@biothings-explorer/query_graph_handler

{ "id": "https://w3id.org/biolink/biolink-model", "name": "Biolink-Model", "description": "Entity and association taxonomy and datamodel for life-sciences data", "license": "https://creativecommons.org/publicdomain/zero/1.0/", "version": "2.1.0", "prefixes": { "Aeolus": "http://translator.ncats.nih.gov/Aeolus_", "alliancegenome": "https://www.alliancegenome.org/", "apollo": "https://github.com/GMOD/Apollo", "biolink": "https://w3id.org/biolink/vocab/", "linkml": "https://w3id.org/linkml/", "CAID": "http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=", "CHADO": "http://gmod.org/wiki/Chado/", "ChemBank": "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=", "chembio": "http://translator.ncats.nih.gov/chembio_", "CHEMBL.MECHANISM": "https://www.ebi.ac.uk/chembl/mechanism/inspect/", "CID": "http://pubchem.ncbi.nlm.nih.gov/compound/", "COAR_RESOURCE": "http://purl.org/coar/resource_type/", "CPT": "https://www.ama-assn.org/practice-management/cpt/", "CTD": "http://translator.ncats.nih.gov/CTD_", "DGIdb": "https://www.dgidb.org/interaction_types", "dcat": "http://www.w3.org/ns/dcat#", "dct": "http://purl.org/dc/terms/", "doi": "https://doi.org/", "DrugCentral": "http://translator.ncats.nih.gov/DrugCentral_", "ECTO": "http://purl.obolibrary.org/obo/ECTO_", "EDAM-DATA": "http://edamontology.org/data_", "EDAM-FORMAT": "http://edamontology.org/format_", "EDAM-OPERATION": "http://edamontology.org/operation_", "EDAM-TOPIC": "http://edamontology.org/topic_", "EFO": "http://www.ebi.ac.uk/efo/EFO_", "ExO": "http://purl.obolibrary.org/obo/ExO_", "fabio": "http://purl.org/spar/fabio/", "foaf": "http://xmlns.com/foaf/0.1/", "foodb.compound": "http://foodb.ca/compounds/", "GAMMA": "http://translator.renci.org/GAMMA_", "gff3": "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#", "GOREL": "http://purl.obolibrary.org/obo/GOREL_", "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/", "hetio": "http://translator.ncats.nih.gov/hetio_", "HsapDv": "http://purl.obolibrary.org/obo/HsapDv_", "ICD0": "http://translator.ncats.nih.gov/ICD0_", "ICD10": "http://translator.ncats.nih.gov/ICD10_", "ICD9": "http://translator.ncats.nih.gov/ICD9_", "interpro": "https://www.ebi.ac.uk/interpro/entry/", "INO": "http://purl.obolibrary.org/obo/INO_", "isbn": "https://www.isbn-international.org/identifier/", "isni": "https://isni.org/isni/", "issn": "https://portal.issn.org/resource/ISSN/", "KEGG.BRITE": "http://www.kegg.jp/entry/", "KEGG.DGROUP": "http://www.kegg.jp/entry/", "KEGG.ENZYME": "http://www.kegg.jp/entry/", "KEGG.GENE": "http://www.kegg.jp/entry/", "KEGG.RCLASS": "http://www.kegg.jp/entry/", "LOINC": "http://loinc.org/rdf/", "medgen": "https://www.ncbi.nlm.nih.gov/medgen/", "MetaCyc": "http://translator.ncats.nih.gov/MetaCyc_", "MI": "http://purl.obolibrary.org/obo/MI_", "MSigDB": "https://www.gsea-msigdb.org/gsea/msigdb/", "NCBIGene": "http://identifiers.org/ncbigene/", "NDDF": "http://purl.bioontology.org/ontology/NDDF/", "NLMID": "https://www.ncbi.nlm.nih.gov/nlmcatalog/?term=", "OBAN": "http://purl.org/oban/", "oboformat": "http://www.geneontology.org/formats/oboInOWL#", "OBOREL": "http://purl.obolibrary.org/obo/RO_", "ORCID": "https://orcid.org/", "ORPHA": "http://www.orpha.net/ORDO/Orphanet_", "os": "https://github.com/cmungall/owlstar/blob/master/owlstar.ttl", "PathWhiz": "http://smpdb.ca/pathways/#", "PATO-PROPERTY": "http://purl.obolibrary.org/obo/pato#", "pav": "http://purl.org/pav/", "PDQ": "https://www.cancer.gov/publications/pdq#", "PHAROS": "http://pharos.nih.gov", "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_", "RTXKG1": "http://kg1endpoint.rtx.ai/", "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=", "