From 73053b9ad95296f04d4dd53bbd3d43bf5b87e369 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 21 Jul 2021 21:34:31 -0700 Subject: [PATCH] update cached biolink model json to v2.1.0 from https://github.com/biolink/biolink-model/blob/2.1.0/biolink-model.yaml. Used https://jsonformatter.org/yaml-to-json to convert to JSON. --- src/biolink.json | 2863 ++++++++++++++++++++++++++++++++++++---------- 1 file changed, 2270 insertions(+), 593 deletions(-) diff --git a/src/biolink.json b/src/biolink.json index cda81634..290530fa 100644 --- a/src/biolink.json +++ b/src/biolink.json @@ -3,12 +3,13 @@ "name": "Biolink-Model", "description": "Entity and association taxonomy and datamodel for life-sciences data", "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "version": "1.7.0", + "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/", - "biolinkml": "https://w3id.org/biolink/biolinkml/", + "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=", @@ -64,6 +65,7 @@ "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/", @@ -100,7 +102,8 @@ "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" + "wgs": "http://www.w3.org/2003/01/geo/wgs84_pos", + "XPO": "http://purl.obolibrary.org/obo/XPO_" }, "default_prefix": "biolink", "default_range": "string", @@ -131,6 +134,113 @@ }, "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": { @@ -148,7 +258,7 @@ } }, "imports": [ - "biolinkml:types" + "linkml:types" ], "types": { "chemical formula value": { @@ -383,6 +493,15 @@ "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" @@ -423,7 +542,7 @@ "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. * 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}", + "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": [ @@ -464,6 +583,28 @@ "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", @@ -848,7 +989,7 @@ }, "has zygosity": { "is_a": "node property", - "domain": "genomic entity", + "domain": "nucleic acid entity", "range": "zygosity" }, "has chemical formula": { @@ -861,17 +1002,17 @@ }, "is metabolite": { "is_a": "node property", - "domain": "chemical substance", + "domain": "molecular entity", "range": "boolean", - "description": "indicates whether a chemical substance is a metabolite", + "description": "indicates whether a molecular entity is a metabolite", "exact_mappings": [ "CHEBI:25212" ] }, "has constituent": { - "description": "one or more chemical substances within a mixture", + "description": "one or more molecular entities within a chemical mixture", "is_a": "node property", - "range": "chemical substance", + "range": "molecular entity", "multivalued": true }, "has drug": { @@ -935,6 +1076,31 @@ "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", @@ -942,6 +1108,10 @@ "multivalued": true, "inherited": true, "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "skos:relatedMatch", "SEMMEDDB:ASSOCIATED_WITH", @@ -959,8 +1129,6 @@ "UBERON_CORE:protects", "GOREL:0002005", "GOREL:0012006", - "BFO:0000068", - "BFO:0000069", "BTO:related_to", "CHEBI:is_conjugate_acid_of", "CHEBI:is_conjugate_base_of", @@ -1106,7 +1274,10 @@ "in_subset": [ "translator_minimal" ], - "inverse": "superclass of", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "close_mappings": [ "LOINC:class_of", "LOINC:has_class" @@ -1151,6 +1322,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "close_mappings": [ "owl:equivalentClass" ], @@ -1172,6 +1347,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "skos:closeMatch", "SEMMEDDB:SAME_AS", @@ -1194,6 +1373,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "skos:exactMatch", "WIKIDATA:Q39893449", @@ -1203,10 +1386,13 @@ "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", - "inverse": "narrow match", "in_subset": [ "translator_minimal" ], + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "skos:broadMatch", "WIKIDATA:Q39894595" @@ -1228,6 +1414,10 @@ "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", "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:0002604" ], @@ -1236,6 +1426,136 @@ "https://github.com/biolink/biolink-model/issues/657" ] }, + "active in": { + "is_a": "related to", + "domain": "gene or gene product", + "range": "cellular component", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, + "exact_mappings": [ + "RO:0002432" + ] + }, + "acts upstream of": { + "is_a": "related to", + "domain": "gene or gene product", + "range": "biological process", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, + "exact_mappings": [ + "RO:0002263" + ] + }, + "has upstream actor": { + "is_a": "related to", + "inverse": "acts upstream of", + "domain": "biological process", + "range": "gene or gene product" + }, + "acts upstream of positive effect": { + "is_a": "acts upstream of", + "domain": "gene or gene product", + "range": "biological process", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, + "exact_mappings": [ + "RO:0004034" + ] + }, + "has positive upstream actor": { + "is_a": "has upstream actor", + "inverse": "acts upstream of positive effect", + "domain": "biological process", + "range": "gene or gene product" + }, + "acts upstream of negative effect": { + "is_a": "acts upstream of", + "domain": "gene or gene product", + "range": "biological process", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, + "exact_mappings": [ + "RO:0004035" + ] + }, + "has negative upstream actor": { + "is_a": "has upstream actor", + "inverse": "acts upstream of negative effect", + "domain": "biological process", + "range": "gene or gene product" + }, + "acts upstream of or within": { + "is_a": "acts upstream of", + "domain": "gene or gene product", + "range": "biological process", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, + "exact_mappings": [ + "RO:0004032" + ] + }, + "has upstream or within actor": { + "is_a": "has upstream actor", + "inverse": "acts upstream of or within", + "domain": "biological process", + "range": "gene or gene product" + }, + "acts upstream of or within positive effect": { + "is_a": "acts upstream of", + "domain": "gene or gene product", + "range": "biological process", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, + "exact_mappings": [ + "RO:0002264" + ] + }, + "has positive upstream or within actor": { + "is_a": "has upstream or within actor", + "inverse": "acts upstream of or within positive effect", + "domain": "biological process", + "range": "gene or gene product" + }, + "acts upstream of or within negative effect": { + "is_a": "acts upstream of", + "domain": "gene or gene product", + "range": "biological process", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": 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" + }, + "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", + "exact_mappings": [ + "IAO:0000142" + ], + "narrow_mappings": [ + "SIO:000628" + ] + }, "contributor": { "is_a": "related to", "domain": "information content entity", @@ -1287,6 +1607,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:0002434" ], @@ -1304,6 +1628,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "WIKIDATA_PROPERTY:P129", "RTXKG1:physically_interacts_with" @@ -1326,6 +1654,15 @@ "PR:non-covalently_bound_to" ] }, + "chemically interacts with": { + "is_a": "physically interacts with", + "domain": "chemical entity", + "range": "chemical entity", + "in_subset": [ + "translator_minimal" + ], + "symmetric": true + }, "molecularly interacts with": { "is_a": "physically interacts with", "domain": "molecular entity", @@ -1334,6 +1671,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "related_mappings": [ "DGIdb:antibody" ], @@ -1359,10 +1700,13 @@ "affects": { "is_a": "related to", "description": "describes an entity that has a direct affect on the state or quality of another existing entity. Use of the 'affects' predicate implies that the affected entity already exists, unlike predicates such as 'affects risk for' and 'prevents, where the outcome is something that may or may not come to be.", - "inverse": "affected by", "in_subset": [ "translator_minimal" ], + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "related_mappings": [ "DRUGBANK:pathway" ], @@ -1410,39 +1754,53 @@ "inverse": "affects" }, "chemical role mixin": { - "description": "A role played by the molecular entity or part thereof within a chemical context.", + "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 molecular entity or part thereof within a biological context.", + "description": "A role played by the chemical entity or part thereof within a biological context.", "mixin": true, - "exact_mappings": [ + "narrow_mappings": [ "CHEBI:24432" ] }, "affects abundance of": { - "description": "holds between two molecular entities where the action or effect of one changes the amount of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one changes the amount of the other within a system of interest", "is_a": "affects", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:affects_abundance_of" ] }, + "abundance affected by": { + "is_a": "affects", + "inverse": "affects abundance of", + "domain": "chemical entity", + "range": "chemical entity" + }, "increases abundance of": { - "description": "holds between two molecular entities where the action or effect of one increases the amount of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one increases the amount of the other within a system of interest", "is_a": "affects abundance of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "related_mappings": [ "UBERGRAPH:is_increase_of" ], @@ -1450,14 +1808,26 @@ "CTD:increases_abundance_of" ] }, + "abundance increased by": { + "is_a": "affects abundance of", + "inverse": "increases abundance of", + "domain": "chemical entity", + "range": "chemical entity" + }, "decreases abundance of": { - "description": "holds between two molecular entities where the action or effect of one decreases the amount of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one decreases the amount of the other within a system of interest", "is_a": "affects abundance of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": [ + { + "tag": "biolink:canonical_predicate", + "value": true + } + ], "related_mappings": [ "UBERGRAPH:is_decrease_of" ], @@ -1465,14 +1835,20 @@ "CTD:decreases_abundance_of" ] }, + "abundance decreased by": { + "is_a": "affects abundance of", + "inverse": "decreases abundance of", + "domain": "chemical entity", + "range": "chemical entity" + }, "affects activity of": { - "description": "holds between two molecular entities where the action or effect of one changes the activity of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one changes the activity of the other within a system of interest", "is_a": "affects", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", "exact_mappings": [ "CTD:affects_activity_of" ], @@ -1484,14 +1860,26 @@ "DGIdb:allosteric_modulator" ] }, + "activity affected by": { + "description": "holds between two chemical entities where the action or effect of one is changed by the activity of the other within a system of interest", + "is_a": "affects", + "domain": "chemical entity", + "range": "chemical entity" + }, + "activity affects": { + "is_a": "affects", + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "activity affected by" + }, "increases activity of": { - "description": "holds between two molecular entities where the action or effect of one increases the activity of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one increases the activity of the other