--- id: https://w3id.org/biolink/vocab/ 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: 4.4.4 ## ------------ ## ## 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/' FMA: 'http://purl.obolibrary.org/obo/FMA_' 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.who.int/browse10/2016/en#/' ICD9: 'http://translator.ncats.nih.gov/ICD9_' icd11: 'http://id.who.int/icd/entity/' icd11.foundation: 'http://id.who.int/icd/entity/' 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/' METPO: 'https://w3id.org/metpo/' 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.DRUG: '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/' uspto-patent: "http://www.uspto.gov/patent/grant/v1/" 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 - https://w3id.org/biolink/biolink-model/attributes types: chemical formula value: uri: xsd:string base: str description: A type of string representing a chemical formula notes: - Should be implemented as a stronger type iri type: uri: xsd:string typeof: uriorcurie description: >- An IRI. label type: uri: xsd:string typeof: string description: >- A type of string that provides a human-readable name for an entity. narrative text: uri: xsd:string typeof: string description: >- A type of string that provides a human-readable description of something. symbol type: uri: xsd:string typeof: string description: >- A type of string that is typically short, used as a human-readable label or symbol for an entity, such as an official gene symbol (e.g., "BRCA1") or a chemical symbol. frequency value: typeof: string uri: UO:0000105 description: >- A quantity expressing the number of occurrences of a repeating event per unit of time (UO:0000105). Typically used for rates such as incidence or event frequency associated with a phenomenon. percentage frequency value: typeof: double uri: UO:0000187 description: >- A frequency value expressed as a percentage (UO:0000187), i.e., a dimensionless ratio multiplied by 100. quotient: aliases: ['ratio'] typeof: double uri: UO:0010006 description: >- A dimensionless value obtained by dividing one quantity by another of the same kind (UO:0010006). Used to represent ratios such as odds ratios, hazard ratios, or relative risks. unit: typeof: string uri: UO:0000000 id_prefixes: - UO exact_mappings: - qud:Unit description: >- A standard of measurement in which the magnitude of a physical quantity is expressed (UO:0000000). Typically drawn from the Units of Measurement Ontology (UO). unit prefix: typeof: string uri: UO:0000046 id_prefixes: - UO description: >- A prefix to a unit indicative of the scaling of the unit, e.g., 'nano' with unit 'meter' implies a unit of 10e-9 meters time type: uri: xsd:string typeof: time description: >- A value representing a point in time, serialised as a lexical representation of xsd:time. biological sequence: uri: xsd:string typeof: string description: >- A string of characters representing a biological macromolecule sequence, such as a nucleic acid sequence (DNA/RNA) using the IUPAC nucleotide alphabet, or a protein sequence using the IUPAC amino-acid alphabet. ## ------------ ## SLOTS ## ------------ slots: node property: abstract: true description: >- A grouping for any property that holds between a node and a value domain: named thing nodes: multivalued: true range: entity description: >- A list of entities that can be a subject or object of an association inlined: true inlined_as_list: true edges: multivalued: true range: association description: >- A list of associations between two entities. inlined: true inlined_as_list: true 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 - 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 binary relation: description: >- Qualifies a value context with a mathematical binary relation. range: BinaryRelationEnum 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 has unit prefix: description: >- relates to scaling of the associated quantitative unit domain: quantity value range: unit prefix 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 ## -------------------- 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: description: >- An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance. 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 hgvs nomenclature: is_a: node property domain: sequence variant multivalued: true description: >- HGVS syntax refers to the specific rules and conventions used by the Human Variant Nomenclature Committee to describe the location and change in DNA, RNA, and protein sequence variants. This slot is used to capture all the different forms of HGVS nomenclature that may be used to describe a sequence variant, including genomic, transcript, and protein HGVS expressions/nomenclatures and is thus multivalued. comments: - >- For more information, please see: https://hgvs-nomenclature.org/stable/background/simple/ and examples: https://hgvs-nomenclature.org/stable/recommendations/summary/. 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: description: >- Indicates whether a chemical reaction is stoichiometrically balanced, i.e. whether the conservation of atoms (and charge) holds between the reactants and the products. 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: description: >- An alternate label for an entity that denotes exactly the same meaning as the primary label and is interchangeable with it in all contexts. is_a: synonym exact_mappings: - oboInOwl:hasExactSynonym broad synonym: description: >- An alternate label for an entity whose meaning is broader (more general) than the primary label but is still useful as a lexical alternative. is_a: synonym exact_mappings: - oboInOwl:hasBroadSynonym narrow synonym: description: >- An alternate label for an entity whose meaning is narrower (more specific) than the primary label, for example naming a particular sub-type. is_a: synonym exact_mappings: - oboInOwl:hasNarrowSynonym related synonym: description: >- An alternate label that is related to the primary label but is neither exactly synonymous nor cleanly broader or narrower; useful as a lexical pointer but not for strict equivalence. Corresponds to oboInOwl:hasRelatedSynonym. 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 subsets: is_a: node property domain: named thing range: string description: >- The set of ontology subsets a term belongs to (e.g. GO slim subsets, MONDO rare disease subset). Carries the values of `oboInOwl:inSubset` annotations from source ontologies through to downstream knowledge graphs. multivalued: true exact_mappings: - oboInOwl:inSubset url: is_a: node property description: >- This slot holds a string representation of a URL for an external resource about the node it is present on. Unlike an 'xref' that is primarily represented by a CURIE, this slot is intended to hold a full URL that can be used to directly access a resource. When linking to an external resource that cannot be represented by a unique CURIE, this slot should be used. However, when the intent is to link to the default URI expansion of a CURIE related to the node it is present on, the xref slot should be used instead. domain: entity range: string 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. multivalued: true domain: retrieval source range: uriorcurie source record urls: is_a: node property description: >- A URL linking to a specific web page or document provided by the source, that contains a record of the knowledge expressed in the Edge. If the knowledge is contained in more than one web page on an Information Resource's site, urls MAY be provided for each. multivalued: true 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', 'date started'] 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: description: >- An abstract grouping for summary numerical measures (e.g. count, total, quotient, percentage, rate) computed over a set of observations or a reference population, used to describe a property of an aggregated entity rather than an individual instance. 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: description: >- The taxonomic rank (e.g. species, genus, family, order, kingdom) assigned to an organism taxon. is_a: node property range: taxonomic rank multivalued: false mappings: - WIKIDATA:P105 has dataset: description: >- Links a dataset version to the underlying dataset that it is a version of. is_a: node property domain: dataset version range: dataset broad_mappings: - dct:source source web page: description: >- A URL of a web page that documents or serves as the landing page for a data source. is_a: node property domain: dataset summary broad_mappings: - dct:source source logo: description: >- A URL referencing an image that serves as the visual logo of a data source. is_a: node property domain: dataset summary slot_uri: schema:logo retrieved on: description: >- The date on which a dataset was retrieved or harvested from its original source, following pav:retrievedOn. is_a: node property domain: dataset range: date exact_mappings: - pav:retrievedOn version of: description: >- Links a dataset version to the dataset summary of which it is a version, edition, or adaptation. is_a: node property domain: dataset version range: dataset summary exact_mappings: - dct:isVersionOf version: description: >- A label identifying a particular release or edition of a dataset or resource, typically following a versioning scheme such as a semantic version string or a release date. is_a: node property domain: dataset broad_mappings: - pav:version - owl:versionInfo license: description: >- A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document. is_a: node property domain: information content entity exact_mappings: - dct:license narrow_mappings: - WIKIDATA_PROPERTY:P275 rights: description: >- A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights. is_a: node property domain: information content entity exact_mappings: - dct:rights format: description: >- The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format. is_a: node property domain: information content entity exact_mappings: - dct:format - WIKIDATA_PROPERTY:P2701 created with: description: >- An identifier (typically a URL or CURIE) of the software tool, service, or pipeline used to create the dataset. is_a: node property domain: dataset exact_mappings: - pav:createdWith download url: description: >- A URL from which the information content entity may be directly downloaded in its native serialization. is_a: node property domain: information content entity slot_uri: dcat:downloadURL dataset download url: description: >- A URL from which the dataset itself may be directly downloaded specialised for the dataset domain. is_a: node property domain: dataset slot_uri: dcat:downloadURL distribution download url: description: >- A URL from which a specific distribution (serialization or format) of a dataset may be directly downloaded; corresponds to dcat:downloadURL specialised for the dataset distribution domain. is_a: node property domain: dataset distribution exact_mappings: - dcat:downloadURL ingest date: description: >- The date on which a dataset version was ingested into the local knowledge graph or downstream data system; a specialization of dct:issued for the ingestion context. is_a: node property domain: dataset version broad_mappings: - dct:issued has distribution: description: >- Links a dataset version to one of its dataset distributions (a specific representation or serialization of the dataset). 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. 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 ## Exposure Events exposure type: is_a: node property description: >- Type of exposure domain: exposure event range: string exposure vehicle: is_a: node property description: >- Type of an exposure event. domain: exposure event range: string exposure route: is_a: node property description: >- Route of exposure. domain: exposure event range: string exposure start age: is_a: node property description: >- Starting age of an exposure event. domain: exposure event range: integer exposure end age: is_a: node property description: >- Ending stage of an exposure event. domain: exposure event range: integer exposure duration: is_a: node property description: >- Duration of an exposure event. domain: exposure event range: time exposure magnitude: is_a: node property description: >- Magnitude of an exposure event, e.g, parts per million of a toxic chemical. domain: exposure event range: string exposure additional condition: is_a: node property description: >- Additional conditions impacting an exposure event. domain: exposure event range: string ## Clinical Trials elevate to prediction: is_a: node property description: >- A boolean flag indicating whether a clinical trial finding should be elevated to a prediction. range: boolean clinical trial phase: is_a: node property description: >- The phase that a clinical trials study represents range: ResearchPhaseEnum clinical trial primary purpose: aliases: ['primary purpose'] is_a: node property description: >- The primary purpose of a clinical trial as determined by clinicaltrials.gov. The most common values are TREATMENT and PREVENTION. Other possible values include BASIC_SCIENCE, SUPPORTIVE_CARE, DIAGNOSTIC, HEALTH_SERVICES_RESEARCH, SCREENING, DEVICE_FEASIBILITY, OTHER, and (null). range: string domain: clinical trial clinical trial intervention model: is_a: node property description: >- The intervention model of a clinical trial as determined by clinicaltrials.gov. The most common values are SINGLE_GROUP, PARALLEL, CROSSOVER, FACTORIAL, and (null). range: string domain: clinical trial clinical trial time perspective: is_a: node property description: >- The time perspective of a clinical trial as determined by clinicaltrials.gov. The most common values are PROSPECTIVE, RETROSPECTIVE, CROSS_SECTIONAL, or OTHER (most common).. range: string domain: clinical trial clinical trial overall status: is_a: node property description: >- The overall status of a clinical trial as determined by clinicaltrials.gov range: ClinicalTrialStatusEnum domain: clinical trial clinical trial intervention boxed warning: is_a: node property description: >- A boolean flag indicating whether a clinical trial intervention has a boxed warning. A boxed warning is the strongest warning that the FDA requires on a prescription drug label. This property should be populated from DailyMed. range: boolean domain: association clinical trial tested intervention: is_a: node property description: >- Records whether the clinical trials are testing the intervention. domain: clinical trial range: string clinical trial brief title: is_a: node property description: >- The brief title of a clinical trial as determined by clinicaltrials.gov range: string domain: clinical trial clinical trial enrollment type: is_a: node property description: >- The enrollment type of a clinical trial as determined by clinicaltrials.gov (actual, anticipated, or estimated) range: string domain: clinical trial clinical trial start date: is_a: node property description: >- The start date of a clinical trial as determined by clinicaltrials.gov range: string domain: clinical trial clinical trial enrollment: is_a: node property description: >- The enrollment number of a clinical trial as determined by clinicaltrials.gov range: integer domain: clinical trial clinical trial age stage: is_a: node property description: >- The age stage of a clinical trial as determined by clinicaltrials.gov (adult, child, older adult) range: ClinicalTrialAgeStageEnum domain: clinical trial multivalued: true clinical trial age range: is_a: node property description: >- The age range of a clinical trial as determined by clinicaltrials.gov range: string domain: clinical trial clinical trial interventions: is_a: node property description: >- connects a clinical trial to one or more interventions being tested in the trial range: clinical intervention multivalued: true domain: clinical trial clinical trial conditions: is_a: node property description: >- connects a clinical trial to one or more conditions being studied in the trial range: disease or phenotypic feature multivalued: true domain: clinical trial ## Biological Entity properties 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 inheritance: is_a: node property description: >- Connects genetic inheritance to a disease or phenotypic feature, as a node property. domain: disease or phenotypic feature range: genetic inheritance exact_mappings: - OMIM:has_inheritance_type has zygosity: description: >- The zygosity characterising a genotype or nucleic acid entity at a particular locus. 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: >- An entity that interacts with an exposure stimulus during an exposure event. exact_mappings: - ExO:0000001 has stressor: is_a: node property domain: exposure event aliases: ['has stimulus'] description: >- An agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure_receptor during an exposure event. exact_mappings: - ExO:0000000 id_prefixes: - ExO 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 response context qualifier: description: >- a biological response (general, study, cohort, etc.) with a specific set of characteristics to constrain an association. is_a: context qualifier range: ResponseEnum response target context qualifier: description: >- a biological response target (a patient, a cohort, a model system, a cell line, a sample of biological material, etc.) is_a: context qualifier range: ResponseTargetEnum 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 # TODO: harmonize with 'response target context qualifier' 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: >- A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food. is_a: node property domain: chemical mixture trade name: description: >- A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor. is_a: node property domain: chemical entity available from: description: >- The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum. is_a: node property multivalued: true range: DrugAvailabilityEnum examples: - value: "over_the_counter" is toxic: description: >- A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure. 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. domain: chemical entity range: chemical role multivalued: true inverse: is chemical role of 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. is chemical role of: is_a: related to at concept level description: >- Holds between a chemical role and a chemical entity that exhibits that role. domain: chemical role range: chemical entity multivalued: true inverse: has chemical role 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: >- A resource (such as a model organism database) from which an animal model representing the given disease or phenotypic feature may be obtained. is_a: node property multivalued: true range: string FDA adverse event level: description: >- The level or severity grade of an adverse event as classified by FDA adverse-event terminology, drawn from FDAIDAAdverseEventEnum; used on adverse-event associations. 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.' range: ApprovalStatusEnum FDA regulatory approvals: description: >- Numbers that identify specific drug applications. Each drug can have multiple approval numbers (for example, as seen with ranitidine having both ANADA200536 and ANDA200536). range: string multivalued: true drug regulatory status world wide: aliases: ['max phase'] range: ApprovalStatusEnum 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 specialization qualifier: is_a: qualifier abstract: true description: >- A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier. examples: - value: CHEBI:5118 description: >- fluoxetine. In a MAXO annotation this would be a specialization in treatment of a disease. For example, fluoxetine would be a specialization of the MAXO term 'serotonin-norepinephrine reuptake inhibitor agent therapy' as a treatment for the HP term 'Fatigable muscle weakness' in the context of the MONDO term 'congenital myasthenic syndrome '4A.' - value: GO:0005634 description: >- nucleus. In an expression annotation this would be a specialization in location of an anatomical entity. For example, "expression in the nucleus of hepatic cells" would be a specialization of "expression in hepatic cells" aspect qualifier: is_a: qualifier abstract: true range: GeneOrGeneProductOrChemicalEntityAspectEnum 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). 