SEMMEDDB": "https://skr3.nlm.nih.gov/SemMedDB", "SIO": "http://semanticscience.org/resource/SIO_", "SNPEFF": "http://translator.ncats.nih.gov/SNPEFF_", "UBERGRAPH": "http://translator.renci.org/ubergraph-axioms.ofn#", "UBERON_CORE": "http://purl.obolibrary.org/obo/uberon/core#", "UMLSSC": "https://metamap.nlm.nih.gov/Docs/SemanticTypes_2018AB.txt/code#", "UMLSSG": "https://metamap.nlm.nih.gov/Docs/SemGroups_2018.txt/group#", "UMLSST": "https://metamap.nlm.nih.gov/Docs/SemanticTypes_2018AB.txt/type#", "VANDF": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/", "VMC": "https://github.com/ga4gh/vr-spec/", "WBVocab": "http://bio2rdf.org/wormbase_vocabulary", "WIKIDATA": "https://www.wikidata.org/wiki/", "WIKIDATA_PROPERTY": "https://www.wikidata.org/wiki/Property:", "wgs": "http://www.w3.org/2003/01/geo/wgs84_pos", "XPO": "http://purl.obolibrary.org/obo/XPO_" }, "default_prefix": "biolink", "default_range": "string", "default_curi_maps": [ "obo_context", "idot_context", "monarch_context", "semweb_context" ], "emit_prefixes": [ "rdf", "rdfs", "xsd", "skos", "OIO", "BIOGRID" ], "enums": { "logical_interpretation_enum": { "permissible_values": { "SomeSome": { "description": "A modifier on a triple that causes the triple to be interpreted as a some-some statement", "meaning": "os:SomeSomeInterpretation" }, "AllSome": { "description": "A modifier on a triple that causes the triple to be interpreted as an all-some statement.", "meaning": "os:AllSomeInterpretation" }, "InverseAllSome": null } }, "reaction_direction_enum": { "permissible_values": { "left_to_right": null, "right_to_left": null, "bidirectional": null, "neutral": null } }, "reaction_side_enum": { "permissible_values": { "left": null, "right": null } }, "phase_enum": { "description": "phase", "permissible_values": { "0": null, "1": null, "2": null } }, "strand_enum": { "description": "strand", "permissible_values": { "+": { "description": "Positive" }, "-": { "description": "Negative" }, ".": { "description": "Unstranded" }, "?": { "description": "Unknown" } } }, "sequence_enum": { "description": "type of sequence", "permissible_values": { "NA": { "description": "nucleic acid" }, "AA": { "description": "amino acid" } } }, "drug_availability_enum": { "description": "", "permissible_values": { "over the counter": { "description": "chemical entity is available over the counter without a prescription." }, "prescription": { "description": "chemical entity is available by prescription." } } }, "FDA_approval_status_enum": { "description": "", "permissible_values": { "Discovery & 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 Monitoring": { "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 approval": null, "post-approval withdrawal": null } } }, "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" } }, "imports": [ "linkml:types" ], "types": { "chemical formula value": { "uri": "xsd:string", "base": "str", "description": "A chemical formula", "notes": [ "Should be implemented as a stronger type" ] }, "category type": { "typeof": "uriorcurie", "description": "A primitive type in which the value denotes a class within the biolink model. The value must be a URI or a CURIE. In a Neo4j representation, the value should be the CURIE for the biolink class, for example biolink:Gene. For an RDF representation, the value should be a URI such as https://w3id.org/biolink/vocab/Gene" }, "iri type": { "typeof": "uriorcurie", "description": "An IRI" }, "label type": { "typeof": "string", "description": "A string that provides a human-readable name for an entity" }, "predicate type": { "typeof": "uriorcurie", "description": "A CURIE from the biolink related_to hierarchy. For