subset: - translator_minimal narrow_mappings: # there is an interesting debate here: are these terms "narrower" a.k.a. more specialized instances of # 'biolink:synonym' or should they be binned into their respective namesake class of mappings? # namely, is 'oboInOwl:hasExactSynonym' an instance 'exact_mappings', etc. - skos:altLabel - gff3:Alias - AGRKB:synonyms - gpi:DB_Object_Synonyms # TODO: RTX contributed terms mapped here... May need review? - HANCESTRO:0330 - IAO:0000136 - RXNORM:has_tradename exact synonym: is_a: synonym exact_mappings: - oboInOwl:hasExactSynonym broad synonym: is_a: synonym exact_mappings: - oboInOwl:hasBroadSynonym narrow synonym: is_a: synonym exact_mappings: - oboInOwl:hasNarrowSynonym related synonym: is_a: synonym exact_mappings: - oboInOwl:hasRelatedSynonym deprecated: range: boolean exact_mappings: - oboInOwl:ObsoleteClass description: >- A boolean flag indicating that an entity is no longer considered current or valid. has topic: aliases: ['topic', 'descriptors'] is_a: node property range: ontology class exact_mappings: - foaf:topic description: >- Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred. See https://github.com/biolink/biolink-model/issues/238 xref: aliases: ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls'] domain: named thing range: uriorcurie 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. multivalued: true in_subset: - translator_minimal narrow_mappings: - gff3:Dbxref - gpi:DB_Xrefs semmed agreement count: is_a: association slot range: integer description: >- The number of times this concept has been asserted in the SemMedDB literature database. in_subset: - translator_minimal support graphs: description: >- A list of knowledge graphs that support the existence of this association. multivalued: true is_a: association slot in_subset: - translator_minimal resource id: is_a: node property description: >- The CURIE for an Information Resource that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge. domain: retrieval source range: uriorcurie in_subset: - translator_minimal resource role: is_a: node property description: >- The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources. domain: retrieval source range: ResourceRoleEnum in_subset: - translator_minimal retrieval source ids: description: >- A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge. multivalued: true range: retrieval source in_subset: - translator_minimal full name: is_a: node property domain: named thing range: label type description: >- a long-form human readable name for a thing upstream resource ids: is_a: node property description: >- An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources. e.g. an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact. domain: retrieval source range: uriorcurie description: aliases: ['definition'] range: narrative text description: >- a human-readable description of an entity in_subset: - translator_minimal slot_uri: dct:description exact_mappings: - IAO:0000115 - skos:definitions narrow_mappings: - gff3:Description systematic synonym: is_a: node property domain: named thing range: label type multivalued: true slot_uri: GOP:systematic_synonym description: >- more commonly used for gene symbols in yeast affiliation: is_a: node property description: >- a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations. domain: agent range: uriorcurie multivalued: true address: is_a: node property description: >- the particulars of the place where someone or an organization is situated. For now, this slot is a simple text "blob" containing all relevant details of the given location for fitness of purpose. For the moment, this "address" can include other contact details such as email and phone number(?). ## Space latitude: is_a: node property range: float description: >- latitude exact_mappings: - wgs:lat longitude: is_a: node property range: float description: >- longitude exact_mappings: - wgs:long ## Time timepoint: aliases: ['duration'] range: time type description: >- a point in time creation date: is_a: node property aliases: ['publication date'] range: date description: >- date on which an entity was created. This can be applied to nodes or edges exact_mappings: - dct:createdOn - WIKIDATA_PROPERTY:P577 update date: is_a: node property range: date description: >- date on which an entity was updated. This can be applied to nodes or edges ## Statistics aggregate statistic: is_a: node property abstract: true has count: description: >- number of things with a particular property is_a: aggregate statistic range: integer exact_mappings: - LOINC:has_count has total: description: >- total number of things in a particular reference set is_a: aggregate statistic range: integer has quotient: is_a: aggregate statistic range: double has percentage: description: >- equivalent to has quotient multiplied by 100 is_a: aggregate statistic range: double ## Properties for Information Content Entity and Publication Nodes has taxonomic rank: is_a: node property range: taxonomic rank multivalued: false mappings: - WIKIDATA:P105 has dataset: is_a: node property domain: dataset version range: dataset broad_mappings: - dct:source source web page: is_a: node property domain: dataset summary broad_mappings: - dct:source source logo: is_a: node property domain: dataset summary slot_uri: schema:logo retrieved on: is_a: node property domain: dataset range: date exact_mappings: - pav:retrievedOn version of: is_a: node property domain: dataset version range: dataset summary exact_mappings: - dct:isVersionOf version: is_a: node property domain: dataset broad_mappings: - pav:version - owl:versionInfo license: is_a: node property domain: information content entity exact_mappings: - dct:license narrow_mappings: - WIKIDATA_PROPERTY:P275 rights: is_a: node property domain: information content entity exact_mappings: - dct:rights format: is_a: node property domain: information content entity exact_mappings: - dct:format - WIKIDATA_PROPERTY:P2701 created with: is_a: node property domain: dataset exact_mappings: - pav:createdWith download url: is_a: node property domain: information content entity slot_uri: dcat:downloadURL dataset download url: is_a: node property domain: dataset slot_uri: dcat:downloadURL distribution download url: is_a: node property domain: dataset distribution exact_mappings: - dcat:downloadURL ingest date: is_a: node property domain: dataset version broad_mappings: - dct:issued has distribution: is_a: node property domain: dataset version range: dataset distribution slot_uri: dct:distribution published in: is_a: node property description: >- CURIE identifier of a broader publication context within which the publication may be placed, e.g. a specified book or journal. domain: publication range: uriorcurie values_from: - NLMID - issn - isbn exact_mappings: - WIKIDATA_PROPERTY:P1433 iso abbreviation: is_a: node property description: >- Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself. domain: publication exact_mappings: - WIKIDATA_PROPERTY:P1160 authors: is_a: node property description: >- connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as "surname, firstname initial.". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication. multivalued: true domain: publication range: agent volume: is_a: node property description: >- volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication domain: publication exact_mappings: - WIKIDATA_PROPERTY:P478 chapter: is_a: node property description: >- chapter of a book domain: book chapter exact_mappings: - WIKIDATA:Q1980247 issue: is_a: node property description: >- issue of a newspaper, a scientific journal or magazine for reference purpose domain: publication exact_mappings: - WIKIDATA_PROPERTY:P433 pages: is_a: node property description: >- page number of source referenced for statement or publication domain: publication multivalued: true exact_mappings: - WIKIDATA_PROPERTY:P304 summary: is_a: node property # since 'abstract' is a linkML keyword denoting a non-instantiable class or slot, # it is generally recommended that knowledge graphs use 'summary' instead to tag a Publication 'abstract' aliases: ['abstract'] description: >- executive summary of a publication domain: publication exact_mappings: - dct:abstract - WIKIDATA:Q333291 keywords: is_a: node property description: >- keywords tagging a publication domain: publication multivalued: true mesh terms: is_a: node property description: >- mesh terms tagging a publication domain: publication range: uriorcurie values_from: - MESH multivalued: true exact_mappings: - dcid:MeSHTerm ## Biology has biological sequence: is_a: node property description: >- connects a genomic feature to its sequence range: biological sequence has gene or gene product: is_a: node property description: >- connects an entity with one or more gene or gene products range: gene multivalued: true has gene: is_a: has gene or gene product description: >- connects an entity associated with one or more genes range: gene multivalued: true has zygosity: is_a: node property domain: nucleic acid entity range: zygosity ## Chemistry, drugs and food has chemical formula: is_a: node property range: chemical formula value description: >- description of chemical compound based on element symbols exact_mappings: - WIKIDATA_PROPERTY:P274 is metabolite: is_a: node property domain: molecular entity range: boolean description: >- indicates whether a molecular entity is a metabolite exact_mappings: - CHEBI:25212 has constituent: description: >- one or more molecular entities within a chemical mixture is_a: node property range: molecular entity multivalued: true has drug: is_a: node property description: >- connects an entity to one or more drugs range: drug multivalued: true has device: is_a: node property description: >- connects an entity to one or more (medical) devices range: device multivalued: true has procedure: is_a: node property description: >- connects an entity to one or more (medical) procedures range: procedure multivalued: true ## Clinical exposures has receptor: is_a: node property domain: exposure event range: organismal entity description: >- the organism or organism part being exposed exact_mappings: - ExO:0000001 has stressor: is_a: node property domain: exposure event aliases: ['has stimulus'] description: >- the process or entity that the receptor is being exposed to exact_mappings: - ExO:0000000 has route: is_a: node property domain: exposure event description: >- the process that results in the stressor coming into direct contact with the receptor exact_mappings: - ExO:0000055 narrow_mappings: - LOINC:has_pharmaceutical_route - SNOMED:has_dose_form_intended_site - SNOMED:has_route_of_administration population context qualifier: description: >- a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association. is_a: qualifier range: population of individual organisms temporal context qualifier: description: >- a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier. is_a: qualifier range: time type temporal interval qualifier: is_a: temporal context qualifier description: >- a constraint of a time interval placed upon the truth value of an association. is supplement: description: >- is_a: node property domain: chemical mixture trade name: description: >- is_a: node property domain: chemical entity available from: description: >- is_a: node property multivalued: true range: DrugAvailabilityEnum is toxic: description: >- is_a: node property multivalued: false range: boolean has chemical role: is_a: related to at concept level description: >- A role is particular behaviour which a chemical entity may exhibit. range: chemical role multivalued: true id_prefixes: - CHEBI comments: >- We expect primarily to use CHEBI chemical roles here; however, we are looking for a mapping between CHEBI And ATC codes to support this slot. max tolerated dose: description: >- The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD. is_a: node property multivalued: false range: string animal model available from: description: >- is_a: node property multivalued: true range: disease or phenotypic feature FDA adverse event level: description: >- is_a: association slot range: FDAIDAAdverseEventEnum highest FDA approval status: description: >- Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.' drug regulatory status world wide: aliases: ['max phase'] description: >- An agglomeration of drug regulatory status worldwide. Not specific to FDA. exact_mappings: - NCIT:C172573 narrow_mappings: - NCIT:R172 - NCIT:regimen_has_accepted_use_for_disease # RTX mapped REPODB terms - REPODB:clinically_tested_approved_unknown_phase - REPODB:clinically_tested_suspended_phase_0 - REPODB:clinically_tested_suspended_phase_1 - REPODB:clinically_tested_suspended_phase_1_or_phase_2 - REPODB:clinically_tested_suspended_phase_2 - REPODB:clinically_tested_suspended_phase_2_or_phase_3 - REPODB:clinically_tested_suspended_phase_3 - REPODB:clinically_tested_terminated_phase_0 - REPODB:clinically_tested_terminated_phase_1 - REPODB:clinically_tested_terminated_phase_1_or_phase_2 - REPODB:clinically_tested_terminated_phase_2 - REPODB:clinically_tested_terminated_phase_2_or_phase_3 - REPODB:clinically_tested_terminated_phase_3 - REPODB:clinically_tested_withdrawn_phase_0 - REPODB:clinically_tested_withdrawn_phase_1 - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2 - REPODB:clinically_tested_withdrawn_phase_2 - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3 - REPODB:clinically_tested_withdrawn_phase_3 routes of delivery: description: >- the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals. multivalued: true range: DrugDeliveryEnum ## ------------------- ## QUALIFIERS ## ------------------- form or variant qualifier: is_a: qualifier abstract: true description: >- A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. examples: - value: mutation - value: late stage - value: severe - value: transplant - value: chemical analog notes: >- please see the ChemicalOrGeneOrGeneProductFormOrVariantEnum (below) for examples of 'form or variant qualifier' terms in the gene->chemical association space. the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘Mutated forms of Gene X’. the qualifier ‘late stage’ combines with a core concept of ‘Disease X’ to express the more specific concept ‘Late Stage forms of Disease X’ the qualifier ‘recombinant’ combines with a core concept of ‘FLT1 Gene’ to express the composed concept ‘Recombinant forms of the FLT1 gene’ the qualifier ‘chemical analog’ combines with a core concept of ‘Ditiocarb’ to express the composed concept ‘analog forms of Ditiocarb’ in_subset: - translator_minimal aspect qualifier: is_a: qualifier abstract: true description: >- Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. examples: - value: stability - value: abundance - value: expression - value: exposure notes: >- for good examples of aspects in the gene-> chemical space, please see the GeneOrGeneProductOrChemicalEntityAspectEnum (below) which lists many aspects that can be used to qualify the gene making the full subject a different ontological type. the qualifier ‘expression’ combines with a core concept of ‘Gene X’ to express the composed concept ‘expression of Gene X’ (Gene → Biological Process) the qualifier ‘exposure’ combines with a core concept of ‘Chemical X’ to express the composed concept ‘exposure to Chemical X’ (Chemical → Exposure Process) the qualifier ‘activity’ combines with a core concept of ‘PPARG’ to express the concept ‘activity of PPARG’ (Gene → function/activity) the qualifier ‘emergency Department Visit’ combines with a core concept of ‘Disease X’ to express the concept ‘Emergency Department visits for Disease X’ (Disease → Clinical Event) the qualifier ‘infection’ combines with a core concept of ‘Giardia’ to express the concept ‘Infection with Giardia’ (Taxon → Biological / Pathological Process) the qualifier ‘severity’ combines with a core concept of ‘DILI’ to express the concept ‘the severity level of DILI’ (Disease → (intrinsic) Characteristic/Quality) the qualifier ‘abundance’ combines with a core concept of ‘BRCA2’ to express the concept ‘abundance of BRCA2’ (Gene → (extrinsic) characteristic/quality) in_subset: - translator_minimal derivative qualifier: is_a: qualifier abstract: true description: >- A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. examples: - value: metabolite in_subset: - translator_minimal part qualifier: is_a: qualifier abstract: true description: >- defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). examples: - value: polyA tail - value: upstream control region in_subset: - translator_minimal context qualifier: is_a: qualifier abstract: true description: >- Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs. examples: - value: cohort x (e.g. a specific population, referenced by an identifier) - value: gut microbiome # OHMI:0000020 in_subset: - translator_minimal direction qualifier: is_a: qualifier abstract: true description: >- Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. notes: >- the qualifier ‘increased’ combines with a core concept of ‘Gene X’ and an aspect of ‘expression’ to express the composed concept ‘increased expression of Gene X’ the qualifier ‘decreased’ combines with a core concept of ‘Protein X’ and an aspect of ‘abundance’ to express the composed concept ‘decreased abundance of Protein X’ in_subset: - translator_minimal mapped predicate: description: >- The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs. predicate mappings: description: >- A collection of relationships that are not used in biolink, but have biolink patterns that can be used to replace them. This is a temporary slot to help with the transition to the fully qualified predicate model in Biolink3. multivalued: true range: predicate mapping inlined_as_list: true exact matches: description: >- A list of terms from different schemas or terminology systems that have an identical meaning. Such terms often describe the same concept from different ontological perspectives. multivalued: true narrow matches: description: >- A list of terms from different schemas or terminology systems that have a narrower meaning. Such terms often describe a more specific concept from different ontological perspectives. multivalued: true broad matches: description: >- A list of terms from different schemas or terminology systems that have a broader meaning. Such terms often describe a more general concept from different ontological perspectives. multivalued: true subject aspect qualifier: description: >- Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement). examples: - value: stability - value: abundance - value: expression - value: exposure is_a: aspect qualifier in_subset: - translator_minimal subject form or variant qualifier: description: >- A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement). examples: - value: mutation - value: late stage - value: severe - value: transplant - value: chemical analog is_a: form or variant qualifier in_subset: - translator_minimal subject part qualifier: description: >- defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement). is_a: part qualifier in_subset: - translator_minimal subject derivative qualifier: description: >- A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement). examples: - value: metabolite is_a: derivative qualifier in_subset: - translator_minimal subject context qualifier: is_a: context qualifier in_subset: - translator_minimal subject direction qualifier: description: >- Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement). is_a: direction qualifier range: DirectionQualifierEnum in_subset: - translator_minimal object aspect qualifier: description: >- Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement). examples: - value: stability - value: abundance - value: expression - value: exposure is_a: aspect qualifier in_subset: - translator_minimal object form or variant qualifier: description: >- A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement). examples: - value: mutation - value: late stage - value: severe - value: transplant - value: chemical analog is_a: form or variant qualifier in_subset: - translator_minimal object part qualifier: description: >- defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement). is_a: part qualifier in_subset: - translator_minimal object derivative qualifier: description: >- A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement). examples: - value: metabolite is_a: derivative qualifier in_subset: - translator_minimal object context qualifier: is_a: context qualifier in_subset: - translator_minimal object direction qualifier: description: >- Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement). is_a: direction qualifier range: DirectionQualifierEnum in_subset: - translator_minimal qualified predicate: is_a: qualifier description: >- Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading. notes: >- to express the statement that “Chemical X causes increased expression of Gene Y”, the core triple is read using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression, object_direction:increased. The predicate ‘affects’ is needed for the core triple reading, but does not make sense in the full statement reading (because “Chemical X affects increased expression of Gene Y'' is not what we mean to say here: it causes increased expression of Gene Y) statement qualifier: is_a: qualifier description: >- A property that qualifies the entirety of the statement made in an association. It applies to both a fully qualified subject and a fully qualified object as well as the predicate and qualified predicate in an association. in_subset: - translator_minimal causal mechanism qualifier: is_a: statement qualifier description: >- A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker') range: CausalMechanismQualifierEnum in_subset: - translator_minimal anatomical context qualifier: is_a: statement qualifier description: >- A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location). notes: >- Anatomical context values can be any term from UBERON. For example, the context qualifier ‘cerebral cortext’ combines with a core concept of ‘neuron’ to express the composed concept ‘neuron in the cerebral cortext’. The species_context_qualifier applies taxonomic context, e.g. species-specific molecular activity. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs. examples: - value: blood # UBERON:0000178 - value: cerebral cortext # UBERON:0000956 in_subset: - translator_minimal species context qualifier: is_a: statement qualifier description: >- A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place. range: organism taxon examples: - value: zebrafish # NCBITaxon:7955 - value: human # NCBITaxon:9606 notes: - Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs. in_subset: - translator_minimal qualifiers: deprecated: true description: >- connects an association to qualifiers that modify or qualify the meaning of that association local_names: ga4gh: annotation qualifier is_a: association slot multivalued: true range: ontology class frequency qualifier: is_a: qualifier description: >- a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject range: frequency value in_subset: - translator_minimal severity qualifier: deprecated: true description: >- a qualifier used in a phenotypic association to state how severe the phenotype is in the subject is_a: qualifier range: severity value in_subset: - translator_minimal sex qualifier: description: >- a qualifier used in a phenotypic association to state whether the association is specific to a particular sex. is_a: qualifier range: biological sex in_subset: - translator_minimal onset qualifier: description: >- a qualifier used in a phenotypic association to state when the phenotype appears is in the subject. notes: >- This is in Biolink to support HP ontology annotations which use "onset" (with terms from HP) as an annotation on a disease to phenotypic feature association. Please only use it for this purpose. If the intent is to describe the onset of a disease in the context of a treatment, use object_aspect_qualifier and object_direction_qualifier to capture "delayed onset" or "exacerbated onset" slot. is_a: qualifier range: onset in_subset: - translator_minimal clinical modifier qualifier: description: >- the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals. is_a: association slot range: clinical modifier sequence variant qualifier: description: >- a qualifier used in an association with the variant is_a: association slot range: sequence variant quantifier qualifier: is_a: association slot range: ontology class description: >- A measurable quantity for the object of the association narrow_mappings: # TODO: RTX contributed terms mapped here... May need review? - LOINC:analyzes - LOINC:measured_by - LOINC:property_of - SEMMEDDB:MEASURES - UMLS:measures catalyst qualifier: is_a: association slot multivalued: true range: macromolecular machine mixin description: >- a qualifier that connects an association between two causally connected entities (for example, two chemical entities, or a chemical entity in that changes location) and the gene product, gene, or complex that enables or catalyzes the change. stage qualifier: description: >- stage during which gene or protein expression of takes place. is_a: statement qualifier range: life stage # path: "object/during" examples: - value: UBERON:0000069 description: larval stage in_subset: - translator_minimal ## -------------------- ## PREDICATES/RELATIONS ## -------------------- related to: description: >- A relationship that is asserted between two named things domain: named thing range: named thing multivalued: true inherited: true symmetric: true annotations: canonical_predicate: true exact_mappings: - UMLS:related_to broad_mappings: - owl:topObjectProperty narrow_mappings: - SEMMEDDB:compared_with - SEMMEDDB:higher_than - SEMMEDDB:lower_than - SEMMEDDB:ADMINISTERED_TO - SEMMEDDB:ASSOCIATED_WITH - BFO:0000054 - UBERON_CORE:protects - GOREL:0002005 - GOREL:0012006 # several of the following terms mapped here by RTX could merit upgrade to new Biolink terms - 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 # RTX contributed terms, perhaps belong somewhere else with more precise semantics? - 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 # bearer_of - 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 # functionally related to - 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 related to at concept level: is_a: related to description: >- Represents a relationship held between terminology components that describe the conceptual model of a domain. annotations: canonical_predicate: true symmetric: true related to at instance level: is_a: related to 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. annotations: canonical_predicate: true symmetric: true associated with: is_a: related to at instance level description: >- Expresses a relationship between two named things where the relationship is typically generated statistically (though not in all cases), and is weaker than its child, 'correlated with', but stronger than its parent, 'related to'. This relationship holds between two concepts represented by variables for which a statistical dependence is demonstrated. E.g. the statement “Atrial Fibrillation (Afib) is associated with Myocardial Infraction (MI)” asserts that having Afib is not statistically independent from whether a patient will also have MI. Note that in Translator associations, the subject and object concepts may map exactly to the statistical variables, or represent related entities for which the variables serve as proxies in an Association (e.g. diseases, chemical entities or processes). annotations: canonical_predicate: true symmetric: true domain: named thing range: named thing narrow_mappings: - RO:0004029 - SNOMEDCT:47429007 superclass of: is_a: related to at concept level inverse: subclass of description: >- holds between two classes where the domain class is a super class of the range class domain: ontology class range: ontology class multivalued: true in_subset: - translator_minimal exact_mappings: - WIKIDATA:Q66088480 - CHEMBL.MECHANISM:superset_of - GO:inverse_isa - RXNORM:inverse_isa - MESH:inverse_isa - VANDF:inverse_isa narrow_mappings: - NCIT:cdrh_parent_of - NCIT:ctcae_5_parent_of - NCIT:subset_includes_concept - OMIM:has_manifestation - SNOMED:has_basic_dose_form - UMLS:RB subclass of: is_a: related to at concept level description: >- holds between two classes where the domain class is a specialization of the range class domain: ontology class range: ontology class multivalued: true in_subset: - translator_minimal annotations: canonical_predicate: true close_mappings: # RTX - LOINC:class_of - LOINC:has_class exact_mappings: - rdfs:subClassOf - SEMMEDDB:ISA - WIKIDATA_PROPERTY:P279 - CHEMBL.MECHANISM:subset_of - GO:isa - MESH:isa - RXNORM:isa - VANDF:isa narrow_mappings: - CHEBI:has_parent_hydride - LOINC:has_archetype - LOINC:has_parent_group - LOINC:is_presence_guidance_for - NCIT:gene_product_has_chemical_classification # RTX mapped terms classes for biomarkers - NCIT:R36 - NCIT:R42 - NCIT:A16 - NCIT:A11 - NCIT:A14 - NCIT:A3 - NDDF:has_dose_form - RXNORM:has_dose_form - RXNORM:has_doseformgroup - SNOMED:entire_anatomy_structure_of - SNOMED:has_dose_form # RTX mapping - rdfs:subPropertyOf same as: is_a: exact match description: >- holds between two entities that are considered equivalent to each other in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true close_mappings: # identical class extension with identical sets of individuals - owl:equivalentClass exact_mappings: # identical individual, or identical class concept/meaning - owl:sameAs - skos:exactMatch # Semantic Medline definition: "comparative predicate" where the equivalence could simply be functional # RTX suggests mapping this to proposed new "biolink:close_match" predicate instead # - SEMMEDDB:same_as - WIKIDATA_PROPERTY:P2888 - CHEMBL.MECHANISM:equivalent_to - MONDO:equivalentTo narrow_mappings: - DRUGBANK:external-identifier close match: is_a: related to at concept level description: >- a list of terms from different schemas or terminology systems that have a semantically similar but not strictly equivalent, broader, or narrower meaning. Such terms often describe the same general concept from different ontological perspectives (e.g. drug as a type of chemical entity versus drug as a type of role borne by a chemical entity). in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true exact_mappings: - skos:closeMatch # Semantic Medline definition: "comparative predicate" where the equivalence could simply be functional - SEMMEDDB:same_as narrow_mappings: - CHEBI:is_enantiomer_of - CHEBI:is_tautomer_of - MEDDRA:classified_as - oboInOwl:hasDbXref - RXNORM:has_quantified_form - UMLS:SY exact match: is_a: close match description: >- holds between two entities that have strictly equivalent meanings, with a high degree of confidence in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true exact_mappings: - skos:exactMatch - WIKIDATA:Q39893449 - WIKIDATA:P2888 broad match: description: >- a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree. is_a: related to at concept level in_subset: - translator_minimal annotations: canonical_predicate: true opposite_of: narrow match exact_mappings: - skos:broadMatch - WIKIDATA:Q39894595 narrow match: description: >- a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree. is_a: related to at concept level inverse: broad match in_subset: - translator_minimal exact_mappings: - skos:narrowMatch - WIKIDATA:Q39893967 annotations: opposite_of: broad match member of: description: >- Defines a mereological relation between a item and a collection. is_a: related to at concept level inverse: has member in_subset: - translator_minimal exact_mappings: - RO:0002350 close_mappings: - skos:member has member: description: >- Defines a mereological relation between a collection and an item. is_a: related to at concept level in_subset: - translator_minimal exact_mappings: - RO:0002351 - skos:member opposite of: description: >- x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). (This description is from RO. Needs to be rephrased). is_a: related to at instance level symmetric: true annotations: canonical_predicate: true exact_mappings: - RO:0002604 see_also: - https://doi.org/10.1101/108977 - https://github.com/biolink/biolink-model/issues/657 affects likelihood of: is_a: related to at instance level description: >- Holds between two entities where the presence or application of one alters the chance that the other will come to be. notes: >- - This predicate implies causation, where the 'affected' entity is something that does not yet exist, and the actions/execution of effector impact the likelihood that this entity may come to be. It is NOT to be used for a statistical associations that describe correlations between two feature variables (use predicates in the 'associated with likelihood of' hierarchy here.) annotations: canonical_predicate: true in_subset: - translator_minimal likelihood affected by: is_a: related to at instance level inverse: affects likelihood of associated with likelihood of: is_a: associated with description: >- A a relationship that holds between two concepts represented by variables for which a statistical dependence is demonstrated, wherein the state or value of one variable predicts the future state or value of the other. E.g. the statement “An Atrial Fibrillation (Afib) diagnosis is associated with likelihood of a Myocardial Infraction (MI) diagnosis” asserts that the state of having Afib is associated with an increased or decreased likelihood that a patient will later exhibit MI. annotations: canonical_predicate: true likelihood associated with: is_a: associated with description: >- inverse: associated with likelihood of associated with increased likelihood of: is_a: associated with likelihood of description: >- Expresses a relationship between two named things where the relationship is typically generated statistically and the state or fact of something is more probable. annotations: canonical_predicate: true increased likelihood associated with: is_a: likelihood associated with description: >- inverse: associated with increased likelihood of associated with decreased likelihood of: is_a: associated with likelihood of description: >- Expresses a relationship between two named things where the relationship is typically generated statistically and the state or fact of something is less probable. annotations: canonical_predicate: true decreased likelihood associated with: is_a: likelihood associated with description: >- inverse: associated with decreased likelihood of target for: is_a: related to at instance level description: >- A gene is a target of a disease when its products are druggable and when a drug interaction with the gene product could have a therapeutic effect annotations: canonical_predicate: true domain: gene range: disease has target: is_a: related to at instance level inverse: target for domain: disease range: gene active in: is_a: related to at instance level domain: gene or gene product range: cellular component annotations: canonical_predicate: true exact_mappings: - RO:0002432 has active component: is_a: related to at instance level inverse: active in domain: cellular component range: gene or gene product acts upstream of: is_a: related to at instance level domain: gene or gene product range: biological process annotations: canonical_predicate: true exact_mappings: - RO:0002263 has upstream actor: is_a: related to at instance level inverse: acts upstream of domain: biological process range: gene or gene product acts upstream of positive effect: is_a: acts upstream of domain: gene or gene product range: biological process annotations: canonical_predicate: true exact_mappings: - RO:0004034 has positive upstream actor: is_a: has upstream actor inverse: acts upstream of positive effect domain: biological process range: gene or gene product acts upstream of negative effect: is_a: acts upstream of domain: gene or gene product range: biological process annotations: canonical_predicate: true exact_mappings: - RO:0004035 has negative upstream actor: is_a: has upstream actor inverse: acts upstream of negative effect domain: biological process range: gene or gene product acts upstream of or within: is_a: acts upstream of domain: gene or gene product range: biological process annotations: canonical_predicate: true exact_mappings: - RO:0002264 has upstream or within actor: is_a: has upstream actor inverse: acts upstream of or within domain: biological process range: gene or gene product acts upstream of or within positive effect: is_a: acts upstream of or within domain: gene or gene product range: biological process annotations: canonical_predicate: true exact_mappings: - RO:0004032 has positive upstream or within actor: is_a: has upstream or within actor inverse: acts upstream of or within positive effect domain: biological process range: gene or gene product acts upstream of or within negative effect: is_a: acts upstream of or within domain: gene or gene product range: biological process annotations: canonical_predicate: true exact_mappings: - RO:0004033 has negative upstream or within actor: is_a: has upstream or within actor inverse: acts upstream of or within negative effect domain: biological process range: gene or gene product ## Publication related predicates mentions: description: >- refers to is a relation between one information content entity and the named thing that it makes reference to. is_a: related to at instance level exact_mappings: - IAO:0000142 narrow_mappings: - SIO:000628 mentioned by: description: >- refers to is a relation between one named thing and the information content entity that it makes reference to. is_a: related to at instance level inverse: mentions ## Publication related predicates contributor: is_a: related to at instance level domain: agent range: information content entity comments: - This is a grouping for predicates relating entities to their associated contributors realizing them abstract: true exact_mappings: - dct:contributor has contributor: inverse: contributor is_a: related to at instance level domain: information content entity range: agent provider: is_a: contributor description: >- person, group, organization or project that provides a piece of information (e.g. a knowledge association). has provider: inverse: provider is_a: has contributor domain: information content entity range: agent publisher: is_a: contributor domain: agent range: publication description: >- organization or person responsible for publishing books, periodicals, podcasts, games or software. Note that in the case of publications which have a containing "published in" node property, the publisher association may not be attached directly to the embedded child publication, but only made in between the parent's publication node and the publisher agent of the encompassing publication (e.g. only from the Journal referenced by the 'published_in' property of an journal article Publication node). exact_mappings: - dct:publisher - WIKIDATA_PROPERTY:P123 has publisher: is_a: has contributor inverse: publisher domain: publication range: agent editor: is_a: contributor domain: agent range: publication description: >- editor of a compiled work such as a book or a periodical (newspaper or an academic journal). Note that in the case of publications which have a containing "published in" node property, the editor association may not be attached directly to the embedded child publication, but only made in between the parent's publication node and the editorial agent of the encompassing publication (e.g. only from the Book referenced by the 'published_in' property of a book chapter Publication node). exact_mappings: - WIKIDATA_PROPERTY:P98 has editor: inverse: editor is_a: has contributor domain: publication range: agent author: is_a: contributor domain: agent range: publication description: >- an instance of one (co-)creator primarily responsible for a written work exact_mappings: - dct:creator - WIKIDATA_PROPERTY:P50 has author: inverse: author is_a: has contributor domain: publication range: agent ## end of Publication related predicates assesses: is_a: related to at instance level aliases: ['was assayed against'] description: >- The effect of a thing on a target was interrogated in some assay. A relationship between some perturbing agent (usually a chemical compound) and some target entity, where the affect of the perturbing agent on the target entity was interrogated in a particular assay. The target might be a particular protein, tissue, phenotype, whole organism, cell line, or other type of biological entity. domain: named thing range: named thing annotations: canonical_predicate: true is assessed by: is_a: related to at instance level inverse: assesses domain: named thing range: named thing interacts with: domain: named thing range: named thing description: >- holds between any two entities that directly or indirectly interact with each other is_a: related to at instance level in_subset: - translator_minimal symmetric: true mixin: true exact_mappings: - SEMMEDDB:INTERACTS_WITH notes: >- please use a more specific child predicate of interacts with, either physically interacts with or genetically interacts with. physically interacts with: is_a: interacts with description: >- holds between two entities that make physical contact as part of some interaction. does not imply a causal relationship. in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true broad_mappings: - WIKIDATA_PROPERTY:P129 close_mappings: - CHEMBL.MECHANISM:binding_agent - CHEMBL.MECHANISM:chelating_agent - CHEMBL.MECHANISM:cross-linking_agent - CHEMBL.MECHANISM:oxidative_enzyme - CHEMBL.MECHANISM:sequestering_agent - CHEMBL.MECHANISM:substrate - DRUGBANK:target narrow_mappings: # Defined more narrowly as "substance interaction", thus specific applies to a subclass entities - DRUGBANK:drug-interaction - FMA:adheres_to - NCIT:A7 - PR:non-covalently_bound_to mixins: - interacts with directly physically interacts with: is_a: physically interacts with description: >- A causal mechanism mediated by a direct contact between the effector and target entities (this contact may be weak or strong, transient or stable). symmetric: true exact_mappings: - RO:0002436 broad_mappings: # Definition of this term is more generic than direct physical molecular interactions: # A is connected to B iff there exists a fiat, material or temporal path between A and B. - SIO:000203 - RO:0002578 narrow_mappings: - PHAROS:drug_targets - DRUGBANK:chelator - CTD:affects_binding - DGIdb:cofactor annotations: canonical_predicate: true binds: deprecated: true is_a: directly physically interacts with description: >- A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction. symmetric: true annotations: canonical_predicate: true close_mappings: - DGIdb:binder indirectly physically interacts with: is_a: physically interacts with symmetric: true annotations: canonical_predicate: true genetically interacts with: is_a: interacts with description: >- holds between two genes whose phenotypic effects are dependent on each other in some way - such that their combined phenotypic effects are the result of some interaction between the activity of their gene products. Examples include epistasis and synthetic lethality. domain: gene range: gene in_subset: - translator_minimal annotations: canonical_predicate: true symmetric: true exact_mappings: - RO:0002435 gene_fusion_with: is_a: genetically interacts with description: >- holds between two independent genes that have fused through translocation, interstitial deletion, or chromosomal inversion to form a new, hybrid gene. Fusion genes are often implicated in various neoplasms and cancers. domain: gene range: gene in_subset: - translator_minimal annotations: canonical_predicate: true symmetric: true genetic_neighborhood_of: is_a: genetically interacts with description: >- holds between two genes located nearby one another on a chromosome. domain: gene range: gene in_subset: - translator_minimal annotations: canonical_predicate: true symmetric: true affects: is_a: related to at instance level description: >- Describes an entity that has an effect on the state or quality of another existing entity. notes: >- Use of the 'affects' predicate implies that the affected entity already exists, unlike predicates such as 'affects likelihood of' and 'prevents' where the effect concerns whether or when something may or may not come into existence. in_subset: - translator_minimal annotations: canonical_predicate: true related_mappings: # Contributed by RTX. Seems possible that a new predicate "biolink:in_pathway" could be justified? - DRUGBANK:pathway exact_mappings: - SEMMEDDB:AFFECTS - DGIdb:affects narrow_mappings: - CTD:prediction_hypothesis - GOREL:0001006 - CTD:inferred - UPHENO:0000001 - RO:0002263 - RO:0002264 - NCIT:R158 - NCIT:R160 - NCIT:R30 - NCIT:R150 - NCIT:R72 - NCIT:R146 - NCIT:R124 - NCIT:R173 - NCIT:R100 - NCIT:R102 - NCIT:R101 - NCIT:R113 - NCIT:R23 - NCIT:R25 - NCIT:gene_mapped_to_disease - NCIT:R133 - RO:0002343 - RO:0002355 - RO:0002591 - RO:0002592 - RO:0012003 - SNOMED:has_pathological_process - UBERGRAPH:is_increase_of # talked to Jim Balhoff, this is a valid mapping - UBERGRAPH:is_decrease_of # talked to Jim Balhoff, this is a valid mapping affected by: is_a: related to at instance level description: >- describes an entity of which the state or quality is affected by another existing entity. inverse: affects associated with sensitivity to: is_a: associated with description: >- A relation that holds between a named thing and a chemical that specifies that the change in the named thing is found to be associated with the degree of sensitivity to treatment by the chemical. domain: named thing range: chemical entity annotations: canonical_predicate: true broad_mappings: - PATO:0000085 # sensitivity toward narrow_mappings: - SNOMEDCT:418038007 # propensity to adverse reaction sensitivity associated with: is_a: associated with inverse: associated with sensitivity to range: named thing domain: chemical entity associated with resistance to: is_a: associated with description: >- A relation that holds between a named thing and a chemical that specifies that the change in the named thing is found to be associated with the degree of resistance to treatment by the chemical. domain: named thing range: chemical entity annotations: canonical_predicate: true resistance associated with: is_a: associated with inverse: associated with resistance to range: named thing domain: chemical entity diagnoses: is_a: related to at instance level description: >- a relationship that identifies the nature of (an illness or other problem) by examination of the symptoms. domain: diagnostic aid range: disease or phenotypic feature annotations: canonical_predicate: true close_mappings: - NCIT:C15220 # diagnosis - SIO:001331 # diagnosis exact_mappings: - DrugCentral:5271 - SEMMEDDB:DIAGNOSES is diagnosed by: is_a: related to at instance level inverse: diagnoses domain: disease or phenotypic feature range: diagnostic aid increases amount or activity of: deprecated: true is_a: related to at instance level mixin: true description: >- A grouping mixin to help with searching for all the predicates that increase the amount or activity of the object. amount or activity increased by: deprecated: true is_a: related to at instance level inverse: increases amount or activity of decreases amount or activity of: deprecated: true is_a: related to at instance level mixin: true description: >- A grouping mixin to help with searching for all the predicates that decrease the amount or activity of the object. amount or activity decreased by: deprecated: true is_a: related to at instance level inverse: decreases amount or activity of ## role mixins for use in tagging corresponding role predicates chemical role mixin: description: >- A role played by the chemical entity or part thereof within a chemical context. mixin: true exact_mappings: - CHEBI:51086 biological role mixin: description: >- A role played by the chemical entity or part thereof within a biological context. mixin: true narrow_mappings: - CHEBI:24432 affects response to: is_a: affects in_subset: - translator_minimal domain: chemical entity or gene or gene product range: chemical entity or gene or gene product inverse: response affected by annotations: canonical_predicate: true exact_mappings: - CTD:affects_response_to response affected by: description: >- holds between two chemical entities where the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) of one is affected by the action of the other. is_a: affected by in_subset: - translator_minimal domain: chemical entity or gene or gene product range: chemical entity or gene or gene product increases response to: description: >- holds between two chemical entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other is_a: affects response to in_subset: - translator_minimal domain: chemical entity or gene or gene product range: chemical entity or gene or gene product annotations: canonical_predicate: true opposite_of: decreases response to exact_mappings: - CTD:increases_response_to response increased by: is_a: response affected by in_subset: - translator_minimal domain: chemical entity or gene or gene product range: chemical entity or gene or gene product inverse: increases response to decreases response to: description: >- holds between two chemical entities where the action or effect of one decreases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other is_a: affects response to in_subset: - translator_minimal domain: chemical entity or gene or gene product range: chemical entity or gene or gene product annotations: canonical_predicate: true opposite_of: increases response to exact_mappings: - CTD:decreases_response_to narrow_mappings: - CTD:decreases_response_to_substance response decreased by: is_a: response affected by in_subset: - translator_minimal domain: chemical entity or gene or gene product range: chemical entity or gene or gene product inverse: decreases response to regulates: is_a: affects description: >- A more specific form of affects, that implies the effect results from a biologically evolved control mechanism. Gene-affects-gene relationships will (almost) always involve regulation. Exogenous/environmental chemical-affects-gene relationships are not cases of regulation in this definition. Instead these would be captured using the 'affects' predicate, or possibly one of the 'interacts with' predicates depending on the nature of the interaction. domain: physical essence or occurrent range: physical essence or occurrent annotations: canonical_predicate: true exact_mappings: - RO:0002448 broad_mappings: # https://www.wikidata.org/wiki/Property:P128 - regulates (molecular biology) - WIKIDATA_PROPERTY:P128 - CHEMBL.MECHANISM:modulator - RO:0002295 - RO:0002332 - RO:0002448 notes: >- The RO definition of 'directly regulates the activity of' is an exact_mapping here because it describes genetic regulation from the point of view of one genetic entity regulating another, as opposed to "RO:0002211" which describes process to process regulation. mixins: - interacts with regulated by: is_a: affected by domain: physical essence or occurrent range: physical essence or occurrent inverse: regulates disrupts: is_a: affects aliases: ['disease causes disruption of'] description: >- describes a relationship where one entity degrades or interferes with the structure, function, or occurrence of another. in_subset: - translator_minimal annotations: canonical_predicate: true opposite_of: enables exact_mappings: - SEMMEDDB:DISRUPTS - CHEMBL.MECHANISM:disrupting_agent narrow_mappings: - RO:0004024 - RO:0004025 disrupted by: is_a: affected by description: >- describes a relationship where the structure, function, or occurrence of one entity is degraded or interfered with by another. inverse: disrupts gene product of: is_a: related to at instance level description: >- definition x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of thatf process is either y or something that is ribosomally translated from x exact_mappings: - RO:0002204 domain: gene product mixin range: gene annotations: canonical_predicate: true inverse: has gene product in_subset: - translator_minimal has gene product: is_a: related to at instance level description: >- holds between a gene and a transcribed and/or translated product generated from it domain: gene range: gene product mixin inverse: gene product of in_subset: - translator_minimal close_mappings: # RTX term tagged as inverse mapping - PR:has_gene_template exact_mappings: - RO:0002205 - WIKIDATA_PROPERTY:P688 - NCIT:gene_encodes_gene_product narrow_mappings: - NCIT:R178 transcribed to: is_a: related to at instance level domain: gene range: transcript description: >- inverse of transcribed from inverse: transcribed from exact_mappings: - RO:0002511 - SIO:010080 transcribed from: is_a: related to at instance level domain: transcript range: gene annotations: canonical_predicate: true inverse: transcribed to description: >- x is transcribed from y if and only if x is synthesized from template y exact_mappings: - RO:0002510 - SIO:010081 translates to: is_a: related to at instance level domain: transcript range: protein annotations: canonical_predicate: true inverse: translation of description: >- x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces x (amino acid chain/polypeptide) close_mappings: - RO:0002513 - SIO:010082 translation of: is_a: related to at instance level domain: protein range: transcript description: >- inverse of translates to inverse: translates to close_mappings: - RO:0002512 - SIO:010083 homologous to: is_a: similar to aliases: ['in homology relationship with'] description: >- holds between two biological entities that have common evolutionary origin comments: - typically used to describe homology relationships between genes or gene products in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true exact_mappings: - RO:HOM0000001 - SIO:010302 narrow_mappings: # This is a tricky one to place; seems narrower than the RO mapping but that mapping, RO:0002158 - UBERON_CORE:sexually_homologous_to paralogous to: is_a: homologous to description: >- a homology relationship that holds between entities (typically genes) that diverged after a duplication event. in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true exact_mappings: - RO:HOM0000011 orthologous to: is_a: homologous to description: >- a homology relationship between entities (typically genes) that diverged after a speciation event. in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true exact_mappings: - RO:HOM0000017 - WIKIDATA_PROPERTY:P684 xenologous to: is_a: homologous to description: >- a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor. in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true exact_mappings: - RO:HOM0000018 coexists with: is_a: related to at instance level description: >- holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true broad_mappings: - SEMMEDDB:COEXISTS_WITH narrow_mappings: - BSPO:0000096 - BSPO:0000097 - BSPO:0000098 - BSPO:0000099 - BSPO:0000100 - BSPO:0000102 - BSPO:0000104 - BSPO:0000110 - BSPO:0000113 - BSPO:0015001 - BSPO:0015002 - BSPO:0015003 - BSPO:0015005 - BSPO:0015006 - BSPO:0015007 - BSPO:0015008 - BSPO:0015009 - BSPO:0015012 - BSPO:0015014 - BSPO:parallel_to - UBERON_CORE:anastomoses_with - UBERON_CORE:anteriorly_connected_to - UBERON_CORE:posteriorly_connected_to - UBERON_CORE:channel_for - UBERON_CORE:channels_from - UBERON_CORE:channels_into - UBERON_CORE:conduit_for - UBERON_CORE:distally_connected_to - UBERON_CORE:extends_fibers_into - UBERON_CORE:filtered_through - UBERON_CORE:indirectly_supplies - UBERON_CORE:proximally_connected_to - UBERON_CORE:synapsed_by - UBERON_CORE:transitively_anteriorly_connected_to - UBERON_CORE:transitively_connected_to - UBERON_CORE:transitively_distally_connected_to - UBERON_CORE:transitively_proximally_connected_to # RTX contributed Environmental Ontology term meaning "partially surrounded by" - ENVO:01001307 - FMA:adjacent_to - FMA:afferent_to - FMA:anterior_to - FMA:anteroinferior_to - FMA:anterolateral_to - FMA:anteromedial_to - FMA:anterosuperior_to # RTX contributed terms (also inverses to one another?) might better be mapped to another term with more precise functional semantics? # Some of these terms also seem to be semantic inverses of one another, thus, perhaps not simple narrow_mappings to Biolink - FMA:arterial_supply_of - FMA:has_arterial_supply - FMA:articulates_with - FMA:attaches_to - FMA:bounded_by - FMA:bounds - FMA:branch_of - FMA:connection_type_of - FMA:continuation_branch_of - FMA:continuous_distally_with - FMA:continuous_proximally_with - FMA:corresponds_to - FMA:development_type_of - FMA:developmental_stage_of - FMA:direct_cell_shape_of - FMA:direct_left_of - FMA:direct_right_of - FMA:distal_to - FMA:drains_into - FMA:efferent_to - FMA:external_to - FMA:formed_by - FMA:forms # these next two RTX mapped terms also seem to be inverses of one another - FMA:full_grown_phenotype_of - FMA:has_full_grown_phenotype # these next two RTX mapped terms also seem to be inverses of one another - FMA:fuses_with - FMA:fusion_of - FMA:has_fusion - FMA:germ_origin_of - FMA:has_germ_origin - FMA:has_adherent - FMA:has_branch - FMA:has_connection_type - FMA:has_continuation_branch - FMA:has_development_type - FMA:has_developmental_stage - FMA:has_direct_cell_shape - FMA:has_inherent_3d_shape - FMA:has_insertion - FMA:has_lymphatic_drainage - FMA:has_nerve_supply - FMA:has_observed_anatomical_entity - FMA:has_origin - FMA:has_primary_segmental_supply - FMA:has_projection - FMA:has_regional_part - FMA:has_related_developmental_entity - FMA:has_secondary_segmental_supply - FMA:has_segmental_composition - FMA:has_segmental_supply - FMA:has_tributary - FMA:has_venous_drainage - FMA:inferior_to - FMA:inferolateral_to - FMA:inferomedial_to - FMA:inherent_3d_shape_of - FMA:insertion_of - FMA:internal_to - FMA:lateral_to - FMA:left_lateral_to - FMA:left_medial_to - FMA:lymphatic_drainage_of - FMA:matures_from - FMA:matures_into - FMA:medial_to - FMA:merges_with - FMA:nerve_supply_of - FMA:origin_of - FMA:posterior_to - FMA:posteroinferior_to - FMA:posterolateral_to - FMA:posteromedial_to - FMA:posterosuperior_to - FMA:primary_segmental_supply_of - FMA:projects_from - FMA:projects_to - FMA:proximal_to - FMA:receives_attachment_from - FMA:receives_drainage_from - FMA:receives_input_from - FMA:receives_projection - FMA:related_part - FMA:right_lateral_to - FMA:right_medial_to - FMA:secondary_segmental_supply_of - FMA:segmental_composition_of - FMA:segmental_supply_of - FMA:sends_output_to - FMA:superior_to - FMA:superolateral_to - FMA:superomedial_to - FMA:surrounded_by - FMA:surrounds - FMA:tributary_of - FMA:venous_drainage_of # These LOINC: terms contributed by RTX were only tagged as 'biolink:has_attribute' # but seem more aligned to the FMA entries in this biolink term, so I leave them here for now - LOINC:has_lateral_anatomic_location - LOINC:has_lateral_location_presence - UBERON_NONAMESPACE:distally_connected_to - UBERON_NONAMESPACE:subdivision_of # These RO terms seem similar to the FMA terms above, so I place them here rather than under 'biolink:related_to' - RO:0002219 - RO:0002220 - RO:0002221 - SO:has_origin # RTX mapped these UBERON terms all here - UBERON:anastomoses_with - UBERON:anteriorly_connected_to - UBERON:channel_for - UBERON:channels_from - UBERON:channels_into - UBERON:conduit_for - UBERON:distally_connected_to - UBERON:existence_starts_and_ends_during - UBERON:extends_fibers_into - UBERON:filtered_through - UBERON:in_central_side_of - UBERON:in_innermost_side_of - UBERON:in_outermost_side_of - UBERON:indirectly_supplies - UBERON:posteriorly_connected_to - UBERON:protects - UBERON:proximally_connected_to - UBERON:sexually_homologous_to in pathway with: description: >- holds between two genes or gene products that are part of in the same biological pathway is_a: coexists with domain: gene or gene product range: gene or gene product in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true related_mappings: # generally pertains to membership of a (subject) component - gene, # metabolite, etc? - in an (object) metabolic pathway - SIO:010532 in complex with: description: >- holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex is_a: coexists with domain: gene or gene product range: gene or gene product in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true related_mappings: # generally pertains to membership of a (subject) protein in an (object) protein complex (doesn't cover RNA-Protein, Lipid-Protein, etc complexes though) - SIO:010497 broad_mappings: # generally pertains to membership of any (subject) constituent molecule in an (object) molecular complex (might also generically cover RNA-Protein, Lipid-Protein, etc complexes) - SIO:010285 in cell population with: description: >- holds between two genes or gene products that are expressed in the same cell type or population is_a: coexists with domain: gene or gene product range: gene or gene product in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true colocalizes with: description: >- holds between two entities that are observed to be located in the same place. is_a: coexists with in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true exact_mappings: - RO:0002325 # Despite the name, note that this particular entity is # NOT a biolink:Association but rather, a biolink:predicate genetic association: deprecated: true deprecated_element_has_exact_replacement: biolink:genetically_associated_with is_a: associated with symmetric: true genetically associated with: is_a: associated with description: >- symmetric: true annotations: canonical_predicate: true description: >- Co-occurrence of a certain allele of a genetic marker and the phenotype of interest in the same individuals at above-chance level exact_mappings: - WIKIDATA_PROPERTY:P2293 in_subset: - translator_minimal gene associated with condition: is_a: genetically associated with description: >- holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with domain: gene range: disease or phenotypic feature annotations: canonical_predicate: true in_subset: - translator_minimal broad_mappings: - GENO:0000840 # broader than a single gene: 'genotype' pathogenic for condition - GENO:0000841 narrow_mappings: # narrower: just diseases, not phenotypic features as well - NCIT:R38 - NCIT:R175 - NCIT:R48 condition associated with gene: is_a: genetically associated with aliases: ['disease associated with gene'] description: >- holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products domain: disease or phenotypic feature range: gene in_subset: - translator_minimal inverse: gene associated with condition narrow_mappings: # RO term implies causality making it narrower - RO:0004000 # narrower since just diseases, not phenotypic features as well - NCIT:R176 contributes to: is_a: related to at instance level description: >- holds between two entities where the occurrence, existence, or activity of one contributes to the occurrence or generation of the other in_subset: - translator_minimal annotations: canonical_predicate: true close_mappings: # RTX contributed mapping tagged as 'inverse' of this Biolink predicate - IDO:0000664 exact_mappings: - RO:0002326 narrow_mappings: - CTD:marker_mechanism - MONDO:predisposes_towards # RTX mapped this to 'biolink:related_to' but this term seems a more precise mapping - RO:0002255 # RTX term 'contributes to condition' mapped to 'biolink:causes' seems more suitable here - RO:0003304 contribution from: is_a: related to at instance level in_subset: - translator_minimal inverse: contributes to causes: description: >- holds between two entities where the occurrence, existence, or activity of one causes the occurrence or generation of the other is_a: contributes to in_subset: - translator_minimal annotations: canonical_predicate: true exact_mappings: - SEMMEDDB:CAUSES - WIKIDATA_PROPERTY:P1542 - SNOMED:cause_of - RO:0003303 broad_mappings: - RO:0002410 - RO:0002506 narrow_mappings: - MONDO:disease_triggers - GOREL:0000040 - MONDO:disease_causes_feature - NCIT:allele_has_abnormality - NCIT:biological_process_has_result_biological_process - NCIT:chemical_or_drug_has_physiologic_effect # RTX mapped terms as 'biolink:part_of' but implied sequence of causality suggests 'biolink:causes'? - NCIT:chemical_or_drug_initiates_biological_process - NCIT:process_initiates_biological_process - NCIT:chromosome_mapped_to_disease - NCIT:disease_has_normal_tissue_origin - NBO-PROPERTY:in_response_to - orphanet:317343 - orphanet:317344 - orphanet:317346 - orphanet:410295 - orphanet:410296 # RTX mapped this term to 'biolink:related_to' but this term seems a more precise mapping - RO:0002256 - RO:0002315 - RO:0002507 - RO:0002509 - RO:0004001 - SNOMED:causative_agent_of - SNOMED:has_realization - UMLS:has_physiologic_effect caused by: description: >- holds between two entities where the occurrence, existence, or activity of one is caused by the occurrence or generation of the other is_a: contribution from aliases: ['disease caused by disruption of', 'disease has basis in dysfunction of', 'realized in response to', 'realized in response to stimulus'] in_subset: - translator_minimal inverse: causes exact_mappings: - WIKIDATA_PROPERTY:P828 narrow_mappings: - RO:0001022 - RO:0002608 - RO:0004019 - RO:0004020 - RO:0004028 - RO:0009501 # TODO: ameliorates and exacerbates inverses. ameliorates condition: aliases: ['ameliorates', 'beneficial for condition', 'therapeutic for condition'] is_a: affects description: >- Holds between an entity and an existing medical condition (disease or phenotypic feature) where the entity is able to ameliorate symptoms, stabilize progression, or cure the condition. notes: >- This predicate describes a narrower view of 'treats' - that covers interventions that are beneficial for existing disease, and excludes interventions that prevent/reduce risk of developing a condition in the future. mixins: - treats domain: chemical or drug or treatment range: disease or phenotypic feature annotations: canonical_predicate: true opposite_of: exacerbates condition exact_mappings: - RO:0003307 condition ameliorated by: inverse: ameliorates condition is_a: affected by domain: disease or phenotypic feature range: chemical or drug or treatment preventative for condition: aliases: ['prophylactic for', 'prevents'] is_a: affects likelihood of mixins: - treats description: >- Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to prevent it manifesting in the first place. domain: chemical or drug or treatment range: disease or phenotypic feature annotations: canonical_predicate: true opposite_of: promotes condition in_subset: - translator_minimal broad_mappings: - SEMMEDDB:PREVENTS condition prevented by: inverse: preventative for condition is_a: affected by domain: disease or phenotypic feature range: chemical or drug or treatment promotes condition: mixin: true is_a: related to at instance level description: >- Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to promote it manifesting in the first place. domain: chemical or drug or treatment range: disease or phenotypic feature annotations: canonical_predicate: true opposite_of: preventative for condition in_subset: - translator_minimal condition promoted by: is_a: likelihood affected by inverse: promotes condition domain: disease or phenotypic feature range: chemical or drug or treatment predisposes to condition: aliases: ['risk factor for'] is_a: affects likelihood of mixins: - promotes condition description: >- Holds between two entities where the presence or application of one increases the chance that the other will come to be. domain: chemical or drug or treatment range: disease or phenotypic feature annotations: canonical_predicate: true in_subset: - translator_minimal broad_mappings: - SEMMEDDB:PREDISPOSES condition predisposed by: is_a: likelihood affected by inverse: predisposes to condition domain: disease or phenotypic feature range: chemical or drug or treatment exacerbates condition: aliases: ['exacerbates', 'detrimental for condition'] is_a: affects description: >- Holds between a substance, procedure, or activity and an existing medical condition (disease or phenotypic feature) where the substance, procedure, or activity worsens some or all aspects of the condition. mixins: - promotes condition domain: chemical or drug or treatment range: disease or phenotypic feature annotations: canonical_predicate: true opposite_of: ameliorates condition exact_mappings: - RO:0003309 broad_mappings: - SEMMEDDB:COMPLICATES condition exacerbated by: inverse: exacerbates condition is_a: affected by domain: disease or phenotypic feature range: chemical or drug or treatment in_subset: - translator_minimal treats: is_a: treats or applied or studied to treat mixin: true aliases: ['is substance that treats', 'indicated for', 'ameliorates or prevents condition'] description: >- Holds between an intervention (substance, procedure, or activity) and a medical condition (disease or phenotypic feature), and states that the intervention is able to ameliorate, stabilize, or cure the condition or delay, prevent, or reduce the risk of it manifesting in the first place. ‘Treats’ edges should be asserted (knowledge_level: assertion) only in cases where there is strong supporting evidence - i.e. the intervention is approved for the condition, passed phase 3 or in phase 4 trials for the condition, or is an otherwise established treatment in the medical community (e.g. a widely-accepted or formally recommended off-label use). In the absence of such evidence, weaker predicates should be used in asserted edges (e.g. ‘in clinical trials for’ or ‘beneficial in models of’). ‘Treats’ edges based on weaker or indirect forms of evidence can however be created as predictions (knowledge_level: prediction) and should point to the more foundational asserted edges that support them. domain: chemical or drug or treatment range: disease or phenotypic feature annotations: canonical_predicate: true in_subset: - translator_minimal related_mappings: - MONDO:disease_responds_to exact_mappings: - DRUGBANK:treats - WIKIDATA_PROPERTY:P2175 narrow_mappings: # "is substance that treats" constrains statements to # a subset of the universe of all possible treatments - RO:0002606 - NCIT:regimen_has_accepted_use_for_disease # RTX mapped REPODB terms - REPODB:clinically_tested_approved_unknown_phase - REPODB:clinically_tested_suspended_phase_0 - REPODB:clinically_tested_suspended_phase_1 - REPODB:clinically_tested_suspended_phase_1_or_phase_2 - REPODB:clinically_tested_suspended_phase_2 - REPODB:clinically_tested_suspended_phase_2_or_phase_3 - REPODB:clinically_tested_suspended_phase_3 - REPODB:clinically_tested_terminated_phase_0 - REPODB:clinically_tested_terminated_phase_1 - REPODB:clinically_tested_terminated_phase_1_or_phase_2 - REPODB:clinically_tested_terminated_phase_2 - REPODB:clinically_tested_terminated_phase_2_or_phase_3 - REPODB:clinically_tested_terminated_phase_3 - REPODB:clinically_tested_withdrawn_phase_0 - REPODB:clinically_tested_withdrawn_phase_1 - REPODB:clinically_tested_withdrawn_phase_1_or_phase_2 - REPODB:clinically_tested_withdrawn_phase_2 - REPODB:clinically_tested_withdrawn_phase_2_or_phase_3 - REPODB:clinically_tested_withdrawn_phase_3 - SNOMED:plays_role broad_mappings: - DRUGBANK:treats - SEMMEDDB:TREATS - WIKIDATA_PROPERTY:P2175 - MONDO:disease_responds_to treated by: mixin: true domain: disease or phenotypic feature range: chemical or drug or treatment # range: chemical or drug or treatment in_subset: - translator_minimal inverse: treats exact_mappings: - WIKIDATA_PROPERTY:P2176 # RTX contributed term tagged as inverse of 'biolink:treats' - MONDO:disease_responds_to narrow_mappings: # "is treated by substance" constrains statements to # subset of the universe of all possible treatments - RO:0002302 studied to treat: is_a: related to at instance level description: >- Holds between an substance, procedure, or activity and a medical condition, and reports that one or more scientific study has been performed to specifically test the potential of the substance, procedure, or activity to treat the medical condition (i.e. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place). notes: >- Predicates in this hierarchy are used in practice when a source reports performance of a study, but there is not sufficient evidence or demonstrated efficacy against the condition to warrant creating a ‘treats’ assertion edge. Note however that a 'studied to treat' edge may be used as evidence to support creation of a separate 'treats' prediction edge. domain: chemical or drug or treatment range: disease or phenotypic feature mixins: - treats or applied or studied to treat annotations: canonical_predicate: true in clinical trials for: is_a: studied to treat description: >- Holds between an intervention and a medical condition, and reports that a clinical trial is being or has been performed in human patients to test the potential of the intervention to treat the medical condition (e.g. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place). notes: >- This predicate should be used when a source reports a clinical trial where the intervention is being or was interrogated, regardless of the phase of the trial, or its ultimate outcome. Information about phase and outcome can be capture using other modeling elements. domain: chemical or drug or treatment range: disease or phenotypic feature mixins: - treats or applied or studied to treat annotations: canonical_predicate: true in_subset: - translator_minimal # TODO: add inverse tested by clinical trials of: is_a: treated in studies by inverse: in clinical trials for domain: disease or phenotypic feature range: chemical or drug or treatment treated in studies by: is_a: treated by inverse: studied to treat domain: disease or phenotypic feature range: chemical or drug or treatment tested by preclinical trials of: is_a: treated in studies by inverse: in preclinical trials for domain: disease or phenotypic feature range: chemical or drug or treatment in preclinical trials for: is_a: studied to treat description: >- Holds between an substance, procedure, or activity and a medical condition, and reports that a pre-clinical study has been performed specifically to test the potential of the substance, procedure, or activity to treat the medical condition (i.e. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place). mixins: - treats or applied or studied to treat domain: chemical or drug or treatment range: disease or phenotypic feature annotations: canonical_predicate: true in_subset: - translator_minimal # TODO: inverse of in_preclincal_trials_for needed beneficial in models for: is_a: in preclinical trials for description: >- Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc). notes: >- This predicate would be used to represent Model Organism Database (MOD) records reporting that an intervention alleviated phenotypes associated with a human disease in a model organism designated as a model of that disease. (e.g. a ZFIN record reporting that treatment with Braf Inhibitors reduced the abnormal brain cell proliferation phenotype of zebrafish used to model the human disease Kabuki Syndrome) . mixins: - treats or applied or studied to treat domain: chemical or drug or treatment range: disease or phenotypic feature annotations: canonical_predicate: true in_subset: - translator_minimal # TODO: need inverse of beneficial_in_models_for models demonstrating benefits for: is_a: tested by preclinical trials of inverse: beneficial in models for domain: disease or phenotypic feature range: chemical or drug or treatment applied to treat: aliases: ['administered to treat', 'used to treat', 'given to treat'] is_a: related to at instance level description: >- Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity was actually taken by one or more patients with the intent of treating the condition. notes: >- This predicate is used simply to report observations of use in the real world, and is agnostic to whether the treatment is approved for or might be effective in treating the condition. The treatment could be taken by a patient on their own accord or prescribed by a clinician, as an off-label or an approved intervention. In practice, it would be used to represent records/statements from patient self-reporting sources like FAERS / AEOLUS where patients directly report the condition for which they took a drug, or statements from a database cataloging instances of off-label prescription of drugs for specific conditions (e.g. here, here, here). mixins: - treats or applied or studied to treat domain: chemical or drug or treatment range: disease or phenotypic feature annotations: canonical_predicate: true in_subset: - translator_minimal # TODO: need an inverse for taken to treat treatment applications from: is_a: related to at instance level inverse: applied to treat domain: disease or phenotypic feature range: chemical or drug or treatment treats or applied or studied to treat: mixin: true description: >- Holds between an substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to treat the condition, has been observed to be taken/prescribed in practice with the intent of treating the condition, or has been interrogated in a scientific study that hypothesized an ability to treat the condition (in humans or other biological systems/organisms). notes: >- This predicate is helpful both as a grouping predicate to aid in searching for broader senses of treating a condition, and as a catch-all for representing sources that are not clear about the sense of treats that is being reported. For example, text-mined statements concerning treatments for disease are based on sentences that can report treatment in any of these different senses and thus require a broader predicate such as this to safely report statement semantics. annotations: canonical_predicate: true in_subset: - translator_minimal exact_mappings: - SEMMEDDB:TREATS subject of treatment application or study for treatment by: mixin: true domain: disease or phenotypic feature range: chemical or drug or treatment inverse: treats or applied or studied to treat correlated with: is_a: associated with description: >- A relationship that holds between two concepts represented by variables for which a statistical dependence is demonstrated using a correlation analysis method. notes: >- These concepts may map exactly to the statistical variables, or represent related entities for which the variables serve as proxies in an Association (e.g. diseases, chemical entities or processes). domain: named thing range: named thing in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true exact_mappings: - RO:0002610 - PATO:correlates_with # proposed positive and negative semantic extensions to the general "correlated with" predicate positively correlated with: is_a: correlated with description: >- A relationship that holds between two concepts represented by variables for which a statistical correlation is demonstrated, wherein variable values move together in the same direction (i.e. increased in one or presence of one correlates with an increase or presence of the other). domain: named thing range: named thing in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true opposite_of: negatively correlated with exact_mappings: - CTD:positive_correlation negatively correlated with: is_a: correlated with description: >- A relationship that holds between two concepts represented by variables for which a statistical correlation is demonstrated, wherein variable values move in opposite directions (i.e. increased in one or presence of one correlates with a decrease or absence of the other). domain: named thing range: named thing in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true opposite_of: positively correlated with exact_mappings: - CTD:negative_correlation occurs together in literature with: is_a: correlated with description: >- holds between two entities where their co-occurrence is correlated by counts of publications in which both occur, using some threshold of occurrence as defined by the edge provider. domain: named thing range: named thing in_subset: translator_minimal symmetric: true annotations: canonical_predicate: true coexpressed with: is_a: correlated with description: >- holds between any two genes or gene products, in which both are generally expressed within a single defined experimental context. domain: gene or gene product range: gene or gene product symmetric: true annotations: canonical_predicate: true has biomarker: is_a: correlated with description: >- holds between a disease or phenotypic feature and a measurable chemical entity that is used as an indicator of the presence or state of the disease or feature. # metabolite domain: disease or phenotypic feature range: chemical entity or gene or gene product in_subset: - translator_minimal inverse: biomarker for narrow_mappings: # some RTX terms contributed as inverses of 'biolink:biomarker_for' - NCIT:disease_has_molecular_abnormality - NCIT:disease_is_marked_by_gene biomarker for: is_a: correlated with description: >- holds between a measurable chemical entity and a disease or phenotypic feature, where the entity is used as an indicator of the presence or state of the disease or feature. domain: chemical entity or gene or gene product range: disease or phenotypic feature annotations: canonical_predicate: true in_subset: - translator_minimal exact_mappings: - NCIT:R39 broad_mappings: # Generic marker definition not specific to biomarkers per say - RO:0002607 narrow_mappings: - NCIT:R47 # RTX term was tagged as 'biolink:actively_involved_in' but maps better here? - NCIT:genetic_biomarker_related_to - NCIT:is_molecular_abnormality_of_disease - orphanet:465410 # It may be helpful to introduce an intermediate predicate in between 'related_to' and 'expressed in' # which would have a domain of 'biological entity' and range of 'anatomical entity', to map predicates # which are biological which have manifestation in an anatomical site, e.g. RO:0004026, RO:0004027 and others expressed in: is_a: located in description: >- holds between a gene or gene product and an anatomical entity in which it is expressed domain: gene or gene product range: anatomical entity multivalued: true annotations: canonical_predicate: true in_subset: - translator_minimal exact_mappings: - RO:0002206 narrow_mappings: - NCIT:R49 - NCIT:R46 expresses: is_a: location of aliases: ['anatomy expresses gene'] description: >- holds between an anatomical entity and gene or gene product that is expressed there domain: anatomical entity range: gene or gene product multivalued: true in_subset: - translator_minimal inverse: expressed in exact_mappings: - RO:0002292 has phenotype: is_a: related to at instance level aliases: ['disease presents symptom'] description: >- holds between a biological entity and a phenotype, where a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). In SNOMEDCT, disorders with keyword 'characterized by' should translate into this predicate. domain: biological entity range: phenotypic feature multivalued: true annotations: canonical_predicate: true notes: - check the range in_subset: - translator_minimal exact_mappings: - RO:0002200 broad_mappings: - NCIT:R115 - NCIT:R108 narrow_mappings: - NCIT:R89 - DOID-PROPERTY:has_symptom - RO:0004022 phenotype of: is_a: related to at instance level domain: phenotypic feature range: biological entity multivalued: true inverse: has phenotype # TODO: predicate inverse for occurs in occurs in: is_a: related to at instance level description: >- holds between a process and a material entity or site within which the process occurs in_subset: - translator_minimal annotations: canonical_predicate: true close_mappings: # These RTX mapped terms tagged as the inverse of "biolink:occurs_in", i.e. Entity/Site contains Process - BFO:0000067 - SNOMED:has_occurrence - UBERON:site_of exact_mappings: - BFO:0000066 - PathWhiz:has_location - SNOMED:occurs_in narrow_mappings: # SemMedDb term 'OCCURS_IN' constrained to something (other than process) occurring in a group or population - SEMMEDDB:OCCURS_IN # SemMedDb term 'PROCESS_IN' constrained specifically to a process occurring in the object concept entity - SEMMEDDB:PROCESS_OF # Uberon term constrained to a 'site' as object concept - UBERON_CORE:site_of - LOINC:has_imaged_location - PathWhiz:in_species - RO:0002231 - RO:0002232 - SNOMED:has_direct_procedure_site - SNOMED:has_direct_site - SNOMED:has_procedure_site contains process: is_a: related to at instance level inverse: occurs in located in: is_a: related to at instance level description: >- holds between a material entity and a material entity or site within which it is located (but of which it is not considered a part) in_subset: - translator_minimal annotations: canonical_predicate: true exact_mappings: - RO:0001025 - FMA:has_location narrow_mappings: - GOREL:0001004 - BSPO:0000107 - BSPO:0000108 - BSPO:0000120 - BSPO:0000121 - BSPO:0000122 - BSPO:0000123 - BSPO:0000124 - BSPO:0000125 - BSPO:0000126 - BSPO:0001100 - BSPO:0001101 - BSPO:0001107 - BSPO:0015101 - BSPO:0015102 - BSPO:0015202 - UBERON_CORE:in_central_side_of - UBERON_CORE:in_innermost_side_of - UBERON_CORE:in_outermost_side_of - NCIT:R100 - EFO:0000784 - FMA:has_location - HMDB:at_cellular_location - HMDB:at_tissue - HMDB:in_biospecimen - LOINC:has_imaging_focus - NCIT:R156 - NCIT:R155 - NCIT:R145 - NCIT:R40 - NCIT:R171 - NCIT:R167 - NCIT:R165 - NCIT:R169 - NCIT:R170 - NCIT:R166 - NCIT:R168 - RO:0002303 - SNOMED:has_finding_site - SNOMED:has_indirect_procedure_site - SNOMED:has_inherent_location domain: named thing range: named thing location of: is_a: related to at instance level aliases: ['site of'] domain: named thing range: named thing description: >- holds between material entity or site and a material entity that is located within it (but not considered a part of it) in_subset: - translator_minimal inverse: located in exact_mappings: - RO:0001015 - SEMMEDDB:LOCATION_OF - WIKIDATA_PROPERTY:P276 # RTX tagged this as an inverse of biolink:located_in - FMA:location_of narrow_mappings: - SNOMED:inherent_location_of - NCIT:Anatomic_Structure_Has_Location_Role disease has location: description: >- A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. is_a: related to exact_mappings: - RO:0004026 - MONDO:disease_has_location location of disease: is_a: related to inverse: disease has location similar to: is_a: related to at instance level description: >- holds between an entity and some other entity with similar features. in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true exact_mappings: - RO:HOM0000000 - SO:similar_to chemically similar to: is_a: similar to description: >- holds between one small molecule entity and another that it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity. in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true narrow_mappings: - CHEBI:has_parent_hydride # subproperty - CHEBI:has_functional_parent # subproperty - CHEBI:is_conjugate_acid_of # subproperty - CHEBI:is_conjugate_base_of # subproperty - CHEBI:is_enantiomer_of # subproperty - CHEBI:is_tautomer_of # subproperty - NCIT:has_salt_form has sequence location: is_a: related to at instance level description: >- holds between two nucleic acid entities when the subject can be localized in sequence coordinates on the object. For example, between an exon and a chromosome/contig. domain: nucleic acid entity range: nucleic acid entity annotations: canonical_predicate: true exact_mappings: - faldo:location sequence location of: is_a: related to at instance level domain: nucleic acid entity range: nucleic acid entity inverse: has sequence location model of: is_a: related to at instance level description: >- holds between a thing and some other thing it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity. annotations: canonical_predicate: true in_subset: - translator_minimal exact_mappings: - RO:0003301 narrow_mappings: - FOODON:00001301 models: is_a: related to at instance level inverse: model of overlaps: is_a: related to at instance level description: >- holds between entities that overlap in their extents (materials or processes) in_subset: - translator_minimal symmetric: true annotations: canonical_predicate: true exact_mappings: - RO:0002131 narrow_mappings: - BSPO:0005001 - CHEMBL.MECHANISM:overlaps_with - RO:0002100 - RO:0002102 - RO:0002433 has part: is_a: overlaps annotations: canonical_predicate: true opposite_of: lacks part description: >- holds between wholes and their parts (material entities or processes) in_subset: - translator_minimal exact_mappings: - BFO:0000051 # term name seems to be 'realizes' but RTX maps this term here - BFO:0000055 - WIKIDATA_PROPERTY:P527 - RO:0001019 - RXNORM:consists_of - RXNORM:has_part broad_mappings: # To 'contain' is 'to have something inside or include something as a part'; slightly broader? - RO:0001019 - FMA:contains - RXNORM:contains narrow_mappings: - BFO:0000117 # RTX term originally mapped to 'biolink:coexists_with'? - FMA:has_constitutional_part - FMA:has_part # Several of the following RTX terms were originally mapped as inverses to 'biolink:part_of'? - FMA:has_member - FOODON:00001563 - FOODON:00002420 - LOINC:has_component - LOINC:has_member - MEDDRA:has_member - MONDO:disease_has_major_feature - NCIT:complex_has_physical_part - NDDF:has_ingredient - PathWhiz:has_element_in_bound # This RTX contributed term was tagged as 'biolink:has_gene_product' but seems more compositional in nature - NCIT:R50 - PathWhiz:has_protein_in_complex - RO:0002104 - RO:0002180 - RO:0002351 - RO:0002473 - RO:0002524 - RO:0002551 - RXNORM:has_ingredient - SNOMED:has_component - UMLS:has_component has plasma membrane part: is_a: has part description: >- Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. exact_mappings: - RO:0002104 annotations: canonical_predicate: true in_subset: - translator_minimal composed primarily of: is_a: related to description: >- x composed_primarily_of_y if:more than half of the mass of x is made from parts of y. exact_mappings: - RO:0002473 annotations: canonical_predicate: true in_subset: - translator_minimal primarily composed of: inverse: composed primarily of is_a: related to plasma membrane part of: is_a: part of inverse: has plasma membrane part part of: is_a: overlaps description: >- holds between parts and wholes (material entities or processes) in_subset: - translator_minimal inverse: has part exact_mappings: - BFO:0000050 - SEMMEDDB:PART_OF - WIKIDATA_PROPERTY:P361 - FMA:part_of - RXNORM:constitutes - RXNORM:part_of broad_mappings: # To 'contain' is 'to have something inside or include something as a part' - RO:0001018 - FMA:contained_in - RXNORM:contained_in narrow_mappings: - BSPO:0001106 - BSPO:0001108 - BSPO:0001113 - BSPO:0001115 - UBERON_CORE:layer_part_of - UBERON_CORE:subdivision_of - UBERON_CORE:trunk_part_of - CHEBI:is_substituent_group_from - CPT:panel_element_of - CPT:panel_element_of_possibly_included - DRUGBANK:component_of - FMA:constitutional_part_of - FMA:member_of - FMA:regional_part_of - FMA:related_developmental_entity_of - LOINC:component_of - LOINC:has_supersystem - LOINC:member_of - LOINC:multipart_of - MEDDRA:member_of - MONDO:part_of_progression_of_disease - NCIT:R82 - NCIT:R27 - NCIT:is_component_of_chemotherapy_regimen - NDDF:ingredient_of - RO:0002007 - RO:0002350 - RO:0002376 - RO:0002380 - RO:0002571 - RO:0002572 - RO:0002576 - RXNORM:ingredient_of - RXNORM:ingredients_of - RXNORM:precise_ingredient_of - SNOMED:active_ingredient_of - SNOMED:basis_of_strength_substance_of - SNOMED:component_of - SNOMED:direct_substance_of - SNOMED:during - SNOMED:focus_of - SNOMED:has_dependent - SNOMED:part_anatomy_structure_of - SNOMED:precise_active_ingredient_of - UBERON:subdivision_of - UMLS:component_of - UMLS:has_owning_affiliate - UMLS:owning_subsection_of - VANDF:ingredient_of has input: is_a: has participant description: >- holds between a process and a continuant, where the continuant is an input into the process domain: biological process or activity range: named thing annotations: canonical_predicate: true opposite_of: has output in_subset: - translator_minimal exact_mappings: - RO:0002233 - SEMMEDDB:USES narrow_mappings: - LOINC:has_fragments_for_synonyms - LOINC:has_system - PathWhiz:has_left_element - RO:0002590 - RO:0004009 - SNOMED:has_finding_method - SNOMED:has_precondition - SNOMED:has_specimen_source_identity - SNOMED:has_specimen_substance - SNOMED:uses_access_device - SNOMED:uses_device - SNOMED:uses_energy - SNOMED:uses_substance is input of: is_a: participates in domain: named thing range: biological process or activity inverse: has input in_subset: - translator_minimal exact_mappings: - RO:0002352 has output: is_a: has participant description: >- holds between a process and a continuant, where the continuant is an output of the process domain: biological process or activity range: named thing annotations: canonical_predicate: true opposite_of: has input in_subset: - translator_minimal exact_mappings: - RO:0002234 narrow_mappings: - NCIT:R31 - OBI:0000299 - PathWhiz:has_right_element - RO:0002296 - RO:0002297 - RO:0002298 - RO:0002299 - RO:0002588 - RO:0004008 is output of: is_a: participates in domain: named thing range: biological process or activity inverse: has output in_subset: - translator_minimal exact_mappings: - RO:0002353 narrow_mappings: - RO:0002354 has participant: is_a: related to at instance level description: >- holds between a process and a continuant, where the continuant is somehow involved in the process domain: biological process or activity range: occurrent annotations: canonical_predicate: true in_subset: - translator_minimal close_mappings: - WIKIDATA_PROPERTY:P2283 exact_mappings: - RO:0000057 - RO:has_participant narrow_mappings: - BFO:0000167 # Several of the following RTX terms tagged as inverse to 'biolink:participates_in' - LOINC:has_subject - NCIT:process_involves_gene - NBO-PROPERTY:has_participant - PathWhiz:has_bound - PathWhiz:has_compound - PathWhiz:has_element_collection - PathWhiz:has_enzyme - OBI:0000293 - PathWhiz:has_nucleic_acid - PathWhiz:has_protein - PathWhiz:has_reaction - RO:0002565 - RO:0004007 - RO:0004020 - RO:0004021 - SNOMED:has_indirect_device - SNOMED:has_procedure_device - SNOMED:has_recipient_category catalyzes: is_a: participates in annotations: canonical_predicate: true exact_mappings: - RO:0002327 has catalyst: is_a: has participant inverse: catalyzes has substrate: is_a: has participant domain: chemical entity or gene or gene product range: chemical entity or gene or gene product annotations: canonical_predicate: true is substrate of: is_a: participates in inverse: has substrate domain: chemical entity or gene or gene product range: chemical entity or gene or gene product participates in: is_a: related to at instance level description: >- holds between a continuant and a process, where the continuant is somehow involved in the process range: biological process or activity domain: occurrent inverse: has participant in_subset: - translator_minimal exact_mappings: - RO:0000056 - BFO:0000056 narrow_mappings: - DRUGBANK:pathway - HMDB:in_pathway - LOINC:is_given_pharmaceutical_substance_for - NCIT:R130 - NCIT:R37 - NCIT:R131 - NCIT:R51 - NCIT:R53 - OBI:0000295 - RO:0002216 - RO:0002505 - SNOMED:has_direct_device actively involved in: is_a: participates in aliases: ['involved in'] description: >- holds between a continuant and a process or function, where the continuant actively contributes to part or all of the process or function it realizes domain: named thing range: biological process or activity annotations: canonical_predicate: true in_subset: - translator_minimal exact_mappings: - RO:0002331 narrow_mappings: - NBO-PROPERTY:by_means - orphanet:317348 - orphanet:317349 - orphanet:327767 - RO:0002503 actively involves: is_a: has participant domain: biological process or activity range: named thing inverse: actively involved in in_subset: - translator_minimal capable of: is_a: actively involved in description: >- holds between a physical entity and process or function, where the continuant alone has the ability to carry out the process or function. domain: named thing range: occurrent annotations: canonical_predicate: true in_subset: - translator_minimal exact_mappings: - RO:0002215 narrow_mappings: - NCIT:R52 - RO:0002500 can be carried out by: is_a: actively involves inverse: capable of domain: occurrent range: named thing enables: is_a: participates in description: >- holds between a physical entity and a process, where the physical entity executes the process domain: physical entity range: biological process or activity annotations: canonical_predicate: true in_subset: - translator_minimal inverse: enabled by exact_mappings: - RO:0002327 enabled by: is_a: has participant description: >- holds between a process and a physical entity, where the physical entity executes the process domain: biological process or activity range: physical entity in_subset: - translator_minimal inverse: enables exact_mappings: - RO:0002333 annotations: opposite_of: prevented by derives into: is_a: related to at instance level aliases: ['is normal cell origin of disease', 'may be normal cell origin of disease'] description: >- holds between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity in_subset: - translator_minimal inverse: derives from exact_mappings: - RO:0001001 - SEMMEDDB:CONVERTS_TO # RTX posted terms as inverse of 'biolink:derives_from' - FMA:derives derives from: is_a: related to at instance level annotations: canonical_predicate: true description: >- holds between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity in_subset: - translator_minimal - samples inverse: derives into exact_mappings: - RO:0001000 - FMA:derives_from - DOID-PROPERTY:derives_from narrow_mappings: - CHEBI:has_functional_parent - SNOMED:has_specimen_source_topography is metabolite of: is_a: derives from description: >- holds between two molecular entities in which the first one is derived from the second one as a product of metabolism domain: molecular entity range: molecular entity in_subset: - translator_minimal inverse: has metabolite comments: - The CHEBI ID represents a role rather than a predicate exact_mappings: - CHEBI:25212 has metabolite: is_a: derives into description: >- holds between two molecular entities in which the second one is derived from the first one as a product of metabolism domain: molecular entity range: molecular entity annotations: canonical_predicate: true in_subset: - translator_minimal comments: - The CHEBI ID represents a role rather than a predicate exact_mappings: - CHEBI:25212 food component of: is_a: part of description: >- holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive) domain: chemical entity range: chemical entity in_subset: - translator_minimal inverse: has food component has food component: is_a: has part description: >- holds between food and one or more chemical entities composing it, irrespective of nutritional value (i.e. could also be a contaminant or additive) domain: chemical entity range: chemical entity annotations: canonical_predicate: true in_subset: - translator_minimal nutrient of: is_a: food component of description: >- holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive) domain: chemical entity range: chemical entity in_subset: - translator_minimal inverse: has nutrient has nutrient: is_a: has food component description: >- one or more nutrients which are growth factors for a living organism domain: chemical entity range: chemical entity annotations: canonical_predicate: true in_subset: - translator_minimal exact_mappings: - WIKIDATA:Q181394 is active ingredient of: is_a: part of description: >- holds between a molecular entity and a drug, in which the former is a part of the latter, and is a biologically active component domain: molecular entity range: drug in_subset: - translator_minimal inverse: has active ingredient mappings: - RO:0002249 has active ingredient: is_a: has part description: >- holds between a drug and a molecular entity in which the latter is a part of the former, and is a biologically active component domain: drug range: molecular entity annotations: canonical_predicate: true opposite_of: is excipient of in_subset: - translator_minimal inverse: is active ingredient of mappings: - RO:0002248 is excipient of: is_a: part of description: >- holds between a molecular entity and a drug in which the former is a part of the latter, and is a biologically inactive component domain: molecular entity range: drug in_subset: - translator_minimal inverse: has excipient mappings: - WIKIDATA:Q902638 has excipient: is_a: has part description: >- holds between a drug and a molecular entities in which the latter is a part of the former, and is a biologically inactive component domain: drug range: molecular entity annotations: canonical_predicate: true in_subset: - translator_minimal mappings: - WIKIDATA:Q902638 manifestation of: is_a: related to at instance level description: >- that part of a phenomenon which is directly observable or visibly expressed, or which gives evidence to the underlying process; used in SemMedDB for linking things like dysfunctions and processes to some disease or syndrome range: disease annotations: canonical_predicate: true in_subset: - translator_minimal exact_mappings: - SEMMEDDB:MANIFESTATION_OF - OMIM:manifestation_of broad_mappings: # Wikidata's definition is slightly broader: "inherent and characteristic embodiment of a given concept" - WIKIDATA_PROPERTY:P1557 narrow_mappings: - SNOMED:has_definitional_manifestation has manifestation: is_a: related to at instance level domain: disease inverse: manifestation of mode of inheritance of: is_a: manifestation of domain: genetic inheritance range: disease or phenotypic feature inverse: has mode of inheritance has mode of inheritance: is_a: has manifestation description: >- Relates a disease or phenotypic feature to its observed genetic segregation and assumed associated underlying DNA manifestation (i.e. autosomal, sex or mitochondrial chromosome). domain: disease or phenotypic feature range: genetic inheritance annotations: # This canonical order reverses that of its parent 'has manifestation' class # but seems a more natural direction in the pertinent edge relationships. canonical_predicate: true in_subset: - translator_minimal produces: is_a: related to at instance level description: >- holds between a material entity and a product that is generated through the intentional actions or functioning of the material entity in_subset: - translator_minimal annotations: canonical_predicate: true related_mappings: - GOREL:0001010 exact_mappings: - RO:0003000 - WIKIDATA_PROPERTY:P1056 - SEMMEDDB:PRODUCES narrow_mappings: - NCIT:R29 - SNOMED:has_process_output - SNOMED:specimen_procedure_of produced by: is_a: related to at instance level inverse: produces exact_mappings: - RO:0003001 consumes: is_a: has input domain: named thing range: named thing annotations: canonical_predicate: true narrow_mappings: - RO:0004009 consumed by: is_a: is input of inverse: consumes domain: named thing range: named thing temporally related to: is_a: related to at instance level description: >- holds between two entities with a temporal relationship domain: occurrent range: occurrent symmetric: true annotations: canonical_predicate: true exact_mappings: - SNOMED:temporally_related_to narrow_mappings: # The These RTX mappings are temporal in nature, but not with precedes ordering, so mapped here - RO:0002082 - RO:0002083 - RO:0002092 - RO:0002093 - RO:0002223 - RO:0002224 - RO:0002229 - RO:0002230 - RO:0002488 - RO:0002489 - RO:0002492 - RO:0002493 - RO:0002496 - RO:0002497 precedes: is_a: temporally related to description: >- holds between two processes, where one completes before the other begins domain: occurrent range: occurrent annotations: canonical_predicate: true inverse: preceded by in_subset: - translator_minimal close_mappings: # the subject of these terms is a material entity, not a process, # but affects a process which causes a second process to occur - RO:0002263 - RO:0002264 exact_mappings: - BFO:0000063 - SEMMEDDB:PRECEDES - SNOMED:occurs_before broad_mappings: # the Wikidata definition is subtly broader, focusing on a series not strictly temporal in nature - WIKIDATA_PROPERTY:P156 narrow_mappings: - FMA:transforms_into - RO:0002090 - RO:0002411 - RO:0002412 preceded by: is_a: temporally related to description: >- holds between two processes, where the other is completed before the one begins domain: occurrent range: occurrent inverse: precedes in_subset: - translator_minimal exact_mappings: - BFO:0000062 broad_mappings: # Contributed by RTX as inverse of 'precedes'. Seems more generic to just processes, so we tag it as 'broad'? - GENEPIO:0001739 narrow_mappings: # RTX contributed mapping was given as the inverse of 'biolink:precedes' - FMA:transforms_from - RO:0002087 - RO:0002285 has variant part: is_a: has part description: holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it annotations: canonical_predicate: true exact_mappings: - GENO:0000382 variant part of: is_a: part of inverse: has variant part related condition: is_a: related to at instance level symmetric: true annotations: canonical_predicate: true exact_mappings: - GENO:0000790 ## Predicates relating variants to genes is sequence variant of: is_a: related to at instance level aliases: ['gene product sequence variation encoded by gene mutant', 'allelic variant of', 'gene product variant of gene product'] description: holds between a sequence variant and a nucleic acid entity domain: sequence variant range: genomic entity annotations: canonical_predicate: true narrow_mappings: - WIKIDATA:P3433 has sequence variant: is_a: related to at instance level inverse: is sequence variant of domain: genomic entity range: sequence variant is missense variant of: is_a: is sequence variant of description: holds between a gene and a sequence variant, such the sequence variant results in a different amino acid sequence but where the length is preserved. domain: sequence variant range: genomic entity annotations: canonical_predicate: true exact_mappings: - SO:0001583 has missense variant: is_a: has sequence variant domain: genomic entity range: sequence variant inverse: is missense variant of is synonymous variant of: is_a: is sequence variant of description: holds between a sequence variant and a gene, such the sequence variant is in the coding sequence of the gene, but results in the same amino acid sequence domain: sequence variant range: genomic entity annotations: canonical_predicate: true exact_mappings: - SO:0001819 has synonymous variant: is_a: has sequence variant domain: genomic entity range: sequence variant inverse: is synonymous variant of aliases: ['stop gained'] is nonsense variant of: is_a: is sequence variant of description: holds between a sequence variant and a gene, such the sequence variant results in a premature stop codon domain: sequence variant range: genomic entity annotations: canonical_predicate: true broad_mappings: # Term definition broader than nonsense codon: A sequence variant whereby # the gene product has diminished or abolished function. - SO:0002054 has nonsense variant: is_a: has sequence variant domain: genomic entity range: sequence variant inverse: is nonsense variant of is frameshift variant of: is_a: is sequence variant of description: holds between a sequence variant and a gene, such the sequence variant causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. domain: sequence variant range: genomic entity annotations: canonical_predicate: true exact_mappings: - SO:0001589 aliases: ['frameshift variant', 'start lost', 'stop lost'] has frameshift variant: is_a: has sequence variant inverse: is frameshift variant of domain: genomic entity range: sequence variant aliases: ['splice region variant', 'splice acceptor variant', 'splice donor variant'] is splice site variant of: is_a: is sequence variant of description: holds between a sequence variant and a gene, such the sequence variant is in the canonical splice site of one of the gene's exons. domain: sequence variant range: genomic entity annotations: canonical_predicate: true exact_mappings: - SO:0001629 has splice site variant: is_a: has sequence variant domain: genomic entity range: sequence variant inverse: is splice site variant of aliases: ['downstream gene variant', 'upstream gene variant'] is nearby variant of: is_a: is sequence variant of description: holds between a sequence variant and a gene sequence that the variant is genomically close to. domain: sequence variant range: genomic entity annotations: canonical_predicate: true has nearby variant: is_a: has sequence variant domain: genomic entity range: sequence variant inverse: is nearby variant of aliases: ['intron variant', '3 prime UTR variant', '5 prime UTR variant', '5 prime UTR premature start codon gain variant', 'non coding transcript exon variant'] is non coding variant of: is_a: is sequence variant of description: holds between a sequence variant and a gene, where the variant does not affect the coding sequence domain: sequence variant range: genomic entity annotations: canonical_predicate: true has non coding variant: is_a: has sequence variant domain: genomic entity range: sequence variant inverse: is non coding variant of # relating disease to process disease has basis in: description: A relation that holds between a disease and an entity where the state of the entity has contribution to the disease. is_a: related to at instance level annotations: canonical_predicate: true narrow_mappings: # These two MONDO terms seem more particular than the predicate - MONDO:disease_has_basis_in_development_of - MONDO:disease_has_basis_in_accumulation_of occurs in disease: is_a: related to at instance level inverse: disease has basis in has adverse event: is_a: affects aliases: ['adverse effect'] description: >- An untoward medical occurrence in a patient or clinical investigation subject that happens during treatment with a therapeutic agent. Adverse events may be caused by something other than the drug or therapy being given and may include abnormal laboratory finding, symptoms, or diseases temporally associated with the treatment, whether or not considered related to the treatment. Adverse events are unintended effects that occur when a medication is administered correctly. domain: chemical or drug or treatment range: disease or phenotypic feature annotations: canonical_predicate: true adverse event of: is_a: affected by domain: disease or phenotypic feature range: chemical or drug or treatment inverse: has adverse event has side effect: aliases: ['adverse drug reaction'] is_a: affects description: >- An unintended, but predictable, secondary effect shown to be correlated with a therapeutic agent, drug or treatment. Side effects happen at normal, recommended doses or treatments, and are unrelated to the intended purpose of the medication. notes: >- Side effects are listed on drug labels. There can be positive side effects, while adverse events are always negative. Aeolus, Sider are both resources that provide side effects. domain: chemical or drug or treatment range: disease or phenotypic feature annotations: canonical_predicate: true exact_mappings: - NCIT:C2861 # side effect is side effect of: is_a: affected by domain: disease or phenotypic feature range: chemical or drug or treatment inverse: has side effect contraindicated in: is_a: related to at instance level description: >- Holds between a substance, procedure, or activity and a medical condition or circumstance, where an authority has established that the substance, procedure, or activity should not be applied as an intervention in patients with the condition or circumstance because it can result in detrimental outcomes. notes: >- This predicate relates the intervention with a specific disease, phenotype, or other medical circumstance that puts patients at high risk for detrimental outcomes. This may be a different condition from the one that the drug would be used to treat (e.g. pseudoephedrine is contraindicated in people with high-blood pressure as a treatment for nasal congestion), a biological state (e.g. isotretinoin is contraindicated in people who are pregnant as a treatment for acne), or being on a different medication (e.g. aspirin is contraindicated in people taking warfarin as a preventative treatment for stroke). domain: chemical or drug or treatment range: biological entity annotations: canonical_predicate: true opposite_of: treats exact_mappings: - NCIT:C37933 chemical entity or drug or treatment: description: >- A union of chemical entities and children, and drug or treatment. mixin: true has contraindication: is_a: related to at instance level domain: biological entity range: chemical or drug or treatment inverse: contraindicated in # The remaining new slots are here because we ran across them somewhere and # they didn't seem to map well to anything else. has not completed: is_a: related to at instance level description: holds between an entity and a process that the entity is capable of, but has not completed exact_mappings: - CL:has_not_completed annotations: opposite_of: has completed canonical_predicate: true not completed by: is_a: related to at instance level inverse: has not completed has completed: is_a: related to at instance level description: holds between an entity and a process that the entity is capable of and has completed annotations: canonical_predicate: true opposite_of: has not completed exact_mappings: - CL:has_completed completed by: is_a: related to at instance level inverse: has completed in linkage disequilibrium with: is_a: related to at instance level description: holds between two sequence variants, the presence of which are correlated in a population symmetric: true annotations: canonical_predicate: true exact_mappings: - NCIT:C16798 has increased amount: is_a: related to at instance level annotations: canonical_predicate: true opposite_of: has decreased amount narrow_mappings: - CL:has_high_plasma_membrane_amount increased amount of: is_a: related to at instance level inverse: has increased amount has decreased amount: is_a: related to at instance level annotations: canonical_predicate: true opposite_of: has increased amount narrow_mappings: - CL:has_low_plasma_membrane_amount decreased amount in: is_a: related to at instance level inverse: has decreased amount lacks part: is_a: related to at instance level annotations: canonical_predicate: true opposite_of: has part exact_mappings: - CL:lacks_part - PR:lacks_part narrow_mappings: - CL:lacks_plasma_membrane_part missing from: is_a: related to at instance level inverse: lacks part develops from: is_a: related to at instance level annotations: canonical_predicate: true close_mappings: # RTX mapping seems to be inverse of 'biolink:develops_from' - RO:0002203 - FMA:develops_into exact_mappings: - BTO:develops_from - DDANAT:develops_from - FMA:develops_from - RO:0002202 narrow_mappings: - RO:0002207 - RO:0002225 # x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - RO:0002226 # x develops_in y if x is located in y whilst x is developing develops into: is_a: related to at instance level inverse: develops from in taxon: aliases: ['instance of', 'is organism source of gene product', 'organism has gene', 'gene found in organism', 'gene product has organism source'] is_a: related to at instance level domain: thing with taxon range: organism taxon annotations: canonical_predicate: 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 exact_mappings: - RO:0002162 - WIKIDATA_PROPERTY:P703 narrow_mappings: - RO:0002160 in taxon label: is_a: node property domain: thing with taxon range: label type description: >- The human readable scientific name for the taxon of the entity. in_subset: - translator_minimal exact_mappings: - WIKIDATA_PROPERTY:P225 annotations: denormalized: true taxon of: is_a: related to at instance level inverse: in taxon domain: organism taxon range: thing with taxon has molecular consequence: is_a: related to at instance level aliases: ['allele has activity'] description: >- connects a sequence variant to a class describing the molecular consequence. E.g. SO:0001583 range: ontology class annotations: canonical_predicate: true narrow_mappings: - NCIT:allele_has_activity is molecular consequence of: is_a: related to at instance level domain: ontology class inverse: has molecular consequence ## -------------------- ## ASSOCIATION SLOTS ## -------------------- association slot: abstract: true domain: association aliases: ['edge property', 'statement property', 'node qualifier', 'edge qualifier', 'statement qualifier'] description: >- any slot that relates an association to another entity qualifier: is_a: association slot description: >- grouping slot for all qualifiers on an edge. useful for testing compliance with association classes in_subset: - translator_minimal original subject: is_a: association slot description: >- used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification. original object: is_a: association slot description: >- used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification. original predicate: aliases: ['original relation', 'relation'] is_a: association slot description: >- used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification. id_prefixes: - RO - BSPO - SIO domain: association range: uriorcurie subject closure: is_a: association slot description: >- Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. multivalued: true domain: association annotations: denormalized: true object closure: is_a: association slot description: >- Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. multivalued: true domain: association examples: - value: ["MONDO:0000167", "MONDO:0005395"] description: >- The object closure of the association between the gene 'BRCA1' and the disease 'breast cancer' is the set of all diseases that are ancestors of 'breast cancer' in the MONDO ontology. Note: typically the "subclass of" and "part of" relations are used to construct the closure, but other relations may be used as well. annotations: denormalized: true subject category: is_a: association slot description: >- Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. multivalued: false domain: association range: ontology class examples: - value: "biolink:Gene" description: >- The subject category of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'biolink:Gene'. annotations: denormalized: true object category: is_a: association slot description: >- Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. multivalued: false domain: association range: ontology class examples: - value: "biolink:Disease" description: >- The object category of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'biolink:Disease'. annotations: denormalized: true subject category closure: is_a: association slot description: >- Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. multivalued: true domain: association range: ontology class examples: - value: ['biolink:Gene", "biolink:NamedThing'] description: >- The subject category closure of the association between the gene 'BRCA1' and the disease 'breast cancer' is the set of all biolink classes that are ancestors of 'biolink:Gene' in the biolink model. Note: typically the "subclass of" and "part of" relations are used to construct the closure, but other relations may be used as well. annotations: denormalized: true object category closure: is_a: association slot description: >- Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. multivalued: true domain: association range: ontology class examples: - value: ['biolink:Disease", "biolink:NamedThing'] description: >- The object category closure of the association between the gene 'BRCA1' and the disease 'breast cancer' is the set of all biolink classes that are ancestors of 'biolink:Disease' in the biolink model. Note: typically the "subclass of" and "part of" relations are used to construct the closure, but other relations may be used as well. annotations: denormalized: true subject label closure: is_a: association slot description: >- Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. multivalued: true domain: association range: string examples: - value: ["BRACA1"] description: >- The subject label closure of the association between the gene 'BRCA1' and the disease 'breast cancer' is the set of all labels that are ancestors of 'BRCA1' in the biolink model. annotations: denormalized: true object label closure: is_a: association slot description: >- Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. multivalued: true domain: association range: string examples: - value: "breast cancer" description: >- The object label closure of the association between the gene 'BRCA1' and the disease 'breast cancer' is the set of all labels that are ancestors of 'breast cancer' in the biolink model. - value: "cancer" annotations: denormalized: true subject namespace: aliases: ["subject prefix"] is_a: association slot description: >- Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. multivalued: false domain: association range: string examples: - value: "NCBIGene" description: >- The subject namespace of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'NCBIGene'. annotations: denormalized: true object namespace: aliases: ["object prefix"] is_a: association slot description: >- Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. multivalued: false domain: association range: string examples: - value: "MONDO" description: >- The object namespace of the association between the gene 'BRCA1' and the disease 'breast cancer' is 'MONDO'. annotations: denormalized: true subject: is_a: association slot local_names: ga4gh: annotation subject neo4j: node with outgoing relationship description: >- connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object. required: true domain: association range: named thing slot_uri: rdf:subject exact_mappings: - owl:annotatedSource - OBAN:association_has_subject object: is_a: association slot description: >- connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object. required: true domain: association range: named thing local_names: ga4gh: descriptor neo4j: node with incoming relationship slot_uri: rdf:object exact_mappings: - owl:annotatedTarget - OBAN:association_has_object predicate: is_a: association slot description: >- A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes. domain: association notes: >- Has a value from the Biolink related_to hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats range: predicate type required: true local_names: ga4gh: annotation predicate translator: predicate slot_uri: rdf:predicate exact_mappings: - owl:annotatedProperty - OBAN:association_has_predicate logical interpretation: is_a: association slot required: false domain: association range: LogicalInterpretationEnum exact_mappings: - os:LogicalInterpretation relation: deprecated: true negated: is_a: association slot range: boolean description: >- if set to true, then the association is negated i.e. is not true has confidence level: is_a: association slot range: confidence level description: >- connects an association to a qualitative term denoting the level of confidence has evidence: is_a: association slot range: evidence type description: >- connects an association to an instance of supporting evidence exact_mappings: - RO:0002558 multivalued: true has supporting study result: is_a: association slot description: >- connects an association to an instance of supporting study result log odds ratio: is_a: association slot description: >- The logarithm of the odds ratio, or the ratio of the odds of event Y occurring in an exposed group versus the odds of event Y occurring in a non-exposed group. range: float log odds ratio 95 ci: is_a: association slot description: >- The ninety-five percent confidence range in which the true log odds ratio for the sample population falls. range: float total sample size: is_a: dataset count description: >- The total number of patients or participants within a sample population. range: integer mechanism of action: is_a: association slot range: boolean description: >- a boolean flag to indicate if the edge is part of a path or subgraph of a knowledge graph that constitutes the mechanism of action for a result. exact_mappings: - NCIT:C54680 - MI:2044 - LOINC:MTHU019741 knowledge source: is_a: association slot description: >- An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property. close_mappings: - pav:providedBy provided by: is_a: node property 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. multivalued: true primary knowledge source: is_a: knowledge source description: >- The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. "aggregator knowledge source" can be used to capture non-primary sources. notes: >- For example: a single ChemicalToGene Edge originally curated by ClinicalTrials.org, is aggregated by ChEMBL, then incorporated into the MolePro KP, then sent via TRAPI message to the ARAGORN ARA, and finally sent to the NCATS ARS. The retrieval path for this Edge is as follows: ARS--retrieved_from--> ARAGORN --retrieved_from--> MolePro --retrieved_from--> ChEMBL --retrieved_from--> ClinicalTrials.gov The "primary knowledge source" for this edge is "infores:clinical-trials-gov". "infores:chembl" and "infores:molecular_data_provider" are listed in the "aggregator knowledge source" property. multivalued: false aggregator knowledge source: is_a: knowledge source description: >- An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form. multivalued: true notes: >- For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, the Edge is passed to the Ranking Agent’s ARAGORN ARA, and then on to the ARS. The retrieval path for this Edge is as follows: ARS--retrieved_from--> ARAGORN --retrieved_from--> ICEES --supporting_data_from--> UNC Data Warehouse This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of data from which the knowledge was derived. The "primary knowledge source" for this edge is "infores:icees-asthma". A "supporting data source" for this KP- generated knowledge is "infores:unc-cdw-health." The "aggregator knowledge source" for this data is "infores:aragorn-ara" supporting data source: is_a: association slot description: >- An Information Resource from which data was retrieved and subsequently used as evidence to generate the knowledge expressed in an Association (e.g. through computation on, reasoning or inference over the retrieved data). multivalued: true notes: >- For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, the Edge is passed to the Ranking Agent’s ARAGORN ARA, and then on to the ARS. The retrieval path for this Edge is as follows: ARS--retrieved_from--> ARAGORN --retrieved_from--> ICEES --supporting_data_from--> UNC Data Warehouse This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of data from which the knowledge was derived. The "primary knowledge source" for this edge is "infores:icees-asthma". A "supporting data source" for this KP- generated knowledge is "infores:unc-cdw-health." The "aggregator knowledge source" for this data is "infores:aragorn-ara" supporting data set: is_a: association slot description: >- A set of data used as evidence to generate the knowledge expressed in an Association (e.g. through computation on, reasoning or inference over the retrieved data). multivalued: true chi squared statistic: is_a: association slot range: float description: >- represents the chi-squared statistic computed from observations exact_mappings: - STATO:0000030 p value: aliases: ['unadjusted p value'] is_a: association slot range: float description: >- A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. exact_mappings: - OBI:0000175 - NCIT:C44185 - EDAM-DATA:1669 evidence count: is_a: association slot description: >- The number of evidence instances that are connected to an association. range: integer dataset count: is_a: association slot description: >- The total number of instances (e.g., number of patients, number of rows, etc) in a dataset/cohort. range: integer examples: - value: 100000 concept count subject: is_a: association slot description: >- The number of instances in a dataset/cohort whose records contain the concept in the subject slot of an association. range: integer examples: - value: 489 concept count object: is_a: association slot description: >- The number of instances in a dataset/cohort whose records contain the concept in the object slot of an association. range: integer concept pair count: is_a: association slot description: >- The number of instances in a dataset/cohort whose records contain both the subject and object concept of an association. range: integer examples: - value: 1731 expected count: is_a: association slot description: >- The expected (calculated) number of instances in a dataset/cohort whose records contain both the subject and object concept of an association if the subject and object concepts are independent. relative frequency subject: is_a: association slot description: >- The frequency at which subject and object concepts co-occur in records within a dataset/cohort, relative to the frequency at which the subject concept appears in these same records. range: float examples: - value: 0.01840490798 relative frequency object: is_a: association slot description: >- The frequency at which subject and object concepts co-occur in records within a dataset/cohort, relative to the frequency at which the object concept appears in these same records. range: string relative frequency subject confidence interval: is_a: association slot description: >- The 99% confidence interval for the relative_frequency_subject calculation (i.e. the range of values within which the true value has a 99% chance of falling) range: string relative frequency object confidence interval: is_a: association slot description: >- The 99% confidence interval for the relative_frequency_object calculation (i.e. the range of values within which the true value has a 99% chance of falling) range: string adjusted p value: is_a: p value description: >- The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<. range: float bonferonni adjusted p value: is_a: adjusted p value description: >- The Bonferroni correction is an adjustment made to P values when several dependent or independent statistical tests are being performed simultaneously on a single data set. To perform a Bonferroni correction, divide the critical P value (α) by the number of comparisons being made. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<. range: float examples: - value: 0.018 supporting text: is_a: association slot description: The segment of text from a document that supports the mined assertion. multivalued: true range: string examples: - value: The administration of 50g/ml bupivacaine promoted maximum breast cancer. supporting documents: deprecated: true is_a: association slot description: >- One or more referenceable documents that report the statement expressed in an Association, or provide information used as evidence supporting this statement. range: uriorcurie multivalued: true examples: - value: PMID:12345678 subject location in text: is_a: association slot description: >- Character offsets for the text span(s) in the supporting text corresponding to the subject concept of the extracted assertion. range: integer examples: - value: 15 multivalued: true object location in text: is_a: association slot description: >- Character offsets for the text span(s) in the supporting text corresponding to the object concept of the extracted assertion range: integer examples: - value: 15 multivalued: true extraction confidence score: is_a: association slot description: >- A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. range: integer examples: - value: 15 supporting document type: is_a: association slot description: >- The document type (e.g., Journal Article, Case Study, Preprint) for the supporting document used in a Text Mining Result. range: string examples: - value: Journal Article supporting document year: is_a: association slot description: >- The document year (typically the publication year) for the supporting document used in a Text Mining Result. range: integer examples: - value: 1999 supporting text section type: is_a: association slot description: >- The section of the supporting text of a Text Mining Result within the supporting document. This is in the form of the name of the document section (e.g., Abstract, Introduction) that contains the supporting text. range: string examples: - value: Introduction ln ratio: is_a: association slot description: the natural log of the ratio of co-occurrence to expected range: float examples: - value: 2.922827136 ln ratio confidence interval: is_a: association slot description: >- The 99% confidence interval for the ln_ratio calculation (i.e. the range of values within which the true value has a 99% chance of falling) range: float examples: - value: 2.922827136 interacting molecules category: is_a: association slot range: ontology class exact_mappings: - MI:1046 values_from: - MI examples: - value: MI:1048 description: smallmolecule-protein expression site: description: >- location in which gene or protein expression takes place. May be cell, tissue, or organ. is_a: association slot range: anatomical entity examples: - value: UBERON:0002037 description: cerebellum phenotypic state: description: >- in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX. is_a: association slot range: disease or phenotypic feature publications: aliases: ['supporting publications', 'supporting documents'] description: >- One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement. comments: >- The notion of a ‘Publication’ is considered broadly to include any document made available for public consumption. It covers journal issues, individual articles, and books - and also things like article pre-prints, white papers, patents, drug labels, web pages, protocol documents, etc. is_a: association slot multivalued: true range: publication associated environmental context: is_a: association slot description: >- An attribute that can be applied to an association where the association holds between two entities located or occurring in a particular environment. For example, two microbial taxa may interact in the context of a human gut; a disease may give rise to a particular phenotype in a particular environmental exposure. # TODO: add examples of values for this property. sequence localization attribute: is_a: association slot domain: genomic sequence localization description: >- An attribute that can be applied to a genome sequence localization edge. These edges connect a nucleic acid entity such as an exon to an entity such as a chromosome. Edge properties are used to ascribe specific positional information and other metadata to the localization. In pragmatic terms this can be thought of as columns in a GFF3 line. interbase coordinate: is_a: sequence localization attribute aliases: ['zero-based', 'half-open', 'space-based'] description: >- A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1. This is applied to a sequence localization edge. range: integer start interbase coordinate: is_a: interbase coordinate description: >- The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0). close_mappings: - faldo:begin annotations: opposite_of: end interbase coordinate end interbase coordinate: is_a: interbase coordinate description: >- The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on. close_mappings: - faldo:end annotations: opposite_of: start interbase coordinate start coordinate: is_a: base coordinate aliases: ['start'] description: >- The position at which the subject genomic entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 1). exact_mappings: - gff3:start close_mappings: - faldo:begin end coordinate: is_a: base coordinate aliases: ['end'] description: >- The position at which the subject genomic entity ends on the chromosome or other entity to which it is located on. exact_mappings: - gff3:end close_mappings: - faldo:end genome build: is_a: sequence localization attribute description: >- The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens. range: StrandEnum exact_mappings: - gff3:strand strand: is_a: sequence localization attribute 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). range: StrandEnum exact_mappings: - gff3:strand phase: is_a: sequence localization attribute domain: coding sequence 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. range: PhaseEnum exact_mappings: - gff3:phase clinical approval status: is_a: association slot description: >- range: ClinicalApprovalStatusEnum max research phase: is_a: association slot range: MaxResearchPhaseEnum supporting study metadata: is_a: association slot description: >- Information about a study used to generate information used as evidence to support the knowledge expressed in an Association. In practice, data creators should use one of the more specific subtypes of this property. abstract: true supporting study method type: is_a: supporting study metadata description: >- A type of method that was applied in a study used to generate the information used as evidence (e.g. a type of experimental assay, or statistical calculation, or computational analysis). range: uriorcurie supporting study method description: is_a: supporting study metadata description: >- A uri or curie pointing to information about the methodology used to generate data supporting an Association. range: uriorcurie supporting study size: is_a: supporting study metadata description: >- The sample size used in a study that provided evidence for the association (e.g. 