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: OHMI:0000020 description: gut microbiome in_subset: - translator_minimal process qualifier: is_a: qualifier abstract: true description: >- Restricts the biological process within which the core concept (or qualified core concept) participates. examples: - value: GO:0009101 description: glycoprotein biosynthetic process 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 range: GeneOrGeneProductOrChemicalEntityAspectEnum in_subset: - translator_minimal subject specialization qualifier: is_a: specialization qualifier description: >- A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier. in_subset: - translator_minimal range: uriorcurie 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). This qualifier is for the subject of an association (or statement). examples: - value: polyA tail - value: upstream control region 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 activity qualifier: is_a: process qualifier in_subset: - translator_minimal subject process qualifier: is_a: process qualifier in_subset: - translator_minimal subject context qualifier: description: >- A qualifier describing the context in which the subject of an association holds. 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). examples: - value: increased - value: downregulated 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 range: GeneOrGeneProductOrChemicalEntityAspectEnum in_subset: - translator_minimal object specialization qualifier: is_a: specialization qualifier description: >- A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier. in_subset: - translator_minimal range: uriorcurie 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). This qualifier is for the object of an association (or statement). examples: - value: polyA tail - value: upstream control region 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 activity qualifier: is_a: process qualifier in_subset: - translator_minimal object process qualifier: is_a: process qualifier in_subset: - translator_minimal object context qualifier: description: >- A qualifier describing the context in which the object of an association holds. 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). examples: - value: increased - value: downregulated 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. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats 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. examples: - value: biolink:causes description: used with `affects` predicate to express causal statements range: uriorcurie 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 examples: - value: agonism - value: inhibition 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. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs. examples: - value: UBERON:0000178 description: blood - value: UBERON:0000956 description: cerebral cortex - value: GO:0005794 description: Golgi apparatus in_subset: - translator_minimal multivalued: true 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: NCBITaxon:7955 description: zebrafish - value: NCBITaxon:9606 description: human 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 disease context qualifier: is_a: context qualifier description: >- A context qualifier representing a disease or condition in which a relationship expressed in an association took place. range: disease examples: - value: MONDO:0004979 description: asthma - value: MONDO:0005148 description: type 2 diabetes mellitus in_subset: - translator_minimal association basis qualifier: is_a: statement qualifier description: >- A statement-level qualifier used with the 'associated with' predicate (or one of its subpredicates) to indicate the biological, clinical, or statistical basis of the asserted association. Use this qualifier when no more specific predicate exists to capture the intended meaning of the association. range: AssociationBasisEnum in_subset: - translator_minimal statistical significance qualifier: is_a: statement qualifier description: >- A statement qualifier that categorizes an association's evidence by statistical significance into coarse bands, as a categorical companion to the numeric 'p value' and 'adjusted p value' slots. It applies only to assessments derived from a quantitative significance statistic (raw p-value, multiple-testing-adjusted p-value, or q-value/FDR), and MUST NOT encode ordinal study-stage, evidence-tier, or confidence-level labels (e.g. clinical trial phases) that are not statistical-significance statements. notes: - >- Enforced via a class rule on `association`: this qualifier may only be set when 'p value' or 'adjusted p value' is also populated (the numeric slots remain authoritative). - >- Bands use conventional defaults (alpha = 0.05); when a source's cutoffs differ, place the value in the closest band and always also populate the numeric slot(s). examples: - value: very_strongly_significant - value: strongly_significant - value: significant - value: suggestive - value: not_significant range: StatisticalSignificanceQualifierEnum 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: >- Indicates a non-causal association between two entities. Such associations are most commonly established through statistical analysis demonstrating that observations of the entities are not statistically independent, but may also be supported by other forms of evidence that establish a meaningful association. When representing a statistical association, the subject and object may correspond directly to the variables analyzed, or to the biological or clinical entities represented/described by those variables (e.g., diseases, genes, chemical entities, biological processes, or phenotypes). The 'association basis qualifier' may be used to constrain the scope of this predicate within a statement if no more specific child predicate provides a more precise semantic context for the association. 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. 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: description: >- Holds between a gene or gene product and a cellular component in which it carries out its molecular function. 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: description: >- Holds between a gene or gene product and a biological process such that the molecular function of the gene product, by way of a chain of causally linked events, is upstream of and contributes to the execution of the process. 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: description: >- Holds between a gene or gene product and a biological process where the molecular function of the gene product is upstream of and has a positive (activating or increasing) effect on the execution of the process. 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: description: >- Holds between a gene or gene product and a biological process where the molecular function of the gene product is upstream of and has a negative (inhibiting or decreasing) effect on the execution of the process. 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: description: >- Holds between a gene or gene product and a biological process when the gene product either acts upstream of the process or participates in it; used when the more specific causal relationship is not known. Corresponds to RO:0002264. 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: description: >- Holds between a gene or gene product and a biological process when the gene product acts upstream of or within the process with a positive (activating or increasing) effect on its execution. Corresponds to RO:0004032. 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: description: >- Holds between a gene or gene product and a biological process when the gene product acts upstream of or within the process with a negative (inhibiting or decreasing) effect on its execution. Corresponds to RO:0004033. 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: description: >- Links an information content entity (such as a dataset, publication, or software artefact) to an agent responsible for making contributions to it. Used as an abstract grouping predicate over more specific contribution roles (author, editor, publisher, provider). Corresponds to dct: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. 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 was tested for effect on: deprecated: "true" is_a: related to at instance level aliases: ['was assayed against', 'was experimentally tested against'] description: >- Reports that the subject was interrogated in an experiment to determine how it may affect the object. 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 was tested for effect of: deprecated: "true" is_a: related to at instance level inverse: was tested for effect on 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 in a physical or functional way. is_a: related to at instance level in_subset: - translator_minimal symmetric: true mixin: true exact_mappings: - SEMMEDDB:INTERACTS_WITH notes: - >- A note on 'interacts with' vs 'affects': These are related but separate relationships. An interaction may or may not involve one interactor exerting an effect on the other. It simply indicates that two entities participate in a physical or functional relationship (e.g. molecular binding, genetic interactions such as epistasis, or pharmacological interactions in which the combined behavior of two drugs differs from that of either drug alone). An 'effect' may be mediated by an interaction or may arise without any direct interaction, through a chain of intermediary events. Any effect or causal influence must be asserted using a predicate in the affects or causes hierarchy. - >- Please use a more specific child predicate of interacts with, either physically interacts with or genetically interacts with or pharmacologically 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 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: description: >- Holds between two entities that physically interact by way of one or more intermediary entities, rather than through direct physical contact. 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 pharmacologically interacts with: aliases: ['drug drug interaction'] is_a: interacts with description: >- holds between two pharmacologically active chemicals (typically drugs), where one alters the availability, efficacy, or toxicity of the other in the body when taken simultaneously - typically by altering how the body processes the chemical (pharmacokinetics) or how the chemical acts on the body (pharmacodynamics). domain: chemical entity range: chemical entity in_subset: - translator_minimal annotations: canonical_predicate: true symmetric: true 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: - >- A note on 'affects' vs 'interacts with': These are related but separate relationships. An interaction may or may not involve one interactor exerting an effect on the other. Effects may be mediated by an interaction or may arise without any direct interaction, through a chain of intermediary events. An affects relationship asserts that one entity directly or indirectly exerts a meaningful influence on the activity, state, abundance, function, or properties of another entity. Unlike an interaction, an effect is directional: the subject changes, modulates, perturbs, regulates, or otherwise influences the object, even if no direct physical interaction occurs. Use interacts_with only when the relationship describes an interaction or association without asserting that one entity exerts an effect on the other. - >- 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 response to: is_a: associated with description: >- A statistical association used to indicate that the object of a statement using this predicate induces a response of some kind in the subject entity. Intentionally broad in definition, this predicate should be used with qualifiers to narrow the type of response (E.g. whether the response is therapeutic, phenotypic, detrimental, resistant, etc. is captured in context, direction, and aspect qualifiers). annotations: canonical_predicate: true response associated with: is_a: associated with inverse: associated with response to associated with sensitivity to: is_a: associated with response to 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: response associated with inverse: associated with sensitivity to range: named thing domain: chemical entity associated with resistance to: is_a: associated with response to 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: response 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 sensitivity to: is_a: related to at instance level description: >- holds between two chemical entities or genes or gene products where the action of one affects the susceptibility/sensitivity of a biological entity or system to the other. in_subset: - translator_minimal domain: chemical entity or gene or gene product range: chemical entity or gene or gene product annotations: canonical_predicate: true exact_mappings: - CTD:affects_response_to sensitivity affected by: is_a: related to at instance level in_subset: - translator_minimal domain: chemical entity or gene or gene product range: chemical entity or gene or gene product inverse: affects sensitivity to increases sensitivity to: description: >- holds between two chemical entities or genes or gene products where the action or effect of one increases the susceptibility/sensitivity of a biological entity or system to the other is_a: affects sensitivity 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 sensitivity to exact_mappings: - CTD:increases_response_to sensitivity increased by: is_a: sensitivity affected by in_subset: - translator_minimal domain: chemical entity or gene or gene product range: chemical entity or gene or gene product inverse: increases sensitivity to decreases sensitivity to: description: >- holds between two chemical entities or genes or gene products where the action or effect of one decreases the susceptibility/sensitivity of a biological entity or system to the other is_a: affects sensitivity 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 sensitivity to exact_mappings: - CTD:decreases_response_to narrow_mappings: - CTD:decreases_response_to_substance sensitivity decreased by: is_a: sensitivity affected by in_subset: - translator_minimal domain: chemical entity or gene or gene product range: chemical entity or gene or gene product inverse: decreases sensitivity 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 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 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 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 range: gene or gene product domain: 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: # indicating the "genetic" basis of an association will now be done using the more general # "associated with" predicate plus a 'association basis qualifier' with the value "genetic". deprecated: "true" is_a: associated with description: >- A statistical association, observed in genetic studies, between a genetic entity such as a gene, locus, or variant and a phenotype, disease, or trait. 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 has preventative intervention: inverse: preventative for condition is_a: likelihood affected by domain: disease or phenotypic feature range: chemical or drug or treatment promotes condition: mixin: true is_a: affects likelihood of 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: mixin: true 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, in some population(s), 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. in some population(s) 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: is_a: subject of treatment application or study for treatment 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 mixins: - subject of treatment application or study for treatment 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 mixins: - subject of treatment application or study for treatment 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 mixins: - subject of treatment application or study for treatment 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 mixins: - subject of treatment application or study for treatment by 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. 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 mixins: - subject of treatment application or study for treatment by inverse: applied to treat domain: disease or phenotypic feature range: chemical or drug or treatment treats or applied or studied to treat: is_a: related to at instance level 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 domain: chemical or drug or treatment range: disease or phenotypic feature subject of treatment application or study for treatment by: is_a: related to at instance level 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 correlation is believed to exist, as 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). Note also that this predicate can be used in the absence of a direct statistical analysis, if there is other evidence suggesting that a correlation is likely to exist. 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. range: gene or gene product domain: 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 - RO:0004029 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: description: >- Holds between a macromolecular machine (typically an enzyme or ribozyme) and a biochemical reaction or process whose rate it accelerates, without itself being consumed, by lowering the activation energy. is_a: participates in annotations: canonical_predicate: true exact_mappings: - RO:0002327 has catalyst: is_a: has participant inverse: catalyzes has substrate: description: >- Holds between a biochemical reaction or catalytic process and a chemical entity that is acted upon (consumed or transformed) by that reaction. 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 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 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 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: description: >- Holds between a process and an entity that is taken in and depleted by the process; for example a metabolite consumed in a biochemical reaction. 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 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: description: >- Links a genotype or genetic variant to a condition (disease or phenotypic feature) that is associated with it. 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: description: >- Holds between an entity and a component that is present at higher amount than in a reference state or sibling entity; used for comparative compositional statements. 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: description: >- Holds between an entity and a component that is present at lower amount than in a reference state or sibling entity; used for comparative compositional statements. 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: description: >- Holds between an entity and a component that is absent from it relative to a reference type; for example a cell type lacking a particular organelle or a protein lacking a particular domain. Corresponds to CL:lacks_part / PR: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: description: >- Holds between two entities where the first develops, by one or more developmental processes, from the second; for example a cell type developing from a precursor cell type or a tissue developing from an embryonic primordium. Corresponds to RO:0002202. 