within a system of interest", "is_a": "affects activity of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", "related_mappings": [ "GAMMA:ec50", "GAMMA:ac50" @@ -1521,14 +1909,23 @@ "DGIdb:stimulator" ] }, + "activity increased by": { + "is_a": "affects activity of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "increases activity of" + }, "decreases activity of": { - "description": "holds between two molecular entities where the action or effect of one decreases the activity of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one decreases the activity of the other within a system of interest", "is_a": "affects activity of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", "related_mappings": [ "GAMMA:ic50", "GAMMA:ki", @@ -1568,26 +1965,44 @@ "DGIdb:inverse_agonist" ] }, + "activity decreased by": { + "is_a": "affects activity of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "decreases activity of" + }, "affects expression of": { - "description": "holds between two molecular entities where the action or effect of one changes the level of expression of the other within a system of interest", + "description": "holds between a chemical entity and a nucleic acid entity where the action or effect of one changes the level of expression of the other within a system of interest", "is_a": "affects", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "genomic entity", + "domain": "chemical entity", + "range": "nucleic acid entity", "exact_mappings": [ "CTD:affects_expression_of" ] }, + "expression affected by": { + "is_a": "affects", + "in_subset": [ + "translator_minimal" + ], + "domain": "nucleic acid entity", + "range": "chemical entity", + "inverse": "affects expression of" + }, "increases expression of": { - "description": "holds between two molecular entities where the action or effect of one increases the level of expression of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one increases the level of expression of the other within a system of interest", "is_a": "affects expression of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "genomic entity", + "domain": "chemical entity", + "range": "nucleic acid entity", "close_mappings": [ "CHEMBL.MECHANISM:releasing_agent" ], @@ -1596,14 +2011,23 @@ "CTD:increases_expression_of" ] }, + "expression increased by": { + "is_a": "expression affected by", + "in_subset": [ + "translator_minimal" + ], + "domain": "nucleic acid entity", + "range": "chemical entity", + "inverse": "increases expression of" + }, "decreases expression of": { - "description": "holds between two molecular entities where the action or effect of one decreases the level of expression of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one decreases the level of expression of the other within a system of interest", "is_a": "affects expression of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "genomic entity", + "domain": "chemical entity", + "range": "nucleic acid entity", "related_mappings": [ "DGIdb:antisense", "DGIdb:antisense_oligonucleotide" @@ -1616,50 +2040,93 @@ "CHEMBL.MECHANISM:antisense_inhibitor" ] }, + "expression decreased by": { + "is_a": "expression affected by", + "in_subset": [ + "translator_minimal" + ], + "domain": "nucleic acid entity", + "range": "chemical entity", + "inverse": "decreases expression of" + }, "affects folding of": { - "description": "holds between two molecular entities where the action or effect of one changes the rate or quality of folding of the other", + "description": "holds between two chemical entities where the action or effect of one changes the rate or quality of folding of the other", "is_a": "affects", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "nucleic acid entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:affects_folding_of" ] }, + "folding affected by": { + "is_a": "affects", + "inverse": "affects folding of", + "domain": "nucleic acid entity", + "range": "chemical entity" + }, "increases folding of": { - "description": "holds between two molecular entities where the action or effect of one increases the rate or quality of folding of the other", + "description": "holds between two chemical entities where the action or effect of one increases the rate or quality of folding of the other", "is_a": "affects folding of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "nucleic acid entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:increases_folding_of" ] }, + "folding increased by": { + "is_a": "affects folding of", + "inverse": "increases folding of", + "domain": "nucleic acid entity", + "range": "chemical entity" + }, "decreases folding of": { - "description": "holds between two molecular entities where the action or effect of one decreases the rate or quality of folding of the other", + "description": "holds between a chemical entity and a nucleic acid entity where the action or effect of one decreases the rate or quality of folding of the other", "is_a": "affects folding of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "nucleic acid entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:decreases_folding_of" ] }, + "folding decreased by": { + "is_a": "affects folding of", + "inverse": "decreases folding of", + "domain": "nucleic acid entity", + "range": "chemical entity" + }, "affects localization of": { - "description": "holds between two molecular entities where the action or effect of one changes the localization of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one changes the localization of the other within a system of interest", "is_a": "affects", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "related_mappings": [ "GAMMA:storage" ], @@ -1668,38 +2135,77 @@ "GOREL:0002003" ] }, + "localization affected by": { + "is_a": "affects", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "affects localization of" + }, "increases localization of": { - "description": "holds between two molecular entities where the action or effect of one increases the proper localization of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one increases the proper localization of the other within a system of interest", "is_a": "affects localization of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:increases_localization_of" ] }, + "localization increased by": { + "is_a": "affects localization of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "increases localization of" + }, "decreases localization of": { - "description": "holds between two molecular entities where the action or effect of one decreases the proper localization of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one decreases the proper localization of the other within a system of interest", "is_a": "affects localization of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:decreases_localization_of" ] }, + "localization decreased by": { + "is_a": "affects localization of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "decreases localization of" + }, "affects metabolic processing of": { - "description": "holds between two molecular entities where the action or effect of one impacts the metabolic processing of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one impacts the metabolic processing of the other within a system of interest", "is_a": "affects", + "domain": "chemical entity", + "range": "chemical entity", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "related_mappings": [ "GAMMA:catalytic_activity" ], @@ -1707,14 +2213,27 @@ "CTD:affects_metabolic_processing_of" ] }, + "metabolic processing affected by": { + "is_a": "affects", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "affects metabolic processing of" + }, "increases metabolic processing of": { - "description": "holds between two molecular entities where the action or effect of one increases the rate of metabolic processing of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one increases the rate of metabolic processing of the other within a system of interest", "is_a": "affects metabolic processing of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:increases_metabolic_processing_of" ], @@ -1722,26 +2241,52 @@ "NCIT:enzyme_metabolizes_chemical_or_drug" ] }, + "metabolic processing increased by": { + "is_a": "affects metabolic processing of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "increases metabolic processing of" + }, "decreases metabolic processing of": { - "description": "holds between two molecular entities where the action or effect of one decreases the rate of metabolic processing of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one decreases the rate of metabolic processing of the other within a system of interest", "is_a": "affects metabolic processing of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:decreases_metabolic_processing_of" ] }, + "metabolic processing decreased by": { + "is_a": "affects metabolic processing of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "decreases metabolic processing of" + }, "affects molecular modification of": { - "description": "holds between two molecular entities where the action or effect of one leads changes in the molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", + "description": "holds between two chemical entities where the action or effect of one leads changes in the molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", "is_a": "affects", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:affects_molecular_modification_of" ], @@ -1779,14 +2324,27 @@ "CTD:affects_carboxylation" ] }, + "molecular modification affected by": { + "is_a": "affects", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "affects molecular modification of" + }, "increases molecular modification of": { - "description": "holds between two molecular entities where the action or effect of one leads to increased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", + "description": "holds between two chemical entities where the action or effect of one leads to increased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", "is_a": "affects molecular modification of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:increases_molecular_modification_of" ], @@ -1826,14 +2384,27 @@ "GAMMA:oxidizer" ] }, + "molecular modification increased by": { + "is_a": "affects molecular modification of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "increases molecular modification of" + }, "decreases molecular modification of": { - "description": "holds between two molecular entities where the action or effect of one leads to decreased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", + "description": "holds between two chemical entities where the action or effect of one leads to decreased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", "is_a": "affects molecular modification of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:decreases_molecular_modification_of" ], @@ -1872,51 +2443,103 @@ "GAMMA:deoxidizer" ] }, + "molecular modification decreased by": { + "is_a": "affects molecular modification of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "decreases molecular modification of" + }, "affects synthesis of": { - "description": "holds between two molecular entities where the action or effect of one impacts the rate of chemical synthesis of the other", + "description": "holds between two chemical entities where the action or effect of one impacts the rate of chemical synthesis of the