example, biolink:related_to, biolink:causes, biolink:treats." }, "narrative text": { "typeof": "string", "description": "A string that provides a human-readable description of something" }, "symbol type": { "typeof": "string" }, "frequency value": { "typeof": "string", "uri": "UO:0000105" }, "percentage frequency value": { "typeof": "double", "uri": "UO:0000187" }, "quotient": { "aliases": [ "ratio" ], "typeof": "double", "uri": "UO:0010006" }, "unit": { "typeof": "string", "uri": "UO:0000000", "id_prefixes": [ "UO" ], "exact_mappings": [ "qud:Unit" ] }, "time type": { "typeof": "time" }, "biological sequence": { "typeof": "string" } }, "slots": { "has attribute": { "description": "connects any entity to an attribute", "domain": "entity", "range": "attribute", "multivalued": true, "in_subset": [ "samples" ], "close_mappings": [ "OBI:0001927" ], "exact_mappings": [ "SIO:000008" ], "narrow_mappings": [ "OBAN:association_has_subject_property", "OBAN:association_has_object_property", "CPT:has_possibly_included_panel_element", "DRUGBANK:category", "EFO:is_executed_in", "HANCESTRO:0301", "LOINC:has_action_guidance", "LOINC:has_adjustment", "LOINC:has_aggregation_view", "LOINC:has_approach_guidance", "LOINC:has_divisor", "LOINC:has_exam", "LOINC:has_method", "LOINC:has_modality_subtype", "LOINC:has_object_guidance", "LOINC:has_scale", "LOINC:has_suffix", "LOINC:has_time_aspect", "LOINC:has_time_modifier", "LOINC:has_timing_of", "NCIT:disease_is_grade", "NCIT:disease_is_stage", "NCIT:eo_disease_has_property_or_attribute", "NCIT:has_data_element", "NCIT:has_pharmaceutical_administration_method", "NCIT:has_pharmaceutical_basic_dose_form", "NCIT:has_pharmaceutical_intended_site", "NCIT:has_pharmaceutical_release_characteristics", "NCIT:has_pharmaceutical_state_of_matter", "NCIT:has_pharmaceutical_transformation", "NCIT:is_qualified_by", "NCIT:qualifier_applies_to", "NCIT:role_has_domain", "NCIT:role_has_range", "INO:0000154", "HANCESTRO:0308", "OMIM:has_inheritance_type", "ORPHA:C016", "ORPHA:C017", "RO:0000053", "RO:0000086", "RO:0000087", "SNOMED:has_access", "SNOMED:has_clinical_course", "SNOMED:has_count_of_base_of_active_ingredient", "SNOMED:has_dose_form_administration_method", "SNOMED:has_dose_form_release_characteristic", "SNOMED:has_dose_form_transformation", "SNOMED:has_finding_context", "SNOMED:has_finding_informer", "SNOMED:has_inherent_attribute", "SNOMED:has_intent", "SNOMED:has_interpretation", "SNOMED:has_laterality", "SNOMED:has_measurement_method", "SNOMED:has_method", "SNOMED:has_priority", "SNOMED:has_procedure_context", "SNOMED:has_process_duration", "SNOMED:has_property", "SNOMED:has_revision_status", "SNOMED:has_scale_type", "SNOMED:has_severity", "SNOMED:has_specimen", "SNOMED:has_state_of_matter", "SNOMED:has_subject_relationship_context", "SNOMED:has_surgical_approach", "SNOMED:has_technique", "SNOMED:has_temporal_context", "SNOMED:has_time_aspect", "SNOMED:has_units", "UMLS:has_structural_class", "UMLS:has_supported_concept_property", "UMLS:has_supported_concept_relationship", "UMLS:may_be_qualified_by" ] }, "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" ] }, "has qualitative value": { "description": "connects an attribute to a value", "domain": "attribute", "range": "named thing", "multivalued": false, "in_subset": [ "samples" ] }, "has quantitative value": { "description": "connects an attribute to a value", "domain": "attribute", "range": "quantity value", "multivalued": true, "exact_mappings": [ "qud:quantityValue" ], "narrow_mappings": [ "SNOMED:has_concentration_strength_numerator_value", "SNOMED:has_presentation_strength_denominator_value", "SNOMED:has_presentation_strength_numerator_value" ], "in_subset": [ "samples" ] }, "has numeric value": { "description": "connects