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 taxon: is_a: node property description: >- A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology. comments: - >- Note there is also a predicate 'in taxon' that can be used to instantiate an edge between a taxon entity and a thing with taxon entity. This is an acceptable practice for KG construction, but for many applications it is more convenient to use this property slot to directly annotate the taxon on the entity itself. in_subset: - translator_minimal range: uriorcurie 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 feature name: is_a: association slot description: >- Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene object feature name: is_a: association slot description: >- Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease 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: "['BRCA1']" 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: >- 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: uriorcurie 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 description: >- connects an association to a qualitative term denoting the level of confidence has confidence score: is_a: association slot range: float description: >- connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about. exact_mappings: - SEPIO:0000168 close_mappings: - SEPIO:0000187 - SEPIO:0000167 has evidence of type: is_a: association slot range: evidence type description: >- Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology. multivalued: true has evidence: is_a: association slot range: information content entity description: >- Connects an association to detailed information providing supporting evidence. exact_mappings: - RO:0002558 multivalued: true inlined: false has study results: is_a: association slot domain: study range: study result multivalued: true inlined_as_list: true description: >- Connects an study to instances of its study result log odds ratio: is_a: node property description: >- The natural logarithm of the odds ratio (OR), or the ratio of the odds of an event Y occurring in an exposed group versus the odds of an event Y occurring in a non-exposed group. range: float log odds ratio 95 ci: is_a: node property description: >- The ninety-five percent confidence range in which the true log odds ratio for the sample population falls. To calculate the 95% confidence interval (CI) for a log odds ratio (a pair of numbers), you need the standard error (SE) of the log odds ratio. This interval helps you understand the precision of your estimate and whether the association is statistically significant. range: float multivalued: true examples: - value: "[0.6996904681742875, 1.6429124024089072]" 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: node property range: float description: >- The chi-squared statistic measures how much observed data deviate from expected values under the null hypothesis. exact_mappings: - STATO:0000030 examples: - value: "26.38523077566414" chi squared dof: is_a: node property description: >- Degrees of freedom (dof) in a chi-squared test referring to the number of values in the final calculation of a statistic that are free to vary range: integer examples: - value: "1" chi squared p: is_a: node property description: >- The chi-square p-value tells you the probability that the observed differences (or associations) in your data occurred by random chance, assuming the null hypothesis is true. range: float examples: - value: "2.7967079822744063e-07" fisher exact odds ratio: is_a: node property description: >- The Fisher Exact Test is used to determine whether there is a non-random association between two categorical variables in a 2×2 contingency table, especially when sample sizes are small. The odds ratio (OR) quantifies the strength of that association. OR = 1 implies No association OR > 1 implies Positive association (Group A more likely to have Outcome 1) OR < 1 implies Negative association (Group A less likely to have Outcome 1) range: float examples: - value: "3.226188583240579" fisher exact p: is_a: node property description: >- The Fisher exact p-value tells you the probability of observing a table as extreme as (or more extreme than) your actual data, assuming that the null hypothesis of independence is true. It's most commonly used for 2×2 contingency tables, especially when sample sizes are small or expected counts are low. range: float examples: - value: "2.8581244515361156e-06" z score: aliases: ['z-score', 'z-value', 'standard score', 'normal score'] is_a: association slot range: float description: >- A measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value. exact_mappings: - STATO:0000104 - NCIT:C68741 - EDAM-DATA:1668 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 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" effect size: is_a: association slot range: float description: >- A quantitative measure of the magnitude and direction of an effect or association between the subject and object of an edge, as estimated by a statistical method. The specific metric used (e.g. Cohen's d, odds ratio, Pearson's r) is indicated by the companion 'effect type' slot. notes: - >- The numeric value here is metric-dependent and should always be interpreted together with 'effect type'. For example, an effect size of 0.8 with effect type 'cohens_d' means a large standardized mean difference, whereas 0.8 with effect type 'pearsons_r' means a strong positive linear correlation. exact_mappings: - STATO:0000085 effect type: is_a: association slot range: EffectTypeEnum description: >- Specifies the statistical metric or method used to compute the numeric value in the companion 'effect size' slot. This disambiguates the effect size value, which is otherwise uninterpretable without knowing the metric (e.g. Cohen's d vs. odds ratio vs. Pearson's r). notes: - >- This slot should only be populated when 'effect size' is also populated. Enforced via a class rule on `association`. examples: - value: cohens_d - value: odds_ratio - value: pearsons_r supporting text: is_a: node property description: The segment of text from a document that supports the mined assertion. multivalued: true range: string examples: - value: "Here, we report two new cases of rivaroxaban-induced hepatitis." 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: node property 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: "33" multivalued: true object location in text: is_a: node property 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: "53" multivalued: true extraction confidence score: is_a: node property 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: float examples: - value: "0.6188385904738642" supporting document type: is_a: node property 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: node property description: >- The document year (typically the publication year) for the supporting document used in a Text Mining Result. range: integer examples: - value: "2018" supporting text section type: is_a: node property 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: abstract 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 allelic requirement: description: >- The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance. is_a: association slot range: string pattern: "^HP:\\d{7}$" comments: - >- This edge property may be used by associations between Genes or SequenceVariants and DiseaseOrPhenotypicFeatures to provide the inheritance pattern and genetic context of the relationship. Terms from the HP mode of inheritance sub-ontology (HP:0000005) should be used in the value of this slot. This slot differs from the predicate "has_mode_of_inheritance", in that the predicate is used to link a disease or phenotype with its general inheritance pattern (how it is typically transmitted from one generation to the next, regardless of the specific genetic variant that is present in an individual or instance). # Affinity Study Result slot definitions pIC50: description: >- Negative base 10 logarithm of the the inhibitory concentration 50% (IC50) measures the concentration needed to block or inhibit a biological response. is_a: node property range: quantity value pEC50: description: >- Negative base 10 logarithm of the molar concentration of a chemical that produces a 50% excitation of a function is_a: node property range: quantity value pAC50: description: >- pAC50 is a base 10 negative logarithmic measure of potency for an activating (agonist) interaction between a molecule (such as a drug or ligand) and a biological target (such as a receptor or enzyme), where AC50 is the concentration (in molar units) of a compound that produces 50% of its maximal activation in a functional assay. is_a: node property range: quantity value pXC50: description: >- In the context of molecular interactions and drug discovery, pXC50 is a generic, base 10 negative logarithmic measure of compound potency that unifies different types of half‑maximal concentration values into a single notation, where XC50 means “the concentration at which 50% of the maximal effect is observed”, and X is a placeholder for the type of effect being measured (e.g., inhibition or activation). The X in pXC50 is intentionally generic and can represent different assay endpoints. is_a: node property range: quantity value pKi: description: >- Negative base 10 logarithm of the equilibrium binding affinity for a ligand that reduces the activity of its binding partner. Ki represents the concentration at which the inhibitor ligand occupies 50% of the receptor sites when no competing ligand is present is_a: node property range: quantity value pKon: description: >- Negative base 10 logarithm of the association rate constant (Kon) describes the rate at which molecules bind to each other. is_a: node property range: quantity value pKoff: description: >- Negative base 10 logarithm of the dissociation rate constant (koff) describes the rate at which they dissociate. is_a: node property range: quantity value pKd: description: >- Negative base 10 logarithm of the equilibrium dissociation constant (KD) which is a measure of the binding affinity and is defined as the ratio of koff to kon. is_a: node property range: quantity value # End of Affinity Study Result slot definitions 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 sources: aliases: ['source retrieval provenance'] description: >- A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org). comments: - >- Note that source retrieval provenance concerns the mechanical retrieval and transformation of data between web accessible information systems. It does not trace the source of knowledge back to specific publications or data sets. And it is not concerned with the reasoning, inference or analysis activities that generate knowledge in the first place (this is instead covered by 'knowledge level' and 'agent type' properties). is_a: association slot multivalued: true range: retrieval source 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: >- The clinical approval status of a chemical entity for treating a specific disease or condition, as captured in the context of the association between the chemical and the disease. range: ClinicalApprovalStatusEnum max research phase: is_a: association slot description: >- The maximum research phase reached for a specific chemical-disease pair, indicating the highest clinical trial phase achieved for the chemical entity's investigation as a treatment for the associated disease or condition. range: ResearchPhaseEnum number of cases: is_a: has count description: >- The number of cases in a study or clinical trial, primarily used in conversion of drug approval data. has studies: is_a: node property range: study description: >- Studies which are components of a given node entity (e.g. a publication) multivalued: true close_mappings: - OBAN:has_study_id has supporting studies: is_a: association slot range: study description: >- Studies that produced information used as evidence to generate the knowledge expressed in an Association. multivalued: true close_mappings: - OBAN:has_study_id study metadata: is_a: node property description: >- Information describing how a study was designed and carried out. In practice, data creators should use one of the more specific subtypes of this property. comments: - This is an abstract slot that groups a set of concrete slots that describe a Study itself. Because each of these properties describes a single study, they are node properties of the Study class rather than association slots. An Association links to the studies that supported it via 'has supporting studies', and the metadata for each of those studies is read off the Study node. abstract: true study method types: is_a: study metadata description: >- Type(s) of methods that were applied in a study (e.g. a type of experimental assay, or statistical calculation, or computational analysis). range: uriorcurie multivalued: true study method description: is_a: study metadata description: >- A uri or curie pointing to information about the methodology used to generate the data produced by a study. range: uriorcurie study size: is_a: study metadata description: >- The sample size used in a study (e.g. 'n' of a cohort for a clinical study). range: integer study cohort: is_a: study metadata description: >- A description of the study population/cohort that was interrogated by a study. range: string study date range: is_a: study metadata description: >- The date range over which data was collected in a study. range: string study context: is_a: study metadata description: >- A term or terms describing the experimental setting/context in which a study was carried out ('context' may be defined by many factors, including taxon, model system, tissue type, disease, etc.). range: string ## Deprecated 'supporting study *' association slots. Each of these describes a single study, but an Association ## may cite several studies via the multivalued 'has supporting studies' slot, leaving no way to say which value ## belongs to which study. They have been replaced by the 'study metadata' node properties above, which hang off ## the Study node itself. None of these slots were ever listed under a class, so none were usable as attributes. supporting study metadata: deprecated: "true" deprecated_element_has_exact_replacement: biolink: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 types: deprecated: "true" deprecated_element_has_exact_replacement: biolink:study_method_types is_a: supporting study metadata description: >- Type(s) of methods that were 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 multivalued: true supporting study method description: deprecated: "true" deprecated_element_has_exact_replacement: biolink: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: deprecated: "true" deprecated_element_has_exact_replacement: biolink: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: deprecated: "true" deprecated_element_has_exact_replacement: biolink:study_cohort is_a: supporting study metadata description: >- A description of a study population/cohort that was interrogated to provide evidence for the association. range: string supporting study date range: deprecated: "true" deprecated_element_has_exact_replacement: biolink: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: deprecated: "true" deprecated_element_has_exact_replacement: biolink: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, 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 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 examples: - value: manual_agent - value: automated_agent - value: computational_model - value: text_mining_agent has biological sex: description: >- The biological sex of the entity regarding a case description from a phenopacket required: false range: biological sex druggable gene category: description: Classification of druggable genes based on knowledge about drug or small molecule activities. range: DruggableGeneCategoryEnum classes: # Add the KGX-specific classes without modifying biolink classes KnowledgeGraph: description: >- A container representing a knowledge graph serialized in KGX (Knowledge Graph Exchange) format. A KnowledgeGraph aggregates a collection of nodes (entities) and edges (relationships between entities) conforming to the KGX specification, enabling interoperable exchange of biomedical knowledge graphs across tools and systems in the Biolink ecosystem. slots: - nodes - edges Node: description: >- A generic node in a KGX-formatted knowledge graph, representing a single entity or concept with a unique identifier. This class serves as the structural superclass for `named thing` in Biolink, providing the minimal KGX-compliant contract (identifier, category, etc.) that any biolink entity participating in a knowledge graph must satisfy. Edge: description: >- A generic edge in a KGX-formatted knowledge graph, representing a directed relationship between a subject node and an object node qualified by a predicate. This class serves as the structural superclass for `association` in Biolink, providing the minimal KGX-compliant contract (subject, predicate, object, and associated metadata) that any biolink relationship participating in a knowledge graph must satisfy. knowledge graph: description: >- A knowledge graph is a structured representation of knowledge in the form of a graph, where nodes represent entities or concepts, and edges represent relationships between them. Knowledge graphs are used to organize and connect information from various sources, enabling better understanding, analysis, and reasoning about complex domains. slots: - nodes - edges tree_root: true abstract: true mapping collection: description: >- An abstract container class that holds a set of predicate mappings. Serves as a top-level root for documents that enumerate how third-party or deprecated predicates should be rewritten to Biolink predicates and their associated qualifiers. 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 - subsets 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, (optional) unit prefix and a numeric value. An optional binary relation qualifier may also be given, to allow capture of relative values, e.g., <1000.0 nM meaning "less than 1000 nanometers" slots: - has unit - has unit prefix - has numeric value - has binary relation examples: - object: # Encoding for <1000.0 nM, meaning "less than 1000 nanometers" has_binary_relation: less_than has_numeric_value: 1000.00 has_unit_prefix: "UO:0000300" # 'nano' has_unit: "UO:0000008" # 'meter' 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 description: antidepressant role biological sex: description: >- An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. 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: description: >- A mixin for quantifying aspects of the strength, frequency, or specificity of a relationship between two entities. mixin: true sensitivity quantifier: description: >- A relationship quantifier that measures the sensitivity of a relationship, such as the proportion of true positives correctly identified in a diagnostic or association context. is_a: relationship quantifier mixin: true specificity quantifier: description: >- A relationship quantifier that measures the specificity of a relationship, such as the proportion of true negatives correctly identified in a diagnostic or association context. 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: description: >- A relationship quantifier that expresses how often a relationship holds, using count, total, quotient, or percentage measures. is_a: relationship quantifier mixin: true slots: - has count - has total - has quotient - has percentage examples: - object: has_count: 42 has_total: 100 has_quotient: 0.42 has_percentage: 42.0 chemical or drug or treatment: description: >- A mixin for entities that represent chemical substances, pharmacological agents, or therapeutic interventions. 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 - exact synonym - broad synonym - narrow synonym - related synonym - equivalent identifiers - information content - taxon 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: description: >- An entity that is the byproduct of an administrative process. is_a: named thing abstract: true study result: is_a: named thing 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. abstract: true 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. ## 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. 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. text mining study result: is_a: study result description: >- A study result that represents information extracted from text using natural language processing techniques. This includes the extracted text, location offsets within the source document, confidence scores, and other metadata related to the text mining process. slots: - supporting text - subject location in text - object location in text - extraction confidence score - supporting document type - supporting document year - supporting text section type examples: - object: id: tmkp:id category: biolink:TextMiningStudyResult supporting_text: - "Here, we report two new cases of rivaroxaban-induced hepatitis." subject_location_in_text: - 33 - 44 object_location_in_text: - 53 - 62 extraction_confidence_score: 0.6188385904738642 supporting_document_year: 2018 supporting_text_section_type: abstract icees study result: is_a: study result description: >- A study result that represents a result, from a supporting Study, which is specifically associated with an Integrated Clinical and Environmental Exposures Service (ICEES) knowledge assertion. slots: - chi squared statistic - chi squared dof - chi squared p - total sample size - fisher exact odds ratio - fisher exact p - log odds ratio - log odds ratio 95 ci protein ligand assay result: is_a: study result description: >- The type of study result describing the strength of interaction affinity - or enzymatic interaction - between a ligand and a target protein. Measured binding or enzymatic assay values are generally stated as the negative base 10 logarithm of the raw measurements. For instance (i.e., in a molecular interaction database like BindingDb) if a ligand inhibits a target protein with a pIC50 of 8.6, then the affinity parameter is pIC50 and the affinity value is 8.6. slots: - pKd - pKi - pIC50 - pEC50 - pAC50 - pXC50 - pKon - pKoff study: is_a: activity description: a detailed investigation and/or analysis slots: - has study results - study method types - study method description - study size - study cohort - study date range - study context 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 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: named thing mixins: - ontology class aliases: ['evidence code'] description: >- Class of evidence that supports an association values_from: - eco exact_mappings: - ECO:0000000 evidence: is_a: information content entity description: >- Dereferences detailed evidence that supports an association ## 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. slots: - authors - pages - summary - keywords - mesh terms - xref - publication type - has studies # 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: description: >- A section of a book that forms a discrete unit of a larger published work and may be independently authored or cited. 