other", "is_a": "affects", + "domain": "chemical entity", + "range": "chemical entity", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:affects_synthesis_of" ] }, + "sythesis affected by": { + "is_a": "affects", + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "affects synthesis of", + "in_subset": [ + "translator_minimal" + ] + }, "increases synthesis of": { - "description": "holds between two molecular entities where the action or effect of one increases the rate of chemical synthesis of the other", + "description": "holds between two chemical entities where the action or effect of one increases the rate of chemical synthesis of the other", "is_a": "affects synthesis of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:increases_synthesis_of" ] }, + "synthesis increased by": { + "is_a": "affects synthesis of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "increases synthesis of" + }, "decreases synthesis of": { - "description": "holds between two molecular entities where the action or effect of one decreases the rate of chemical synthesis of the other", + "description": "holds between two chemical entities where the action or effect of one decreases the rate of chemical synthesis of the other", "is_a": "affects synthesis of", + "domain": "chemical entity", + "range": "chemical entity", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:decreases_synthesis_of", "GAMMA:inhibition_of_synthesis" ] }, + "synthesis decreased by": { + "is_a": "affects synthesis of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "decreases synthesis of" + }, "affects degradation of": { - "description": "holds between two molecular entities where the action or effect of one impacts the rate of degradation of the other within a system of interest, where chemical degradation is defined act or process of simplifying or breaking down a molecule into smaller parts, either naturally or artificially (Oxford English Dictionary, UK, 1995)", + "description": "holds between two chemical entities where the action or effect of one impacts the rate of degradation of the other within a system of interest, where chemical degradation is defined act or process of simplifying or breaking down a molecule into smaller parts, either naturally or artificially (Oxford English Dictionary, UK, 1995)", "is_a": "affects", + "domain": "chemical entity", + "range": "chemical entity", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:affects_degradation_of" ], @@ -1925,14 +2548,27 @@ "CTD:affects_hydrolysis" ] }, + "degradation affected by": { + "is_a": "affects", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "affects degradation of" + }, "increases degradation of": { - "description": "holds between two molecular entities where the action or effect of one increases the rate of degradation of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one increases the rate of degradation of the other within a system of interest", "is_a": "affects degradation of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "related_mappings": [ "GAMMA:substrate", "CHEMBL.MECHANISM:substrate" @@ -1951,14 +2587,27 @@ "GOREL:0002004" ] }, + "degradation increased by": { + "is_a": "affects degradation of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "increases degradation of" + }, "decreases degradation of": { - "description": "holds between two molecular entities where the action or effect of one decreases the rate of degradation of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one decreases the rate of degradation of the other within a system of interest", "is_a": "affects degradation of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:decreases_degradation_of" ], @@ -1967,29 +2616,53 @@ "CTD:decreases_hydrolysis" ] }, + "degradation decreased by": { + "is_a": "affects degradation of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "decreases degradation of" + }, "affects mutation rate of": { - "description": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity impacts the rate of mutation of the genomic entity within a system of interest", + "description": "holds between a chemical entity and a nucleic acid entity where the action or effect of the chemical entity impacts the rate of mutation of the nucleic acid entity within a system of interest", "is_a": "affects", + "domain": "chemical entity", + "range": "nucleic acid entity", + "broad_mappings": null, "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "genomic entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:affects_mutation_rate_of" - ], - "broad_mappings": [ - "CTD:affects_mutagenesis" ] }, + "mutation rate affected by": { + "is_a": "affects", + "in_subset": [ + "translator_minimal" + ], + "domain": "nucleic acid entity", + "range": "chemical entity", + "inverse": "affects mutation rate of" + }, "increases mutation rate of": { - "description": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity increases the rate of mutation of the genomic entity within a system of interest", + "description": "holds between a chemical entity and a nucleic acid entity where the action or effect of the chemical entity increases the rate of mutation of the nucleic acid entity within a system of interest", "is_a": "affects mutation rate of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "genomic entity", + "domain": "chemical entity", + "range": "nucleic acid entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:increases_mutation_rate_of" ], @@ -1997,14 +2670,26 @@ "CTD:increases_mutagenesis" ] }, + "mutation rate increased by": { + "in_subset": [ + "translator_minimal" + ], + "domain": "nucleic acid entity", + "range": "chemical entity", + "inverse": "increases mutation rate of" + }, "decreases mutation rate of": { - "description": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity decreases the rate of mutation of the genomic entity within a system of interest", + "description": "holds between a chemical entity and a nucleic acid entity where the action or effect of the chemical entity decreases the rate of mutation of the nucleic acid entity within a system of interest", "is_a": "affects mutation rate of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "genomic entity", + "domain": "chemical entity", + "range": "nucleic acid entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:decreases_mutation_rate_of" ], @@ -2012,38 +2697,77 @@ "CTD:decreases_mutagenesis" ] }, + "mutation rate decreased by": { + "is_a": "affects mutation rate of", + "in_subset": [ + "translator_minimal" + ], + "domain": "nucleic acid entity", + "range": "chemical entity", + "inverse": "decreases mutation rate of" + }, "affects response to": { - "description": "holds between two molecular entities where the action or effect of one impacts the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other", + "description": "holds between two chemical entities where the action or effect of one impacts the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other", "is_a": "affects", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:affects_response_to" ] }, + "response affected by": { + "is_a": "affects", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "affects response to" + }, "increases response to": { - "description": "holds between two molecular entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other", + "description": "holds between two chemical entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other", "is_a": "affects response to", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:increases_response_to" ] }, + "response increased by": { + "is_a": "affects response to", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "increases response to" + }, "decreases response to": { - "description": "holds between two molecular entities where the action or effect of one decreases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other", + "description": "holds between two chemical entities where the action or effect of one decreases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other", "is_a": "affects response to", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:decreases_response_to" ], @@ -2052,14 +2776,27 @@ "GAMMA:desensitize_the_target" ] }, + "response decreased by": { + "is_a": "affects response to", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "decreases response to" + }, "affects splicing of": { - "description": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity impacts the splicing of the mRNA", + "description": "holds between a chemical entity and an mRNA where the action or effect of the chemical entity impacts the splicing of the mRNA", "is_a": "affects", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", + "domain": "chemical entity", "range": "transcript", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:affects_RNA_splicing" ], @@ -2067,14 +2804,27 @@ "CTD:affects_splicing_of" ] }, + "splicing affected by": { + "is_a": "affects", + "in_subset": [ + "translator_minimal" + ], + "domain": "transcript", + "range": "chemical entity", + "inverse": "affects splicing of" + }, "increases splicing of": { - "description": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity increases the proper splicing of the mRNA", + "description": "holds between a chemical entity and an mRNA where the action or effect of the chemical entity increases the proper splicing of the mRNA", "is_a": "affects splicing of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", + "domain": "chemical entity", "range": "transcript", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:increases_RNA_splicing" ], @@ -2082,14 +2832,27 @@ "CTD:increases_splicing_of" ] }, + "splicing increased by": { + "is_a": "affects splicing of", + "in_subset": [ + "translator_minimal" + ], + "domain": "transcript", + "range": "chemical entity", + "inverse": "increases splicing of" + }, "decreases splicing of": { - "description": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity decreases the proper splicing of the mRNA", + "description": "holds between a chemical entity and an mRNA where the action or effect of the chemical entity decreases the proper splicing of the mRNA", "is_a": "affects splicing of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", + "domain": "chemical entity", "range": "transcript", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:decreases_RNA_splicing" ], @@ -2097,14 +2860,27 @@ "CTD:decreases_splicing_of" ] }, + "splicing decreased by": { + "is_a": "affects splicing of", + "in_subset": [ + "translator_minimal" + ], + "domain": "transcript", + "range": "chemical entity", + "inverse": "decreases splicing of" + }, "affects stability of": { - "description": "holds between two molecular entities where the action or effect of one impacts the stability of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one impacts the stability of the other within a system of interest", "is_a": "affects", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "close_mappings": [ "GAMMA:stabilization" ], @@ -2112,14 +2888,27 @@ "CTD:affects_stability_of" ] }, + "stability affected by": { + "is_a": "affects", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "affects stability of" + }, "increases stability of": { - "description": "holds between two molecular entities where the action or effect of one increases the stability of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one increases the stability of the other within a system of