a quantity value to a number", "domain": "quantity value", "range": "double", "multivalued": false, "exact_mappings": [ "qud:quantityValue" ], "in_subset": [ "samples" ] }, "has unit": { "description": "connects a quantity value to a unit", "domain": "quantity value", "range": "unit", "multivalued": false, "close_mappings": [ "EFO:0001697", "OBO:uo#is_unit_of" ], "exact_mappings": [ "qud:unit", "IAO:0000039" ], "narrow_mappings": [ "SNOMED:has_concentration_strength_denominator_unit", "SNOMED:has_concentration_strength_numerator_unit", "SNOMED:has_presentation_strength_denominator_unit", "SNOMED:has_presentation_strength_numerator_unit", "SNOMED:has_unit_of_presentation" ], "in_subset": [ "samples" ] }, "base coordinate": { "is_a": "sequence localization attribute", "aliases": [ "one-based", "fully-closed" ], "description": "A position in the base coordinate system. Base coordinates start at position 1 instead of position 0.", "range": "integer" }, "node property": { "description": "A grouping for any property that holds between a node and a value", "domain": "named thing" }, "id": { "identifier": true, "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": [ "alliancegenome:primaryId", "gff3:ID", "gpi:DB_Object_ID" ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "range": "iri type", "in_subset": [ "translator_minimal", "samples" ], "exact_mappings": [ "WIKIDATA_PROPERTY:P854" ] }, "type": { "slot_uri": "rdf:type", "exact_mappings": [ "alliancegenome:soTermId", "gff3:type", "gpi:DB_Object_Type" ] }, "category": { "is_a": "type", "domain": "entity", "range": "category type", "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis 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`, ...\nIn 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" ] }, "name": { "aliases": [ "label", "display name", "title" ], "description": "A human-readable name for an attribute or 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" ] }, "source": { "description": "a lightweight analog to the association class 'has provider' slot, which is the string name, or the authoritative (i.e. database) namespace, designating the origin of the entity to which the slot belongs.", "range": "label type", "in_subset": [ "translator_minimal" ] }, "filler": { "is_a": "node property", "range": "named thing", "description": "The value in a property-value tuple" }, "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": "reaction_direction_enum", "narrow_mappings": [ "NCIT:C42677" ] }, "reaction balanced": { "is_a": "association slot", "range": "boolean" }, "reaction side": { "description": "the side of a reaction being modeled (ie: left or right)", "is_a": "association slot", "range": "reaction_side_enum" }, "symbol": { "is_a": "node property", "domain": "named thing", "description": "Symbol for a particular thing", "exact_mappings": [ "alliancegenome: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": [ "skos:altLabel", "gff3:Alias", "alliancegenome:synonyms", "gpi:DB_Object_Synonyms", "oboInOwl:hasExactSynonym", "oboInOwl:hasNarrowSynonym", "oboInOwl:hasBroadSynonym", "oboInOwl:hasRelatedSynonym", "HANCESTRO:0330", "IAO:0000136", "RXNORM:has_tradename" ] }, "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": { "is_a": "node property", "aliases": [ "dbxref", "Dbxref", "DbXref" ], "domain": "named thing", "range": "iri type", "description": "Alternate CURIEs for a thing", "multivalued": true, "in_subset": [ "translator_minimal" ], "narrow_mappings": [ "gff3:Dbxref", "gpi:DB_Xrefs" ] }, "full name": { "is_a": "node property", "domain": "named thing", "range": "label type", "description": "a long-form human readable name for a thing" }, "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(?)