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 - source record urls - 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: >- A list of upstream InformationResources from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. source record urls: description: >- One or more URLs that link to a specific web page or document provided by the InformationResource, that contains a record of the knowledge expressed in the Edge. examples: - object: id: urn:uuid:id category: biolink:RetrievalSource resource_id: infores:text-mining-provider-targeted resource_role: primary_knowledge_source upstream_resource_ids: - infores:pubmed ## 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 - MAXO:0000001 id_prefixes: - CPT - MAXO 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 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: description: >- A process that occurs within or involves the components of an environmental system. is_a: planetary entity mixins: - occurrent exact_mappings: - ENVO:02500000 environmental feature: description: >- A system or entity in the natural environment that has the disposition to environ one or more material entities. 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: description: >- A heterogeneous substance that contains genomic material or is the product of a biological process. 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: description: >- A generically dependent continuant that carries biological sequence that is part of or derived from a genome. mixin: true slots: - has biological sequence in_subset: - translator_minimal narrow_mappings: - STY:T028 # Gene or Genome - GENO:0000897 # Genomic Entity epigenomic entity: description: >- A mixin for entities that represent epigenomic modifications or features associated with heritable changes in gene expression that do not involve changes to the DNA sequence itself. mixin: true slots: - has biological sequence in_subset: - translator_minimal narrow_mappings: molecular entity: is_a: chemical entity mixins: - ontology class 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: - CHEBI - UNII - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - PHARMGKB.DRUG - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY - BIGG.METABOLITE - foodb.compound - KEGG.GLYCAN - KEGG.DRUG - KEGG.ENVIRON - 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 - routes of delivery - chembl prodrug - chembl black box warning - chembl natural product - chembl availability type - chembl chirality - chembl drug warning 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: - CHEBI - UNII - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - PHARMGKB.DRUG - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY - BIGG.METABOLITE - foodb.compound - KEGG.GLYCAN - KEGG.DRUG - KEGG.ENVIRON - 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 - UNII - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - PHARMGKB.DRUG - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY - BIGG.METABOLITE - foodb.compound - KEGG.GLYCAN - KEGG.DRUG - KEGG.ENVIRON - KEGG - UMLS in_subset: - model_organism_database - translator_minimal chemical mixture: is_a: chemical entity mixins: - ontology class 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 in_subset: - translator_minimal id_prefixes: - CHEBI - UNII - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - PHARMGKB.DRUG - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY - BIGG.METABOLITE - foodb.compound - KEGG.GLYCAN - KEGG.DRUG - KEGG.ENVIRON - KEGG - 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: - CHEBI - UNII - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - PHARMGKB.DRUG - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY - BIGG.METABOLITE - foodb.compound - KEGG.GLYCAN - KEGG.DRUG - KEGG.ENVIRON - KEGG - UMLS 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 - UMLS pathway: description: >- A hierarchical ordering of connected molecular reactions (steps) that represent a specific biological process, such as signaling or metabolism. 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: description: >- A biological or chemical function within a living organism. 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: description: >- The internally coordinated responses (actions or inactions) of organisms (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. 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: - CHEBI - UNII - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - PHARMGKB.DRUG - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY - BIGG.METABOLITE - foodb.compound - foodb.food - KEGG.GLYCAN - KEGG.DRUG - KEGG.ENVIRON - KEGG - UMLS 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 - CHEBI - UNII - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - PHARMGKB.DRUG - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY - BIGG.METABOLITE - foodb.compound - KEGG.GLYCAN - KEGG.ENVIRON - KEGG.ENVIRON - KEGG ## Food environmental food contaminant: description: >- Any unwanted chemical in food. The term includes agrochemicals and industrial chemicals that may contaminate foodstuffs during their production, transportation or storage. is_a: chemical entity exact_mappings: - CHEBI:78299 related_mappings: # substance role - CHEBI:78299 id_prefixes: - CHEBI - UNII - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - PHARMGKB.DRUG - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY - BIGG.METABOLITE - foodb.compound - foodb.food - KEGG.GLYCAN - KEGG.DRUG - KEGG.ENVIRON - KEGG - UMLS food additive: description: >- Any substance which is added to food to preserve or enhance its flavour and/or appearance. is_a: chemical entity exact_mappings: - CHEBI:64047 related_mappings: # substance role - CHEBI:64047 id_prefixes: - CHEBI - UNII - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - PHARMGKB.DRUG - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY - BIGG.METABOLITE - foodb.compound - foodb.food - KEGG.GLYCAN - KEGG.DRUG - KEGG.ENVIRON - KEGG - UMLS food: is_a: chemical mixture description: >- A substance of plant, animal, or artificial origin consumed by a living organism to provide essential nutrients, energy, and support growth and the processes of life, or to satisfy other health needs or provide a social or organoleptic experience. exact_mappings: - CHEBI:33290 - FOODON:00002403 id_prefixes: - foodb.food - foodb.compound - FOODON - CHEBI - UNII - PUBCHEM.COMPOUND - CHEMBL.COMPOUND - DRUGBANK - MESH - CAS - DrugCentral - GTOPDB - HMDB - KEGG.COMPOUND - PHARMGKB.DRUG - ChemBank - PUBCHEM.SUBSTANCE - SIDER.DRUG - INCHI - INCHIKEY - BIGG.METABOLITE - KEGG.GLYCAN - KEGG.DRUG - KEGG.ENVIRON - KEGG - UMLS ## 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 characteristic of a phenotype (e.g., weight, size, shape, color) that can be observed, measured, or compared across organisms or conditions. examples: - value: "PATO:0000128" broad_mappings: - PATO:0001995 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. 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. comments: - >- see: https://github.com/OBOFoundry/COB/pull/211 exact_mappings: - NCBITaxon:10239 - STY:T005 # Virus cellular organism: is_a: organismal entity mixins: - subject of investigation description: >- An organism that contains one or more cells belonging to the cellular lineages of life (Archaea, Bacteria, or Eukaryota), whose body consists of one or more cells. Distinguished from acellular biological entities such as viruses and viroids. comments: - >- see: https://github.com/OBOFoundry/COB/pull/211 exact_mappings: - NCBITaxon:131567 mammal: deprecated: "true" is_a: cellular organism mixins: - subject of investigation exact_mappings: - NCBITaxon:40674 # mammal - STY:T015 # mammal - NCIT:C14234 # Mamalia - FOODON:03411134 # mammal human: deprecated: "true" is_a: mammal mixins: - subject of investigation exact_mappings: - STY:T016 - NCBITaxon:9606 - SIO:000485 - NCIT:C14225 plant: deprecated: "true" is_a: cellular organism exact_mappings: - NCIT:C14258 # plant - STY:T002 # plant - PO:0000003 # whole plant - NCIT:C79659 # plant, whole invertebrate: deprecated: "true" is_a: cellular organism exact_mappings: - NCIT:C14228 # invertebrate - OMIT:0008565 # invertebrates - FOODON:00002452 # invertebrate animals - STY:T011 related_mappings: - NCBITaxon:1767184 # unidentified invertebrate vertebrate: deprecated: "true" is_a: cellular organism exact_mappings: - STY:T010 - NCBITaxon:7742 # vertebrata - OMIT:0015545 # vertebrates related_mappings: - NCBITaxon:2662825 # unclassified vertebrata (in:vertebrates) fungus: deprecated: "true" is_a: cellular organism exact_mappings: - STY:T004 - NCIT:C14209 - FOODON:03411261 narrow_mappings: - FOODON:03315605 # fungus (edible) - NCBITaxon:1670606 # fungus metagenome life stage: is_a: organismal entity mixins: - ontology class 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, Charles Darwin, my pet cat. examples: - value: 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 mixins: - ontology class slots: - inheritance description: >- A disease or an individual phenotypic feature, grouped as a single class to accommodate source vocabularies and assertions that do not distinguish the two. Prefer the more specific subclasses disease or phenotypic feature when the distinction is known. related_mappings: # UMLS Semantic Type "Finding" - more specialized use of 'disease or phenotypic feature' - STY:T033 disease: aliases: ['condition', 'disorder', 'medical condition'] description: >- A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. 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. 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 - icd11 - icd11.foundation - 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 often 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 - ontology class description: >- A part of a cellular organism at or above the granularity of a protein complex. This is a grouping class with three concrete subclasses that should be preferred when applicable: "biolink:Cell" for whole cells, "biolink:CellularComponent" for subcellular and intracellular structures (organelles, membranes, bacterial flagella, etc.), and "biolink:GrossAnatomcialStructure" for multicellular parts (tissues, organs, body parts). Excludes viral and other acellular biological entities. examples: - value: UBERON:0000178 description: blood - value: UBERON:0002553 description: anatomical cavity 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 - FMA in_subset: - model_organism_database cellular component: aliases: ['cell component', 'cell part'] is_a: anatomical entity description: >- A location in or around a cell examples: - value: GO:0005739 description: mitochondrion - value: GO:0005634 description: nucleus - value: GO:0005886 description: plasma membrane - value: GO:0009288 description: bacterial-type flagellum - value: GO:0031012 description: extracellular matrix 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: description: >- The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. is_a: anatomical entity examples: - value: CL:0000540 description: neuron - value: CL:0000236 description: B cell 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: description: >- A cultured cell population that is genetically stable and homogeneous, sharing a common propagation history through successive passages in culture. is_a: organismal entity mixins: - subject of investigation exact_mappings: - CLO:0000031 id_prefixes: - CLO gross anatomical structure: description: >- An anatomical structure that has more than one cell as a part. aliases: ['tissue', 'organ'] is_a: anatomical entity examples: - value: UBERON:0000955 description: brain - value: UBERON:0002107 description: liver - value: UBERON:0000479 description: tissue - value: PO:0009046 description: flower - value: PO:0009025 description: leaf - value: FAO:0001001 description: hypha 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 # model organism anatomy ontologies that include gross structures (organs, tissues), # mirroring the model-organism prefixes on anatomical entity (see #1746) - EMAPA # mouse, e.g. subclasses of EMAPA:35949 "organ" and EMAPA:35868 "tissue" - MA # mouse adult anatomy - ZFA # zebrafish - FBbt # fly - WBbt # c. elegans - XAO # frog ## 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 close_mappings: - DRUGBANK:target gene or gene product or gene family: is_a: macromolecular machine mixin description: >- A union of gene family or gene loci or gene products, useful to define the association between a gene or gene product or gene family and some other general class of entity. mixin: true 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 - gene or gene product or gene family - 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 - CHEMBL.TARGET - 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. 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: description: >- A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. 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 - NCIT - 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. comments: - >- 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. 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, altering its structure, activity, localization, or interactions. mixins: - gene product isoform mixin id_prefixes: - MOD - UNIMOD exact_mappings: - MOD:00000 # protein modification (PSI-MOD root) examples: - value: MOD:00696 description: phosphorylated residue - value: MOD:01148 description: ubiquitinylated lysine protein family: description: >- A set of proteins coding for diverse functions which, by virtue of their high degree of sequence similarity, are believed to have evolved from a single ancestral gene. 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. consensus sequences. RNA product: is_a: transcript description: >- High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds typically synthesized by a DNA- or RNA-dependent RNA polymerase that constitutes the product of a gene. Distinct in emphasis from `biolink:Transcript`, which denotes the informational output of transcription at the gene-model level rather than the chemical species itself. examples: - value: RNACENTRAL:URS00005EB5B7_9606 - value: mirbase:MI0000060 mixins: - gene product mixin exact_mappings: - CHEBI:33697 # ribonucleic acid - WIKIDATA:Q11053 # RNA id_prefixes: - RNACENTRAL - mirbase 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: description: >- An RNA transcript that does not encode for a protein rather the RNA molecule is the functional gene product. is_a: RNA product id_prefixes: - RNACENTRAL - NCBIGene - ENSEMBL exact_mappings: - SO:0000655 - SIO:001235 microRNA: description: >- A small (~22 nucleotide) RNA molecule that is the endogenous transcript of a miRNA gene. Produced from precursor molecules that form hairpin structures, which are processed (typically via the Dicer pathway) to yield a single miRNA molecule. miRNAs function by triggering cleavage of target molecules or acting as translational repressors. is_a: noncoding RNA product exact_mappings: - SO:0000276 - SIO:001397 - WIKIDATA:Q310899 id_prefixes: - MIR - HGNC - WormBase - mirbase 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 - gene or gene product or gene family - 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: description: >- An allelic state describing the degree of similarity between features at a single locus, specifically whether alleles at the same location on paired chromosomes are identical or different. 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 - hgvs nomenclature 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: study description: >- A clinical trial is a research study that prospectively assigns human participants or groups of humans to one or more health-related interventions to evaluate the effects on health outcomes. exact_mappings: - NCIT:C71104 - SIO:001000 slots: - clinical trial phase - clinical trial primary purpose - clinical trial intervention model - clinical trial overall status - clinical trial brief title - clinical trial enrollment type - clinical trial start date - clinical trial enrollment - clinical trial age stage - clinical trial age range - clinical trial tested intervention - clinical trial interventions - clinical trial conditions - creation date id_prefixes: - CLINICALTRIALS clinical intervention: description: >- A medical procedure, treatment, or action taken by healthcare professionals to modify the course of a disease or condition. 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: description: >- The admission and care of a patient in a hospital for observation, diagnosis, or treatment. 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 slots: - has biological sex 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: named thing mixins: - ontology class aliases: ['exposure', 'experimental condition'] slots: - timepoint - exposure type - exposure vehicle - exposure route - exposure start age - exposure end age - exposure duration - exposure magnitude - exposure additional condition 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 slot_usage: id: description: >- Could generally be a CURIE from a suitable exposure ontology like ECTO. exact_mappings: - XCO:0000000 in_subset: - model_organism_database # TODO - confirm that genomic backgrounds are exposures genomic background exposure: is_a: exposure event mixins: - 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: exposure event description: >- A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome. 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: exposure event description: >- An abnormal anatomical structure, when viewed as an exposure, represented as a precondition, leading to or influencing an outcome. disease or phenotypic feature exposure: is_a: exposure event mixins: - pathological entity mixin description: >- A disease or phenotypic feature state, when viewed as an exposure, represented as a precondition, leading to or influencing an outcome,. chemical exposure: is_a: 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: exposure event description: >- A complex chemical exposure is an intake of a chemical mixture, 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. 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: exposure event mixins: - 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: exposure event aliases: ['viral exposure', 'bacterial exposure'] description: >- An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses). geographic exposure: is_a: environmental exposure 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: 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: exposure event description: >- A behavioral exposure is a factor relating to behavior impacting an individual. socioeconomic exposure: is_a: exposure event description: >- A socioeconomic exposure is a factor relating to social and financial status of an affected individual. 