interest", "is_a": "affects stability of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "close_mappings": [ "CHEMBL.MECHANISM:stabiliser" ], @@ -2127,26 +2916,52 @@ "CTD:increases_stability_of" ] }, + "stability increased by": { + "is_a": "affects stability of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "increases stability of" + }, "decreases stability of": { - "description": "holds between two molecular entities where the action or effect of one decreases the stability of the other within a system of interest", + "description": "holds between two chemical entities where the action or effect of one decreases the stability of the other within a system of interest", "is_a": "affects stability of", + "domain": "chemical entity", + "range": "chemical entity", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:decreases_stability_of" ] }, + "stability decreased by": { + "is_a": "affects stability of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "decreases stability of" + }, "affects transport of": { - "description": "holds between two molecular entities where the action or effect of one impacts the rate of transport of the other across some boundary in a system of interest", + "description": "holds between two chemical entities where the action or effect of one impacts the rate of transport of the other across some boundary in a system of interest", "is_a": "affects", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:affects_transport_of" ], @@ -2156,14 +2971,27 @@ "RO:0002345" ] }, + "transport affected by": { + "is_a": "affects", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "affects transport of" + }, "increases transport of": { - "description": "holds between two molecular entities where the action or effect of one increases the rate of transport of the other across some boundary in a system of interest", + "description": "holds between two chemical entities where the action or effect of one increases the rate of transport of the other across some boundary in a system of interest", "is_a": "affects transport of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "close_mappings": [ "GAMMA:carrier", "GAMMA:transporter" @@ -2172,26 +3000,52 @@ "CTD:increases_transport_of" ] }, + "transport increased by": { + "is_a": "affects transport of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "increases transport of" + }, "decreases transport of": { - "description": "holds between two molecular entities where the action or effect of one decreases the rate of transport of the other across some boundary in a system of interest", + "description": "holds between two chemical entities where the action or effect of one decreases the rate of transport of the other across some boundary in a system of interest", "is_a": "affects transport of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:decreases_transport_of" ] }, + "transport decreased by": { + "is_a": "affects transport of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "decreases transport of" + }, "affects secretion of": { - "description": "holds between two molecular entities where the action or effect of one impacts the rate of secretion of the other out of a cell, gland, or organ", + "description": "holds between two chemical entities where the action or effect of one impacts the rate of secretion of the other out of a cell, gland, or organ", "is_a": "affects", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:affects_secretion_of" ], @@ -2199,14 +3053,27 @@ "CTD:affects_export" ] }, + "secretion affected by": { + "is_a": "affects", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "affects secretion of" + }, "increases secretion of": { - "description": "holds between two molecular entities where the action or effect of one increases the rate of secretion of the other out of a cell, gland, or organ", + "description": "holds between two chemical entities where the action or effect of one increases the rate of secretion of the other out of a cell, gland, or organ", "is_a": "affects secretion of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:increases_secretion_of" ], @@ -2214,14 +3081,27 @@ "CTD:increases_export" ] }, + "secretion increased by": { + "is_a": "affects secretion of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "increases secretion of" + }, "decreases secretion of": { - "description": "holds between two molecular entities where the action or effect of one decreases the rate of secretion of the other out of a cell, gland, or organ", + "description": "holds between two chemical entities where the action or effect of one decreases the rate of secretion of the other out of a cell, gland, or organ", "is_a": "affects secretion of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:decreases_secretion_of" ], @@ -2229,14 +3109,27 @@ "CTD:decreases_export" ] }, + "secretion decreased by": { + "is_a": "affects secretion of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "decreases secretion of" + }, "affects uptake of": { - "description": "holds between two molecular entities where the action or effect of one impacts the rate of uptake of the other into of a cell, gland, or organ", + "description": "holds between two chemical entities where the action or effect of one impacts the rate of uptake of the other into of a cell, gland, or organ", "is_a": "affects", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:affects_uptake_of" ], @@ -2244,14 +3137,27 @@ "CTD:affects_import" ] }, + "uptake affected by": { + "is_a": "affects", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "affects uptake of" + }, "increases uptake of": { - "description": "holds between two molecular entities where the action or effect of one increases the rate of uptake of the other into of a cell, gland, or organ", + "description": "holds between two chemical entities where the action or effect of one increases the rate of uptake of the other into of a cell, gland, or organ", "is_a": "affects uptake of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:increases_uptake_of" ], @@ -2259,14 +3165,27 @@ "CTD:increases_import" ] }, + "uptake increased by": { + "is_a": "affects uptake of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "increases uptake of" + }, "decreases uptake of": { - "description": "holds between two molecular entities where the action or effect of one decreases the rate of uptake of the other into of a cell, gland, or organ", + "description": "holds between two chemical entities where the action or effect of one decreases the rate of uptake of the other into of a cell, gland, or organ", "is_a": "affects uptake of", "in_subset": [ "translator_minimal" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:decreases_uptake_of" ], @@ -2274,6 +3193,15 @@ "CTD:decreases_import" ] }, + "uptake decreased by": { + "is_a": "affects uptake of", + "in_subset": [ + "translator_minimal" + ], + "domain": "chemical entity", + "range": "chemical entity", + "inverse": "decreases uptake of" + }, "regulates": { "comments": [ "This is a grouping for process-process and entity-entity regulation." @@ -2281,7 +3209,10 @@ "mixin": true, "domain": "physical essence or occurrent", "range": "physical essence or occurrent", - "inverse": "regulated by", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "close_mappings": [ "RO:0002334" ], @@ -2309,8 +3240,11 @@ "This is a grouping for positive process-process and entity-entity regulation." ], "is_a": "regulates", - "inverse": "positively regulated by", "mixin": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "close_mappings": [ "RO:0002336" ], @@ -2336,8 +3270,11 @@ "This is a grouping for negative process-process and entity-entity regulation." ], "is_a": "regulates", - "inverse": "negatively regulated by", "mixin": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "close_mappings": [ "RO:0002335" ], @@ -2368,7 +3305,10 @@ ], "domain": "occurrent", "range": "occurrent", - "inverse": "process regulated by process", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:0002211" ] @@ -2384,7 +3324,10 @@ "mixins": [ "positively regulates" ], - "inverse": "process positively regulated by process", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:0002213" ] @@ -2398,7 +3341,10 @@ "mixins": [ "negatively regulates" ], - "inverse": "process negatively regulated by process", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:0002212" ] @@ -2415,9 +3361,13 @@ "mixins": [ "regulates" ], - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", "inverse": "entity regulated by entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "local_names": { "translator": "regulates", "ro": "activity directly regulates activity of" @@ -2434,8 +3384,8 @@ }, "entity regulated by entity": { "is_a": "affected by", - "domain": "molecular entity", - "range": "molecular entity", + "domain": "chemical entity", + "range": "chemical entity", "inverse": "entity regulates entity" }, "entity positively regulates entity": { @@ -2446,7 +3396,10 @@ "mixins": [ "positively regulates" ], - "inverse": "entity positively regulated by entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "local_names": { "translator": "positively regulates", "ro": "activity directly positively regulates activity of" @@ -2479,7 +3432,10 @@ "mixins": [ "negatively regulates" ], - "inverse": "entity negatively regulated by entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "local_names": { "translator": "negatively regulates", "ro": "activity directly negatively regulates activity of" @@ -2507,7 +3463,10 @@ "in_subset": [ "translator_minimal" ], - "inverse": "disrupted by", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "SEMMEDDB:DISRUPTS", "SEMMEDDB:disrupts", @@ -2526,12 +3485,16 @@ }, "gene product of": { "is_a": "related to", - "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 that process is either y or something that is ribosomally translated from x", + "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": { + "tag": "biolink:canonical_predicate", + "value": true + }, "inverse": "has gene product", "in_subset": [ "translator_minimal" @@ -2542,10 +3505,10 @@ "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" ], - "inverse": "gene product of", "close_mappings": [ "PR:has_gene_template" ], @@ -2573,7 +3536,10 @@ "is_a": "related to", "domain": "transcript", "range": "gene", - "inverse": "transcribed to", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "description": "x is transcribed from y if and only if x is synthesized from template y", "exact_mappings": [ "RO:0002510", @@ -2584,8 +3550,11 @@ "is_a": "related to", "domain": "transcript", "range": "protein", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": 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)", - "inverse": "translation of", "close_mappings": [ "RO:0002513", "SIO:010082" @@ -2615,6 +3584,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:HOM0000001", "SIO:010302" @@ -2630,6 +3603,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:HOM0000011" ] @@ -2641,6 +3618,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:HOM0000017", "WIKIDATA_PROPERTY:P684" @@ -2653,6 +3634,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:HOM0000018" ] @@ -2664,6 +3649,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "SEMMEDDB:COEXISTS_WITH", "SEMMEDDB:coexists_with" @@ -2846,6 +3835,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "related_mappings": [ "SIO:010532" ] @@ -2859,6 +3852,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "related_mappings": [ "SIO:010497" ], @@ -2874,7 +3871,11 @@ "in_subset": [ "translator_minimal" ], - "symmetric": true + "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + } }, "colocalizes with": { "description": "holds between two entities that are observed to be located in the same place.", @@ -2883,6 +3884,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:00002325" ] @@ -2890,6 +3895,10 @@ "genetic association": { "is_a": "related to", "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": 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" @@ -2900,10 +3909,13 @@ "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": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], - "inverse": "condition associated with gene", "exact_mappings": [ "RTXKG1:gene_associated_with_condition" ], @@ -2934,16 +3946,28 @@ "affects risk for": { "is_a": "related to", "description": "holds between two entities where exposure to one entity alters the chance of developing the other", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ] }, + "risk affected by": { + "is_a": "related to", + "inverse": "affects risk for" + }, "predisposes": { "is_a": "affects risk for", "description": "holds between two entities where exposure to one entity increases the chance of developing the other", "in_subset": [ "translator_minimal" ], + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "SEMMEDDB:PREDISPOSES", "SEMMEDDB:predisposes" @@ -2955,6 +3979,10 @@ "in_subset": [ "translator_minimal" ], + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "close_mappings": [ "IDO:0000664" ], @@ -2968,22 +3996,32 @@ "RO:0003304" ] }, + "contribution from": { + "is_a": "related to", + "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" ], - "inverse": "caused by", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ - "RO:0002506", "SEMMEDDB:CAUSES", "SEMMEDDB:causes", "WIKIDATA_PROPERTY:P1542", "SNOMED:cause_of" ], "broad_mappings": [ - "RO:0002410" + "RO:0002410", + "RO:0002506" ], "narrow_mappings": [ "MONDO:disease_triggers", @@ -3042,6 +4080,10 @@ "description": "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.", "domain": "biological entity", "range": "disease or phenotypic feature", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:0003307", "CTD:therapeutic" @@ -3052,6 +4094,10 @@ "description": "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.", "domain": "biological entity", "range": "disease or phenotypic feature", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:0003309" ] @@ -3061,13 +4107,16 @@ "is substance that treats" ], "is_a": "ameliorates", - "description": "holds between a therapeutic procedure or chemical substance and a disease or phenotypic feature that it is used to treat", - "domain": "chemical or drug or treatement", + "description": "holds between a therapeutic procedure or chemical entity and a disease or phenotypic feature that it is used to treat", + "domain": "chemical or drug or treatment", "range": "disease or phenotypic feature", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], - "inverse": "treated by", "related_mappings": [ "MONDO:disease_responds_to" ], @@ -3077,9 +4126,6 @@ "SEMMEDDB:treats", "WIKIDATA_PROPERTY:P2175" ], - "broad_mappings": [ - "RO:0003307" - ], "narrow_mappings": [ "RO:0002606", "NCIT:regimen_has_accepted_use_for_disease", @@ -3108,9 +4154,9 @@ }, "treated by": { "is_a": "related to", - "description": "holds between a disease or phenotypic feature and a therapeutic process or chemical substance that is used to treat the condition", + "description": "holds between a disease or phenotypic feature and a therapeutic process or chemical entity that is used to treat the condition", "domain": "disease or phenotypic feature", - "range": "treatment", + "range": "chemical or drug or treatment", "in_subset": [ "translator_minimal" ], @@ -3124,9 +4170,13 @@ ] }, "approved to treat": { - "description": "holds between a therapeutic procedure or chemical substance and a disease or phenotypic feature for which it is approved for treatment to some level of clinical trial. Note that in terms of REPODB narrow mappings, terms containing 'suspended', 'terminated' or 'withdrawn' should be mapped onto associations using this term for which 'negated: true' is asserted.", + "description": "holds between a therapeutic procedure or chemical entity and a disease or phenotypic feature for which it is approved for treatment to some level of clinical trial. Note that in terms of REPODB narrow mappings, terms containing 'suspended', 'terminated' or 'withdrawn' should be mapped onto associations using this term for which 'negated: true' is asserted.", "is_a": "treats", - "inverse": "approved for treatment by", + "domain": "chemical or drug or treatment", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "NCIT:C172573" ], @@ -3155,14 +4205,18 @@ ] }, "approved for treatment by": { - "description": "holds between a disease or phenotypic feature and a therapeutic process or chemical substance that is approved for treatment of the condition (or not, if negated) to some level of clinical trial", + "description": "holds between a disease or phenotypic feature and a therapeutic process or chemical entity that is approved for treatment of the condition (or not, if negated) to some level of clinical trial", "is_a": "treated by", + "range": "chemical or drug or treatment", "inverse": "approved to treat" }, "prevents": { "is_a": "affects risk for", - "description": "holds between an entity whose application or use reduces the likelihood of a potential outcome. Typically used to associate a chemical substance, exposure, activity, or medical intervention that can prevent the onset a disease or phenotypic feature.", - "inverse": "prevented by", + "description": "holds between an entity whose application or use reduces the likelihood of a potential outcome. Typically used to associate a chemical entity, exposure, activity, or medical intervention that can prevent the onset a disease or phenotypic feature.", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], @@ -3188,6 +4242,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:0002610", "PATO:correlates_with" @@ -3213,6 +4271,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:positive_correlation" ] @@ -3226,6 +4288,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:negative_correlation" ] @@ -3235,13 +4301,17 @@ "description": "holds between any two genes or gene products, in which both are generally expressed within a single defined experimental context.", "domain": "gene or gene product", "range": "gene or gene product", - "symmetric": true + "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + } }, "has biomarker": { "is_a": "correlated with", - "description": "holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.", + "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": "molecular entity", + "range": "chemical entity", "in_subset": [ "translator_minimal" ], @@ -3254,13 +4324,16 @@ }, "biomarker for": { "is_a": "correlated with", - "description": "holds between a measurable molecular 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": "molecular entity", + "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", "range": "disease or phenotypic feature", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], - "inverse": "has biomarker", "exact_mappings": [ "NCIT:R39" ], @@ -3280,10 +4353,13 @@ "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", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], - "inverse": "expresses", "exact_mappings": [ "RO:0002206" ], @@ -3312,7 +4388,10 @@ "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).", "domain": "biological entity", "range": "phenotypic feature", - "inverse": "phenotype of", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "notes": [ "check the range" ], @@ -3357,6 +4436,10 @@ "in_subset": [ "translator_minimal" ], + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "close_mappings": [ "BFO:0000067", "SNOMED:has_occurrence", @@ -3388,7 +4471,10 @@ "in_subset": [ "translator_minimal" ], - "inverse": "location of", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:0001025", "FMA:has_location" @@ -3465,6 +4551,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:HOM0000000", "SO:similar_to" @@ -3472,11 +4562,15 @@ }, "chemically similar to": { "is_a": "similar to", - "description": "holds between one chemical substances and another that it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity.", + "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": { + "tag": "biolink:canonical_predicate", + "value": true + }, "narrow_mappings": [ "CHEBI:has_parent_hydride", "CHEBI:has_functional_parent", @@ -3489,16 +4583,30 @@ }, "has sequence location": { "is_a": "related to", - "description": "holds between two genomic entities when the subject can be localized in sequence coordinates on the object. For example, between an exon and a chromosome/contig.", - "domain": "genomic entity", - "range": "genomic entity", + "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": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "faldo:location" ] }, + "sequence location of": { + "is_a": "related to", + "domain": "nucleic acid entity", + "range": "nucleic acid entity", + "inverse": "has sequence location" + }, "model of": { - "is_a": "similar to", - "description": "holds between an entity and some other entity it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity.", + "is_a": "related to", + "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": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], @@ -3509,6 +4617,10 @@ "FOODON:00001301" ] }, + "models": { + "is_a": "related to", + "inverse": "model of" + }, "overlaps": { "is_a": "related to", "description": "holds between entities that overlap in their extents (materials or processes)", @@ -3516,6 +4628,10 @@ "translator_minimal" ], "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "RO:0002131" ], @@ -3529,11 +4645,14 @@ }, "has part": { "is_a": "overlaps", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "description": "holds between wholes and their parts (material entities or processes)", "in_subset": [ "translator_minimal" ], - "inverse": "part of", "exact_mappings": [ "BFO:0000051", "BFO:0000055", @@ -3657,6 +4776,11 @@ "is_a": "has participant", "description": "holds between a process and a continuant, where the continuant is an input into the process", "domain": "occurrent", + "range": "biological process or activity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], @@ -3684,10 +4808,24 @@ "SNOMED:uses_substance" ] }, + "is input of": { + "is_a": "has participant", + "domain": "biological process or activity", + "range": "occurrent", + "inverse": "has input", + "in_subset": [ + "translator_minimal" + ] + }, "has output": { "is_a": "has participant", "description": "holds between a process and a continuant, where the continuant is an output of the process", "domain": "occurrent", + "range": "biological process or activity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], @@ -3711,14 +4849,26 @@ "RO:0004008" ] }, + "is output of": { + "is_a": "has participant", + "range": "occurrent", + "domain": "biological process or activity", + "inverse": "has output", + "in_subset": [ + "translator_minimal" + ] + }, "has participant": { "is_a": "related to", "description": "holds between a process and a continuant, where the continuant is