'n' of a cohort for a clinical study). range: integer supporting study cohort: is_a: supporting study metadata description: >- A description of a study population/cohort that was interrogated to provide evidence for the association (e.g. the inclusion and exclusion criteria). range: string supporting study date range: is_a: supporting study metadata description: >- The date range over which data was collected in a study that provided evidence for an Association. range: string supporting study context: is_a: supporting study metadata description: >- A term or terms describing the experimental setting/context in which evidence supporting the Association was generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue type, disease, etc.). range: string knowledge level: aliases: ['knowledge type'] is_a: association slot description: >- Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true. notes: >- The notion of a 'level' of knowledge can in one sense relate to the strength of a statement - i.e. how confident we are that it says something true about our domain of discourse. Here, we can generally consider Assertions to be stronger than Entailments to be stronger than Predictions. But in another sense, 'level' of knowledge can refer to the scope or specificity of what a statement expresses - on a spectrum from context-specific results of a data analysis, to generalized assertions of knowledge or fact. Here, Statistical Associations and Observations represent more foundational statements that are only slightly removed from the data on which they are based (the former reporting the direct results of an analysis in terms of correlations between variables in the data, and the latter describing phenomena that were observed/reported to have occurred). domain: association range: KnowledgeLevelEnum multivalued: false required: true ifabsent: string(not_provided) examples: - value: knowledge_assertion - value: prediction - value: statistical_association agent type: is_a: association slot description: >- Describes the high-level category of agent who originally generated a statement of knowledge or other type of information. notes: >- Note that this property indicates the type of agent who produced a final statement of knowledge, which is often different from the agent oragents who produced information used as evidence to support generation of this knowledge. For example, if a human curator concludes that a particular gene variant causes a medical condition - based on their interpretation of information produced by computational modeling tools, automated data analysis pipelines, and robotic laboratory assay systems - the agent_type for this statement is 'manual agent' - despite all of the evidence being created by automated agents. But if any of these systems is programmed to generate knowledge statements directly and without human assistance, the statement would be attributed to an 'automated_agent'. domain: association range: AgentTypeEnum multivalued: false required: true ifabsent: string(not_provided) examples: - value: manual_agent - value: automated_agent - value: computational_model - value: text_mining_agent classes: mapping collection: description: >- A collection of deprecated mappings. abstract: true slots: - predicate mappings tree_root: true predicate mapping: description: >- A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place. slots: - mapped predicate - subject aspect qualifier - subject direction qualifier - subject form or variant qualifier - subject part qualifier - subject derivative qualifier - subject context qualifier - predicate - qualified predicate - object aspect qualifier - object direction qualifier - object form or variant qualifier - object part qualifier - object derivative qualifier - object context qualifier - causal mechanism qualifier - anatomical context qualifier - species context qualifier - exact match - narrow match - broad match ## ---------- ## ATTRIBUTES ## ---------- ## Ontology Classes ontology class: mixin: true slots: - id 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. exact_mappings: - owl:Class - schema:Class 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 see_also: - https://github.com/biolink/biolink-model/issues/486 examples: - value: UBERON:0000955 description: >- the class 'brain' from the Uberon anatomy ontology id_prefixes: - MESH - UMLS - KEGG.BRITE ## br/ko number annotation: description: >- Biolink Model root class for entity annotations. abstract: true quantity value: is_a: annotation description: >- A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value slots: - has unit - has numeric value # Alignment attempted of the biolink:Attribute model # to the proposed TRAPI Release 1.1 Attribute schema, i.e. # # attribute_name: "assertionAuthoredBy", # attribute_type: SEPIO:0000130, # value: "ORCID:12345", # value_type: "wd:Q51044", # value_type_name: "ORCID ID" # url: https://orcid.org/12345 # source: ORCID attribute: is_a: named thing mixins: - ontology class 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. slots: - name # 'attribute_name' - has attribute type # 'attribute_type' # 'value', 'value_type', 'value_type_name' # extracted from either of the next two slots - has quantitative value - has qualitative value - iri # 'url' slot_usage: 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. id_prefixes: - EDAM-DATA - EDAM-FORMAT - EDAM-OPERATION - EDAM-TOPIC exact_mappings: - SIO:000614 in_subset: - samples chemical role: is_a: attribute description: >- A role played by the molecular entity or part thereof within a chemical context. id_prefixes: - CHEBI exact_mappings: - CHEBI:51086 examples: - value: CHEBI:35469 # antidepressant role biological sex: is_a: attribute exact_mappings: - PATO:0000047 phenotypic sex: is_a: biological sex description: >- An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present. exact_mappings: - PATO:0001894 genotypic sex: is_a: biological sex description: >- An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes. exact_mappings: - PATO:0020000 severity value: deprecated: true is_a: attribute description: >- describes the severity of a phenotypic feature or disease relationship quantifier: mixin: true sensitivity quantifier: is_a: relationship quantifier mixin: true specificity quantifier: is_a: relationship quantifier mixin: true pathognomonicity quantifier: is_a: specificity quantifier description: >- A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease mixin: true frequency quantifier: is_a: relationship quantifier mixin: true slots: - has count - has total - has quotient - has percentage chemical or drug or treatment: mixin: true id_prefixes: - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - CHEBI - MAXO ## ------ ## THINGS ## ------ entity: description: >- Root Biolink Model class for all things and informational relationships, real or imagined. abstract: true slots: - id - iri - category - type # rdf:type - name - description - has attribute - deprecated # evidence code(s)? named thing: is_a: entity description: "a databased entity or concept/class" slots: - provided by - xref - full name - synonym slot_usage: category: required: true exact_mappings: - BFO:0000001 - WIKIDATA:Q35120 # UMLS Semantic Group "Objects" - UMLSSG:OBJC # Entity - STY:T071 - dcid:Thing relationship type: is_a: ontology class description: >- An OWL property used as an edge label taxonomic rank: description: >- A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom) is_a: ontology class id_prefixes: - TAXRANK mappings: - WIKIDATA:Q427626 organism taxon: aliases: ['taxon', 'taxonomic classification'] 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. is_a: named thing slots: - has taxonomic rank slot_usage: has taxonomic rank: range: taxonomic rank multivalued: false mappings: - WIKIDATA:P105 values_from: - NCBITaxon exact_mappings: - WIKIDATA:Q16521 - STY:T001 - bioschemas:Taxon narrow_mappings: - dcid:BiologicalSpecies id_prefixes: - NCBITaxon - MESH - UMLS in_subset: - model_organism_database ## Temporal Entities event: is_a: named thing description: >- Something that happens at a given place and time. exact_mappings: - NCIT:C25499 # UMLS "Event" - STY:T051 ## Administrative Entities administrative entity: is_a: named thing abstract: true study result: abstract: true description: >- A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence. notes: The data/metadata included in a Study Result object are typically a subset of data from a larger study data set, that are selected by a curator because they may be useful as evidence for deriving knowledge about a specific focus of the study. The notion of a 'study' here is defined broadly to include any research activity at any scale that is aimed at generating knowledge or hypotheses. This may include a single assay or computational analyses, or a larger scale clinical trial or experimental research investigation. is_a: information content entity study: description: a detailed investigation and/or analysis is_a: activity exact_mappings: - NCIT:C63536 close_mappings: - SIO:001066 - SEPIO:0000004 narrow_mappings: - SIO:000994 study variable: is_a: information content entity description: a variable that is used as a measure in the investigation of a study narrow_mappings: - NCIT:C142192 # specifies clinical study close_mappings: - STATO:0000258 - SIO:000367 common data element: is_a: information content entity description: >- A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home) close_mappings: - NCIT:C19984 ## epc result sets concept count analysis result: is_a: study result description: >- A result of a concept count analysis. observed expected frequency analysis result: is_a: study result description: >- A result of a observed expected frequency analysis. relative frequency analysis result: is_a: study result description: >- A result of a relative frequency analysis. text mining result: is_a: study result description: >- A result of text mining. chi squared analysis result: is_a: study result description: >- A result of a chi squared analysis. log odds analysis result: is_a: study result description: >- A result of a log odds ratio analysis. agent: is_a: administrative entity aliases: ['group'] description: >- person, group, organization or project that provides a piece of information (i.e. a knowledge association) slots: - affiliation - address exact_mappings: - prov:Agent - dct:Agent narrow_mappings: # Organization - UMLSSG:ORGA - STY:T092 # Health Care Related Organization - STY:T093 # Professional Society - STY:T094 # Self-help or Relief Organization - STY:T095 # Group - STY:T096 slot_usage: id: required: true description: >- Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code. values_from: # CURIE space for publishers - isbn # CURIE space for authors - ORCID - ScopusID - ResearchID - GSID # Institutional agents - isni name: description: >- it is recommended that an author's 'name' property be formatted as "surname, firstname initial." id_prefixes: - isbn - ORCID - ScopusID - ResearchID - GSID - isni ## General Information Entities information content entity: aliases: ['information', 'information artefact', 'information entity'] abstract: true is_a: named thing description: >- a piece of information that typically describes some topic of discourse or is used as support. slots: - license - rights - format - creation date id_prefixes: - doi exact_mappings: - IAO:0000030 narrow_mappings: # UMLS Semantic Group "Concepts & Ideas" - UMLSSG:CONC # Conceptual Entity - STY:T077 # Idea or Concept - STY:T078 # Temporal Concept - STY:T079 # Qualitative Concept - STY:T080 # Quantitative Concept - STY:T081 # Spatial Concept - STY:T082 # Regulation or Law - STY:T089 # Group Attribute - STY:T102 # Functional Concept - STY:T169 # Language - STY:T171 # Classification - STY:T185 dataset: description: >- an item that refers to a collection of data from a data source. is_a: information content entity exact_mappings: - IAO:0000100 - dctypes:Dataset - schema:dataset - dcid:Dataset dataset distribution: is_a: information content entity description: >- an item that holds distribution level information about a dataset. slots: - distribution download url exact_mappings: - dcat:Distribution dataset version: description: >- an item that holds version level information about a dataset. is_a: information content entity slots: - has dataset - ingest date - has distribution dataset summary: description: >- an item that holds summary level information about a dataset. is_a: information content entity slots: - source web page - source logo confidence level: is_a: information content entity description: >- Level of confidence in a statement values_from: - cio exact_mappings: - CIO:0000028 # statement confidence - SEPIO:0000187 close_mappings: # assertion confidence levels - SEPIO:0000167 evidence type: is_a: information content entity aliases: ['evidence code'] description: >- Class of evidence that supports an association values_from: - eco exact_mappings: - ECO:0000000 ## Publications # TODO: to review additional ontology relating to Publications, such as http://www.sparontologies.net/ontologies publication: is_a: information content entity description: >- Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). slots: - authors - pages - summary - keywords - mesh terms - xref - publication type # In addition to embedded slots, instances of 'contributor association' # may be used to more extensively document publisher, editor and author details slot_usage: id: description: >- Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN. name: description: >- the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case). publication type: required: true pages: multivalued: true description: >- When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book. exact_mappings: - IAO:0000311 narrow_mappings: - IAO:0000013 # UMLS Semantic Type "Intellectual Product" - STY:T170 id_prefixes: - PMID - PMC - doi - NLMID in_subset: - model_organism_database book: is_a: publication description: >- This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. slot_usage: id: required: true description: >- Books should have industry-standard identifier such as from ISBN. type: description: >- Should generally be set to an ontology class defined term for 'book'. id_prefixes: - isbn - NLMID in_subset: - model_organism_database book chapter: is_a: publication slots: - published in - volume - chapter slot_usage: published in: required: true description: >- The enclosing parent book containing the chapter should have industry-standard identifier from ISBN. in_subset: - model_organism_database serial: aliases: ['journal'] is_a: publication description: >- This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. slots: - iso abbreviation - volume - issue slot_usage: id: required: true description: >- Serials (journals) should have industry-standard identifier such as from ISSN. type: description: >- Should generally be set to an ontology class defined term for 'serial' or 'journal'. id_prefixes: - issn - NLMID in_subset: - model_organism_database article: is_a: publication description: >- a piece of writing on a particular topic presented as a stand-alone section of a larger publication slots: - published in - iso abbreviation - volume - issue slot_usage: published in: required: true description: >- The enclosing parent serial containing the article should have industry-standard identifier from ISSN. iso abbreviation: description: >- Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent. exact_mappings: - SIO:000154 - fabio:article id_prefixes: # By inheritance, a DOI may be used as a publication identifier; there may be other relevant namespaces - PMID in_subset: - model_organism_database journal article: is_a: article description: >- an article, typically presenting results of research, that is published in an issue of a scientific journal. exact_mappings: - IAO:0000013 - fabio:JournalArticle id_prefixes: - PMID - PMCID - doi patent: is_a: publication description: >- a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time. exact_mappings: - SIO:000153 - IAO:0000313 - fabio:Patent web page: is_a: publication description: >- a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features. exact_mappings: - SIO:000302 - NCIT-OBO:C142749 - fabio:WebPage preprint publication: is_a: publication description: >- a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal. exact_mappings: - EFO:0010558 - fabio:Preprint drug label: is_a: publication description: >- a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc. broad_mappings: - NCIT-OBO:C41203 retrieval source: is_a: information content entity description: >- Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved. slots: - resource id - resource role - upstream resource ids - xref slot_usage: resource id: required: true description: >- The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge. resource role: required: true description: >- The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge. upstream resource ids: description: >- The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge. ## Top Level Abstractions of Material & Process Entities physical essence or occurrent: description: >- Either a physical or processual entity. mixin: true physical essence: description: >- Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge. is_a: physical essence or occurrent mixin: true physical entity: is_a: named thing mixins: - physical essence description: >- An entity that has material reality (a.k.a. physical essence). exact_mappings: # Physical Object - STY:T072 narrow_mappings: # Manufactured Object - STY:T073 occurrent: description: >- A processual entity. # biolink:Occurrent is most consistently used as a mixin thus it should # be declared as such and cannot inherit from the non-mixin biolink:NamedThing is_a: physical essence or occurrent mixin: true exact_mappings: - BFO:0000003 activity and behavior: is_a: occurrent mixin: true description: >- Activity or behavior of any independent integral living, organization or mechanical actor in the world exact_mappings: # Activities & Behaviors - UMLSSG:ACTI activity: is_a: named thing mixins: - activity and behavior 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. exact_mappings: - prov:Activity - NCIT:C43431 # Activity - STY:T052 narrow_mappings: # Daily or Recreational Activity - STY:T056 # Occupational Activity - STY:T057 # Governmental or Regulatory Activity - STY:T064 # Machine Activity - STY:T066 # Research Activity - STY:T062 # Educational Activity - STY:T065 # Health Care Activity - STY:T058 procedure: is_a: named thing mixins: - activity and behavior description: >- A series of actions conducted in a certain order or manner exact_mappings: # Procedures - UMLSSG:PROC - dcid:MedicalProcedure narrow_mappings: # Laboratory Procedure - STY:T059 # Diagnostic Procedure - STY:T060 # Therapeutic or Preventive Procedure - STY:T061 # Molecular Biology Research Technique - STY:T063 id_prefixes: - CPT phenomenon: is_a: named thing mixins: - occurrent description: >- a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question broad_mappings: # the inclusion of 'process' in the definition of these # terms broadens them, relative to 'phenomenon' # Phenomenon or Process - STY:T067 # Human-caused Phenomenon or Process - STY:T068 # Natural Phenomenon or Process - STY:T070 exact_mappings: # Phenomena - UMLSSG:PHEN narrow_mappings: # Laboratory or Test Result - STY:T034 # Biologic Function - STY:T038 # Environmental Effect of Humans - STY:T069 device: is_a: named thing description: >- A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment narrow_mappings: # Devices - UMLSSG:DEVI # Medical Device - STY:T074 # Research Device - STY:T075 # Drug Delivery Device - STY:T203 # Biomedical or Dental Material - STY:T122 diagnostic aid: is_a: named thing description: >- A device or substance used to help diagnose disease or injury exact_mappings: - STY:T130 # Diagnostic Aid - SNOMED:2949005 # Diagnostic aid ## Scientific Studies study population: is_a: population of individual organisms description: >- A group of people banded together or treated as a group as participants in a research study. close_mappings: - WIKIDATA:Q7229825 subject of investigation: mixin: true description: >- An entity that has the role of being studied in an investigation, study, or experiment material sample: aliases: ['biospecimen', 'sample', 'biosample', 'physical sample'] is_a: physical entity mixins: - subject of investigation 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] exact_mappings: - OBI:0000747 - SIO:001050 id_prefixes: - BIOSAMPLE - GOLD.META ## Earth Sciences planetary entity: is_a: named thing description: >- Any entity or process that exists at the level of the whole planet environmental process: is_a: planetary entity mixins: - occurrent exact_mappings: - ENVO:02500000 environmental feature: is_a: planetary entity exact_mappings: - ENVO:01000254 geographic location: is_a: planetary entity description: >- a location that can be described in lat/long coordinates slots: - latitude - longitude exact_mappings: # Geographic Areas - UMLSSG:GEOG # Geographic Area - STY:T083 geographic location at time: is_a: geographic location description: >- a location that can be described in lat/long coordinates, for a particular time slots: - timepoint ## Biological Sciences thing with taxon: mixin: true 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 slots: - in taxon - in taxon label biological entity: is_a: named thing aliases: ['bioentity'] abstract: true mixins: - thing with taxon narrow_mappings: - WIKIDATA:Q28845870 # UMLS Semantic Type "Experimental Model of Disease" - STY:T050 # SIO term is 'biological entity' but less inclusive than the Biolink scope - SIO:010046 - STY:T129 # (imft, full name: Immunologic Factor genomic entity: mixin: true slots: - has biological sequence in_subset: - translator_minimal narrow_mappings: - STY:T028 # Gene or Genome - GENO:0000897 # Genomic Entity epigenomic entity: mixin: true slots: - has biological sequence in_subset: - translator_minimal narrow_mappings: molecular entity: is_a: chemical entity description: >- A molecular entity is a chemical entity composed of individual or covalently bonded atoms. slots: - is metabolite narrow_mappings: - STY:T088 # Carbohydrate - STY:T085 # Molecular Sequence - CHEBI:23367 # Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, # radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. - bioschemas:MolecularEntity in_subset: - translator_minimal id_prefixes: - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - UNII - CHEBI - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - KEGG.GLYCAN # G number - KEGG.DRUG # D number - KEGG.ENVIRON # E number - KEGG - UMLS chemical entity: is_a: named thing mixins: - physical essence - chemical or drug or treatment # issue 701 - chemical entity or gene or gene product - chemical entity or protein or polypeptide description: >- A chemical entity is a physical entity that pertains to chemistry or biochemistry. slots: - trade name - available from - max tolerated dose - is toxic - has chemical role exact_mappings: - CHEBI:24431 - SIO:010004 # Chemical entity - WIKIDATA:Q79529 # Chemical substance - STY:T103 # Chemical broad_mappings: - STY:T167 # Substance, children include food, body substance, chemical. narrow_mappings: - WIKIDATA:Q43460564 - STY:T123 # (bacs, full name: Biologically Active Substance) - STY:T131 # (hops, full name: Hazardous or Poisonous Substance) in_subset: - translator_minimal id_prefixes: - UNII - CHEBI - MESH - CAS # CAS numbers are given for things like plant extracts as well. - ncats.drug - PHARMGKB.CHEMICAL - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - KEGG.GLYCAN # G number - KEGG.DRUG # D number - KEGG.ENVIRON # E number - KEGG - UMLS small molecule: is_a: molecular entity aliases: ['chemical substance'] description: >- A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion). narrow_mappings: - STY:T196 # Element, Ion, or Isotope - CHEBI:59999 - bioschemas:ChemicalSubstance - STY:T125 # (horm, full name: Hormone) - STY:T197 # (inch, full name: Inorganic Chemical) - STY:T109 # (orch, full name: Organic Chemical) - STY:T118 # (carb, full name: Carbohydrate) - note that this term is missing from newer SRDEF files (depreciated?), but is still used by the SEMMEDDB data files) - STY:T111 # (eico, full name: Eicosanoid) - same note as above - STY:T119 # (lipd, full name: Lipid) - same note as above - STY:T124 # (nsba, full name: Neuroreactive Substance or Biogenic Amine) - same note as above - STY:T115 # (opco, full name: Organophosphorus Compound) - same note as above - STY:T110 # (strd, full name: Steroid) - same note as above - STY:T127 # vitamin id_prefixes: - CHEBI - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - UNII - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - BIGG.METABOLITE - UMLS - foodb.compound - KEGG.GLYCAN # G number - KEGG.DRUG # D number - KEGG.ENVIRON # E number - KEGG - UMLS slot_usage: id: examples: - value: CHEBI:29101 description: sodium ion in_subset: - model_organism_database - translator_minimal chemical mixture: is_a: chemical entity description: >- A chemical mixture is a chemical entity composed of two or more molecular entities. slots: - is supplement - highest FDA approval status - drug regulatory status world wide - routes of delivery in_subset: - translator_minimal id_prefixes: - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - UNII - CHEBI - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - KEGG.GLYCAN ## G number - KEGG.DRUG ## D number - KEGG - KEGG.ENVIRON ## E number - UMLS close_mappings: - dcid:ChemicalCompound narrow_mappings: - NCIT:C20401 # monoclonal antibody - SNOMEDCT:49616005 # monoclonal antibody (substance) nucleic acid entity: is_a: molecular entity description: >- A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included. aliases: ['sequence feature', 'genomic entity'] mixins: - genomic entity - thing with taxon - physical essence - ontology class exact_mappings: - SO:0000110 narrow_mappings: - STY:T086 # Nucleotide Sequence - STY:T114 # Nucleic Acid, Nucleoside, or Nucleotide in_subset: - model_organism_database - translator_minimal id_prefixes: - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - UNII - CHEBI - MESH - CAS - GTOPDB - HMDB - KEGG - KEGG.COMPOUND - ChemBank - PUBCHEM.SUBSTANCE - INCHI - INCHIKEY # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - KEGG.GLYCAN # G number - KEGG.ENVIRON # E number - ChemBank - SIDER.DRUG - BIGG.METABOLITE - foodb.compound - UMLS regulatory region: aliases: ['regulatory element'] description: >- A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene is_a: biological entity mixins: - genomic entity - chemical entity or gene or gene product - physical essence - ontology class exact_mappings: - SO:0005836 - SIO:001225 - WIKIDATA:Q3238407 accessible dna region: aliases: ['dnase-seq accessible region', 'atac-seq accessible region'] description: >- A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose is_a: regulatory region mixins: - genomic entity - chemical entity or gene or gene product - physical essence - ontology class exact_mappings: - SO:0002231 transcription factor binding site: aliases: ['tf binding site', 'binding site'] description: >- A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription is_a: regulatory region mixins: - genomic entity - chemical entity or gene or gene product - physical essence - ontology class exact_mappings: - SO:0000235 molecular mixture: is_a: chemical mixture description: >- A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry. in_subset: - translator_minimal id_prefixes: - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - UNII - CHEBI - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - KEGG.GLYCAN ## G number - KEGG.DRUG ## D number - KEGG - KEGG.ENVIRON ## E number - UMLS - ncats.drug complex molecular mixture: is_a: chemical mixture description: >- A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry. in_subset: - translator_minimal id_prefixes: - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - UNII - CHEBI - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - KEGG.GLYCAN ## G number - KEGG.DRUG ## D number - KEGG - KEGG.ENVIRON ## E number - UMLS biological process or activity: description: >- Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system. is_a: biological entity mixins: - occurrent - ontology class id_prefixes: - GO - REACT slots: - has input - has output - enabled by molecular activity: description: >- An execution of a molecular function carried out by a gene product or macromolecular complex. is_a: biological process or activity aliases: ['molecular function', 'molecular event', 'reaction'] mixins: - occurrent - ontology class slot_usage: has input: range: molecular entity description: >- A chemical entity that is the input for the reaction has output: range: molecular entity description: >- A chemical entity that is the output for the reaction enabled by: range: macromolecular machine mixin description: >- The gene product, gene, or complex that catalyzes the reaction exact_mappings: - GO:0003674 # UMLS Semantic Type "Molecular Function" - STY:T044 broad_mappings: - STY:T045 # Genetic Function id_prefixes: - GO - REACT - RHEA - metacyc.reaction - EC - TCDB - KEGG.REACTION ## R number - KEGG - KEGG.ORTHOLOGY ## in particular for gut microbiome use case in issue #888 - UMLS - BIGG.REACTION - SEED.REACTION - METANETX.REACTION biological process: is_a: biological process or activity mixins: - occurrent - ontology class description: >- One or more causally connected executions of molecular functions exact_mappings: - GO:0008150 - SIO:000006 - WIKIDATA:Q2996394 broad_mappings: - WIKIDATA:P682 id_prefixes: - GO - REACT - metacyc.reaction - KEGG.MODULE ## M number - KEGG pathway: is_a: biological process mixins: - ontology class exact_mappings: - PW:0000001 - WIKIDATA:Q4915012 narrow_mappings: - SIO:010526 - GO:0007165 id_prefixes: - GO - REACT - KEGG - SMPDB - MSigDB - PHARMGKB.PATHWAYS - WIKIPATHWAYS - FB # FlyBase FBgg* - PANTHER.PATHWAY - KEGG.PATHWAY - ncats.bioplanet physiological process: aliases: ['physiology'] is_a: biological process mixins: - ontology class close_mappings: exact_mappings: # Physiologic Function - STY:T039 - WIKIDATA:Q30892994 narrow_mappings: # Organism Function - STY:T040 # Organ or Tissue Function - STY:T042 # Cell Function - STY:T043 # Genetic Function - STY:T045 id_prefixes: - GO - REACT behavior: is_a: biological process mixins: - ontology class - activity and behavior exact_mappings: - GO:0007610 # Behavior - STY:T053 narrow_mappings: # Mental Process - STY:T041 # Social Behavior - STY:T054 # Individual Behavior - STY:T055 ## (Bio)chemistry processed material: is_a: chemical mixture description: >- A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing. exact_mappings: - OBI:0000047 id_prefixes: - UMLS - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - UNII - CHEBI - MESH - CAS - GTOPDB - HMDB - KEGG - KEGG.COMPOUND - ChemBank - PUBCHEM.SUBSTANCE - INCHI - INCHIKEY # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - KEGG.GLYCAN # G number - KEGG.ENVIRON # E number - ChemBank - SIDER.DRUG - BIGG.METABOLITE - foodb.compound - UMLS - foodb.food drug: is_a: molecular mixture mixins: - chemical or drug or treatment - ontology class description: >- A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease comments: - The CHEBI ID represents a role rather than a substance broad_mappings: # Pharmacologic Substance: Any natural, endogenously-derived, # synthetic or semi synthetic compound with pharmacologic activity. - STY:T121 exact_mappings: - WIKIDATA:Q12140 - CHEBI:23888 # UMLS Semantic Type "Clinical Drug" - STY:T200 - dcid:Drug narrow_mappings: # Antibiotic - STY:T195 id_prefixes: - ncats.drug - RXCUI - NDC - UMLS - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - UNII - CHEBI - MESH - CAS - GTOPDB - HMDB - KEGG - KEGG.COMPOUND - ChemBank - PUBCHEM.SUBSTANCE - INCHI - INCHIKEY # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - KEGG.GLYCAN # G number - KEGG.ENVIRON # E number - ChemBank - SIDER.DRUG - BIGG.METABOLITE - foodb.compound ## Food environmental food contaminant: is_a: chemical entity related_mappings: # substance role - CHEBI:78299 id_prefixes: - ncats.drug - RXCUI - NDC - UMLS - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - UNII - CHEBI - MESH - CAS - GTOPDB - HMDB - KEGG - KEGG.COMPOUND - ChemBank - PUBCHEM.SUBSTANCE - INCHI - INCHIKEY # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - KEGG.GLYCAN # G number - KEGG.ENVIRON # E number - ChemBank - SIDER.DRUG - BIGG.METABOLITE - foodb.compound food additive: is_a: chemical entity related_mappings: # substance role - CHEBI:64047 id_prefixes: - ncats.drug - RXCUI - NDC - UMLS - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - UNII - CHEBI - MESH - CAS - GTOPDB - HMDB - KEGG - KEGG.COMPOUND - ChemBank - PUBCHEM.SUBSTANCE - INCHI - INCHIKEY # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - KEGG.GLYCAN # G number - KEGG.ENVIRON # E number - ChemBank - SIDER.DRUG - BIGG.METABOLITE - foodb.compound food: is_a: chemical mixture description: >- A substance consumed by a living organism as a source of nutrition id_prefixes: - foodb.food - foodb.compound - FOODON - UMLS - NCIT - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - UNII - CHEBI - MESH - CAS - GTOPDB - HMDB - KEGG - KEGG.COMPOUND - ChemBank - PUBCHEM.SUBSTANCE - INCHI - INCHIKEY # - iupac # is not actually a CURIE namespace but only a naming convention for chemistry # - SMILES # is not actually a CURIE namespace but only a query language for chemistry - KEGG.GLYCAN # G number - KEGG.ENVIRON # E number - ChemBank - SIDER.DRUG - BIGG.METABOLITE exact_mappings: # Food - STY:T168 ## Biology and Biomedical Sciences ## Biological Attributes organism attribute: is_a: attribute description: >- describes a characteristic of an organismal entity. exact_mappings: # Organism Attribute - STY:T032 phenotypic quality: aliases: ['phenotypic properties'] is_a: organism attribute description: >- A property of a phenotype examples: - value: weight mappings: - PATO:0000001 genetic inheritance: aliases: ['inheritance'] is_a: biological entity description: >- The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc. exact_mappings: - HP:0000005 - GENO:0000141 - NCIT:C45827 close_mappings: - STY:T045 id_prefixes: - HP - GENO - NCIT ## Biological Entities organismal entity: description: >- A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities abstract: true is_a: biological entity mixins: - subject of investigation slot_usage: has attribute: description: >- may often be an organism attribute exact_mappings: - WIKIDATA:Q7239 # UMLS Semantic Group "Living Beings" # Several of the associated semantic types here are probably not # that relevant to the Biolink world, but we keep them here for now. - UMLSSG:LIVB - CARO:0001010 narrow_mappings: - STY:T008 # animal bacterium: is_a: organismal entity description: >- A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile. exact_mappings: - NCBITaxon:1869227 - STY:T007 # Bacterium virus: is_a: organismal entity mixins: - subject of investigation description: >- A virus is a microorganism that replicates itself as a microRNA and infects the host cell. exact_mappings: - NCBITaxon:10239 - STY:T005 # Virus cellular organism: is_a: organismal entity mixins: - subject of investigation description: >- exact_mappings: - NCBITaxon:131567 mammal: is_a: cellular organism mixins: - subject of investigation description: >- A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex exact_mappings: - NCBITaxon:40674 # mammal - STY:T015 # mammal - NCIT:C14234 # Mamalia - FOODON:03411134 # mammal human: is_a: mammal mixins: - subject of investigation description: >- A member of the the species Homo sapiens. exact_mappings: - STY:T016 - NCBITaxon:9606 - SIO:000485 - NCIT:C14225 plant: is_a: cellular organism description: >- exact_mappings: - NCIT:C14258 # plant - STY:T002 # plant - PO:0000003 # whole plant - NCIT:C79659 # plant, whole invertebrate: is_a: cellular organism description: >- An animal lacking a vertebral column. This group consists of 98% of all animal species. exact_mappings: - NCIT:C14228 # invertebrate - OMIT:0008565 # invertebrates - FOODON:00002452 # invertebrate animals - STY:T011 related_mappings: - NCBITaxon:1767184 # unidentified invertebrate vertebrate: is_a: cellular organism description: >- A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column. exact_mappings: - STY:T010 - NCBITaxon:7742 # vertebrata - OMIT:0015545 # vertebrates related_mappings: - NCBITaxon:2662825 # unclassified vertebrata (in:vertebrates) fungus: is_a: cellular organism description: >- A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds). exact_mappings: - STY:T004 - NCIT:C14209 - FOODON:03411261 narrow_mappings: - FOODON:03315605 # fungus (edible) - NCBITaxon:1670606 # fungus metagenome life stage: is_a: organismal entity description: >- A stage of development or growth of an organism, including post-natal adult stages exact_mappings: - UBERON:0000105 narrow_mappings: # constrained to human life cycles - HsapDv:0000000 in_subset: - model_organism_database id_prefixes: - HsapDv - MmusDv - ZFS - FBdv - WBls - UBERON individual organism: aliases: ['organism'] description: >- An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576 is_a: organismal entity mixins: - subject of investigation exact_mappings: - SIO:010000 # Organism - STY:T001 narrow_mappings: # Wikidata considers its definition of 'individual' to be constrained to human persons? - WIKIDATA:Q795052 - foaf:Person id_prefixes: - ORCID population of individual organisms: description: >- A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes. local_names: ga4gh: population is_a: organismal entity mixins: - subject of investigation exact_mappings: - PCO:0000001 - SIO:001061 # UMLS Semantic Type "Population Group" - STY:T098 - OBI:0000181 id_prefixes: - HANCESTRO in_subset: - model_organism_database disease or phenotypic feature: aliases: ['phenome'] is_a: biological entity description: >- Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature. union_of: - disease - phenotypic feature narrow_mappings: # UMLS Semantic Type "Finding" - more specialized use of 'disease or phenotypic feature' - STY:T033 disease: aliases: ['condition', 'disorder', 'medical condition'] description: >- A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. is_a: disease or phenotypic feature exact_mappings: - MONDO:0000001 - DOID:4 - NCIT:C2991 - WIKIDATA:Q12136 - SIO:010299 - UMLSSG:DISO - STY:T047 - dcid:Disease narrow_mappings: - STY:T019 # Acquired Abnormality - STY:T020 # Mental or behavioral disfunction - STY:T048 # (Cell or Molecular Dysfunction) - STY:T049 # (Neoplastic Process) - STY:T191 # disease susceptibility - MONDO:0042489 id_prefixes: - MONDO - DOID - OMIM - OMIM.PS - orphanet - EFO - UMLS - MESH - MEDDRA - NCIT - SNOMEDCT - medgen - ICD10 - ICD9 - KEGG.DISEASE ## H number - HP - MP - PHARMGKB.DISEASE in_subset: - model_organism_database - translator_minimal phenotypic feature: aliases: ['sign', 'symptom', 'phenotype', 'trait', 'endophenotype'] is_a: disease or phenotypic feature description: >- A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment. examples: - value: MP:0001262 description: decreased body weight exact_mappings: - UPHENO:0001001 - SIO:010056 - WIKIDATA:Q104053 - UMLS:C4021819 - NCIT:C16977 - SNOMEDCT:8116006 # documented as phenotypic finding and phenotype, also referred to as "SCTID:8116006" at SNOMEDCT - MESH:D010641 # phenotype narrow_mappings: - STY:T184 # Sign or Symptom - WIKIDATA:Q169872 # Sign or Symptom # presentation of a disease in clinical medicine - WIKIDATA:Q25203551 - ZP:00000000 # zebrafish phenotype - FBcv:0001347 # fly phenotype - HP:0000118 # human phenotype - MP:0000001 # mouse phenotype - WBPhenotype:0000886 # worm phenotype - XPO:00000000 # frog phenotype - FYPO:0000001 # fission yeast phenotype - APO:0000017 # phenotype - TO:0000387 # more narrowly defined here for plants; our definition conflates trait and phenotype. - STY:T190 broad_mappings: - BFO:0000019 # quality - PATO:0000001 # quality id_prefixes: - HP - EFO # covered by BFO quality mapping - NCIT - UMLS - MEDDRA # can not find a mapping - MP - ZP - UPHENO - APO - FBcv - WBPhenotype - SNOMEDCT - MESH - XPO - FYPO - TO in_subset: - model_organism_database behavioral feature: description: >- A phenotypic feature which is behavioral in nature. is_a: phenotypic feature exact_mappings: - NBO:0000243 anatomical entity: is_a: organismal entity mixins: - physical essence description: >- A subcellular location, cell type or gross anatomical part exact_mappings: - UBERON:0001062 - WIKIDATA:Q4936952 # UMLS Semantic Group "Anatomy" - UMLSSG:ANAT # UMLS Semantic Type "Anatomical Structure" - STY:T017 - FMA:62955 # anatomical entity - CARO:0000000 # anatomical entity - SIO:001262 # anatomical entity - STY:T029 # Body Location or Region - STY:T030 # Body Space or Junction narrow_mappings: - ZFA:0100000 # zebrafish anatomical entity - FBbt:10000000 # fly anatomical entity - EMAPA:0 # mouse anatomical entity - MA:0000001 # mouse anatomical entity - XAO:0000000 # frog anatomical entity - WBbt:0000100 # c. elegans anatomical entity - NCIT:C12219 # human anatomical entity - GO:0110165 # cellular anatomical entity, also used directly in CL - STY:T031 # Body Substance related_mappings: - SNOMEDCT:123037004 # body structure id_prefixes: - UBERON - GO - CL - UMLS - MESH - NCIT - EMAPA - ZFA - FBbt - WBbt in_subset: - model_organism_database cellular component: aliases: ['cell component', 'cell part'] is_a: anatomical entity description: >- A location in or around a cell exact_mappings: - GO:0005575 - SIO:001400 - WIKIDATA:Q5058355 # Cell Component - STY:T026 broad_mappings: - WIKIDATA:P681 id_prefixes: - GO - MESH - UMLS - NCIT - SNOMEDCT - CL - UBERON cell: is_a: anatomical entity exact_mappings: - GO:0005623 - CL:0000000 - SIO:010001 - WIKIDATA:Q7868 # UMLS Semantic Type "Cell" - STY:T025 - MESH:D002477 # cells id_prefixes: - CL - PO - UMLS - NCIT - MESH - UBERON - SNOMEDCT - MESH cell line: is_a: organismal entity mixins: - subject of investigation exact_mappings: - CLO:0000031 id_prefixes: - CLO gross anatomical structure: aliases: ['tissue', 'organ'] is_a: anatomical entity exact_mappings: - UBERON:0010000 - WIKIDATA:Q4936952 narrow_mappings: # UMLS Semantic Type "Body Part, Organ, or Organ Component" - STY:T023 # UMLS Semantic Type "Tissue" - STY:T024 # Embryonic Structure - STY:T018 id_prefixes: - UBERON - UMLS - MESH - NCIT - PO - FAO ## entity mixins chemical entity or gene or gene product: 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. mixin: true chemical entity or protein or polypeptide: description: >- A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities. mixin: true macromolecular machine mixin: 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. mixin: true slots: - name slot_usage: name: range: symbol type description: >- genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name gene or gene product: description: >- A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another is_a: macromolecular machine mixin mixin: true id_prefixes: - CHEMBL.TARGET - IUPHAR.FAMILY 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. is_a: biological entity mixins: - gene or gene product - genomic entity - chemical entity or gene or gene product - physical essence - ontology class slots: - symbol - xref exact_mappings: - SO:0000704 - SIO:010035 - WIKIDATA:Q7187 - dcid:Gene id_prefixes: - NCBIGene - ENSEMBL - HGNC - MGI - ZFIN - dictyBase - WB - WormBase # we have two prefixes here as wormbase supports WormBase:WBGene00000898 # and alliancegenome.org and identifiers.org supports WB:WBGene00000898. - FB - RGD - SGD - PomBase - OMIM - KEGG.GENES ## org:gene - UMLS - Xenbase - AspGD - PHARMGKB.GENE in_subset: - translator_minimal - model_organism_database narrow_mappings: - bioschemas:gene broad_mappings: - NCIT:C45822 gene product mixin: description: >- The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules. is_a: gene or gene product mixin: true slots: - synonym - xref exact_mappings: - WIKIDATA:Q424689 - GENO:0000907 - NCIT:C26548 id_prefixes: - UniProtKB - gtpo - PR gene product isoform mixin: description: >- This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms. is_a: gene product mixin mixin: true macromolecular complex: description: >- A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. is_a: biological entity mixins: - macromolecular machine mixin exact_mappings: - GO:0032991 - WIKIDATA:Q22325163 id_prefixes: - INTACT - GO - PR - REACT - ComplexPortal in_subset: - model_organism_database ## Genomic Classes nucleosome modification: is_a: biological entity description: >- A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A. mixins: - gene product isoform mixin - genomic entity - epigenomic entity genome: is_a: biological entity mixins: - genomic entity - physical essence - ontology class description: >- A genome is the sum of genetic material within a cell or virion. exact_mappings: - SO:0001026 - SIO:000984 - WIKIDATA:Q7020 close_mappings: - dcid:GenomeAssemblyUnit in_subset: - model_organism_database exon: is_a: biological entity description: >- A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. exact_mappings: - SO:0000147 - SIO:010445 - WIKIDATA:Q373027 transcript: is_a: biological entity description: >- An RNA synthesized on a DNA or RNA template by an RNA polymerase. exact_mappings: - SO:0000673 - SIO:010450 - WIKIDATA:Q7243183 - dcid:RNATranscript id_prefixes: - ENSEMBL # ENSEMBL:ENST for human - FB # FlyBase:FBtr in_subset: - model_organism_database coding sequence: is_a: biological entity mixins: - genomic entity exact_mappings: - SO:0000316 - SIO:001390 polypeptide: aliases: ['amino acid entity'] is_a: biological entity description: >- A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule. mixins: - chemical entity or gene or gene product - chemical entity or protein or polypeptide id_prefixes: - UniProtKB - PR - ENSEMBL # ENSEMBL:ENSP* - FB # FlyBase FBpp* - UMLS in_subset: - model_organism_database narrow_mappings: - SO:0000104 # polypeptide defined in SO conflates protein and polypeptide # Amino Acid, Peptide, or Protein - STY:T116 # Amino Acid Sequence - STY:T087 protein: description: >- A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA is_a: polypeptide mixins: - gene product mixin id_prefixes: - UniProtKB - PR - ENSEMBL # ENSEMBL:ENSP* - FB # FlyBase FBpp* - UMLS - MESH - ncats.drug broad_mappings: - bioschemas:Protein exact_mappings: - PR:000000001 - SIO:010043 - WIKIDATA:Q8054 narrow_mappings: # Enzyme - STY:T126 # Receptor - STY:T192 protein isoform: aliases: ['proteoform'] is_a: protein description: >- Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/ mixins: - gene product isoform mixin id_prefixes: - UniProtKB # UniProtKB:([A-Z0-9]+-\d+) - UNIPROT.ISOFORM - PR - ENSEMBL protein domain: is_a: biological entity description: >- A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain. mixins: - gene grouping mixin - chemical entity or gene or gene product exact_mappings: - NCIT:C13379 - SIO:001379 - UMLS:C1514562 posttranslational modification: is_a: biological entity description: >- A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination. mixins: - gene product isoform mixin protein family: is_a: biological entity exact_mappings: - NCIT:C26004 - WIKIDATA:Q2278983 narrow_mappings: - SIO:001380 - NCIT:C20130 - WIKIDATA:Q417841 mixins: - gene grouping mixin - chemical entity or gene or gene product nucleic acid sequence motif: aliases: ['consensus sequence'] is_a: biological entity description: >- A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences. RNA product: is_a: transcript mixins: - gene product mixin exact_mappings: - CHEBI:33697 # This SIO term here also mapped to 'biolink:Transcript'; however, # since this 'biolink:RNAProduct' relates more to the biochemical # essence of RNA, then map the SIO term instead to 'biolink:Transcript' # - SIO:010450 - WIKIDATA:Q11053 id_prefixes: - RNACENTRAL RNA product isoform: is_a: RNA product description: >- Represents a protein that is a specific isoform of the canonical or reference RNA mixins: - gene product isoform mixin id_prefixes: - RNACENTRAL noncoding RNA product: is_a: RNA product id_prefixes: - RNACENTRAL - NCBIGene - ENSEMBL exact_mappings: - SO:0000655 - SIO:001235 microRNA: is_a: noncoding RNA product exact_mappings: - SO:0000276 - SIO:001397 - WIKIDATA:Q310899 id_prefixes: - MIR - HGNC - WormBase in_subset: - model_organism_database siRNA: aliases: ['small interfering RNA', 'RNAi'] description: >- A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. is_a: noncoding RNA product exact_mappings: - SO:0000646 - WIKIDATA:Q203221 id_prefixes: - MIR - HGNC - WormBase in_subset: - model_organism_database gene grouping mixin: description: >- any grouping of multiple genes or gene products mixin: true slots: - has gene or gene product gene family: aliases: ['orthogroup', 'protein family'] is_a: biological entity exact_mappings: - NCIT:C26004 - WIKIDATA:Q2278983 narrow_mappings: # These term definitions focus only on proteins; # the 'biolink:GeneFamily' term would be more inclusive # to describe gene loci, non-coding RNA, etc. - SIO:001380 - NCIT:C20130 - WIKIDATA:Q417841 mixins: - gene grouping mixin - chemical entity or gene or gene product description: >- any grouping of multiple genes or gene products related by common descent id_prefixes: - PANTHER.FAMILY - HGNC.FAMILY - FB # FlyBase FBgg* - interpro # note: may be better to introduce a protein domain/family - CATH - CDD - HAMAP - PFAM - PIRSF - PRINTS - PRODOM - PROSITE - SMART - SUPFAM - TIGRFAM - CATH.SUPERFAMILY - RFAM ## RNAs only - KEGG.ORTHOLOGY ## aka KEGG.KO: K number - EGGNOG - COG in_subset: - model_organism_database zygosity: is_a: attribute exact_mappings: - GENO:0000133 genotype: is_a: biological entity mixins: - physical essence - genomic entity - ontology class description: >- An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background comments: - Consider renaming as genotypic entity slots: - has zygosity exact_mappings: - GENO:0000536 - SIO:001079 id_prefixes: - ZFIN - FB # FlyBase FBba* in_subset: - model_organism_database haplotype: is_a: biological entity mixins: - genomic entity - physical essence - ontology class description: >- A set of zero or more Alleles on a single instance of a Sequence[VMC] # slots: # - completeness exact_mappings: - GENO:0000871 - SO:0001024 - VMC:Haplotype sequence variant: aliases: ['allele'] local_names: agr: allele is_a: biological entity mixins: - genomic entity - physical essence - ontology class description: >- A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. comments: - This class is for modeling the specific state at a locus. A single DBSNP rs ID could correspond to more than one sequence variants (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743) exact_mappings: # slightly broader semantics than SO:0001059 - 'sequence alteration' # describes a sequence feature that may have 1..* sequence alterations - WIKIDATA:Q15304597 close_mappings: - dcid:Allele - SO:0001060 - VMC:Allele - GENO:0000002 - SIO:010277 - SO:0001060 id_prefixes: - CAID # ClinGen Allele Registry - CLINVAR - WIKIDATA # - CIViC needs IRI mapping - DBSNP - MGI - ZFIN - FB - RGD - AGRKB - SPDI - WB - WormBase - PHARMGKB.VARIANT alt_descriptions: AGR: >- An entity that describes a single affected, endogenous allele. These can be of any type that matches that definition VMC: >- A contiguous change at a Location slots: - has gene slot_usage: has gene: multivalued: true description: Each allele can be associated with any number of genes has biological sequence: description: >- The state of the sequence w.r.t a reference sequence id: examples: - value: ZFIN:ZDB-ALT-980203-1091 description: ti282a allele from ZFIN - value: CLINVAR:17681 description: NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp) in_subset: - model_organism_database snv: aliases: ['single nucleotide variant', 'single nucleotide polymorphism', 'snp'] is_a: sequence variant description: >- SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist exact_mappings: - SO:0001483 reagent targeted gene: aliases: ['sequence targeting reagent'] is_a: biological entity description: >- A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi. mixins: - genomic entity - physical essence - ontology class exact_mappings: - GENO:0000504 in_subset: - model_organism_database ## -------------------- ## Clinical ## Attributes, Cohort, ## Exposures & Outcomes ## -------------------- ## Clinical Attributes clinical attribute: is_a: attribute description: >- Attributes relating to a clinical manifestation exact_mappings: # Clinical Attribute - STY:T201 clinical measurement: is_a: clinical attribute description: >- A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot. slot_usage: has attribute type: required: true multivalued: false values_from: - EFO - LOINC exact_mappings: - EFO:0001444 clinical modifier: is_a: clinical attribute description: >- Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects exact_mappings: clinical course: is_a: clinical attribute description: >- The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual exact_mappings: - HP:0031797 onset: is_a: clinical course description: >- The age group in which (disease) symptom manifestations appear. notes: >- This class is in Biolink to support HP ontology annotations which use "onset" (with terms from HP) as an annotation on a disease to phenotypic feature association. This should be the primary use case for this class. exact_mappings: - HP:0003674 clinical entity: is_a: named thing description: >- Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities clinical trial: is_a: clinical entity clinical intervention: is_a: clinical entity clinical finding: is_a: phenotypic feature description: >- this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations. slot_usage: has attribute: range: clinical attribute id_prefixes: - LOINC - NCIT - EFO hospitalization: is_a: clinical intervention exact_mappings: - SNOMEDCT:32485007 - WIKIDATA:Q3140971 socioeconomic attribute: is_a: attribute description: >- Attributes relating to a socioeconomic manifestation ## Cohorts case: aliases: ['patient', 'proband'] is_a: individual organism description: >- An individual (human) organism that has a patient role in some clinical context. mixins: - subject of investigation cohort: is_a: study population description: >- A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time. mixins: - subject of investigation exact_mappings: - WIKIDATA:Q1303415 narrow_mappings: # Professional or Occupational Group - STY:T097 # Family Group - STY:T099 # Age Group - STY:T100 # Patient or Disabled Group - STY:T101 ## Exposures exposure event: is_a: ontology class aliases: ['exposure', 'experimental condition'] mixin: true slots: - timepoint description: >- A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes exact_mappings: - XCO:0000000 in_subset: - model_organism_database # TODO - confirm that genomic backgrounds are exposures genomic background exposure: is_a: attribute mixins: - exposure event - gene grouping mixin - physical essence - genomic entity - thing with taxon - ontology class description: >- A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome. pathological entity mixin: description: >- A pathological (abnormal) structure or process. mixin: true exact_mappings: - MPATH:0 narrow_mappings: - HP:0000118 pathological process: description: >- A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. is_a: biological process mixins: - pathological entity mixin exact_mappings: - OBI:1110122 - NCIT:C16956 - MPATH:596 narrow_mappings: # metastasis - NCIT:C19151 - EFO:0009708 - STY:T046 - STY:T037 pathological process exposure: is_a: attribute mixins: - exposure event description: >- A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease. pathological anatomical structure: description: >- An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. is_a: anatomical entity mixins: - pathological entity mixin exact_mappings: - MPATH:603 pathological anatomical exposure: is_a: attribute mixins: - exposure event description: >- An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome. disease or phenotypic feature exposure: is_a: attribute mixins: - exposure event - pathological entity mixin description: >- A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer. chemical exposure: is_a: attribute mixins: - exposure event slots: - has quantitative value description: >- A chemical exposure is an intake of a particular chemical entity. exact_mappings: # this ECTO term is not visibly defined but # the 9000000-series identifiers seems to be the # numeric space of chemical exposure definitions - ECTO:9000000 - SIO:001399 complex chemical exposure: is_a: attribute description: >- A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug. drug exposure: is_a: chemical exposure aliases: ['drug intake', 'drug dose', 'medication intake'] description: >- A drug exposure is an intake of a particular drug. mixins: - exposure event broad_mappings: # slightly broader than just drug effects on a biological system - SIO:001005 exact_mappings: - ECTO:0000509 # TODO: deprecate? drug to gene interaction exposure: description: >- drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome. is_a: drug exposure mixins: - gene grouping mixin treatment: aliases: ['medical action', 'medical intervention'] # 'named thing' seems too generic here but not sure what applies better here is_a: named thing mixins: - exposure event - chemical or drug or treatment description: >- A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures slots: - has drug - has device - has procedure exact_mappings: - OGMS:0000090 - SIO:001398 broad_mappings: - MAXO:0000058 biotic exposure: is_a: attribute aliases: ['viral exposure', 'bacterial exposure'] mixins: - exposure event description: >- An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses). geographic exposure: is_a: environmental exposure mixins: - exposure event description: >- A geographic exposure is a factor relating to geographic proximity to some impactful entity. close_mappings: - dcid:GeologicalEvent narrow_mappings: - dcid:IceStoremEvent - dcid:LakeEffectSnowEvent - dcid:LandslideEvent - dcid:MarineDenseFogEvent - dcid:MarineLighteningEvent - dcid:MarineStrongWindEvent - dcid:MarineThunderstormWindEvent - dcid:StormEvent - dcid:StormSurgeTideEvent - dcid:StrongWindEvent - dcid:ThunderstormWindEvent - dcid:TornadoEvent - dcid:TropicalDepressionEvent - dcid:WinterStoremEvent environmental exposure: is_a: attribute mixins: - exposure event description: >- A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants. behavioral exposure: is_a: attribute mixins: - exposure event description: >- A behavioral exposure is a factor relating to behavior impacting an individual. socioeconomic exposure: is_a: attribute mixins: - exposure event description: >- A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty). slot_usage: has attribute: range: socioeconomic attribute required: true ## Outcomes outcome: mixin: true description: >- An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes. pathological process outcome: mixins: - outcome description: >- An outcome resulting from an exposure event which is the manifestation of a pathological process. pathological anatomical outcome: mixins: - outcome description: >- An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure. disease or phenotypic feature outcome: mixins: - outcome description: >- Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype. behavioral outcome: mixins: - outcome description: >- An outcome resulting from an exposure event which is the manifestation of human behavior. hospitalization outcome: mixins: - outcome description: >- An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization. mortality outcome: mixins: - outcome description: >- An outcome of death from resulting from an exposure event. epidemiological outcome: mixins: - outcome description: >- An epidemiological outcome, such as societal disease burden, resulting from an exposure event. related_mappings: - NCIT:C19291 socioeconomic outcome: mixins: - outcome description: >- An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event ## ------------ ## ASSOCIATIONS ## ------------ association: is_a: entity description: >- A typed association between two entities, supported by evidence comments: - This is roughly the model used by biolink and ontobio at the moment slots: - subject - predicate - object - negated - qualifier - qualifiers # deprecated - publications - has evidence - knowledge source - primary knowledge source - aggregator knowledge source - knowledge level - agent type - timepoint - original subject - original predicate - original object # denormalized fields - subject category - object category - subject closure - object closure - subject category closure - object category closure - subject namespace - object namespace - subject label closure - object label closure - retrieval source ids slot_usage: type: description: rdf:type of biolink:Association should be fixed at rdf:Statement category: range: uriorcurie required: false exact_mappings: - OBAN:association - rdf:Statement - owl:Axiom chemical entity assesses named thing association: is_a: association slot_usage: subject: range: chemical entity object: range: named thing predicate: subproperty_of: assesses contributor association: is_a: association defining_slots: - subject - predicate - object description: >- Any association between an entity (such as a publication) and various agents that contribute to its realisation slot_usage: subject: range: information content entity description: >- information content entity which an agent has helped realise predicate: subproperty_of: contributor description: >- generally one of the predicate values 'provider', 'publisher', 'editor' or 'author' object: range: agent description: >- agent helping to realise the given entity (e.g. such as a publication) qualifiers: description: >- this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author' genotype to genotype part association: is_a: association defining_slots: - subject - object description: >- Any association between one genotype and a genotypic entity that is a sub-component of it slot_usage: predicate: subproperty_of: has variant part subject: range: genotype description: >- parent genotype object: range: genotype description: >- child genotype genotype to gene association: description: >- Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality is_a: association defining_slots: - subject - object slot_usage: predicate: description: >- the relationship type used to connect genotype to gene subject: range: genotype description: >- parent genotype object: range: gene description: >- gene implicated in genotype genotype to variant association: description: >- Any association between a genotype and a sequence variant. is_a: association defining_slots: - subject - object slot_usage: predicate: description: >- the relationship type used to connect genotype to gene subject: range: genotype description: >- parent genotype object: range: sequence variant description: >- gene implicated in genotype gene to gene association: aliases: ['molecular or genetic interaction'] description: >- abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction. abstract: true is_a: association defining_slots: - subject - object slot_usage: subject: range: gene or gene product description: >- the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa. object: range: gene or gene product description: >- the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa. gene to gene homology association: description: >- A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same) is_a: gene to gene association defining_slots: - subject - predicate - object slot_usage: subject: range: gene or gene product predicate: subproperty_of: homologous to symmetric: true description: >- homology relationship type object: range: gene or gene product gene to gene family association: description: >- Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships. is_a: association defining_slots: - subject - predicate - object slot_usage: subject: range: gene object: range: gene family predicate: subproperty_of: member of symmetric: false description: >- membership of the gene in the given gene family. gene expression mixin: description: >- Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs. mixin: true slots: - quantifier qualifier - expression site - stage qualifier - phenotypic state slot_usage: quantifier qualifier: description: >- Optional quantitative value indicating degree of expression. gene to gene coexpression association: description: >- Indicates that two genes are co-expressed, generally under the same conditions. is_a: gene to gene association defining_slots: - subject - predicate - object mixins: - gene expression mixin slot_usage: predicate: subproperty_of: coexpressed with symmetric: true pairwise gene to gene interaction: description: >- An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation) is_a: gene to gene association defining_slots: - subject - predicate - object slot_usage: predicate: subproperty_of: interacts with symmetric: true description: "interaction relationship type" narrow_mappings: - dcid:ProteinProteinInteraction pairwise molecular interaction: description: >- An interaction at the molecular level between two physical entities is_a: pairwise gene to gene interaction slots: - interacting molecules category defining_slots: - subject - predicate - object slot_usage: subject: range: molecular entity id: description: >- identifier for the interaction. This may come from an interaction database such as IMEX. examples: - value: WB:WBInteraction000538741 values_from: - IMEX - BioGRID predicate: subproperty_of: interacts with description: "interaction relationship type" examples: - value: RO:0002447 description: the subject molecular phosphorylates the object molecule object: range: molecular entity cell line to entity association mixin: description: >- An relationship between a cell line and another entity mixin: true slots: - subject - predicate - object defining_slots: - subject slot_usage: subject: range: cell line # TODO: figure out what gives with subject range cell line to disease or phenotypic feature association: is_a: association mixins: - cell line to entity association mixin - entity to disease or phenotypic feature association mixin description: >- An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype. slot_usage: subject: # - range: cell line # - range: disease or phenotypic feature range: disease or phenotypic feature chemical entity to entity association mixin: description: >- An interaction between a chemical entity and another entity mixin: true slots: - subject - predicate - object defining_slots: - subject slot_usage: subject: range: chemical entity or gene or gene product description: "the chemical entity that is an interactor" drug to entity association mixin: description: >- An interaction between a drug and another entity is_a: chemical entity to entity association mixin mixin: true slots: - subject - predicate - object defining_slots: - subject slot_usage: subject: range: drug description: "the drug that is an interactor" chemical to entity association mixin: description: >- An interaction between a chemical entity and another entity is_a: chemical entity to entity association mixin mixin: true slots: - subject - predicate - object defining_slots: - subject slot_usage: subject: range: chemical entity or gene or gene product description: "the chemical entity or entity that is an interactor" case to entity association mixin: description: >- An abstract association for use where the case is the subject mixin: true slots: - subject - predicate - object defining_slots: - subject slot_usage: subject: range: case description: "the case (e.g. patient) that has the property" chemical to chemical association: description: >- A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another. is_a: association slots: - subject - predicate - object defining_slots: - subject - object mixins: - chemical to entity association mixin slot_usage: object: range: chemical entity description: "the chemical element that is the target of the statement" reaction to participant association: description: is_a: chemical to chemical association slots: - stoichiometry - reaction direction - reaction side slot_usage: subject: range: molecular entity defining_slots: - subject - predicate - object reaction to catalyst association: description: is_a: reaction to participant association slot_usage: object: range: gene or gene product chemical to chemical derivation association: description: >- A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P is_a: chemical to chemical association defining_slots: - subject - predicate - object slots: - catalyst qualifier slot_usage: subject: range: chemical entity description: >- the upstream chemical entity object: range: chemical entity description: >- the downstream chemical entity predicate: subproperty_of: derives into catalyst qualifier: description: >- this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical. chemical to disease or phenotypic feature association: description: >- An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype. is_a: association narrow_mappings: - SIO:000993 defining_slots: - subject - object mixins: - chemical to entity association mixin - entity to disease or phenotypic feature association mixin slot_usage: object: range: disease or phenotypic feature description: "the disease or phenotype that is affected by the chemical" chemical or drug or treatment to disease or phenotypic feature association: description: >- This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect. is_a: association defining_slots: - subject - predicate - object mixins: - chemical to entity association mixin - entity to disease or phenotypic feature association mixin slots: - FDA adverse event level slot_usage: predicate: subproperty_of: has adverse event chemical or drug or treatment side effect disease or phenotypic feature association: description: >- This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect. is_a: chemical or drug or treatment to disease or phenotypic feature association defining_slots: - subject - predicate - object mixins: - chemical to entity association mixin - entity to disease or phenotypic feature association mixin slot_usage: predicate: subproperty_of: has side effect gene to pathway association: description: >- An interaction between a gene or gene product and a biological process or pathway. is_a: association defining_slots: - subject - object mixins: - gene to entity association mixin slot_usage: subject: range: gene or gene product description: "the gene or gene product entity that participates or influences the pathway" object: range: pathway description: "the pathway that includes or is affected by the gene or gene product" molecular activity to pathway association: description: >- Association that holds the relationship between a reaction and the pathway it participates in. is_a: association slot_usage: subject: range: molecular activity object: range: pathway predicate: subproperty_of: part of chemical to pathway association: description: >- An interaction between a chemical entity and a biological process or pathway. is_a: association exact_mappings: - SIO:001250 defining_slots: - subject - object mixins: - chemical to entity association mixin slot_usage: subject: range: chemical entity description: "the chemical entity that is affecting the pathway" object: range: pathway description: "the pathway that is affected by the chemical" named thing associated with likelihood of named thing association: # TODO: better name description: >- is_a: association slots: - subject - subject aspect qualifier - subject context qualifier - predicate - object - object aspect qualifier - object context qualifier - population context qualifier defining_slots: - subject - subject aspect qualifier - subject context qualifier - predicate - object - object aspect qualifier - object context qualifier - population context qualifier slot_usage: predicate: subproperty_of: associated with subject aspect qualifier: # TODO: range subject context qualifier: range: ontology class object aspect qualifier: # TODO: range object context qualifier: range: ontology class chemical gene interaction association: description: >- describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction) is_a: association exact_mappings: - SIO:001257 mixins: - chemical to entity association mixin slots: - subject form or variant qualifier - subject part qualifier - subject derivative qualifier - subject context qualifier - object form or variant qualifier - object part qualifier - object context qualifier - anatomical context qualifier slot_usage: subject: range: chemical entity object: range: gene or gene product predicate: subproperty_of: physically interacts with subject form or variant qualifier: range: ChemicalOrGeneOrGeneProductFormOrVariantEnum subject part qualifier: range: GeneOrGeneProductOrChemicalPartQualifierEnum subject derivative qualifier: range: ChemicalEntityDerivativeEnum subject context qualifier: range: anatomical entity object form or variant qualifier: range: ChemicalOrGeneOrGeneProductFormOrVariantEnum object part qualifier: range: GeneOrGeneProductOrChemicalPartQualifierEnum object context qualifier: range: anatomical entity anatomical context qualifier: range: anatomical entity chemical affects gene association: description: >- Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.) is_a: association slots: - subject form or variant qualifier - subject part qualifier - subject derivative qualifier - subject aspect qualifier - subject context qualifier - subject direction qualifier - object form or variant qualifier - object part qualifier - object aspect qualifier - object context qualifier - object direction qualifier - causal mechanism qualifier - anatomical context qualifier - qualified predicate - species context qualifier slot_usage: subject: range: chemical entity subject form or variant qualifier: range: ChemicalOrGeneOrGeneProductFormOrVariantEnum subject part qualifier: range: GeneOrGeneProductOrChemicalPartQualifierEnum subject derivative qualifier: range: ChemicalEntityDerivativeEnum subject aspect qualifier: range: GeneOrGeneProductOrChemicalEntityAspectEnum subject context qualifier: range: anatomical entity subject direction qualifier: range: DirectionQualifierEnum predicate: subproperty_of: affects qualified predicate: subproperty_of: causes object: range: gene or gene product object form or variant qualifier: range: ChemicalOrGeneOrGeneProductFormOrVariantEnum object part qualifier: range: GeneOrGeneProductOrChemicalPartQualifierEnum object aspect qualifier: range: GeneOrGeneProductOrChemicalEntityAspectEnum object context qualifier: range: anatomical entity object direction qualifier: range: DirectionQualifierEnum causal mechanism qualifier: range: CausalMechanismQualifierEnum anatomical context qualifier: range: anatomical entity species context qualifier: range: organism taxon gene affects chemical association: description: >- Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.) examples: value: subject: TRPC4 predicate: affects qualified_predicte: causes object: Barium object_aspect_qualifier: transport object_direction_qualifier: increased is_a: association slots: - subject form or variant qualifier - subject part qualifier - subject derivative qualifier - subject aspect qualifier - subject context qualifier - subject direction qualifier - object form or variant qualifier - object part qualifier - object aspect qualifier - object context qualifier - object direction qualifier - object derivative qualifier - causal mechanism qualifier - anatomical context qualifier - qualified predicate - species context qualifier slot_usage: subject: range: gene or gene product subject form or variant qualifier: range: ChemicalOrGeneOrGeneProductFormOrVariantEnum subject part qualifier: range: GeneOrGeneProductOrChemicalPartQualifierEnum subject aspect qualifier: range: GeneOrGeneProductOrChemicalEntityAspectEnum subject context qualifier: range: anatomical entity subject direction qualifier: range: DirectionQualifierEnum predicate: subproperty_of: affects qualified predicate: subproperty_of: causes object: range: chemical entity object form or variant qualifier: range: ChemicalOrGeneOrGeneProductFormOrVariantEnum object part qualifier: range: GeneOrGeneProductOrChemicalPartQualifierEnum object derivative qualifier: range: ChemicalEntityDerivativeEnum object aspect qualifier: range: GeneOrGeneProductOrChemicalEntityAspectEnum object context qualifier: range: anatomical entity object direction qualifier: range: DirectionQualifierEnum causal mechanism qualifier: range: CausalMechanismQualifierEnum anatomical context qualifier: range: anatomical entity species context qualifier: range: organism taxon drug to gene association: description: >- An interaction between a drug and a gene or gene product. is_a: association related_mappings: - SIO:001257 defining_slots: - subject - object mixins: - drug to entity association mixin slot_usage: object: range: gene or gene product description: "the gene or gene product that is affected by the drug" material sample to entity association mixin: description: >- An association between a material sample and something. mixin: true slots: - subject - predicate - object defining_slots: - subject slot_usage: subject: range: material sample description: >- the material sample being described material sample derivation association: description: >- An association between a material sample and the material entity from which it is derived. is_a: association slots: - subject - predicate - object defining_slots: - subject - predicate slot_usage: subject: range: material sample description: >- the material sample being described object: description: >- the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material. predicate: description: >- derivation relationship subproperty_of: derives from material sample to disease or phenotypic feature association: description: >- An association between a material sample and a disease or phenotype. is_a: association mixins: - material sample to entity association mixin - entity to disease or phenotypic feature association mixin defining_slots: - subject - object disease to entity association mixin: mixin: true slots: - subject - predicate - object defining_slots: - subject slot_usage: subject: range: disease description: "disease class" values_from: ['mondo', 'omim', 'orphanet', 'ncit', 'doid'] examples: - value: MONDO:0017314 description: "Ehlers-Danlos syndrome, vascular type" entity to exposure event association mixin: description: >- An association between some entity and an exposure event. mixin: true slots: - subject - predicate - object defining_slots: - object slot_usage: object: range: exposure event disease to exposure event association: description: >- An association between an exposure event and a disease. is_a: association mixins: - disease to entity association mixin - entity to exposure event association mixin defining_slots: - subject - object entity to outcome association mixin: description: >- An association between some entity and an outcome mixin: true slots: - subject - predicate - object defining_slots: - object slot_usage: object: range: outcome exposure event to outcome association: description: >- An association between an exposure event and an outcome. is_a: association mixins: - entity to outcome association mixin slots: - population context qualifier - temporal context qualifier defining_slots: - subject - object frequency qualifier mixin: mixin: true description: >- Qualifier for frequency type associations slots: - frequency qualifier - subject - predicate - object entity to feature or disease qualifiers mixin: description: >- Qualifiers for entity to disease or phenotype associations. mixin: true is_a: frequency qualifier mixin slots: - subject aspect qualifier - subject direction qualifier - object aspect qualifier - object direction qualifier - qualified predicate feature or disease qualifiers to entity mixin: description: >- Qualifiers for disease or phenotype to entity associations. mixin: true is_a: frequency qualifier mixin slots: - subject aspect qualifier - subject direction qualifier - object aspect qualifier - object direction qualifier - qualified predicate entity to phenotypic feature association mixin: mixin: true is_a: entity to feature or disease qualifiers mixin mixins: - frequency quantifier slots: - subject - predicate - object - sex qualifier defining_slots: - object slot_usage: object: range: phenotypic feature values_from: ['upheno', 'hp', 'mp', 'wbphenotype'] examples: - value: HP:0002487 description: Hyperkinesis - value: WBPhenotype:0000180 description: axon morphology variant - value: MP:0001569 description: abnormal circulating bilirubin level phenotypic feature to entity association mixin: mixin: true is_a: feature or disease qualifiers to entity mixin mixins: - frequency quantifier defining_slots: - subject slot_usage: subject: range: phenotypic feature values_from: ['upheno', 'hp', 'mp', 'wbphenotype'] examples: - value: HP:0002487 description: Hyperkinesis - value: WBPhenotype:0000180 description: axon morphology variant - value: MP:0001569 description: abnormal circulating bilirubin level slots: - sex qualifier information content entity to named thing association: description: >- association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property). is_a: association defining_slots: - subject - object slot_usage: subject: domain: publication object: range: named thing predicate: subproperty_of: mentions in_subset: - model_organism_database entity to disease association mixin: description: >- mixin class for any association whose object (target node) is a disease mixin: true is_a: entity to feature or disease qualifiers mixin defining_slots: - object slot_usage: object: range: disease description: "disease" examples: - value: MONDO:0020066 description: "Ehlers-Danlos syndrome" disease or phenotypic feature to entity association mixin: mixin: true slots: - subject - predicate - object defining_slots: - subject slot_usage: subject: range: disease or phenotypic feature description: "disease or phenotype" examples: - value: MONDO:0017314 description: "Ehlers-Danlos syndrome, vascular type" - value: MP:0013229 description: "abnormal brain ventricle size" disease or phenotypic feature to location association: description: >- An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site. is_a: association mixins: - disease or phenotypic feature to entity association mixin slot_usage: object: range: anatomical entity description: >- anatomical entity in which the disease or feature is found. examples: - value: UBERON:0002048 description: "lung" disease or phenotypic feature to genetic inheritance association: description: >- An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance. is_a: association mixins: - disease or phenotypic feature to entity association mixin slot_usage: predicate: subproperty_of: has mode of inheritance object: range: genetic inheritance description: >- genetic inheritance associated with the specified disease or phenotypic feature. examples: - value: HP:0001417 description: "X-linked inheritance" entity to disease or phenotypic feature association mixin: mixin: true slots: - subject - predicate - object defining_slots: - object slot_usage: object: range: disease or phenotypic feature description: "disease or phenotype" examples: - value: MONDO:0017314 description: "Ehlers-Danlos syndrome, vascular type" - value: MP:0013229 description: "abnormal brain ventricle size" genotype to entity association mixin: mixin: true slots: - subject - predicate - object defining_slots: - subject slot_usage: subject: range: genotype description: "genotype that is the subject of the association" genotype to phenotypic feature association: is_a: association defining_slots: - subject - object description: >- Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment mixins: - entity to phenotypic feature association mixin - genotype to entity association mixin slot_usage: predicate: subproperty_of: has phenotype subject: range: genotype description: >- genotype that is associated with the phenotypic feature # ie: smoke exposure to coughing phenotype? is this a denormalization? exposure event to phenotypic feature association: is_a: association defining_slots: - subject - object description: >- Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype. mixins: - entity to phenotypic feature association mixin slot_usage: subject: range: exposure event disease to phenotypic feature association: is_a: association slots: - onset qualifier defining_slots: - subject - object description: >- An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way. mixins: - frequency quantifier - entity to phenotypic feature association mixin - disease to entity association mixin close_mappings: - dcid:DiseaseSymptomAssociation slot_usage: subject: range: disease object: range: phenotypic feature case to phenotypic feature association: description: >- An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype. is_a: association defining_slots: - subject - object mixins: - entity to phenotypic feature association mixin - case to entity association mixin behavior to behavioral feature association: description: >- An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior. is_a: association defining_slots: - subject - object slot_usage: subject: range: behavior description: >- behavior that is the subject of the association object: range: behavioral feature description: >- behavioral feature that is the object of the association mixins: - entity to phenotypic feature association mixin gene to entity association mixin: mixin: true slots: - subject - predicate - object defining_slots: - subject slot_usage: subject: range: gene or gene product description: >- gene that is the subject of the association variant to entity association mixin: slots: - subject - predicate - object local_names: ga4gh: variant annotation mixin: true defining_slots: - subject slot_usage: subject: range: sequence variant description: >- a sequence variant in which the allele state is associated with some other entity examples: - value: CLINVAR:38077 description: "CLINVAR representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)" - value: ClinGen:CA024716 description: "chr13:g.32921033G>C (hg19) in ClinGen" gene to disease or phenotypic feature association: is_a: association mixins: - entity to phenotypic feature association mixin - gene to entity association mixin narrow_mappings: - WBVocab:Gene-Phenotype-Association - dcid:DiseaseGeneAssociation - SIO:000983 slots: - subject aspect qualifier - object direction qualifier slot_usage: subject: range: gene or gene product description: "gene in which variation is correlated with the phenotypic feature" examples: - value: HGNC:2197 description: "COL1A1 (Human)" subject aspect qualifier: range: GeneOrGeneProductOrChemicalEntityAspectEnum object: range: disease or phenotypic feature object direction qualifier: range: DirectionQualifierEnum predicate: subproperty_of: affects comments: - NCIT:R176 refers to the inverse relationship - for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype - if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children. gene to phenotypic feature association: is_a: gene to disease or phenotypic feature association exact_mappings: - WBVocab:Gene-Phenotype-Association defining_slots: - subject - object mixins: - entity to phenotypic feature association mixin - gene to entity association mixin slot_usage: subject: range: gene or gene product description: "gene in which variation is correlated with the phenotypic feature" examples: - value: HGNC:2197 description: "COL1A1 (Human)" object: range: phenotypic feature gene to disease association: is_a: gene to disease or phenotypic feature association comments: - NCIT:R176 refers to the inverse relationship exact_mappings: - SIO:000983 close_mappings: - dcid:DiseaseGeneAssociation defining_slots: - subject - object mixins: - entity to disease association mixin - gene to entity association mixin slot_usage: subject: range: gene or gene product description: >- gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model object: range: disease causal gene to disease association: is_a: gene to disease association defining_slots: - subject - object mixins: - entity to disease association mixin - gene to entity association mixin slot_usage: subject: range: gene or gene product description: >- gene in which variation is shown to cause the disease. object: range: disease correlated gene to disease association: is_a: gene to disease association defining_slots: - subject - object mixins: - entity to disease association mixin - gene to entity association mixin slot_usage: subject: range: gene or gene product description: >- gene in which variation is shown to correlate with the disease. object: range: disease druggable gene to disease association: is_a: gene to disease association slot_usage: subject: range: gene or gene product description: >- gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state. predicate: subproperty_of: target for has evidence: range: DruggableGeneCategoryEnum defining_slots: - subject - object - predicate mixins: - entity to disease association mixin - gene to entity association mixin phenotypic feature to disease association: is_a: association slot_usage: predicate: subproperty_of: associated with defining_slots: - subject - predicate - object mixins: - entity to disease association mixin - phenotypic feature to entity association mixin variant to gene association: description: >- An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium) is_a: association defining_slots: - subject - predicate - object mixins: - variant to entity association mixin slot_usage: object: range: gene predicate: subproperty_of: genetically associated with variant to gene expression association: description: >- An association between a variant and expression of a gene (i.e. e-QTL) is_a: variant to gene association defining_slots: - subject - predicate - object mixins: - gene expression mixin slot_usage: predicate: subproperty_of: affects variant to population association: description: >- An association between a variant and a population, where the variant has particular frequency in the population is_a: association defining_slots: - subject - object mixins: - variant to entity association mixin - frequency quantifier - frequency qualifier mixin slot_usage: subject: range: sequence variant description: >- an allele that has a certain frequency in a given population examples: - value: "NC_000017.11:g.43051071A>T" description: >- 17:41203088 A/C in gnomad object: range: population of individual organisms description: >- the population that is observed to have the frequency examples: - value: HANCESTRO:0010 description: African has quotient: description: >- frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency examples: - value: "0.0001666" has count: description: >- number in object population that carry a particular allele, aka allele count examples: - value: "4" description: 4 individuals in gnomad set has total: description: >- number all populations that carry a particular allele, aka allele number examples: - value: "24014" description: 24014 individuals in gnomad set population to population association: description: >- An association between a two populations is_a: association defining_slots: - subject - object slot_usage: subject: range: population of individual organisms description: >- the population that form the subject of the association object: range: population of individual organisms description: >- the population that form the object of the association predicate: # subproperty_of: ??? description: >- A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used variant to phenotypic feature association: is_a: association defining_slots: - subject - object mixins: - variant to entity association mixin - entity to phenotypic feature association mixin slot_usage: subject: range: sequence variant description: >- a sequence variant in which the allele state is associated in some way with the phenotype state variant to disease association: is_a: association comments: - TODO decide no how to model pathogenicity defining_slots: - subject - object mixins: - variant to entity association mixin - entity to disease association mixin slot_usage: subject: description: >- a sequence variant in which the allele state is associated in some way with the disease state examples: - value: CLINVAR:52241 description: "NM_000059.3(BRCA2):c.7007G>C (p.Arg2336Pro)" predicate: description: >- E.g. is pathogenic for subproperty_of: related condition object: description: >- a disease that is associated with that variant examples: - value: MONDO:0016419 description: hereditary breast cancer genotype to disease association: is_a: association comments: - TODO decide no how to model pathogenicity defining_slots: - subject - object mixins: - genotype to entity association mixin - entity to disease association mixin slot_usage: subject: description: >- a genotype that is associated in some way with a disease state predicate: description: >- E.g. is pathogenic for subproperty_of: related condition object: description: >- a disease that is associated with that genotype examples: - value: MONDO:0016419 description: hereditary breast cancer model to disease association mixin: description: >- This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease mixin: true slots: - subject - predicate - object slot_usage: subject: description: >- The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits similar features, or a gene that when mutated exhibits features of the disease predicate: subproperty_of: model of description: >- The relationship to the disease gene as a model of disease association: is_a: gene to disease association defining_slots: - subject - predicate - object mixins: - model to disease association mixin - entity to disease association mixin slot_usage: subject: range: gene or gene product description: >- A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease. variant as a model of disease association: is_a: variant to disease association defining_slots: - subject - predicate - object mixins: - model to disease association mixin - entity to disease association mixin slot_usage: subject: range: sequence variant description: >- A variant that has a role in modeling the disease. genotype as a model of disease association: is_a: genotype to disease association defining_slots: - subject - predicate - object mixins: - model to disease association mixin - entity to disease association mixin slot_usage: subject: range: genotype description: >- A genotype that has a role in modeling the disease. cell line as a model of disease association: is_a: cell line to disease or phenotypic feature association defining_slots: - subject - predicate - object mixins: - model to disease association mixin - entity to disease association mixin slot_usage: subject: range: cell line description: >- A cell line derived from an organismal entity with a disease state that is used as a model of that disease. organismal entity as a model of disease association: is_a: association defining_slots: - subject - predicate - object mixins: - model to disease association mixin - entity to disease association mixin slot_usage: subject: range: organismal entity description: >- A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease. organism to organism association: is_a: association defining_slots: - subject - predicate - object slot_usage: subject: range: individual organism object: range: individual organism description: >- An association between two individual organisms. taxon to taxon association: is_a: association defining_slots: - subject - predicate - object slot_usage: subject: range: organism taxon object: range: organism taxon description: >- An association between individuals of different taxa. gene has variant that contributes to disease association: is_a: gene to disease association defining_slots: - subject - predicate - object slots: - subject form or variant qualifier slot_usage: subject: range: gene or gene product description: >- A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease. object: range: disease predicate: subproperty_of: contributes to gene to expression site association: is_a: association defining_slots: - subject - predicate - object description: >- An association between a gene and a gene expression site, possibly qualified by stage/timing info. notes: - "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" see_also: "https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee" slots: - stage qualifier - quantifier qualifier slot_usage: subject: range: gene or gene product description: >- Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location. object: range: anatomical entity description: "location in which the gene is expressed" examples: - value: UBERON:0002037 description: cerebellum predicate: description: "expression relationship" subproperty_of: expressed in stage qualifier: range: life stage description: "stage at which the gene is expressed in the site" examples: - value: UBERON:0000069 description: larval stage quantifier qualifier: description: >- can be used to indicate magnitude, or also ranking sequence variant modulates treatment association: is_a: association description: >- An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used. comments: - An alternate way to model the same information