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 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 - sources - has evidence of type - has evidence - knowledge source - primary knowledge source - aggregator knowledge source - knowledge level - agent type - timepoint - original subject - original predicate - original object - subject feature name - object feature name # 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 - p value - adjusted p value - statistical significance qualifier - effect size - effect type - supporting text - has supporting studies - update date - has confidence score - stringdb combined score - stringdb experimental score - stringdb coexpression score - elevate to prediction - evidence count - semmed agreement count - association basis qualifier slot_usage: type: description: rdf:type of biolink:Association should be fixed at rdf:Statement category: range: uriorcurie required: false sources: inlined_as_list: true has supporting studies: inlined: true rules: - description: >- A statistical significance qualifier may only be set when at least one numeric p-value slot (p value or adjusted p value) is also populated. preconditions: slot_conditions: statistical significance qualifier: {} postconditions: any_of: - slot_conditions: p value: {} - slot_conditions: adjusted p value: {} - description: >- An effect type may only be set when the companion effect size slot is also populated, because the effect type disambiguates the numeric value and is meaningless without it. preconditions: slot_conditions: effect type: {} postconditions: slot_conditions: effect size: {} exact_mappings: - OBAN:association - rdf:Statement - owl:Axiom examples: - object: subject: NCBIGene:6910 # TBX5 predicate: biolink:acts_upstream_of object: GO:1901846 # positive regulation of cell communication by electrical coupling involved in cardiac conduction category: biolink:Association knowledge_level: knowledge_assertion agent_type: manual_agent publications: ["PMID:15289437"] - object: subject: NCBIGene:4357 # MPST predicate: biolink:enables object: GO:0005515 # protein binding category: biolink:Association knowledge_level: knowledge_assertion agent_type: manual_agent publications: ["PMID:32296183"] - object: subject: CHEBI:114566 # 2-imino-N,8-dimethyl-5-oxo-1-propan-2-yl-3-dipyrido[1,2-d:3',4'-f]pyrimidinecarboxamide predicate: biolink:subclass_of object: CHEBI:38166 # organic heteropolycyclic compound category: biolink:Association knowledge_level: knowledge_assertion agent_type: manual_agent disease associated with response to chemical entity association: description: >- A statistical association between a disease and a chemical entity where the chemical entity has a therapeutic or adverse effect on the disease progression, symptoms or outcomes in a patient, cell line, or any model system. is_a: association slots: - response context qualifier - response target context qualifier defining_slots: - subject - predicate - object - response context qualifier - response target context qualifier slot_usage: subject: range: disease object: range: chemical entity predicate: subproperty_of: associated with response to chemical entity assesses named thing association: deprecated: "true" is_a: association slot_usage: subject: range: chemical entity object: range: named thing predicate: subproperty_of: was tested for effect on 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: >- parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction. is_a: association slots: - subject aspect qualifier - subject direction qualifier - object aspect qualifier - object direction qualifier - causal mechanism qualifier - qualified predicate - species context qualifier - subject - subject activity qualifier - subject process qualifier - subject context qualifier - predicate - qualified predicate - object - object activity qualifier - object process qualifier - object context qualifier 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. subject activity qualifier: range: molecular activity subject process qualifier: range: biological process subject context qualifier: range: anatomical entity 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. object activity qualifier: range: molecular activity object process qualifier: range: biological process object context qualifier: range: anatomical entity 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 family to gene or gene product or gene family association: description: >- Relationship between a gene family and a contained gene or gene product or gene family. is_a: association defining_slots: - subject - predicate - object slot_usage: subject: range: gene family object: range: gene or gene product predicate: subproperty_of: has part symmetric: false description: >- membership of a gene or gene product, or strict subset relationship gene family, in the given gene family. gene or gene product or gene family to biological process or activity association: description: >- Relationship between a gene or gene product or gene family to a specified biological process or activity (e.g. molecular activity, biological process or pathway). is_a: association defining_slots: - subject - predicate - object slot_usage: subject: range: gene or gene product or gene family object: range: biological process or activity predicate: subproperty_of: participates in symmetric: false description: >- participation of a gene or gene product or gene family in a given biological process or activity (e.g., gene product participates in biological process; gene catalyzes molecular activity; gene family is actively involved in a pathway). biological process or activity to gene or gene product or gene family association: description: >- Relationship between a biological processor activity (e.g. molecular activity, biological process or pathway) to gene or gene product or gene family. is_a: association defining_slots: - subject - predicate - object slot_usage: subject: range: biological process or activity object: range: gene or gene product or gene family predicate: subproperty_of: has participant symmetric: false description: >- Relationship in which a biological process has the participation of a gene or gene product or gene family in a (e.g., pathway has participant gene product). biological process or activity to biological process or activity association: description: >- Classification relationship between biological processes or activities (e.g. coupling of two molecular activities; assignment of molecular activity to a pathway; implicating a pathway in a biological process; etc.) is_a: association defining_slots: - subject - predicate - object slot_usage: subject: range: biological process or activity object: range: biological process or activity predicate: subproperty_of: subclass of symmetric: false description: >- One biological processes or activities is a subclass of another. 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: deprecated: "true" 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 entity to chemical entity 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 - species context qualifier defining_slots: - subject - object slot_usage: object: range: chemical entity description: "the chemical element that is the target of the statement" examples: - object: subject: CHEBI:85990 # panobinostat predicate: biolink:has_metabolite object: PUBCHEM.COMPOUND:155543741 # (E)-3-[4-[[2-(1a-methyl-2H-oxireno[2,3-b]indol-6b-yl)ethylamino]methyl]phenyl]-N-hydroxyprop-2-enamide category: biolink:ChemicalEntityToChemicalEntityAssociation knowledge_level: knowledge_assertion agent_type: manual_agent publications: ["PMID:22344701"] species_context_qualifier: NCBITaxon:9606 - object: subject: CHEBI:85973 # edoxaban predicate: biolink:has_metabolite object: UNII:9O1PTP64VA category: biolink:ChemicalEntityToChemicalEntityAssociation knowledge_level: knowledge_assertion agent_type: manual_agent publications: ["PMID:22936313"] species_context_qualifier: NCBITaxon:9606 reaction to participant association: description: >- An association between a biochemical reaction and a participating molecular entity, qualified by the stoichiometry, the side (reactant vs. product) on which the participant appears, and the direction of the reaction. is_a: chemical entity to chemical entity association slots: - stoichiometry - reaction direction - reaction side slot_usage: subject: range: molecular entity defining_slots: - subject - predicate - object reaction to catalyst association: description: >- A specialization of reaction-to-participant association in which the participant is a gene or gene product (e.g., an enzyme) that catalyses the reaction. is_a: reaction to participant association slot_usage: object: range: gene or gene product chemical entity 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 entity to chemical entity 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 entity 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: - entity to disease or phenotypic feature association mixin slots: - clinical approval status - max research phase slot_usage: object: range: disease or phenotypic feature description: "the disease or phenotype that is affected by the chemical" examples: - object: subject: CHEBI:167638 # 2-hydroxy-5-{1-hydroxy-2-[(4-phenylbutan-2-yl)amino]ethyl}benzamide predicate: biolink:contraindicated_in object: UMLS:C0271149 # Secondary angle-closure glaucoma category: biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation knowledge_level: knowledge_assertion agent_type: manual_validation_of_automated_agent - object: subject: CHEBI:25879 # pentaerythritol tetranitrate predicate: biolink:contraindicated_in object: UMLS:C0234976 # Lowered convulsive threshold category: biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation knowledge_level: knowledge_assertion agent_type: manual_validation_of_automated_agent - object: subject: PUBCHEM.COMPOUND:134612761 # macimorelin predicate: biolink:diagnoses object: UMLS:C1720505 # Adult growth hormone deficiency category: biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation knowledge_level: knowledge_assertion agent_type: manual_validation_of_automated_agent - object: subject: CHEBI:82720 # empagliflozin predicate: biolink:preventative_for_condition object: UMLS:C1320716 # Cardiovascular event category: biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation knowledge_level: knowledge_assertion agent_type: manual_validation_of_automated_agent - object: subject: CHEBI:6919 # mezlocillin predicate: biolink:treats object: EFO:1001421 # Serratia Infections category: biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation knowledge_level: knowledge_assertion agent_type: manual_validation_of_automated_agent - object: subject: CHEBI:135361 # methscopolamine predicate: biolink:treats object: MONDO:0005324 # seasonal allergic rhinitis category: biolink:ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation knowledge_level: knowledge_assertion agent_type: manual_validation_of_automated_agent 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 chemical or treatment is used to treat, or is being studied to treat, the disease or phenotypic feature. is_a: association defining_slots: - subject - predicate - object mixins: - entity to disease or phenotypic feature association mixin - entity to feature or disease qualifiers mixin slot_usage: predicate: subproperty_of: treats or applied or studied to treat chemical or drug or treatment adverse event association: description: >- This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is an untoward medical occurrence that happens during treatment, whether or not considered related to the treatment. is_a: association defining_slots: - subject - predicate - object mixins: - entity to disease or phenotypic feature association mixin - entity to feature or disease qualifiers mixin slots: - FDA adverse event level slot_usage: predicate: subproperty_of: has adverse event chemical or drug or treatment side effect association: description: >- This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is an unintended, but predictable, secondary effect of the treatment. is_a: association defining_slots: - subject - predicate - object mixins: - entity to disease or phenotypic feature association mixin - entity to feature or disease qualifiers 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 entity 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 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" chemical entity to biological process association: description: >- An association between a chemical entity and a biological process, where the chemical entity has some effect on the biological process. is_a: association slots: - species context qualifier - anatomical context qualifier - qualified predicate - object direction qualifier slot_usage: subject: range: chemical entity description: "the chemical entity that affects the biological process" object: range: biological process description: "the biological process that is affected by the chemical entity" predicate: subproperty_of: related to at instance level named thing associated with likelihood of named thing association: # TODO: better name description: >- An association in which the subject entity is linked to the likelihood of the object entity occurring, manifesting, or being observed. Subject and object may each be qualified by aspect and context, and the association may be further qualified by a population context. 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 an 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 broad_mappings: - SIO:001257 ## chemical-gene association slots: - subject form or variant qualifier - subject part qualifier - subject derivative qualifier - subject context qualifier - qualified predicate - object direction qualifier - object aspect qualifier - object form or variant qualifier - object part qualifier - object context qualifier - anatomical context qualifier - species context qualifier - causal mechanism qualifier - dgidb interaction score - dgidb evidence score slot_usage: subject: range: chemical entity object: range: gene or gene product predicate: subproperty_of: 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 direction qualifier: range: DirectionQualifierEnum object aspect qualifier: range: GeneOrGeneProductOrChemicalEntityAspectEnum object form or variant qualifier: range: ChemicalOrGeneOrGeneProductFormOrVariantEnum object part qualifier: range: GeneOrGeneProductOrChemicalPartQualifierEnum object context qualifier: range: anatomical entity anatomical context qualifier: range: anatomical entity causal mechanism qualifier: range: CausalMechanismQualifierEnum examples: - object: subject: CHEBI:135370 # aprindine predicate: biolink:directly_physically_interacts_with object: UniProtKB:P0DP23 # CALM1_HUMAN Calmodulin-1 (sprot) category: biolink:ChemicalGeneInteractionAssociation knowledge_level: knowledge_assertion agent_type: manual_agent - object: subject: CHEBI:4779 # emedastine predicate: biolink:directly_physically_interacts_with object: NCBIGene:3269 # HRH1 category: biolink:ChemicalGeneInteractionAssociation knowledge_level: knowledge_assertion agent_type: manual_agent publications: ["http://www.accessdata.fda.gov/drugsatfda_docs/label/2003/20706slr011_emadine_lbl.pdf"] - object: subject: UNII:OP35X9610Y # ACP-001 predicate: biolink:interacts_with object: NCBIGene:2690 # GHR category: biolink:ChemicalGeneInteractionAssociation knowledge_level: knowledge_assertion agent_type: manual_agent publications: ["https://www.accessdata.fda.gov/drugsatfda_docs/label/2021/761177Orig1s000lbl.pdf"] macromolecular machine has substrate association: is_a: association description: >- Describes the relationship between an enzyme (usually a macromolecular complex or gene product) and the molecules it acts on (substrate). The substrate can be a chemical, a polypeptide, or a protein. notes: - >- Using macromolecular machine should cover cases of gene-protein conflation. 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: macromolecular machine mixin predicate: subproperty_of: has substrate object: range: chemical entity or protein or polypeptide examples: - object: subject: NCBIGene:6530 # SLC6A2 predicate: biolink:has_substrate object: CHEBI:5557 # guanethidine category: biolink:MacromolecularMachineHasSubstrateAssociation knowledge_level: knowledge_assertion agent_type: manual_agent - object: subject: NCBIGene:50719 # Slc7a5 predicate: biolink:has_substrate object: UNII:UID84303EL # borofalan (10B) category: biolink:MacromolecularMachineHasSubstrateAssociation knowledge_level: knowledge_assertion agent_type: manual_agent gene regulates gene association: is_a: association description: >- Describes a regulatory relationship between two genes or gene products. slots: - object aspect qualifier - object direction qualifier - qualified predicate - species context qualifier - causal mechanism qualifier slot_usage: subject: range: chemical entity or gene or gene product predicate: subproperty_of: regulates object: range: chemical entity or gene or gene product object aspect qualifier: range: GeneOrGeneProductOrChemicalEntityAspectEnum required: true description: >- the aspect of the object gene or gene product that is being regulated, must be a descendant of "activity_or_abundance"" object direction qualifier: range: DirectionQualifierEnum required: true qualified predicate: subproperty_of: causes required: true examples: - value: >- { subject: NCBIGene:551, predicate: regulates, qualified_predicate: causes, object: NCBIGene:1636, object_aspect_qualifier: activity_or_abundance, object_direction_qualifier: downregulated } description: >- AVP (NCBIGene:551) regulates ACE (NCBIGene:1636), with qualified predicate 'causes', object aspect qualifier 'activity_or_abundance', and object direction qualifier 'downregulated'. process regulates process association: is_a: association description: >- Describes a regulatory relationship between two genes or gene products. slot_usage: subject: range: biological process predicate: subproperty_of: regulates object: range: biological process chemical affects biological entity association: description: >- Describes an effect that a chemical has on a biological entity (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: biological entity 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 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: chemical affects biological entity association slots: - dgidb interaction score - dgidb evidence score - evidence count - supporting documents examples: - object: subject: PUBCHEM.COMPOUND:168290237 # 1-[4-(4-ethoxyphenyl)-4-(2H-tetrazol-5-yl)piperidin-1-yl]prop-2-en-1-one predicate: biolink:affects object: NCBIGene:200424 # TET3 category: biolink:ChemicalAffectsGeneAssociation knowledge_level: knowledge_assertion agent_type: automated_agent publications: ["PMID:35978680"] object_aspect_qualifier: activity object_direction_qualifier: decreased causal_mechanism_qualifier: inhibition qualified_predicate: biolink:causes species_context_qualifier: NCBITaxon:9606 - object: subject: CHEBI:91447 # 4-methyl-3-[[1-methyl-6-(3-pyridinyl)-4-pyrazolo[3,4-d]pyrimidinyl]amino]-N-[3-(trifluoromethyl)phenyl]benzamide predicate: biolink:directly_physically_interacts_with object: NCBIGene:3313 # HSPA9 category: biolink:ChemicalAffectsGeneAssociation knowledge_level: knowledge_assertion agent_type: automated_agent publications: ["PMID:29928781"] causal_mechanism_qualifier: binding species_context_qualifier: NCBITaxon:9606 - object: subject: UNII:5V9KLZ54CY # Vinblastine predicate: biolink:has_substrate object: NCBIGene:5244 # ABCB4 category: biolink:ChemicalAffectsGeneAssociation knowledge_level: knowledge_assertion agent_type: manual_agent publications: ["PMID:20190787"] species_context_qualifier: NCBITaxon:9606 - object: subject: CHEMBL.COMPOUND:CHEMBL1743027 # GIRENTUXIMAB predicate: biolink:interacts_with object: NCBIGene:768 # CA9 category: biolink:ChemicalAffectsGeneAssociation knowledge_level: knowledge_assertion agent_type: manual_agent publications: ["http://www.wilex.de/portfolio-english/rencarex/therapeutic-target/", "PMID:11941456"] species_context_qualifier: NCBITaxon:9606 - object: subject: CHEBI:3546 # cepharanthine predicate: biolink:affects object: NCBIGene:4790 # NFKB1 category: biolink:ChemicalAffectsGeneAssociation knowledge_level: knowledge_assertion agent_type: manual_agent object_aspect_qualifier: activity object_direction_qualifier: decreased causal_mechanism_qualifier: inhibition qualified_predicate: biolink:causes chemical gene sensitivity association: description: >- Describes a relationship in which a chemical entity affects the sensitivity or susceptibility of a biological system to a gene or gene product (e.g. a chemical that increases or decreases the response to a gene or gene product). This covers 'response to substance' style interactions from sources such as CTD that map to the 'affects sensitivity to' predicate hierarchy, as opposed to the abundance/activity/processing effects covered by ChemicalAffectsGeneAssociation. is_a: association broad_mappings: - SIO:001257 ## chemical-gene association slots: - subject form or variant qualifier - subject part qualifier - subject derivative qualifier - subject aspect qualifier - subject direction qualifier - object form or variant qualifier - object part qualifier - object derivative qualifier - object aspect qualifier - object direction qualifier - qualified predicate - anatomical context qualifier - species context qualifier - evidence count - supporting documents slot_usage: subject: range: chemical entity object: range: gene or gene product predicate: subproperty_of: affects sensitivity to description: >- must be a descendant of 'affects sensitivity to' (e.g. 