somehow involved in the process", "domain": "occurrent", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], - "inverse": "participates in", "close_mappings": [ "WIKIDATA_PROPERTY:P2283" ], @@ -3749,14 +4899,36 @@ "SNOMED:has_recipient_category" ] }, + "catalyzes": { + "is_a": "has participant", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + } + }, + "is catalyst of": { + "is_a": "participates in", + "inverse": "catalyzes" + }, + "has substrate": { + "is_a": "has participant", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + } + }, + "is substrate of": { + "is_a": "participates in", + "inverse": "has substrate" + }, "participates in": { "is_a": "related to", "description": "holds between a continuant and a process, where the continuant is somehow involved in the process", "range": "occurrent", + "inverse": "has participant", "in_subset": [ "translator_minimal" ], - "inverse": "has participant", "exact_mappings": [ "RO:0000056", "BFO:0000056", @@ -3781,7 +4953,12 @@ "actively involved in": { "is_a": "participates 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": "molecular activity", "range": "occurrent", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], @@ -3804,10 +4981,26 @@ "RO:0002503" ] }, + "actively involves": { + "is_a": "participates in", + "domain": "occurrent", + "range": "molecular activity", + "inverse": "actively involved in", + "exact_mappings": [ + "RO:0002331" + ], + "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.", "range": "occurrent", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], @@ -3825,6 +5018,10 @@ "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": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], @@ -3864,6 +5061,10 @@ }, "derives from": { "is_a": "related to", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": 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", @@ -3882,9 +5083,9 @@ }, "is metabolite of": { "is_a": "derives from", - "description": "holds between two chemical substances in which the first one is derived from the second one as a product of metabolism", - "domain": "chemical substance", - "range": "chemical substance", + "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" ], @@ -3898,13 +5099,16 @@ }, "has metabolite": { "is_a": "derives into", - "description": "holds between two chemical substances in which the second one is derived from the first one as a product of metabolism", - "domain": "chemical substance", - "range": "chemical substance", + "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": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], - "inverse": "is metabolite of", "comments": [ "The CHEBI ID represents a role rather than a predicate" ], @@ -3914,9 +5118,9 @@ }, "food component of": { "is_a": "part of", - "description": "holds between a one or more chemical substances present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)", - "domain": "chemical substance", - "range": "chemical substance", + "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" ], @@ -3924,19 +5128,22 @@ }, "has food component": { "is_a": "has part", - "description": "holds between food and one or more chemical substances composing it, irrespective of nutritional value (i.e. could also be a contaminant or additive)", - "domain": "chemical substance", - "range": "chemical substance", + "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": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" - ], - "inverse": "food component of" + ] }, "nutrient of": { "is_a": "food component of", - "description": "holds between a one or more chemical substances present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)", - "domain": "chemical substance", - "range": "chemical substance", + "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" ], @@ -3945,20 +5152,23 @@ "has nutrient": { "is_a": "has food component", "description": "one or more nutrients which are growth factors for a living organism", - "domain": "chemical substance", - "range": "chemical substance", + "domain": "chemical entity", + "range": "chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], - "inverse": "nutrient of", "exact_mappings": [ "WIKIDATA:Q181394" ] }, "is active ingredient of": { "is_a": "part of", - "description": "holds between a chemical substance and a drug, in which the former is a part of the latter, and is a biologically active component", - "domain": "chemical substance", + "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" @@ -3970,9 +5180,13 @@ }, "has active ingredient": { "is_a": "has part", - "description": "holds between a drug and a chemical substance in which the latter is a part of the former, and is a biologically active component", + "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": "chemical substance", + "range": "molecular entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], @@ -3983,8 +5197,8 @@ }, "is excipient of": { "is_a": "part of", - "description": "holds between a chemical substance and a drug in which the former is a part of the latter, and is a biologically inactive component", - "domain": "chemical substance", + "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" @@ -3996,13 +5210,16 @@ }, "has excipient": { "is_a": "has part", - "description": "holds between a drug and a chemical substances in which the latter is a part of the former, and is a biologically inactive component", + "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": "chemical substance", + "range": "molecular entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], - "inverse": "is excipient of", "mappings": [ "WIKIDATA:Q902638" ] @@ -4011,6 +5228,10 @@ "is_a": "related to", "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": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], @@ -4026,12 +5247,21 @@ "SNOMED:has_definitional_manifestation" ] }, + "has manifestation": { + "is_a": "related to", + "domain": "disease", + "inverse": "manifestation of" + }, "produces": { "is_a": "related to", "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": { + "tag": "biolink:canonical_predicate", + "value": true + }, "related_mappings": [ "GOREL:0001010" ], @@ -4054,12 +5284,29 @@ "RO:0003001" ] }, + "consumes": { + "is_a": "has input", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, + "narrow_mappings": [ + "RO:0004009" + ] + }, + "consumed by": { + "inverse": "consumes" + }, "temporally related to": { "is_a": "related to", "description": "holds between two entities with a temporal relationship", "domain": "occurrent", "range": "occurrent", "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "SNOMED:temporally_related_to" ], @@ -4085,7 +5332,10 @@ "description": "holds between two processes, where one completes before the other begins", "domain": "occurrent", "range": "occurrent", - "inverse": "preceded by", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "in_subset": [ "translator_minimal" ], @@ -4132,10 +5382,14 @@ }, "directly interacts with": { "is_a": "interacts with", - "description": "Holds between molecular entities that physically and directly interact\nwith each other", - "domain": "molecular entity", - "range": "molecular entity", + "description": "Holds between chemical entities that physically and directly interact with each other", + "domain": "chemical entity", + "range": "chemical entity", "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "related_mappings": [ "GAMMA:kd", "GAMMA:kb", @@ -4173,30 +5427,50 @@ }, "affects expression in": { "is_a": "affects", - "description": "Holds between a variant and an anatomical entity where the expression of the variant\nis located in.", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, + "description": "Holds between a variant and an anatomical entity where the expression of the variant is located in.", "exact_mappings": [ "GTEx:affects_expression_in" ] }, "has variant part": { "is_a": "has part", - "description": "holds between a genomic entity and a genotypic entity that is a sub-component of it", + "description": "holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "GENO:0000382" ] }, + "variant part of": { + "is_a": "part of", + "inverse": "has variant part" + }, "related condition": { "is_a": "related to", "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "GENO:0000790" ] }, "is sequence variant of": { "is_a": "related to", - "description": "holds between a sequence variant and a genomic entity", + "description": "holds between a sequence variant and a nucleic acid entity", "domain": "sequence variant", - "range": "genomic entity", + "range": "nucleic acid entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "narrow_mappings": [ "NCIT:gene_product_sequence_variation_encoded_by_gene_mutant", "NCIT:gene_product_variant_of_gene_product", @@ -4204,11 +5478,21 @@ "WIKIDATA:P3433" ] }, + "has sequence variant": { + "is_a": "related to", + "inverse": "is sequence variant of", + "domain": "nucleic acid 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\nresults in a different amino acid sequence but where the length is preserved.", + "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": "gene", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "SO:0001583", "SNPEFF:missense_variant" @@ -4218,11 +5502,21 @@ "SNPEFF:structural_interaction_variant" ] }, + "has missense variant": { + "is_a": "is sequence variant of", + "domain": "gene", + "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\nis in the coding sequence of the gene, but results in the same amino acid sequence", + "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": "gene", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "SO:0001819", "SNPEFF:synonymous_variant" @@ -4232,11 +5526,21 @@ "SNPEFF:stop_retained_variant" ] }, + "has synonymous variant": { + "is_a": "is sequence variant of", + "domain": "gene", + "range": "sequence variant", + "inverse": "is synonymous variant of" + }, "is nonsense variant of": { "is_a": "is sequence variant of", - "description": "holds between a sequence variant and a gene, such the sequence variant\nresults in a premature stop codon", + "description": "holds between a sequence variant and a gene, such the sequence variant results in a premature stop codon", "domain": "sequence variant", "range": "gene", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "SNPEFF:stop_gained" ], @@ -4244,11 +5548,21 @@ "SO:0002054" ] }, + "has nonsense variant": { + "is_a": "is sequence variant of", + "domain": "gene", + "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\ncauses a disruption of the translational reading frame, because the number of\nnucleotides inserted or deleted is not a multiple of three.", + "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": "gene", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "SO:0001589", "SNPEFF:frameshift_variant" @@ -4258,11 +5572,21 @@ "SNPEFF:stop_lost" ] }, + "has frameshift variant": { + "is_a": "is sequence variant of", + "inverse": "is frameshift variant of", + "domain": "gene", + "range": "sequence 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\nis in the canonical splice site of one of the gene's exons.", + "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": "gene", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "SO:0001629" ], @@ -4272,11 +5596,21 @@ "SNPEFF:splice_donor_variant" ] }, + "has splice site variant": { + "is_a": "is sequence variant of", + "domain": "gene", + "range": "sequence variant", + "inverse": "is splice