could be via a qualifier defining_slots: - subject - object abstract: true slot_usage: subject: range: sequence variant description: "variant that modulates the treatment of some disease" object: range: treatment description: "treatment whose efficacy is modulated by the subject variant" functional association: is_a: association description: >- An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed. slot_usage: subject: range: macromolecular machine mixin description: >- gene, product or macromolecular complex that has the function associated with the GO term examples: - value: ZFIN:ZDB-GENE-050417-357 description: twist1b object: range: ontology class description: >- class describing the activity, process or localization of the gene product values_from: - go examples: - value: GO:0016301 description: kinase activity - value: GO:0045211 description: postsynaptic membrane macromolecular machine to entity association mixin: description: >- an association which has a macromolecular machine mixin as a subject mixin: true slots: - subject - predicate - object slot_usage: subject: domain: macromolecular machine mixin macromolecular machine to molecular activity association: description: >- A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution. is_a: functional association mixins: - macromolecular machine to entity association mixin slot_usage: object: range: molecular activity macromolecular machine to biological process association: description: >- A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it. is_a: functional association mixins: - macromolecular machine to entity association mixin slot_usage: object: range: biological process macromolecular machine to cellular component association: description: >- A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component. is_a: functional association mixins: - macromolecular machine to entity association mixin slot_usage: object: range: cellular component molecular activity to chemical entity association: is_a: association description: >- Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples slot_usage: subject: range: molecular activity object: range: chemical entity molecular activity to molecular activity association: is_a: association description: >- Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples slot_usage: subject: range: molecular activity object: range: molecular activity gene to go term association: aliases: ['functional association'] is_a: functional association exact_mappings: - WBVocab:Gene-GO-Association defining_slots: - subject - object slot_usage: subject: range: gene description: >- gene, product or macromolecular complex that has the function associated with the GO term examples: - value: ZFIN:ZDB-GENE-050417-357 description: twist1b object: range: ontology class description: >- class describing the activity, process or localization of the gene product values_from: - go examples: - value: GO:0016301 description: kinase activity entity to disease association: is_a: association exact_mappings: slots: - clinical approval status - max research phase defining_slots: - subject - object entity to phenotypic feature association: is_a: association exact_mappings: slots: - clinical approval status - max research phase defining_slots: - subject - object ## ----------------- ## SEQUENCE FEATURES ## ----------------- sequence association: is_a: association description: >- An association between a sequence feature and a nucleic acid entity it is localized to. genomic sequence localization: is_a: sequence association description: >- A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig. slot_usage: subject: aliases: ['sequence feature'] range: nucleic acid entity object: aliases: ['reference'] range: nucleic acid entity # typically a chromosome use monochrom predicate: subproperty_of: has sequence location slots: - start interbase coordinate - end interbase coordinate - genome build - strand - phase broad_mappings: - dcid:Chromosome exact_mappings: - dcid:GenomeAnnotation sequence feature relationship: is_a: association defining_slots: - subject - object description: >- For example, a particular exon is part of a particular transcript or gene slot_usage: subject: range: nucleic acid entity object: range: nucleic acid entity # typically a chromosome exact_mappings: - CHADO:feature_relationship transcript to gene relationship: is_a: sequence feature relationship defining_slots: - subject - object description: >- A gene is a collection of transcripts slot_usage: subject: range: transcript object: range: gene gene to gene product relationship: is_a: sequence feature relationship defining_slots: - subject - object description: >- A gene is transcribed and potentially translated to a gene product slot_usage: subject: range: gene object: range: gene product mixin predicate: subproperty_of: has gene product exon to transcript relationship: is_a: sequence feature relationship defining_slots: - subject - object description: >- A transcript is formed from multiple exons slot_usage: subject: range: exon object: range: transcript chemical entity or gene or gene product regulates gene association: is_a: association description: >- A regulatory relationship between two genes slots: - object direction qualifier slot_usage: predicate: description: >- the direction is always from regulator to regulated subproperty_of: regulates subject: range: chemical entity or gene or gene product role: regulatory gene object: range: gene or gene product role: regulated gene object direction qualifier: range: DirectionQualifierEnum anatomical entity to anatomical entity association: # schema: gocam is_a: association abstract: true defining_slots: - subject - object slot_usage: subject: range: anatomical entity object: range: anatomical entity anatomical entity to anatomical entity part of association: # schema: gocam is_a: anatomical entity to anatomical entity association description: >- A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms defining_slots: - predicate slot_usage: subject: range: anatomical entity description: >- the part object: range: anatomical entity description: >- the whole predicate: subproperty_of: part of anatomical entity to anatomical entity ontogenic association: is_a: anatomical entity to anatomical entity association description: >- A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship. defining_slots: - predicate slot_usage: subject: range: anatomical entity description: >- the structure at a later time object: range: anatomical entity description: >- the structure at an earlier time predicate: subproperty_of: develops from organism taxon to entity association: mixin: true description: >- An association between an organism taxon and another entity slots: - subject - predicate - object defining_slots: - subject slot_usage: subject: range: organism taxon description: >- organism taxon that is the subject of the association organism taxon to organism taxon association: is_a: association abstract: true mixins: - organism taxon to entity association description: >- A relationship between two organism taxon nodes defining_slots: - subject - object slot_usage: subject: range: organism taxon object: range: organism taxon organism taxon to organism taxon specialization: is_a: organism taxon to organism taxon association description: >- A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo defining_slots: - predicate slot_usage: subject: range: organism taxon role: child taxon description: >- the more specific taxon object: range: organism taxon role: parent taxon description: >- the more general taxon predicate: subproperty_of: subclass of organism taxon to organism taxon interaction: is_a: organism taxon to organism taxon association description: >- An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens defining_slots: - predicate slots: - associated environmental context slot_usage: subject: range: organism taxon role: interactor taxon description: >- the taxon that is the subject of the association object: range: organism taxon role: interactee taxon description: >- the taxon that is the subject of the association predicate: subproperty_of: interacts with associated environmental context: description: >- the environment in which the two taxa interact organism taxon to environment association: is_a: association abstract: true mixins: - organism taxon to entity association slot_usage: subject: range: organism taxon role: interactor taxon description: >- the taxon that is the subject of the association object: role: environmental context description: >- the environment in which the organism occurs predicate: description: >- predicate describing the relationship between the taxon and the environment enums: ClinicalApprovalStatusEnum: description: permissible_values: approved_for_condition: fda_approved_for_condition: is_a: approved_for_condition not_approved_for_condition: post_approval_withdrawal: is_a: not_approved_for_condition off_label_use: is_a: not_approved_for_condition not_provided: MaxResearchPhaseEnum: permissible_values: pre_clinical_research_phase: description: >- Biolink 'pre_clinical_research' is the union of both the `FDA discovery and development phase` and `FDA preclinical research phase`. Discovery involves researchers finding new possibilities for medication through testing molecular compounds, noting unexpected effects from existing treatments, or the creation of new technology that allows novel ways of targeting medical products to sites in the body. Drug development occurs after researchers identify potential compounds for experiments Preclinical Research Phase. Once researchers have examined the possibilities a new drug may contain, they must do preliminary research to determine its potential for harm (toxicity). This is categorized as preclinical research and can be one of two types: in vitro or in vivo. notes: >- DrugBank calls this 'experimental'. clinical_trial_phase: description: >- Clinical research involves trials of the drug on people, and it is one of the most involved stages in the drug development and approval process. Clinical trials must answer specific questions and follow a protocol determined by the drug researcher or manufacturer. clinical_trial_phase_1: is_a: clinical_trial_phase description: >- In the FDA Clinical Trial Phase, the Clinical Trial Phase 1 involves 20 – 100 study participants and lasts several months. This phase is used to determine the safety and dosage of the drug, and about 70% of these drugs move on to the next clinical research phase. clinical_trial_phase_2: is_a: clinical_trial_phase description: >- In the FDA Clinical Trial Phase, the Clinical Trial Phase 2 involves up to several hundred people, who must have the disease or condition the drug supposes to treat. This phase can last from a few months to two years, and its purpose is to monitor the efficacy of the drug, as well as note side effects that may occur. clinical_trial_phase_3: is_a: clinical_trial_phase description: >- In the FDA Clinical Trial Phase, the Clinical Trial Phase 3 involves 300 – 3000 volunteers and can last up to four years. It is used to continue monitoring the efficacy of the drug, as well as exploring any longer-term adverse reactions. clinical_trial_phase_4: is_a: clinical_trial_phase description: >- In the FDA Clinical Trial Phase, the Clinical Trial Phase 4 involves several thousands of volunteers who have the disease or condition and continues to monitor safety and efficacy. If a drug passes this phase, it goes on to FDA review. not_provided: DirectionQualifierEnum: permissible_values: increased: upregulated: is_a: increased close_mappings: - RO:0002336 exact_mappings: - RO:0002213 narrow_mappings: - RO:0004032 - RO:0004034 - RO:0002629 decreased: downregulated: is_a: decreased exact_mappings: - RO:0004035 - RO:0002212 close_mappings: - RO:0002335 broad_mappings: - RO:0004033 ChemicalEntityDerivativeEnum: permissible_values: metabolite: ChemicalOrGeneOrGeneProductFormOrVariantEnum: permissible_values: genetic_variant_form: is_a: modified_form modified_form: loss_of_function_variant_form: is_a: genetic_variant_form gain_of_function_variant_form: is_a: genetic_variant_form polymorphic_form: is_a: genetic_variant_form snp_form: is_a: polymorphic_form analog_form: is_a: modified_form GeneOrGeneProductOrChemicalPartQualifierEnum: permissible_values: 3_prime_utr: 5_prime_utr: polya_tail: promoter: enhancer: exon: intron: GeneOrGeneProductOrChemicalEntityAspectEnum: permissible_values: activity_or_abundance: description: >- Used in cases where the specificity of the relationship can not be determined to be either activity or abundance. In general, a more specific value from this enumeration should be used. abundance: is_a: activity_or_abundance activity: is_a: activity_or_abundance expression: is_a: abundance synthesis: is_a: abundance degradation: cleavage: is_a: degradation hydrolysis: is_a: degradation metabolic_processing: mutation_rate: stability: folding: localization: transport: secretion: is_a: transport uptake: is_a: transport splicing: molecular_interaction: molecular_modification: acetylation: is_a: molecular_modification acylation: is_a: molecular_modification alkylation: is_a: molecular_modification amination: is_a: molecular_modification carbamoylation: is_a: molecular_modification ethylation: is_a: molecular_modification glutathionylation: is_a: molecular_modification glycation: is_a: molecular_modification glycosylation: is_a: molecular_modification glucuronidation: is_a: molecular_modification n_linked_glycosylation: is_a: molecular_modification o_linked_glycosylation: is_a: molecular_modification hydroxylation: is_a: molecular_modification lipidation: is_a: molecular_modification farnesylation: is_a: molecular_modification geranoylation: is_a: molecular_modification myristoylation: is_a: molecular_modification palmitoylation: is_a: molecular_modification prenylation: is_a: molecular_modification methylation: is_a: molecular_modification nitrosation: is_a: molecular_modification nucleotidylation: is_a: molecular_modification phosphorylation: is_a: molecular_modification ribosylation: is_a: molecular_modification ADP-ribosylation: is_a: molecular_modification sulfation: is_a: molecular_modification sumoylation: is_a: molecular_modification ubiquitination: is_a: molecular_modification oxidation: is_a: molecular_modification reduction: is_a: molecular_modification carboxylation: is_a: molecular_modification CausalMechanismQualifierEnum: permissible_values: binding: description: >- A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction. inhibition: is_a: binding description: >- A causal mechanism in which the effector binds to the target and negatively effects its normal function, e.g. prevention of enzymatic reaction or activation of downstream pathway. close_mappings: - DGIdb:inhibitor - SEMMEDDB:INHIBITS narrow_mappings: - DGIdb:blocker - DGIdb:channel_blocker - DGIdb:gating_inhibitor - CHEMBL.MECHANISM:antisense_inhibitor - CHEMBL.MECHANISM:blocker - CHEMBL.MECHANISM:inhibitor - CHEMBL.MECHANISM:negative_allosteric_modulator - CHEMBL.MECHANISM:negative_modulator - DGIdb:negative_modulator antibody_inhibition: is_a: inhibition description: >- A causal mechanism in which an antibody specifically binds to and interferes with the target. antagonism: is_a: inhibition description: >- A causal mechanism in which the effector binds to a receptor and prevents activation by an agonist through competing for the binding site. close_mappings: - DGIdb:antagonist - CHEMBL.MECHANISM:antagonist narrow_mappings: - CHEMBL.MECHANISM:allosteric_antagonist molecular_channel_blockage: is_a: inhibition description: >- A causal mechanism in which the effector binds to a molecular channel and prevents or reduces transport of ions through it. inverse_agonism: is_a: inhibition description: >- A causal mechanism in which the effector binds to the same receptor-binding site as an agonist and antagonizes its effects, often exerting the opposite effect of the agonist by suppressing spontaneous receptor signaling. close_mappings: - CHEMBL.MECHANISM:inverse_agonist - DGIdb:inverse_agonist negative_allosteric_modulation: is_a: inhibition description: >- A causal mechanism in which the effector reduces or prevents the action of the endogenous ligand of a receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition) close_mappings: - CHEMBL.MECHANISM:negative_allosteric_modulator - DGIdb:inhibitory_allosteric_modulator narrow_mappings: - DGIdb:negative_modulator agonism: is_a: activation description: >- A causal mechanism in which the effector binds and activates a receptor to mimic the effect of an endogenous ligand. close_mappings: - CHEMBL.MECHANISM:agonist - DGIdb:agonist narrow_mappings: - CHEMBL.MECHANISM:partial_agonist - DGIdb:partial_agonist molecular_channel_opening: is_a: activation description: >- A causal mechanism in which the effector binds to a molecular channel and facilitates transport of ions through it. close_mappings: - CHEMBL.MECHANISM:opener positive_allosteric_modulation: is_a: activation description: >- A causal mechanism in which the effector enhances the action of the endogenous ligand of a receptor by binding to a site distinct from that ligand (i.e. non-competitive inhibition) close_mappings: - CHEMBL.MECHANISM:positive_allosteric_modulator - CHEMBL.MECHANISM:positive_modulator - DGIdb:positive_allosteric_modulator broad_mappings: - DGIdb:modulator - DGIdb:allosteric_modulator potentiation: is_a: binding description: >- A causal mechanism in which the effector binds to and enhances or intensifies the effect of some other chemical or drug on its target. close_mappings: activation: is_a: binding description: >- A causal mechanism in which the effector binds to and positively affects the normal functioning of its target. close_mappings: - CHEMBL.MECHANISM:activator - DGIdb:activator inducer: is_a: binding description: >- A causal mechanism in which the effector binds to and increases the activity/rate of an enzyme that processes drugs in the body. close_mappings: - DGIdb:inducer transcriptional_regulation: description: >- A causal mechanism mediated by through the control of target gene transcription signaling_mediated_control: description: >- A causal mechanism mediated by the activation or control of signaling events that influence the some aspect of the target entity (e.g. its activity, processing, transport, etc) stabilization: is_a: activation close_mappings: - CHEMBL.MECHANISM:stabiliser stimulation: is_a: activation close_mappings: - DGIdb:stimulator - SEMMEDDB:STIMULATES - DGIdb:stimulator releasing_activity: is_a: activation close_mappings: - CHEMBL:MECHANISM:releasing_agent LogicalInterpretationEnum: permissible_values: some_some: description: >- A modifier on a triple that causes the triple to be interpreted as a some-some statement meaning: os:SomeSomeInterpretation all_some: description: >- A modifier on a triple that causes the triple to be interpreted as an all-some statement. meaning: os:AllSomeInterpretation inverse_all_some: ReactionDirectionEnum: permissible_values: left_to_right: right_to_left: bidirectional: neutral: ReactionSideEnum: permissible_values: left: right: PhaseEnum: description: phase permissible_values: 0: 1: 2: StrandEnum: description: strand permissible_values: "+": description: Positive "-": description: Negative ".": description: Unstranded "?": description: Unknown SequenceEnum: description: type of sequence permissible_values: "na": description: nucleic acid "aa": description: amino acid DruggableGeneCategoryEnum: permissible_values: "tclin": description: >- These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action. "tbio": description: >- These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy the activity thresholds detailed below. "tchem": description: >- These targets do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy one or more of the following criteria: target is above the cutoff criteria for Tdark target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s) with an Experimental Evidence code "tdark": description: >- These are targets about which virtually nothing is known. They do not have known drug or small molecule activities that satisfy the activity thresholds detailed below AND satisfy two or more of the following criteria: A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or less than or equal to 50 Antibodies available according to http://antibodypedia.com. DrugAvailabilityEnum: description: >- permissible_values: "over_the_counter": description: >- chemical entity is available over the counter without a prescription. "prescription": description: chemical entity is available by prescription. DrugDeliveryEnum: permissible_values: "inhalation": "oral": "absorption_through_the_skin": "intravenous_injection": ResourceRoleEnum: description: >- The role played by the information reource in serving as a source for an edge in a TRAPI message. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources. This enumeration is found in Biolink Model, but is repeated here for convenience. permissible_values: "primary_knowledge_source": "aggregator_knowledge_source": "supporting_data_source": in_subset: - translator_minimal FDAIDAAdverseEventEnum: description: >- please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32 permissible_values: "life_threatening_adverse_event": description: >- An adverse event or suspected adverse reaction is considered 'life-threatening' if, in the view of either the investigator or sponsor, its occurrence places the patient or subject at immediate risk of death. It does not include an adverse event or suspected adverse reaction that, had it occurred in a more severe form, might have caused death. "serious_adverse_event": description: >- An adverse event or suspected adverse reaction is considered 'serious' if, in the view of either the investigator or sponsor, it results in any of the following outcomes: Death, a life-threatening adverse event, inpatient hospitalization or prolongation of existing hospitalization, a persistent or significant incapacity or substantial disruption of the ability to conduct normal life functions, or a congenital anomaly/birth defect. Important medical events that may not result in death, be life-threatening, or require hospitalization may be considered serious when, based upon appropriate medical judgment, they may jeopardize the patient or subject and may require medical or surgical intervention to prevent one of the outcomes listed in this definition. Examples of such medical events include allergic bronchospasm requiring intensive treatment in an emergency room or at home, blood dyscrasias or convulsions that do not result in inpatient hospitalization, or the development of drug dependency or drug abuse. "suspected_adverse_reaction": description: >- means any adverse event for which there is a reasonable possibility that the drug caused the adverse event. For the purposes of IND safety reporting, 'reasonable possibility' means there is evidence to suggest a causal relationship between the drug and the adverse event. Suspected adverse reaction implies a lesser degree of certainty about causality than adverse reaction, which means any adverse event caused by a drug. "unexpected_adverse_event": description: >- An adverse event or suspected adverse reaction is considered 'unexpected' if it is not listed in the investigator brochure or is not listed at the specificity or severity that has been observed; or, if an investigator brochure is not required or available, is not consistent with the risk information described in the general investigational plan or elsewhere in the current application, as amended. For example, under this definition, hepatic necrosis would be unexpected (by virtue of greater severity) if the investigator brochure referred only to elevated hepatic enzymes or hepatitis. Similarly, cerebral thromboembolism and cerebral vasculitis would be unexpected (by virtue of greater specificity) if the investigator brochure listed only cerebral vascular accidents. 'Unexpected', as used in this definition, also refers to adverse events or suspected adverse reactions that are mentioned in the investigator brochure as occurring with a class of drugs or as anticipated from the pharmacological properties of the drug, but are not specifically mentioned as occurring with the particular drug under investigation. in_subset: - translator_minimal AgentTypeEnum: permissible_values: manual_agent: description: >- A human agent who is responsible for generating a statement of knowledge. The human may utilize computationally generated information as evidence for the resulting knowledge, but the human is the one who ultimately interprets/reasons with this evidence to produce a statement of knowledge. automated_agent: description: >- An automated agent, typically a software program or tool, that is responsible for generating a statement of knowledge. Human contribution to the knowledge creation process ends with the definition and coding of algorithms or analysis pipelines that get executed by the automated agent. data_analysis_pipeline: is_a: automated_agent description: >- An automated agent that executes an analysis workflow over data and reports the direct results of the analysis. These typically report statistical associations/correlations between variables in the input dataset, and do not interpret/infer broader conclusions from associations the analysis reveals in the data. notes: >- If an analysis pipeline includes any rules for generating broader conclusions based on the dataset-specific statistical correlations it calculates (e.g. create a 'treats' edge when the analysis reveals a drug-disease correlation in the data with statistical scores that meet a certain threshold) - we would consider this agent to be a Computational Model rather than just a Data Analysis Pipeline. computational_model: is_a: automated_agent description: >- An automated agent that generates knowledge statements (typically predictions) based on rules/logic explicitly encoded in an algorithm (e.g. heuristic models, supervised classifiers), or learned from patterns observed in data (e.g. ML models, unsupervised classifiers). notes: >- The bar is quite low relatively for what is considered to be a ‘computational model’ by our definition. Even agents/tools that apply simple rules or logic to the output of an ingest or analysis pipeline to allow for a stronger or more general conclusion to be stated can qualify an agent as a model. For example, an ingest pipeline that applies rules to its ingest of clinical trials data to create a 'treats' prediction edge when the source reports a drug to be in phase 2 or 3 trials represents a computational model because it is automatically drawing a stronger conclusion than the source reports, based on logic encoded in the ingest pipeline. Similarly, a data analysis pipeline that is extended with rules to automatically generate broader conclusions based on dataset-specific statistical correlations (e.g. create a 'treats' edge when the analysis reveals a drug-disease correlation in the data with statistical scores that meet a certain threshold), would also qualify as a computational model by our definition. text_mining_agent: is_a: automated_agent description: >- An automated agent that uses Natural Language Processing to recognize concepts and/or relationships in text, and report them using formally encoded semantics (e.g. as an edge in a knowledge graph). notes: >- The original statement in the source text is typically made by a human / manual agent, but if a specific encoding of this knowledge is produced by a text-mining tool, it has an agent_type of 'text_mining_agent'. Examples of text mining agents include SemmedDB, and the Translator Text-Mining Knowledge Provider. Note that text-mining tools are prone to erroneous interpretation of concepts and relationships, and can fail to provide important details about the context in which the original knowledge was reported - so users should always consult the source text for a text-mined statement to assess its veracity and relevance. image_processing_agent: is_a: automated_agent description: >- An automated agent that processes images to generate textual statements of knowledge derived from the image and/or expressed in text the image depicts (e.g. via OCR). manual_validation_of_automated_agent: description: >- A human agent reviews and validates/approves the veracity of knowledge that is initially generated by an automated agent. notes: >- This term applies when a human was only involved in evaluating the veracity of a knowledge statement that was generated by an automated agent. It is important to indicate when such manual review has occurred, because it can give a user more confidence in an automated statement. not_provided: description: >- The agent type is not provided, typically because it cannot be determined from available information if the agent that generated the knowledge is manual or automated. in_subset: - translator_minimal KnowledgeLevelEnum: permissible_values: knowledge_assertion: aliases: ['assertion'] description: >- A statement of purported fact that is put forth by an agent as true, based on assessment of direct evidence. Assertions are likely but not definitively true. notes: >- Knowledge Assertions are supported by direct evidence deemed sufficient by some agent to support a confidence assertion of truth. Our certainty in this truth is not absolute, but is typically higher than for Predictions. logical_entailment: aliases: ['deductive_inference'] description: >- A statement reporting a conclusion that follows logically from premises representing established facts or knowledge assertions (e.g. fingernail part of finger, finger part of hand --> fingernail part of hand). notes: >- These statements report entailed conclusions derived through dedictive inference. They are not directly asserted by a source, but logically follow from statement(s) a source does make - and are necessarily true if their supporting premises are true. In practice, these will primarily be entailments based on logic encoded in ontologies. Examples include propagation of annotated knowledge to hierarchically-related concepts, across paths through a graph constructed from transitive relationships, or sets of relationships that support property chain inference. prediction: aliases: ['hypothesis'] description: >- A statement of a possible fact based on probabilistic forms of reasoning over more indirect forms of evidence, that lead to more speculative conclusions. notes: >- Predictions typically result from non-deductive forms of reasoning - e.g. inductive and deductive inference, or statistical inference where conclusions are drawn about a broader/global population based on data from a representative cohort. For example, a prediction that a drug may treat a particular disease based on its chemical similarity to known drugs that treat the disease, and the fact that it can inhibit proteins in a pathway that is associated with the disease As Predictions are based on weaker forms of inference and evidence, they are typically considered lower confidence statements as compared to Knowledge Assertions and Logical Entailments. statistical_association: description: >- A statement that reports concepts representing variables in a dataset to be statistically associated with each other in a particular cohort (e.g. 'Metformin Treatment (variable 1) is correlated with Diabetes Diagnosis (variable 2) in EHR dataset X'). notes: >- Such statements report the direct results of some statistical analysis. Their scope is limited tp the cohort/dataset interrogated in the analysis, and they do not make broader claims or draw more meaningful conclusions about the domain of discourse. Note however that such Statistical Associations can be used as evidence to support a more pointed/precise Prediction or Assertion of knowledge. For example, e.g. a Statistical Association between 'Metformin Prescription' and 'Diabetes Diagnosis' in EHR records could support a Prediction that 'Metformin treats Diabetes', or 'Metformin causes Diabetes'. This 'treats' edge may have a knowledge_level of 'Prediction', but the provider could use the 'evidence_type' edge property to indicate that this prediction is based on a 'Statistical Association'. Because Statistical Associations directly report analysis-specific results, we can consider them to be inherently true statements, whose broader utility is dependent on subsequent generalization of the reported result to a broader population, and/or interpretation of the result as support for a more meaningful statements about the domain of discourse. observation: description: >- A statement reporting (and possibly quantifying) a phenomenon that was observed to occur - absent any analysis or interpretation that generates a statistical association or supports a broader conclusion or inference. notes: >- An observation that "56362 people self-reported taking melatonin to treat migraines" is agnostic to whether melatonin is an effective or approved treatment - it only claims that it was taken for this purpose. Such observations, however, may be used as the basis for predicting that a drug may be efficacious against a disease. not_provided: description: >- The knowledge level is not provided, typically because it cannot be determined from available. information. notes: >- This term is most often applied for text-mined edges, as NLP tools are typically not able to detect a specific knowledge level for the concept relationships they extract (e.g. whether the author was predicting or asserting a relationship, or merely observed it to occur). in_subset: - translator_minimal