'increases sensitivity to' or 'decreases sensitivity to') subject form or variant qualifier: range: ChemicalOrGeneOrGeneProductFormOrVariantEnum subject part qualifier: range: GeneOrGeneProductOrChemicalPartQualifierEnum subject derivative qualifier: range: ChemicalEntityDerivativeEnum subject aspect qualifier: range: GeneOrGeneProductOrChemicalEntityAspectEnum subject direction qualifier: range: DirectionQualifierEnum qualified predicate: subproperty_of: causes object form or variant qualifier: range: ChemicalOrGeneOrGeneProductFormOrVariantEnum object part qualifier: range: GeneOrGeneProductOrChemicalPartQualifierEnum object derivative qualifier: range: ChemicalEntityDerivativeEnum object aspect qualifier: range: GeneOrGeneProductOrChemicalEntityAspectEnum object direction qualifier: range: DirectionQualifierEnum anatomical context qualifier: range: anatomical entity species context qualifier: range: organism taxon examples: - object: subject: CHEBI:28748 # doxorubicin predicate: biolink:increases_sensitivity_to object: NCBIGene:7157 # TP53 category: biolink:ChemicalGeneSensitivityAssociation knowledge_level: knowledge_assertion agent_type: manual_agent species_context_qualifier: NCBITaxon:9606 - object: subject: CHEBI:45863 # paclitaxel predicate: biolink:decreases_sensitivity_to object: NCBIGene:5243 # ABCB1 category: biolink:ChemicalGeneSensitivityAssociation knowledge_level: knowledge_assertion agent_type: manual_agent species_context_qualifier: NCBITaxon:9606 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: - object: subject: NCBIGene:6616 # SNAP25 predicate: biolink:affects object: CHEMBL.COMPOUND:CHEMBL3707322 # LETIBOTULINUMTOXINA category: biolink:GeneAffectsChemicalAssociation knowledge_level: knowledge_assertion agent_type: manual_agent publications: ["CHEMBL.DOCUMENT:CHEMBL2107839", "https://www.accessdata.fda.gov/drugsatfda_docs/label/2024/761225s000lbl.pdf"] subject_aspect_qualifier: hydrolysis subject_direction_qualifier: increased qualified_predicate: biolink:causes species_context_qualifier: NCBITaxon:9606 - object: subject: CHEBI:3172 # bretylium predicate: biolink:has_substrate object: NCBIGene:6530 # SLC6A2 category: biolink:GeneAffectsChemicalAssociation knowledge_level: knowledge_assertion agent_type: manual_agent publications: ["ISBN:9780702034718 PP. 190-191", "PMID:18071295", "PMID:9142404"] species_context_qualifier: NCBITaxon:9606 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: chemical entity or 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: description: >- A mixin applied to any association whose subject (source node) is a disease. 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 - disease context qualifier entity to feature or variant qualifiers mixin: description: >- Qualifiers for entity to variant 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 feature or gene qualifiers mixin: description: >- Qualifiers for entity to gene 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: description: >- A mixin applied to any association whose object (target node) is a phenotypic feature. mixin: true is_a: entity to feature or disease qualifiers mixin mixins: - frequency quantifier slots: - subject - predicate - object - sex qualifier defining_slots: - subject - predicate - 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: description: >- A mixin applied to any association whose subject (source node) is a phenotypic feature. 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 phenotypic feature to phenotypic feature association: description: >- Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships. is_a: association mixins: - phenotypic feature to entity association mixin - entity to phenotypic feature association mixin defining_slots: - subject - predicate - object 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 - disease context qualifier - subject specialization qualifier - object specialization qualifier - anatomical context qualifier defining_slots: - subject - predicate - 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 disease to disease association: is_a: association defining_slots: - subject - object description: >- An association between two diseases. Captures clinical or biological relationships such as comorbidity, sequela, post-infectious complication, shared susceptibility, or differential diagnosis. The precise relationship is carried by the predicate (e.g. ``associated with``, ``contributes to``, ``risk affected by``, ``temporally related to``); use this class whenever both ends of the association are diseases, rather than the more specific ``disease to phenotypic feature association`` (which forces the object to be a phenotypic feature) or a generic ``association``. mixins: - disease to entity association mixin - entity to disease association mixin slot_usage: subject: range: disease description: "the disease that is the source/context of the association" examples: - value: MONDO:0005688 description: "campylobacteriosis (subject of: associated with Guillain-Barré syndrome as a post-infectious sequela)" object: range: disease description: "the related disease" examples: - value: MONDO:0016218 description: "Guillain-Barré syndrome (object of: campylobacteriosis associated with Guillain-Barré syndrome)" predicate: subproperty_of: associated with 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 - predicate - object mixins: - entity to phenotypic feature association mixin - case to entity association mixin slots: - negated - onset qualifier case to disease association: is_a: association mixins: - case to entity association mixin description: "An association between a Case (patient) and a Disease" slot_usage: object: range: disease slots: - subject - predicate - object - onset qualifier case to variant association: is_a: association mixins: - case to entity association mixin description: "Association between a Case and a Genetic Variant" slot_usage: object: range: sequence variant has zygosity: range: zygosity slots: - subject - predicate - object - has zygosity case to gene association: is_a: association mixins: - case to entity association mixin description: "Association between a Case and a Gene (e.g., indicating a gene of interest for the case)" slot_usage: object: range: gene or gene product slots: - subject - predicate - object 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 phenotypic feature association: description: >- An association between a gene or gene product and a phenotypic feature, where variation in the gene is correlated with the phenotypic feature. is_a: association slots: - subject form or variant qualifier - subject aspect qualifier - object direction qualifier - allelic requirement narrow_mappings: - dcid:DiseaseGeneAssociation - SIO:000983 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)" subject form or variant qualifier: range: ChemicalOrGeneOrGeneProductFormOrVariantEnum subject aspect qualifier: range: GeneOrGeneProductOrChemicalEntityAspectEnum object: range: phenotypic feature object direction qualifier: range: DirectionQualifierEnum predicate: range: GeneToPhenotypicFeaturePredicateEnum 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 disease association: description: >- An association between a gene or gene product and a disease, where variation in the gene is correlated with the disease. examples: - object: subject: NCBIGene:60 # ACTB predicate: biolink:associated_with object: MONDO:0017579 # Baraitser-Winter cerebrofrontofacial syndrome category: biolink:GeneToDiseaseAssociation knowledge_level: knowledge_assertion agent_type: manual_agent - object: subject: UniProtKB:P11274-1 # breakpoint cluster region protein isoform h1 (human) predicate: biolink:associated_with object: MONDO:0011996 # chronic myelogenous leukemia, BCR-ABL1 positive category: biolink:GeneToDiseaseAssociation knowledge_level: knowledge_assertion agent_type: manual_agent is_a: association exact_mappings: - SIO:000983 close_mappings: - dcid:DiseaseGeneAssociation defining_slots: - subject - object mixins: - gene to entity association mixin slots: - subject form or variant qualifier - subject aspect qualifier - object direction qualifier - allelic requirement - qualified predicate - diseases confidence score - gene2phenotype confidence category slot_usage: subject: range: gene or gene product description: "gene in which variation is correlated with the disease" subject form or variant qualifier: range: ChemicalOrGeneOrGeneProductFormOrVariantEnum subject aspect qualifier: range: GeneOrGeneProductOrChemicalEntityAspectEnum object direction qualifier: range: DirectionQualifierEnum object: range: disease predicate: range: GeneToDiseasePredicateEnum 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 disease - if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children. causal gene to disease association: description: >- An association between a gene and a disease where variation in the gene has been shown to have a causal role in the disease. is_a: association defining_slots: - subject - object slots: - subject form or variant qualifier - subject aspect qualifier - object direction qualifier - allelic requirement - qualified predicate mixins: - 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: description: >- An association between a gene (or gene product) and a disease for which the gene is statistically correlated with the disease rather than asserted as causal. Such associations typically derive from GWAS, co-occurrence analyses, or other statistical methods, and are annotated with scores such as a z-score or a diseases confidence score. is_a: association defining_slots: - subject - object - predicate slots: - z score - diseases confidence score - subject form or variant qualifier - subject aspect qualifier - object direction qualifier - allelic requirement - qualified predicate 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 predicate: subproperty_of: correlated with examples: - object: subject: NCBIGene:8506 # CNTNAP1 predicate: biolink:occurs_together_in_literature_with object: MONDO:0004585 # polyhydramnios category: biolink:CorrelatedGeneToDiseaseAssociation knowledge_level: text_co_occurrence agent_type: data_analysis_pipeline - object: subject: UniProtKB:Q2KHT3-1 # protein CLEC16A isoform h1 (human) predicate: biolink:occurs_together_in_literature_with object: MONDO:0005578 # arthritic joint disease category: biolink:CorrelatedGeneToDiseaseAssociation knowledge_level: text_co_occurrence agent_type: data_analysis_pipeline druggable gene to disease association: description: >- An association between a gene (or gene product) and a disease in which the gene is classified by its druggability (e.g., via the IDG/Pharos target development-level tiers). is_a: gene to disease association slots: - druggable gene category 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 defining_slots: - subject - object - predicate mixins: - entity to disease association mixin - gene to entity association mixin phenotypic feature to disease association: description: >- An association between a phenotypic feature (sign or symptom) and a disease, where the phenotypic feature is a manifestation or clinical indicator of the disease. 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: description: >- An association between a sequence variant and a phenotypic feature, in which the allele state of the variant is linked to the manifestation of the phenotype. 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: description: >- An association between a sequence variant and a disease, in which the allele state of the variant is linked to the disease state. 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: description: >- An association between a genotype and a disease, in which the genotype (typically a combination of alleles at one or more loci) is linked to the disease state. 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: description: >- An association in which a gene (e.g., a model-organism ortholog of a known disease gene) serves as a model of a human disease - for example, because mutants of the gene recapitulate core features of the disease. 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: description: >- An association in which a sequence variant serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it. 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: description: >- An association in which a genotype serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it. 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: description: >- An association in which a cell line - typically derived from an organismal entity with a disease state - serves as a model for that disease in experimental settings. 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: description: >- An association in which an organismal entity (e.g., a strain or breed) serves as a model of a disease, either because it has a natural predisposition to the disease or was bred or engineered specifically to recapitulate it. 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: description: >- An association between two individual organisms (e.g., symbiosis, parasitism, predation, or other inter-organism relationships). 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: description: >- An association between two organism taxa, capturing ecological or evolutionary relationships between the taxa (e.g., a host-pathogen relationship or shared habitat). 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: description: >- A gene-to-disease association that is asserted on the grounds that the gene harbours a sequence variant that contributes to the disease. Qualifies the gene with the form or variant that underlies the contribution. 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 - object specialization 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 - species context qualifier 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: description: >- A functional association between a gene (or gene product or macromolecular complex) and a Gene Ontology (GO) term describing the molecular function, biological process, or cellular component in which it participates. 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 examples: - object: subject: NCBIGene:25595 # Map2 predicate: biolink:active_in object: GO:0015630 # microtubule cytoskeleton category: biolink:GeneToGoTermAssociation knowledge_level: prediction agent_type: manual_validation_of_automated_agent - object: subject: NCBIGene:20502 # Slc16a2 predicate: biolink:acts_upstream_of object: GO:0042403 # thyroid hormone metabolic process category: biolink:GeneToGoTermAssociation knowledge_level: prediction agent_type: manual_validation_of_automated_agent - object: subject: NCBIGene:308911 # Rrp8 predicate: biolink:acts_upstream_of_negative_effect object: GO:1903450 # regulation of G1 to G0 transition category: biolink:GeneToGoTermAssociation knowledge_level: prediction agent_type: manual_validation_of_automated_agent - object: subject: NCBIGene:101148 # Samtor predicate: biolink:acts_upstream_of_or_within object: GO:0031669 # cellular response to nutrient levels category: biolink:GeneToGoTermAssociation knowledge_level: prediction agent_type: manual_validation_of_automated_agent - object: subject: NCBIGene:18072 # Nhlh2 predicate: biolink:acts_upstream_of_or_within_positive_effect object: GO:0006915 # apoptotic process category: biolink:GeneToGoTermAssociation knowledge_level: knowledge_assertion agent_type: manual_agent publications: ["PMID:17573818"] - object: subject: NCBIGene:12168 # Bmpr2 predicate: biolink:colocalizes_with object: GO:0005901 # caveola category: biolink:GeneToGoTermAssociation knowledge_level: prediction agent_type: automated_agent - object: subject: NCBIGene:303888 # Osbpl11 predicate: biolink:contributes_to object: GO:0160270 # phosphatidylserine-phosphatidylinositol-4-phosphate exchange activity category: biolink:GeneToGoTermAssociation knowledge_level: prediction agent_type: manual_validation_of_automated_agent - object: subject: NCBIGene:12193 # Zfp36l2 predicate: biolink:enables object: GO:0046872 # metal ion binding category: biolink:GeneToGoTermAssociation knowledge_level: prediction agent_type: automated_agent - object: subject: NCBIGene:258177 # Or4c117 predicate: biolink:located_in object: GO:0016020 # membrane category: biolink:GeneToGoTermAssociation knowledge_level: prediction agent_type: automated_agent publications: ["PMID:14611657"] entity to disease association: description: >- An association between any entity and a disease, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases. is_a: association exact_mappings: slots: - clinical approval status - max research phase - FDA regulatory approvals - number of cases defining_slots: - subject - object examples: - object: subject: CHEBI:50681 # methotrexate(2-) predicate: biolink:in_clinical_trials_for object: MONDO:0971091 # acute megakaryoblastic leukemia in adult category: biolink:EntityToDiseaseAssociation knowledge_level: knowledge_assertion agent_type: manual_agent - object: subject: CHEBI:9150 # simvastatin predicate: biolink:treats object: UMLS:C0520863 # Diastolic dysfunction category: biolink:EntityToDiseaseAssociation knowledge_level: knowledge_assertion agent_type: manual_agent - object: subject: CHEBI:28077 # rifampicin predicate: biolink:applied_to_treat object: MONDO:0005011 # Crohn disease category: biolink:EntityToDiseaseAssociation knowledge_level: observation agent_type: manual_validation_of_automated_agent - object: subject: RXCUI:1367436 # 21 DAY ethinyl estradiol 0.000625 MG/HR / etonogestrel 0.005 MG/HR Vaginal System predicate: biolink:contraindicated_in object: MONDO:0004981 # atrial fibrillation category: biolink:EntityToDiseaseAssociation knowledge_level: knowledge_assertion agent_type: manual_validation_of_automated_agent publications: ["a280f164-2833-4f37-96e3-a857c91f77f2"] entity to phenotypic feature association: description: >- An association between any entity and a phenotypic feature, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases. is_a: association exact_mappings: slots: - clinical approval status - max research phase - FDA regulatory approvals - number of cases defining_slots: - subject - object examples: - object: subject: GTOPDB:13663 # ponsegromab predicate: biolink:in_clinical_trials_for object: NCIT:C146753 # Fatigue, CTCAE 5.0 category: biolink:EntityToPhenotypicFeatureAssociation knowledge_level: knowledge_assertion agent_type: manual_agent - object: subject: CHEBI:6339 # etoricoxib predicate: biolink:treats object: HP:0001822 # Hallux valgus category: biolink:EntityToPhenotypicFeatureAssociation knowledge_level: knowledge_assertion agent_type: manual_agent - object: subject: CHEBI:78538 # tafamidis predicate: biolink:applied_to_treat object: MONDO:0005294 # peripheral vascular disease category: biolink:EntityToPhenotypicFeatureAssociation knowledge_level: observation agent_type: manual_validation_of_automated_agent - object: subject: RXCUI:617430 # amoxicillin 80 MG/ML / clavulanate 11.4 MG/ML Oral Suspension predicate: biolink:contraindicated_in object: HP:0001410 # Decreased liver function category: biolink:EntityToPhenotypicFeatureAssociation knowledge_level: knowledge_assertion agent_type: manual_validation_of_automated_agent publications: - "2970fe7e-9e1f-47aa-85ad-663ee15c7e06" - "a5fa252a-d39e-4099-a230-b665fbb97a80" - "b897c800-24a2-4e76-8668-498c5515c3d0" - "babf3b8d-f2ce-407d-9407-728c45eb19ee" - "d74e93e5-11c9-434e-a60c-4a4f911dd0f8" ## ----------------- ## 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 description: >- An abstract parent class for associations between two anatomical entities, such as part-of, develops-from, or other mereological and ontogenic relationships. is_a: association abstract: true defining_slots: - subject - object slot_usage: subject: range: anatomical entity object: range: anatomical entity anatomical entity has part anatomical entity 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, that is, the subject is has the object entity as a part (the expected predicate is "biolink:has_part" or suitable predicate slots inheriting from it, i.e., "biolink:has_plasma_membrane_part", "biolink:has_variant_part", etc.). This includes relationships between cells and cellular components, between issues and cells, whole organisms and tissues. defining_slots: - predicate slot_usage: subject: range: anatomical entity description: >- the whole object: range: anatomical entity description: >- the part predicate: subproperty_of: has part anatomical entity part of anatomical entity 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, that is, the subject is a part of the object entity (the expected predicate is "biolink:part_of" or suitable predicate slots inheriting from it, i.e., "biolink:plasma_membrane_part_of", "biolink:variant_part_of", etc.). 