." }, "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" ] }, "timepoint": { "is_a": "node property", "range": "time type", "description": "a point in time" }, "creation date": { "is_a": "node property", "aliases": [ "publication date" ], "range": "date", "description": "date on which an entity was created. This can be applied to nodes or edges", "exact_mappings": [ "dct:createdOn", "WIKIDATA_PROPERTY:P577" ] }, "update date": { "is_a": "node property", "range": "date", "description": "date on which an entity was updated. This can be applied to nodes or edges" }, "aggregate statistic": { "is_a": "node property", "abstract": true }, "has count": { "description": "number of things with a particular property", "is_a": "aggregate statistic", "range": "integer", "exact_mappings": [ "LOINC:has_count" ] }, "has total": { "description": "total number of things in a particular reference set", "is_a": "aggregate statistic", "range": "integer" }, "has quotient": { "is_a": "aggregate statistic", "range": "double" }, "has percentage": { "description": "equivalent to has quotient multiplied by 100", "is_a": "aggregate statistic", "range": "double" }, "has dataset": { "is_a": "node property", "domain": "dataset version", "range": "dataset", "slot_uri": "dct:source" }, "source web page": { "is_a": "node property", "domain": "dataset summary", "broad_mappings": [ "dct:source" ] }, "source logo": { "is_a": "node property", "domain": "dataset summary", "slot_uri": "schema:logo" }, "retrieved on": { "is_a": "node property", "domain": "dataset", "range": "date", "exact_mappings": [ "pav:retrievedOn" ] }, "version of": { "is_a": "node property", "domain": "dataset version", "range": "dataset summary", "exact_mappings": [ "dct:isVersionOf" ] }, "version": { "is_a": "node property", "domain": "dataset", "broad_mappings": [ "pav:version", "owl:versionInfo" ] }, "license": { "is_a": "node property", "domain": "information content entity", "exact_mappings": [ "dct:license" ], "narrow_mappings": [ "WIKIDATA_PROPERTY:P275" ] }, "rights": { "is_a": "node property", "domain": "information content entity", "exact_mappings": [ "dct:rights" ] }, "format": { "is_a": "node property", "domain": "information content entity", "exact_mappings": [ "dct:format", "WIKIDATA_PROPERTY:P2701" ] }, "created_with": { "is_a": "node property", "domain": "dataset", "exact_mappings": [ "pav:createdWith" ] }, "download url": { "is_a": "node property", "domain": "information content entity", "slot_uri": "dcat:downloadURL" }, "dataset download url": { "is_a": "node property", "domain": "dataset", "slot_uri": "dcat:downloadURL" }, "distribution download url": { "is_a": "node property", "domain": "dataset distribution", "exact_mappings": [ "dcat:downloadURL" ] }, "ingest date": { "is_a": "node property", "domain": "dataset version", "slot_uri": "pav:version" }, "has distribution": { "is_a": "node property", "domain": "dataset version", "range": "dataset distribution", "slot_uri": "dct:distribution" }, "published in": { "is_a": "node property", "description": "CURIE identifier of a broader publication context within which the publication may be placed, e.g. a specified book or journal.", "domain": "publication", "range": "uriorcurie", "values_from": [ "NLMID", "issn", "isbn" ], "exact_mappings": [ "WIKIDATA_PROPERTY:P1433" ] }, "iso abbreviation": { "is_a": "node property", "description": "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself.", "domain": "publication", "exact_mappings": [ "WIKIDATA_PROPERTY:P1160" ] }, "authors": { "is_a": "node property", "singular_name": "author", "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" }, "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", "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 }, "has biological sequence": { "is_a": "node property", "description": "connects a genomic feature to its sequence", "range": "biological sequence" }, "has gene or gene product": { "is_a": "node property", "description": "connects an entity with one or more gene or gene products", "range": "gene", "multivalued": true }, "has gene": { "is_a": "has gene or gene product", "description": "connects an entity associated with one or more genes", "range": "gene", "multivalued": true }, "has zygosity": { "is_a": "node property", "domain": "nucleic acid entity", "range": "zygosity" }, "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 }, "has receptor": { "is_a": "node property", "domain": "exposure event", "range": "organismal entity", "description": "the organism or organism part being exposed", "exact_mappings": [ "ExO:0000001" ] }, "has stressor": { "is_a": "node property", "domain": "exposure event", "aliases": [ "has stimulus" ], "description": "the process or entity that the receptor is being exposed to", "exact_mappings": [ "ExO:0000000" ] }, "has route": { "is_a": "node property", "domain": "exposure event", "description": "the process that results in the stressor coming into direct contact with the receptor", "exact_mappings": [ "ExO:0000055" ], "narrow_mappings": [ "LOINC:has_pharmaceutical_route", "SNOMED:has_dose_form_intended_site", "SNOMED:has_route_of_administration" ] }, "has population context": { "description": "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.", "is_a": "association slot", "range": "population of individual organisms" }, "has temporal context": { "description": "a constraint of time placed upon the truth value of an association.", "is_a": "association slot", "range": "time type" }, "is supplement": { "description": "", "is_a": "node property", "range": "chemical mixture" }, "trade name": { "description": "", "is_a": "node property", "range": "chemical entity" }, "available from": { "description": "", "is_a": "node property", "multivalued": true, "range": "drug_availability_enum" }, "animal model available from": { "description": "", "is_a": "node property", "multivalued": true, "range": "disease or phenotypic feature" }, "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, 'FDA approval status.'" }, "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": { "tag": "biolink:canonical_predicate", "value": true }, "exact_mappings": [ "skos:relatedMatch", "SEMMEDDB:ASSOCIATED_WITH", "SEMMEDDB:associated_with", "UMLS:related_to" ], "broad_mappings": [ "owl:topObjectProperty" ], "narrow_mappings": [ "SEMMEDDB:compared_with", "SEMMEDDB:higher_than", "SEMMEDDB:lower_than", "BFO:0000054", "UBERON_CORE:protects", "GOREL:0002005", "GOREL:0012006", "BTO:related_to", "CHEBI:is_conjugate_acid_of", "CHEBI:is_conjugate_base_of", "CPT:has_add_on_code", "CPT:mapped_to", "EFO:0006351", "FMA:connected_to", "FMA:continuous_with", "FMA:homonym_of", "FMA:related_developmental_entity_of", "RO:0002093", "RO:0002092", "RO:0002084", "GOREL:0002005", "GOREL:0012006", "HCPCS:mapped_to", "HMDB:disease", "HMDB:has_protein_association", "IAO:0000136", "LOINC:has_answer", "LOINC:has_challenge", "LOINC:has_evaluation", "LOINC:mapped_to", "LOINC:mth_has_expanded_form", "MESH:RO", "MESH:has_mapping_qualifier", "MESH:mapped_to", "MONDO:disease_shares_features_of", "NCIT:disease_may_have_associated_disease", "NCIT:human_disease_maps_to_eo_disease", "NCIT:is_abnormal_cell_of_disease", "NCIT:is_related_to_endogenous_product", "OBO:core#connected_to", "OBO:core#innervated_by", "OBO:envo#has_increased_levels_of", "OBO:has_role", "OBO:nbo#is_about", "RO:0000053", "PATO-PROPERTY:decreased