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 chemical entity to anatomical entity association: is_a: association description: >- An association between a chemical entity (other than 'gene or gene product or gene family', for example, a metabolite) and an anatomical entity, such as a tissue or subcellular location. defining_slots: - subject - object slot_usage: subject: range: chemical entity object: range: anatomical entity gene or gene product or gene family to anatomical entity association: is_a: association description: >- An association between a gene or gene product or gene family and an anatomical entity. defining_slots: - subject - object slot_usage: subject: range: gene or gene product or gene family object: range: anatomical entity biological process or activity to anatomical entity association: is_a: association description: >- An association between a biological process or activity and an anatomical entity. defining_slots: - subject - object slot_usage: subject: range: biological process or activity object: range: anatomical entity 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: description: >- An abstract association between an organism taxon and an environmental context (e.g., a habitat, biome, or ecological setting) in which the taxon occurs. 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: BinaryRelationEnum: description: >- Mathematical binary relation qualifiers of a value in its context. permissible_values: less_than: equal_to: greater_than: ResponseEnum: description: >- A response to a treatment or intervention permissible_values: therapeutic_response: description: >- A positive response to a treatment or intervention negative: description: >- A negative response to a treatment or intervention ResponseTargetEnum: description: >- The target of a treatment or intervention permissible_values: cohort: description: >- A group of individuals that are the target of a treatment or intervention cell line: description: >- A cell line that is the target of a treatment or intervention individual: description: >- An individual that is the target of a treatment or intervention sample: description: >- A biological materialsample that is the target of a treatment or intervention ClinicalTrialStatusEnum: description: > Enumeration of clinical trial statuses indicating the recruitment state, availability, or regulatory status of a clinical study or intervention. permissible_values: ACTIVE_NOT_RECRUITING: description: The study is ongoing but not currently recruiting participants. APPROVED_FOR_MARKETING: description: The intervention has received regulatory approval for marketing. AVAILABLE: description: The intervention or data is available for use or distribution. COMPLETED: description: The study has ended normally and participants are no longer being examined or treated. ENROLLING_BY_INVITATION: description: Participants are being enrolled by invitation only. NO_LONGER_AVAILABLE: description: The intervention or data is no longer available. NOT_YET_RECRUITING: description: The study has not yet started recruiting participants. RECRUITING: description: The study is currently recruiting participants. SUSPENDED: description: The study has been temporarily halted but may resume. TEMPORARILY_NOT_AVAILABLE: description: The intervention or data is not currently available but may become available later. TERMINATED: description: The study has stopped prematurely and will not start again. UNKNOWN: description: The recruitment or availability status is unknown. WITHDRAWN: description: The study was halted before enrolling its first participant. ClinicalTrialAgeStageEnum: description: >- Enumeration of age stages or populations commonly used in clinical trials to categorize participant demographics and target populations. permissible_values: adult: child: older_adult: ApprovalStatusEnum: description: >- An enumeration of regulatory and development milestones for a drug or therapeutic, spanning discovery, preclinical research, FDA clinical trial phases (1-4), special review designations (e.g., fast track, breakthrough therapy, priority review), regular FDA approval, and post-approval withdrawal. permissible_values: "discovery_and_development_phase": description: >- Discovery & Development 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": description: >- 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. "fda_clinical_research_phase": description: >- Clinical Research Phase. 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. "fda_review_phase_4": description: >- FDA Review "fda_post_market_safety_review": description: >- FDA Post-Market Safety Monitoring. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations. "fda_clinical_research_phase_1": description: >- In the FDA Clinical Research Phase, the Clinical Research 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. "fda_clinical_research_phase_2": description: >- In the FDA Clinical Research Phase, the Clinical Research 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. "fda_clinical_research_phase_3": description: >- In the FDA Clinical Research Phase, the Clinical Research 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. "fda_clinical_research_phase_4": description: >- In the FDA Clinical Research Phase, the Clinical Research 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. "fda_fast_track": description: >- Fast track is a process designed to facilitate the development, and expedite the review of drugs to treat serious conditions and fill an unmet medical need. The purpose is to get important new drugs to the patient earlier. Fast Track addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track "fda_breakthrough_therapy": description: >- Breakthrough Therapy designation is a process designed to expedite the development and review of drugs that are intended to treat a serious condition and preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over available therapy on a clinically significant endpoint(s). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy "fda_accelerated_approval": description: >- When studying a new drug, it can sometimes take many years to learn whether a drug actually provides a real effect on how a patient survives, feels, or functions. A positive therapeutic effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”. Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint. Using a surrogate endpoint enabled the FDA to approve these drugs faster. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval "fda_priority_review": description: >- Prior to approval, each drug marketed in the United States must go through a detailed FDA review process. In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving the drug review time and created a two-tiered system of review times – Standard Review and Priority Review. A Priority Review designation means FDA’s goal is to take action on an application within 6 months (compared to 10 months under standard review). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review "regular_fda_approval": description: >- Regular FDA Approval. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations. "post_approval_withdrawal": ClinicalApprovalStatusEnum: description: >- An enumeration describing whether a chemical or therapy is approved for use in treating a specific condition (e.g., FDA-approved for a condition, not approved, off-label use, or withdrawn following approval). 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: ResearchPhaseEnum: description: >- An enumeration of research phases describing the stage of investigation for a drug or therapy, spanning preclinical research through clinical trial phases 1 through 4 (including phase 1/2 and phase 2/3 combinations). 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_1_to_2: is_a: clinical_trial_phase description: >- A study that tests the safety, side effects, and best dose of a new treatment. Phase I/II clinical trials also test how well a certain type of cancer or other disease responds to a new treatment. In the phase II part of the clinical trial, patients usually receive the highest dose of treatment that did not cause harmful side effects in the phase I part of the clinical trial. Combining phases I and II may allow research questions to be answered more quickly or with fewer patients. Also called phase 1/phase 2 clinical trial. see_also: - https://www.cancer.gov/publications/dictionaries/cancer-terms/def/phase-i-ii-clinical-trial 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_2_to_3: is_a: clinical_trial_phase description: >- A study that tests how well a new treatment works for a certain type of cancer or other disease and compares the new treatment with a standard treatment. Phase II/III clinical trials may also provide more information about the safety and side effects of the new treatment. Combining phases II and III may allow research questions to be answered more quickly or with fewer patients. Also called phase 2/phase 3 clinical trial. see_also: - https://www.cancer.gov/publications/dictionaries/cancer-terms/def/phase-ii-iii-clinical-trial 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: description: >- An enumeration of values that qualify a change or effect by its direction, i.e., whether the referenced quantity or activity is increased (including up-regulated) or decreased (including down-regulated). 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: description: >- An enumeration of relationships by which one chemical entity is derived from another, e.g., a metabolite produced from a parent compound. permissible_values: metabolite: ChemicalOrGeneOrGeneProductFormOrVariantEnum: description: >- An enumeration used as a qualifier to indicate a specific form or variant of a chemical, gene, or gene product involved in an association (e.g., modified form, loss-of-function variant, gain-of-function variant, dominant-negative variant, polymorphic form, SNP form, mutant form, or analog form). permissible_values: genetic_variant_form: is_a: modified_form modified_form: loss_of_function_variant_form: is_a: genetic_variant_form non_loss_of_function_variant_form: is_a: genetic_variant_form gain_of_function_variant_form: is_a: non_loss_of_function_variant_form dominant_negative_variant_form: is_a: non_loss_of_function_variant_form polymorphic_form: is_a: genetic_variant_form snp_form: is_a: polymorphic_form mutant_form: is_a: genetic_variant_form analog_form: is_a: modified_form GeneOrGeneProductOrChemicalPartQualifierEnum: description: >- An enumeration used as a qualifier to indicate a particular structural or functional part of a gene, gene product, or chemical (e.g., 3' UTR, 5' UTR, poly-A tail, promoter, enhancer, exon, or intron). permissible_values: 3_prime_utr: 5_prime_utr: polya_tail: promoter: enhancer: exon: intron: GeneOrGeneProductOrChemicalEntityAspectEnum: description: >- An enumeration used as a qualifier to indicate the specific aspect of a gene, gene product, or chemical entity that is affected or measured in an association. Values cover activity and abundance (expression, synthesis, degradation, stability, localization, transport), molecular interactions, and a wide range of molecular modifications such as phosphorylation, methylation, acetylation, ubiquitination, and other post-translational or chemical modifications. 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: hydrolysis: is_a: cleavage metabolic_processing: mutation_rate: stability: folding: localization: transport: absorption: aggregation: interaction: release: isomerization: secretion: is_a: transport uptake: is_a: transport splicing: molecular_interaction: guanyl_nucleotide_exchange: is_a: molecular_interaction adenyl_nucleotide_exchange: is_a: 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 EffectTypeEnum: description: >- An enumeration of statistical metrics and estimators used to quantify the magnitude and direction of an effect or association between the subject and object of an edge. The numeric result is stored in the companion 'effect size' slot. permissible_values: # --- Regression / omics coefficients --- regression_coefficient: description: >- The coefficient of an independent variable in a regression model, representing the expected change in the dependent variable per unit change in the predictor. Commonly reported as a beta coefficient in eQTL, pQTL, mQTL, and GWAS analyses. close_mappings: - STATO:0000565 log2_fold_change: description: >- The base-2 logarithm of the ratio of a quantity (e.g. gene expression, protein abundance, metabolite concentration) between two conditions. The standard effect size in differential expression and differential abundance analyses across transcriptomics, proteomics, and metabolomics. close_mappings: - STATO:0000169 # --- Mendelian randomization estimators --- wald_ratio: description: >- A single-variant Mendelian randomization estimator computed as the ratio of the genetic variant-outcome association to the genetic variant-exposure association. inverse_variance_weighted: description: >- A Mendelian randomization estimator that combines per-variant Wald ratios using inverse-variance weighting, assuming all instruments are valid (no horizontal pleiotropy). mr_egger: description: >- A Mendelian randomization estimator based on Egger regression that allows for directional horizontal pleiotropy by fitting an intercept term; a non-zero intercept indicates pleiotropic bias. weighted_median: description: >- A robust Mendelian randomization estimator that provides a consistent causal estimate when at least 50% of the instrument weight comes from valid variants. # --- Standardized mean differences --- standardized_mean_difference: description: >- The difference between two group means divided by a pooled standard deviation, used when the predictor is categorical and the outcome is continuous. close_mappings: - STATO:0000100 cohens_d: is_a: standardized_mean_difference description: >- A standardized mean difference using the square root of the average of the two group variances as the denominator, with a small-sample correction for n < 50. close_mappings: - STATO:0000618 hedges_g: is_a: standardized_mean_difference description: >- A standardized mean difference with a Gamma-function correction on the pooled standard deviation to reduce small-sample bias. close_mappings: - STATO:0000319 glasss_delta: is_a: standardized_mean_difference description: >- A standardized mean difference using only the control group's standard deviation as the denominator, preferred when group variances differ substantially. close_mappings: - STATO:0000320 strictly_standardized_mean_difference: is_a: standardized_mean_difference description: >- The ratio of the mean difference to the standard deviation of the difference between two groups (SSMD), widely used in high-content screening for hit selection and quality control. close_mappings: - STATO:0000135 # --- Correlation coefficients --- correlation_coefficient: description: >- A normalized measure of association between two variables, ranging from -1 to +1, computed as covariance divided by the product of standard deviations. close_mappings: - STATO:0000142 pearsons_r: is_a: correlation_coefficient description: >- A parametric correlation coefficient for two continuous, normally distributed variables with a linear relationship. close_mappings: - STATO:0000280 spearmans_rho: is_a: correlation_coefficient description: >- A nonparametric rank correlation coefficient measuring monotonic dependence between two variables. close_mappings: - STATO:0000201 kendalls_tau: is_a: correlation_coefficient description: >- A rank correlation coefficient based on concordant and discordant pairs, suitable for ordinal data. close_mappings: - STATO:0000240 polychoric_correlation: is_a: correlation_coefficient description: >- A correlation coefficient estimating the association between two latent continuous variables from observed ordinal data. close_mappings: - STATO:0000269 matthews_correlation_coefficient: is_a: correlation_coefficient description: >- A correlation-based measure of binary classification quality (also known as the phi coefficient), ranging from -1 to +1. close_mappings: - STATO:0000524 goodman_kruskal_gamma: is_a: correlation_coefficient description: >- A rank correlation measure for ordinal or continuous variables based on the difference between concordant and discordant pairs, excluding ties. close_mappings: - STATO:0000612 r2_linkage_disequilibrium: is_a: correlation_coefficient description: >- A squared correlation coefficient over two dichotomous variables used as a measure of linkage disequilibrium. close_mappings: - STATO:0000123 # --- Risk / ratio measures --- odds_ratio: description: >- The ratio of the odds of an outcome in an exposed group to the odds in an unexposed group, measuring association strength between two binary variables. close_mappings: - STATO:0000182 relative_risk: description: >- The ratio of event probability in an exposed group to event probability in an unexposed group (also called risk ratio). close_mappings: - STATO:0000245 hazard_ratio: description: >- The ratio of hazard rates between two groups over time, commonly reported in survival analysis and time-to-event omics studies. close_mappings: - STATO:0000677 # --- Variance-explained measures --- eta_squared: description: >- The proportion of total variance in the dependent variable attributable to a predictor in the sample (a biased estimator analogous to R-squared). close_mappings: - STATO:0000317 omega_squared: description: >- A less biased estimator of the proportion of variance explained by a predictor, providing a better population-level estimate than eta-squared. close_mappings: - STATO:0000318 root_mean_square_standardized_effect: description: >- The square root of the average of squared standardized effects in an analysis of variance context (RMSSE, Psi). close_mappings: - STATO:0000316 StatisticalSignificanceQualifierEnum: description: >- An enumeration used as a qualifier to categorize the statistical significance of an association's supporting evidence into coarse bands (e.g., very strongly significant, strongly significant, significant, suggestive, not significant), conventionally anchored to alpha = 0.05. The underlying numeric value lives in the 'p value' and 'adjusted p value' slots, which remain authoritative. permissible_values: very_strongly_significant: description: >- A significance band denoting that the association meets the most stringent conventional threshold (significance statistic at or below 0.001), such that, under the null hypothesis of no association, an effect at least this large would be expected in no more than about one in a thousand comparable studies. strongly_significant: description: >- A significance band denoting that the association meets a stringent conventional threshold (significance statistic at or below 0.01). significant: description: >- A significance band denoting that the association meets the standard conventional threshold (significance statistic at or below alpha = 0.05), such that, under the null hypothesis, an effect at least this large would be expected in no more than about one in twenty comparable studies. suggestive: description: >- A significance band denoting a borderline result (significance statistic above 0.05 but at or below roughly 0.10, sometimes extended to 0.20 in fields such as genetics) that is suggestive of, but does not conclusively support, an association. not_significant: description: >- A significance band denoting that the association does not meet the conventional threshold (significance statistic above 0.05), such that there is insufficient evidence to rule out the null hypothesis of no association. CausalMechanismQualifierEnum: description: >- An enumeration used as a qualifier to specify the causal or pharmacologic mechanism by which an effect is exerted in an association (e.g., agonism, antagonism, inverse agonism, allosteric modulation, activation, inhibition, and their competitive or partial variants). permissible_values: modulation: description: >- A causal mechanism that effects the normal functioning of a protein in some way e.g., mixed agonist/antagonist or unclear whether action is positive or negative allosteric_modulation: is_a: modulation description: >- A modulation mechanism that occurs when a chemical exerts an effect on a protein targets via a different binding site than the natural ('orthosteric') ligand site. mixed_allosteric_modulation: is_a: allosteric_modulation description: >- An allosteric modulation mechanism that occurs when a chemical may exert an activating effect or an inhibitory effect in different conditions / contexts (e.g. concentration, receptor conformational state, signaling pathway context, receptor subtype, cellular environment). biphasic_allosteric_modulation: is_a: mixed_allosteric_modulation description: >- A mixed allosteric modulation mechanism that occurs when a chemical exerts an activating effect at lower concentrations, and an inhibitory effect at higher concentrations. mixed_agonism: is_a: modulation description: >- An modulation mechanism in which the effector acts as both an agonist (activating a receptor) and an antagonist (blocking a receptor) at different receptor sites. positive_modulation: is_a: modulation description: >- A modulation mechanism that positively effects the normal functioning of a target by increasing or enhancing its activity or abundance, or its sensitivity to other factors that do so. potentiation: is_a: positive_modulation description: >- A positive modulation mechanism in which the effector binds to and enhances or intensifies the effect of some other chemical or drug on its target. induction: is_a: positive_modulation description: >- A positive modulation 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 cofactor: is_a: positive_modulation description: >- A positive modulation mechanism in which the effector (usually some non-protein chemical compound or metallic ion) is required for a target enzyme's biological/catalytic activity. activation: is_a: positive_modulation description: >- A positive modulation mechanism in which the effector binds to and positively affects the normal functioning of its target. close_mappings: - CHEMBL.MECHANISM:activator - DGIdb:activator positive_allosteric_modulation: is_a: activation description: >- A positive modulation 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 agonism: is_a: activation description: >- An activation 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 partial_agonism: is_a: agonism description: >- An agonism mechanism in which the effector binds to and only partially activates a receptor (relative to the response to a full agonist) biased_agonism: is_a: agonism description: >- An agonism mechanism in which the effector binds to a receptor and activates certain signaling pathways while ignoring others, allowing it to produce a desired effect without unwanted side effects. antibody_agonism: is_a: agonism description: >- An agonism mechanism in which the effector is an antobody that binds and activates a receptor to mimic the effect of an endogenous ligand. molecular_channel_opening: is_a: activation description: >- An activation mechanism in which the effector binds to a molecular channel and facilitates transport of ions through it. close_mappings: - CHEMBL.MECHANISM:opener stimulation: is_a: activation description: >- An activation mechanism in which the effector directly or indirectly affects its target, stimulating a physiological response. close_mappings: - DGIdb:stimulator - SEMMEDDB:STIMULATES - DGIdb:stimulator guanyl_nucleotide_exchange: is_a: activation description: >- An activation mechanism in which the effector catalyzes the exchange of guanosine diphosphate (GDP) for guanosine triphosphate (GTP) in a guanine nucleotide-binding protein (G-protein). negative_modulation: is_a: modulation description: >- A modulation mechanism that negatively effects the normal functioning of a target by decreasing or impeding its activity or abundance, or its sensitivity to other factors that do so. narrow_mappings: - DGIdb:negative_modulator negative_gene_editing_modulation: is_a: negative_modulation description: >- A negative modulation mechanism in which the effector elicits the negative modulation of its target through a gene editing activity. gtpase_activation: is_a: negative_modulation description: >- An activation mechanism in which the effector accelerates the intrinsic GTPase activity of a G-protein, promoting the conversion of the active, GTP-bound form to the inactive, GDP-bound form, thereby terminating a signaling event. Note that this is a negative modulation mechanism because the target is the G-protein whose activity is attenuated through gtpase activation. atpase_activation: is_a: negative_modulation description: >- An activation mechanism in which the effector accelerates the intrinsic ATPase activity of a target protein, promoting the conversion of the active, ATP-bound form to the inactive, ADP-bound form, thereby terminating a signaling event. Note that this is a negative modulation mechanism because the target is the protein whose activity is attenuated through atpase activation. antisense_oligonucleotide_inhibition: is_a: negative_modulation description: >- A negative modulation mechanism in which an antisense oligonucleotide effector prevents translation of a complementary mRNA sequence through binding and targeting it for degradation. Note that while this is called "inhibition', it is not inhibition in the classic biochemical sense that requires a direct interaction between effector and target. rna_interference_inhibition: is_a: negative_modulation description: >- A negative modulation mechanism in which an effector small interfering RNA (siRNA) molecule finds and destroys messenger RNA (mRNA) with a complementary sequence, preventing a specific gene from being translated into a protein. Note that while this is called "inhibition', it is not inhibition in the classic biochemical sense that requires a direct interaction between effector and target. suppression: is_a: negative_modulation description: >- A negative modulation mechanism in which the effector directly or indirectly affects its target, suppressing a physiological process. feedback_inhibition: is_a: negative_modulation description: >- An negative modulation mechanism in which the end product of a metabolic pathway inhibits an enzyme early in that same pathway, which stops the production of the final product when it's no longer needed. inhibition: is_a: negative_modulation description: >- A negative modulation 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: >- An inhibition mechanism in which an antibody effector specifically binds to and interferes with the target. antagonism: is_a: inhibition description: >- An inhibition 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 allosteric_antagonism: is_a: antagonism description: >- An inhibition mechanism in which the effector binds to a receptor at an allosteric site and prevents activation by a positive allosteric modulator at that site. non_competitive_antagonism: is_a: antagonism description: >- An inhibition mechanism in which the effector binds a site distinct from the agonist's binding site (non-orthosteric), or irreversibly/insurmountably inactivates the receptor - reduces the receptor’s maximal response (Emax) in a way that cannot be overcome by adding more agonist. competitive_inhibition: is_a: inhibition description: >- An inhibition mechanism in which the effector binds to a target molecule (such as an enzyme) and prevents the binding of a substrate (or another binding partner) and vice versa. noncompetitive_inhibition: is_a: inhibition description: >- An inhibition mechanism in which the effector binds to a target molecule (such as an enzyme) at a site other than the active site, in a way that reduces the activity of the target. negative_allosteric_modulation: is_a: noncompetitive_inhibition description: >- A noncompetitive inhibition 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, and causing a conformational change that affects ligand binding. close_mappings: - CHEMBL.MECHANISM:negative_allosteric_modulator - DGIdb:inhibitory_allosteric_modulator gating_inhibition: is_a: inhibition description: >- An inhibition mechanism mediated by the transition of ion channels between their open (conducting) and closed (non-conducting) conformational states. irreversible_inhibition: is_a: inhibition description: >- An inhibition mechanism in which an effector permanently binds to a target, permanently disrupting its activity. molecular_channel_blockage: is_a: inhibition description: >- An inhibition 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: >- An inhibition 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 binding: is_a: modulation description: >- A modulation mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction (typically non-covalent). covalent_binding: is_a: modulation description: >- A modulation mechanism mediated by a direct covalent binding interaction between effector and target chemical or biomolecular entity. adduction: is_a: covalent_binding description: >- A covalent binding mechanism in which a drug-protein adduct forms by the covalent binding of electrophilic drugs or their reactive metabolite(s) to a target protein. crosslinking: is_a: covalent_binding description: >- A covalent binding mechanism in which an effector induces cross-linking of target proteins or nucleic acids - covalently joining them into a rigid structure. transglutamination: is_a: covalent_binding description: >- A covalent binding mechanism involving formation of a covalent bond between a glutamine residue and an amine as catalyzed by a transglutaminase. disuphide_binding: is_a: covalent_binding description: >- A covalent binding mechanism involving a covalent bond formed between two cysteine residues in or between proteins. stabilization: is_a: modulation description: >- A modulation mechanism in which the effector increases the conformational stability of a protein or complex. close_mappings: - CHEMBL.MECHANISM:stabiliser chaperone_mediated_stabilization: is_a: stabilization description: >- destabilization: is_a: modulation description: >- A modulation mechanism in which a chaperone molecule directly binds to a partially folded biosynthetic intermediate to stabilize the protein and allow it to complete the folding process to yield a functional protein. degradation: is_a: modulation description: >- A modulation mechanism that controls protein and cellular component levels through the regulated breakdown and recycling of molecules. cleavage: is_a: modulation description: >- A modulation mechanism in which an effector promotes degeneration of the target protein through cleaving of the peptide bonds. hydrolysis: is_a: modulation description: >- A modulation mechanism in which an effector cleaves its target through a chemical reaction where a molecule of water is used to break a bond. disruption: is_a: modulation description: >- A modulation mechanism in which an effector destabilizes or disrupts a protein complex, macromolecular assembly, cell membrane etc. opening: is_a: modulation description: >- A modulation mechanism in which an effector positively effects the normal functioning of an ion channel e.g., facilitates transport of ions through the channel. multitarget_modulation: is_a: modulation description: >- A modulation mechanism in which an effector achieves a physiological effect through simultaneous interaction with multiple gene targets. chelation: is_a: modulation description: >- A modulation mechanism in which an effector binds to a metal ion target, reducing its availability/reactivity for further interactions. release: is_a: modulation description: >- A modulation mechanism in which an effector reverses the normal functioning of a transporter, causing release of the substrate, rather than uptake close_mappings: - CHEMBL:MECHANISM:releasing_agent sequestration: is_a: modulation description: >- A modulation mechanism in which an effector binds to a substance such as a drug, toxin or metabolite and reduces its availability for further interactions. oxidoreduction: is_a: modulation description: >- A modulation mechanism in which in which electrons are transferred between molecules catalyzed by an oxidoreductase enzyme. exogenous_protein: is_a: modulation description: >- A modulation mechanism in which a protein from an exogenous source acts as a substitute or supplement for a specific protein which is absent or has reduced function in an affected target/subject. exogenous_gene: is_a: modulation description: >- A modulation mechanism in which a nucleic acid from an exogenous source acts as a substitute or supplement for a specific gene which is absent or has reduced function in an affected target/subject. transcriptional_regulation: is_a: modulation description: >- A modulation mechanism mediated by through the control of target gene transcription. translational_regulation: is_a: modulation description: >- A modulation mechanism mediated by through the control of target gene translation. catalytic_activity: is_a: modulation description: >- A modulation mechanism mediated by through the catalytic activity of the effector on the target. chemical_modification: is_a: modulation description: >- A modulation mechanism mediated by a protein/complex effector altering a small molecule by modifying it or converting it to something else. relocalization: is_a: modulation description: >- A modulation mechanism mediated by an effector that alters the localization of a target in the cell or body. isomerization: is_a: modulation description: >- A modulation mechanism mediated by an effector that alters the isomeric conformation of a target. signaling_mediated_control: is_a: modulation description: >- A modulation 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.). immune_system_modulation: is_a: modulation description: >- A modulation mechanism in which the actions of the effector on the immune system ultimately mediate the affects a target. vaccine_antigen: is_a: immune_system_modulation description: >- An immune system modulation mechanism in which a vaccine mediates its effect through the activation of the immune system against the target. post_transcriptional_regulation: is_a: modulation description: >- A modulation mechanism which controls expression of a target gene at the RNA level after a gene has been transcribed into messenger RNA (mRNA). molecular_modification: is_a: modulation description: >- A modulation mechanism through which an effect is mediated by the modification of a target, through addition of chemical moieties such phosphate groups, ubiquitin, lipids, etc., which alter its activity or cellular behavior. phosphorylation: is_a: molecular_modification dephosphorylation: is_a: molecular_modification neddylation: is_a: molecular_modification deneddylation: is_a: molecular_modification lipidation: is_a: molecular_modification palmitoylation: is_a: lipidation myristoylation: is_a: lipidation tyrosination: is_a: molecular_modification carboxylation: is_a: molecular_modification ubiquitination: is_a: molecular_modification monoubiquitination: is_a: ubiquitination polyubiquitination: is_a: ubiquitination deubiquitination: is_a: molecular_modification sulfation: is_a: molecular_modification reduction: is_a: molecular_modification description: >- A molecular modification mechanism in which an effector modifies a target substrate via a reduction reaction. oxidation: is_a: molecular_modification description: >- A molecular modification mechanism in which an effector modifies a target substrate via an oxidation reaction. acetylation: is_a: molecular_modification deacetylation: is_a: molecular_modification glycosylation: is_a: molecular_modification deglycosylation: is_a: molecular_modification methylation: is_a: molecular_modification trimethylation: is_a: methylation demethylation: is_a: molecular_modification sumoylation: is_a: molecular_modification desumoylation: is_a: molecular_modification ADP-ribosylation: is_a: molecular_modification de-ADP-ribosylation: is_a: molecular_modification ampylation: is_a: molecular_modification description: >- A molecular modification involving the addition of an adenylyl (AMP) moiety to a substrate protein residue. hydroxylation: is_a: molecular_modification s_nitrosylation: is_a: molecular_modification LogicalInterpretationEnum: description: >- An enumeration of logical interpretations that can be applied to a triple to indicate whether the relation should be read as existential on both sides (some-some), universal-existential (all-some), or its inverse (inverse all-some). 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: description: >- An enumeration of possible directions for a biochemical reaction, indicating whether it proceeds left-to-right, right-to-left, is bidirectional (reversible), or has no net direction. permissible_values: left_to_right: right_to_left: bidirectional: neutral: ReactionSideEnum: description: >- An enumeration indicating on which side of a biochemical reaction a participant appears - the left-hand (reactant/substrate) side or the right-hand (product) side, as written. 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: description: >- An enumeration of druggability categories for gene targets as defined by the IDG (Illuminating the Druggable Genome) / Pharos target development level classification: Tclin (targets of approved drugs), Tchem (targets with potent bioactives), Tbio (targets with biological knowledge), and Tdark (poorly characterized targets). 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 the 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: >- An enumeration describing how a drug or chemical entity may be obtained, distinguishing products that are available over the counter from those that require a prescription. 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: description: >- An enumeration of routes by which a drug is administered or delivered to a patient, including inhalation, oral, transdermal absorption, and various forms of injection (intravenous, subcutaneous, intramuscular). permissible_values: inhalation: oral: absorption_through_the_skin: injection: intravenous_injection: is_a: injection subcutaneous_injection: is_a: injection intramuscular_injection: is_a: 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: description: >- An enumeration of agent types responsible for generating a statement of knowledge, as defined by the Translator Knowledge Level / Agent Type (KL/AT) standard. Values distinguish human (manual) agents from automated agents (including data analysis pipelines, computational models, text-mining agents, image-processing agents) and mixed cases such as manual validation of automated output. 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: description: >- An enumeration characterizing the type of knowledge expressed in a statement and the kind of evidence and reasoning that supports it, as defined by the Translator Knowledge Level / Agent Type (KL/AT) standard. Values include knowledge assertion, logical entailment, prediction, statistical association, text co-occurrence, direct observation, and not-provided. 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. text_co_occurrence: description: >- A statement reporting that mentions of two concepts in some corpus of text (e.g. the biomedical literature) occur together at a statistically significant frequency - suggesting that a real-world biological or clinical relationship may exist between the concepts. notes: - >- Such statements often utilize NLP/text-mining to identify concept mentions in text, but the reported statement is generated by a data analysis pipeline that performs calculations on mention counts and determines the strength of their correlation. 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 GeneToPhenotypicFeaturePredicateEnum: description: >- Enumeration of predicates permissible for use in gene to phenotypic feature associations. This constrains the relationship types that can be used between genes and phenotypic features. permissible_values: "biolink:causes": "biolink:contributes_to": "biolink:associated_with": "biolink:has_phenotype": GeneToDiseasePredicateEnum: description: >- Enumeration of predicates permissible for use in gene to disease associations. This constrains the relationship types that can be used between genes and diseases. permissible_values: "biolink:contributes_to": "biolink:associated_with": "biolink:affects": AssociationBasisEnum: description: >- Permissible values for the 'association basis qualifier', indicating the nature or basis of an association asserted using the 'associated with' predicate or one of its subpredicates. permissible_values: statistical: description: >- An association based on statistical dependence (i.e., non-independence), derived from analysis of observational or experimental data using an appropriate statistical method. functional: description: >- An association based on the participation of two biological entities in a common biological function, process, pathway, reaction, molecular complex, interaction, gene expression program, or other functional system. Functionally associated entities need not interact directly or contribute in the same direction to the shared function; they are related by their involvement in the same biological phenomenon. genetic: description: >- An association based on the relationship of two biological entities through inherited genetic variation. Examples include associations between genetic variants and phenotypes, diseases, traits, gene expression levels, protein abundance, or other molecular or organismal phenotypes. Such associations do not necessarily imply causation or direct biological function and are typically identified through genetic association studies, including genome-wide association studies (GWAS), phenome-wide association studies (PheWAS), and quantitative trait locus (QTL) mapping (e.g., eQTL and pQTL analyses). in_subset: - translator_minimal