site variant of" + }, "is nearby variant of": { "is_a": "is sequence variant of", - "description": "holds between a sequence variant and a gene sequence that the variant\nis genomically close to.", + "description": "holds between a sequence variant and a gene sequence that the variant is genomically close to.", "domain": "sequence variant", "range": "gene", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "GAMMA:0000102" ], @@ -4285,11 +5619,21 @@ "SNPEFF:upstream_gene_variant" ] }, + "has nearby variant": { + "is_a": "is sequence variant of", + "domain": "gene", + "range": "sequence variant", + "inverse": "is nearby variant of" + }, "is non coding variant of": { "is_a": "is sequence variant of", - "description": "holds between a sequence variant and a gene, where the variant does\nnot affect the coding sequence", + "description": "holds between a sequence variant and a gene, where the variant does not affect the coding sequence", "domain": "sequence variant", "range": "gene", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "GAMMA:0000103" ], @@ -4301,9 +5645,19 @@ "SNPEFF:intron_variant" ] }, + "has non coding variant": { + "is_a": "is sequence variant of", + "domain": "gene", + "range": "sequence variant", + "inverse": "is non coding variant of" + }, "disease has basis in": { - "description": "A relation that holds between a disease and an entity where the state\nof the entity has contribution to the disease.", + "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", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "narrow_mappings": [ "MONDO:disease_has_basis_in_development_of", "MONDO:disease_has_basis_in_accumulation_of" @@ -4311,74 +5665,150 @@ }, "causes adverse event": { "is_a": "causes", - "description": "holds between a drug and a disease or phenotype that can be caused\nby the drug", + "description": "holds between a drug and a disease or phenotype that can be caused by the drug", "domain": "drug", "range": "disease or phenotypic feature", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "Aeolus:0000001" ] }, + "adverse event caused by": { + "is_a": "causes", + "domain": "disease or phenotypic feature", + "range": "drug", + "inverse": "causes adverse event" + }, "contraindicated for": { "is_a": "related to", - "description": "Holds between a drug and a disease or phenotype, such that a person\nwith that disease should not be treated with the drug.", + "description": "Holds between a drug and a disease or phenotype, such that a person with that disease should not be treated with the drug.", "domain": "drug", "range": "disease or phenotypic feature", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "DrugCentral:0000001", "RTXKG1:contraindicated_for" ] }, + "has contraindication": { + "is_a": "related to", + "domain": "disease or phenotypic feature", + "range": "drug", + "inverse": "contraindicated for" + }, "has not completed": { "is_a": "related to", - "description": "holds between an entity and a process that the entity is capable of,\nbut has not completed", + "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": { + "tag": "biolink:canonical_predicate", + "value": true + } + }, + "not completed by": { + "is_a": "related to", + "inverse": "has not completed" }, "has completed": { "is_a": "related to", - "description": "holds between an entity and a process that the entity is capable of\nand has completed", + "description": "holds between an entity and a process that the entity is capable of and has completed", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CL:has_completed", "RTXKG1:has_completed" ] }, + "completed by": { + "is_a": "related to", + "inverse": "has completed" + }, "decreases molecular interaction": { "is_a": "molecularly interacts with", - "description": "indicates that the source decreases the molecular interaction between\nthe target and some other molecular entity", + "description": "indicates that the source decreases the molecular interaction between the target and some other chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:decreases_molecular_interaction_with" ] }, + "molecular interaction decreased by": { + "is_a": "molecularly interacts with", + "inverse": "decreases molecular interaction" + }, "increases molecular interaction": { "is_a": "molecularly interacts with", - "description": "indicates that the source increases the molecular interaction between\nthe target and some other molecular entity", + "description": "indicates that the source increases the molecular interaction between the target and some other chemical entity", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CTD:increases_molecular_interaction_with" ] }, + "molecular interaction increased by": { + "is_a": "molecularly interacts with", + "inverse": "increases molecular interaction" + }, "in linkage disequilibrium with": { "is_a": "related to", - "description": "holds between two sequence variants, the presence of which are correlated\nin a population", + "description": "holds between two sequence variants, the presence of which are correlated in a population", "symmetric": true, + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "NCIT:C16798" ] }, "has increased amount": { "is_a": "related to", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "narrow_mappings": [ "CL:has_high_plasma_membrane_amount" ] }, + "increased amount of": { + "is_a": "related to", + "inverse": "has increased amount" + }, "has decreased amount": { "is_a": "related to", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "narrow_mappings": [ "CL:has_low_plasma_membrane_amount" ] }, + "decreased amount in": { + "is_a": "related to", + "inverse": "has decreased amount" + }, "lacks part": { "is_a": "related to", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "exact_mappings": [ "CL:lacks_part", "PR:lacks_part", @@ -4388,8 +5818,16 @@ "CL:lacks_plasma_membrane_part" ] }, + "missing from": { + "is_a": "related to", + "inverse": "lacks part" + }, "develops from": { "is_a": "related to", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "close_mappings": [ "RO:0002203", "FMA:develops_into" @@ -4406,6 +5844,10 @@ "RO:0002226" ] }, + "develops into": { + "is_a": "related to", + "inverse": "develops from" + }, "in taxon": { "aliases": [ "instance of" @@ -4413,6 +5855,10 @@ "is_a": "related to", "domain": "thing with taxon", "range": "organism taxon", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "in_subset": [ "translator_minimal" @@ -4437,10 +5883,19 @@ "is_a": "related to", "description": "connects a sequence variant to a class describing the molecular consequence. E.g. SO:0001583", "range": "ontology class", + "annotations": { + "tag": "biolink:canonical_predicate", + "value": true + }, "narrow_mappings": [ "NCIT:allele_has_activity" ] }, + "is molecular consequence of": { + "is_a": "related to", + "domain": "ontology class", + "inverse": "has molecular consequence" + }, "association slot": { "abstract": true, "domain": "association", @@ -4450,18 +5905,6 @@ ], "description": "any slot that relates an association to another entity" }, - "association_id": { - "is_a": "association slot", - "identifier": true, - "deprecated": "This slot is deprecated in favor of 'id' slot.", - "deprecated_element_has_exact_replacement": "id", - "description": "A unique identifier for an association", - "in_subset": [ - "translator_minimal" - ], - "domain": "association", - "alias": "id" - }, "subject": { "is_a": "association slot", "local_names": { @@ -4509,19 +5952,6 @@ "OBAN:association_has_predicate" ] }, - "edge label": { - "deprecated": "This slot is deprecated in favor of 'predicate' slot.", - "deprecated_element_has_exact_replacement": "predicate", - "is_a": "association slot", - "domain": "association", - "range": "predicate type", - "required": true, - "local_names": { - "ga4gh": "annotation predicate", - "translator": "predicate" - }, - "slot_uri": "rdf:predicate" - }, "logical interpretation": { "is_a": "association slot", "required": false, @@ -4561,8 +5991,18 @@ "RO:0002558" ] }, + "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.", + "range": "information resource", + "multivalued": true, + "close_mappings": [ + "pav:providedBy" + ] + }, "provided by": { "is_a": "association slot", + "deprecated": "This slot is deprecated and replaced by a set of more precise slots for describing the source retrieval provenance of an Association. These include 'knowledge source' and its descendants 'primary knowledge source', 'original knowledge source', and 'aggregator knowledge source'.", "description": "connects an association to the agent (person, organization or group) that provided it", "range": "agent", "multivalued": true, @@ -4570,6 +6010,30 @@ "pav:providedBy" ] }, + "primary knowledge source": { + "is_a": "knowledge source", + "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).", + "range": "information resource", + "multivalued": false + }, + "original knowledge source": { + "is_a": "primary knowledge source", + "description": "The Information Resource that created the original record of the knowledge expressed in an Association (e.g. via curation of the knowledge from the literature, or generation of the knowledge de novo through computation, reasoning, inference over data).", + "range": "information resource", + "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.", + "range": "information resource", + "multivalued": true + }, + "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).", + "range": "information resource", + "multivalued": true + }, "association type": { "is_a": "association slot", "range": "category type", @@ -4710,33 +6174,87 @@ "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 genomic 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." + "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", - "description": "A position in interbase coordinates. This is applied to a sequence localization edge.", + "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 genomic entity starts on the chromosome or other entity to which it is located on." + "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" + ] }, "end interbase coordinate": { "is_a": "interbase coordinate", - "description": "The position at which the subject genomic entity ends on the chromosome or other entity to which it is located on." + "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" + ] + }, + "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." + "description": "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens.", + "range": "strand_enum", + "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)." + "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": "strand_enum", + "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." + "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": "phase_enum", + "exact_mappings": [ + "gff3:phase" + ] + }, + "FDA approval status": { + "is_a": "association slot", + "description": "", + "range": "FDA_approval_status_enum" } }, "classes": { @@ -4749,7 +6267,7 @@ ], "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" + "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" @@ -4860,7 +6378,7 @@ "has percentage" ] }, - "chemical or drug or treatement": { + "chemical or drug or treatment": { "mixin": true }, "entity": { @@ -4989,6 +6507,15 @@ "model_organism_database" ] }, + "event": { + "is_a": "named thing", + "description": "Something that happens at a given place and time.", + "exact_mappings": [ + "NCIT:C25499", + "UMLSSC:T051", + "UMLSST:evnt" + ] + }, "administrative entity": { "is_a": "named thing", "abstract": true @@ -5018,9 +6545,7 @@ "UMLSSC:T095", "UMLSST:shro", "UMLSSC:T096", - "UMLSST:grup", - "UMLSSC:T097", - "UMLSST:prog" + "UMLSST:grup" ], "slot_usage": { "id": { @@ -5158,6 +6683,16 @@ "ECO:0000000" ] }, + "information resource": { + "is_a": "information content entity", + "aliases": [ + "knowledgebase" + ], + "description": "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb.", + "in_subset": [ + "translator_minimal" + ] + }, "publication": { "is_a": "information content entity", "description": "Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web, as well as printed materials, either directly or in one of the Publication Biolink category subclasses.", @@ -5422,7 +6957,9 @@ "UMLSSC:T075", "UMLSST:resd", "UMLSSC:T203", - "UMLSST:drdd" + "UMLSST:drdd", + "UMLSSC:T122", + "UMLSST:bodm" ] }, "study population": { @@ -5498,6 +7035,9 @@ }, "biological entity": { "is_a": "named thing", + "aliases": [ + "bioentity" + ], "abstract": true, "narrow_mappings": [ "WIKIDATA:Q28845870", @@ -5513,36 +7053,169 @@ "in taxon" ] }, + "genomic entity": { + "mixin": true, + "is_a": "thing with taxon", + "slots": [ + "has biological sequence" + ], + "in_subset": [ + "translator_minimal" + ], + "narrow_mappings": [ + "UMLSSC:T028", + "GENO:0000897" + ] + }, "molecular entity": { - "is_a": "biological entity", + "is_a": "chemical entity", + "description": "A molecular entity is a chemical entity composed of individual or covalently bonded atoms.", + "slots": [ + "is metabolite" + ], + "narrow_mappings": [ + "UMLSSC:T088", + "UMLSSC:T085" + ], + "in_subset": [ + "translator_minimal" + ] + }, + "chemical entity": { + "is_a": "named thing", + "abstract": true, "mixins": [ - "thing with taxon", "physical essence", - "ontology class" + "chemical or drug or treatment", + "chemical entity or gene or gene product", + "chemical entity or protein or polypeptide" ], - "aliases": [ - "bioentity" + "description": "A chemical entity is a physical entity that pertains to chemistry or biochemistry.", + "slots": [ + "trade name", + "available from" ], - "description": "A gene, gene product, small molecule or macromolecule (including protein complex)\"", "exact_mappings": [ - "CHEBI:24431" + "CHEBI:24431", + "SIO:010004", + "WIKIDATA:Q79529" ], "narrow_mappings": [ - "SIO:010341", "WIKIDATA:Q43460564", - "UMLSSG:CHEM", - "UMLSSC:T085", - "UMLSST:mosq", - "UMLSSC:T123", - "UMLSST:bacs", + "UMLSSC:T103", + "UMLSSC:T120", + "UMLSSC:T104", + "UMLSSC:T197", + "UMLSSC:T109", "UMLSSC:T125", - "UMLSST:horm", - "UMLSSC:T126", - "UMLSST:enzy", + "UMLSSC:T123", "UMLSSC:T129", - "UMLSST:imft", - "UMLSSC:T192", - "UMLSST:rcpt" + "UMLSSC:T131" + ], + "broad_mappings": [ + "UMLSSC:T167" + ], + "in_subset": [ + "translator_minimal" + ] + }, + "chemical substance": { + "deprecated": "This class is deprecated in favor of 'small molecule.'" + }, + "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": [ + "UMLSSC:T196" + ], + "id_prefixes": [ + "PUBCHEM.COMPOUND", + "CHEMBL.COMPOUND", + "UNII", + "CHEBI", + "DRUGBANK", + "MESH", + "CAS", + "DrugCentral", + "GTOPDB", + "HMDB", + "KEGG.COMPOUND", + "ChemBank", + "Aeolus", + "PUBCHEM.SUBSTANCE", + "SIDER.DRUG", + "INCHI", + "INCHIKEY", + "KEGG.GLYCAN", + "KEGG.DRUG", + "KEGG.DGROUP", + "KEGG.ENVIRON" + ], + "slot_usage": { + "id": { + "examples": [ + { + "value": "CHEBI:29101", + "description": "sodium ion" + } + ] + } + }, + "in_subset": [ + "model_organism_database", + "translator_minimal" + ] + }, + "chemical mixture": { + "is_a": "chemical entity", + "description": "A chemical mixture is a chemical entity composed of two or more molecular entities.", + "slots": [ + "is supplement", + "highest FDA approval status" + ], + "in_subset": [ + "translator_minimal" + ] + }, + "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", + "physical essence", + "ontology class" + ], + "exact_mappings": [ + "SO:0000110" + ], + "narrow_mappings": [ + "UMLSSC:T086", + "UMLSSC:T114" + ], + "in_subset": [ + "model_organism_database", + "translator_minimal" + ] + }, + "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" + ] + }, + "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" ] }, "biological process or activity": { @@ -5576,11 +7249,11 @@ ], "slot_usage": { "has input": { - "range": "chemical substance", + "range": "molecular entity", "description": "A chemical entity that is the input for the reaction" }, "has output": { - "range": "chemical substance", + "range": "molecular entity", "description": "A chemical entity that is the output for the reaction" }, "enabled by": { @@ -5660,9 +7333,7 @@ "mixins": [ "ontology class" ], - "close_mappings": [ - "UMLSSG:PHYS" - ], + "close_mappings": null, "exact_mappings": [ "UMLSSC:T039", "UMLSST:phsf", @@ -5686,7 +7357,8 @@ "behavior": { "is_a": "biological process", "mixins": [ - "ontology class" + "ontology class", + "activity and behavior" ], "exact_mappings": [ "GO:0007610", @@ -5708,106 +7380,17 @@ "GO:0016265" ] }, - "mixture": { - "mixin": true, - "description": "The physical combination of two or more molecular entities in which the identities are retained and are mixed in the form of solutions, suspensions and colloids.", - "slots": [ - "has constituent" - ] - }, - "chemical substance": { - "is_a": "molecular entity", - "mixins": [ - "ontology class" - ], - "description": "May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part", - "slots": [ - "is metabolite" - ], - "broad_mappings": [ - "UMLSSC:T167", - "UMLSST:sbst" - ], - "exact_mappings": [ - "SIO:010004", - "WIKIDATA:Q79529", - "UMLSSC:T103", - "UMLSST:chem" - ], - "narrow_mappings": [ - "UMLSSC:T104", - "UMLSST:chvs", - "UMLSSC:T109", - "UMLSST:orch", - "UMLSSC:T114", - "UMLSST:nnon", - "UMLSSC:T120", - "UMLSST:chvf", - "UMLSSC:T122", - "UMLSST:bodm", - "UMLSSC:T130", - "UMLSST:irda", - "UMLSSC:T131", - "UMLSST:hops", - "UMLSSC:T196", - "UMLSST:elii", - "UMLSSC:T197", - "UMLSST:inch" - ], - "id_prefixes": [ - "PUBCHEM.COMPOUND", - "CHEMBL.COMPOUND", - "UNII", - "CHEBI", - "DRUGBANK", - "MESH", - "CAS", - "DrugCentral", - "GTOPDB", - "HMDB", - "KEGG.COMPOUND", - "ChemBank", - "Aeolus", - "PUBCHEM.SUBSTANCE", - "SIDER.DRUG", - "INCHI", - "INCHIKEY", - "KEGG.GLYCAN", - "KEGG.DRUG", - "KEGG.DGROUP", - "KEGG.ENVIRON" - ], - "in_subset": [ - "model_organism_database" - ] - }, - "carbohydrate": { - "deprecated": "This class will be removed from the Biolink model", - "is_a": "chemical substance", - "exact_mappings": [ - "UMLSSC:T088", - "UMLSST:crbs" - ], - "id_prefixes": [ - "PUBCHEM.SUBSTANCE" - ] - }, "processed material": { - "is_a": "chemical substance", - "mixins": [ - "mixture", - "ontology class" - ], - "description": "A chemical substance (often a mixture) processed for consumption for nutritional, medical or technical use.", + "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" ] }, "drug": { - "is_a": "molecular entity", + "is_a": "molecular mixture", "mixins": [ - "mixture", - "chemical or drug or treatement", + "chemical or drug or treatment", "ontology class" ], "description": "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease", @@ -5834,27 +7417,20 @@ "PHARMGKB.DRUG" ] }, - "food component": { - "deprecated": "Food component is replaced by a slot/role of chemical substance and will be removed from the Biolink model.", - "is_a": "chemical substance", - "related_mappings": [ - "CHEBI:78295" - ] - }, "environmental food contaminant": { - "is_a": "chemical substance", + "is_a": "chemical entity", "related_mappings": [ "CHEBI:78299" ] }, "food additive": { - "is_a": "chemical substance", + "is_a": "chemical entity", "related_mappings": [ "CHEBI:64047" ] }, "nutrient": { - "is_a": "chemical substance", + "is_a": "chemical entity", "related_mappings": [ "CHEBI:33284" ] @@ -5880,10 +7456,7 @@ ] }, "food": { - "is_a": "molecular entity", - "mixins": [ - "mixture" - ], + "is_a": "chemical mixture", "description": "A substance consumed by a living organism as a source of nutrition", "id_prefixes": [ "foodb.compound" @@ -5893,17 +7466,6 @@ "UMLSST:food" ] }, - "metabolite": { - "deprecated": "Metabolite is replaced by a slot/role of chemical substance and will be removed from the Biolink model.", - "is_a": "chemical substance", - "description": "Any intermediate or product resulting from metabolism. Includes primary and secondary metabolites.", - "comments": [ - "The CHEBI ID represents a role rather than a substance" - ], - "exact_mappings": [ - "CHEBI:25212" - ] - }, "organism attribute": { "is_a": "attribute", "description": "describes a characteristic of an organismal entity.", @@ -5932,7 +7494,7 @@ ] }, "organismal entity": { - "description": "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding molecular entities", + "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", "slot_usage": { @@ -6000,14 +7562,6 @@ "UMLSST:popg", "OBI:0000181" ], - "narrow_mappings": [ - "UMLSSC:T099", - "UMLSST:famg", - "UMLSSC:T100", - "UMLSST:aggp", - "UMLSSC:T101", - "UMLSST:podg" - ], "id_prefixes": [ "HANCESTRO" ], @@ -6124,7 +7678,8 @@ "FBcv", "WBPhenotype", "SNOMEDCT", - "MESH" + "MESH", + "XPO" ], "in_subset": [ "model_organism_database" @@ -6247,10 +7802,21 @@ ], "id_prefixes": [ "UBERON", + "UMLS", + "MESH", + "NCIT", "PO", "FAO" ] }, + "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 mixin. 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, @@ -6275,9 +7841,13 @@ }, "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": "genomic entity", + "is_a": "biological entity", "mixins": [ - "gene or gene product" + "gene or gene product", + "genomic entity", + "chemical entity or gene or gene product", + "physical essence", + "ontology class" ], "aliases": [ "locus" @@ -6296,18 +7866,19 @@ "NCBIGene", "ENSEMBL", "HGNC", - "UniProtKB", "MGI", "ZFIN", "dictyBase", "WB", "WormBase", "FB", - "FB", "RGD", "SGD", "POMBASE", - "KEGG.GENE" + "OMIM", + "KEGG.GENE", + "UMLS", + "Xenbase" ], "in_subset": [ "model_organism_database" @@ -6355,32 +7926,13 @@ "model_organism_database" ] }, - "genomic entity": { - "is_a": "molecular entity", - "aliases": [ - "sequence feature" - ], - "description": "an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)", - "slots": [ - "has biological sequence" - ], - "exact_mappings": [ - "UMLSSG:GENE", - "SO:0000110", - "GENO:0000897" - ], - "narrow_mappings": [ - "UMLSSC:T028", - "UMLSST:gngm", - "UMLSSC:T086", - "UMLSST:nusq" - ], - "in_subset": [ - "model_organism_database" - ] - }, "genome": { - "is_a": "genomic entity", + "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", @@ -6392,7 +7944,7 @@ ] }, "exon": { - "is_a": "genomic entity", + "is_a": "nucleic acid 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", @@ -6401,7 +7953,7 @@ ] }, "transcript": { - "is_a": "genomic entity", + "is_a": "nucleic acid entity", "description": "An RNA synthesized on a DNA or RNA template by an RNA polymerase.", "exact_mappings": [ "SO:0000673", @@ -6417,41 +7969,65 @@ ] }, "coding sequence": { - "is_a": "genomic entity", + "is_a": "nucleic acid entity", "exact_mappings": [ "SO:0000316", "SIO:001390" ] }, - "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": "genomic entity", + "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": [ - "gene product mixin" + "thing with taxon", + "chemical entity or gene or gene product", + "chemical entity or protein or polypeptide" ], - "aliases": [ - "polypeptide" + "id_prefixes": [ + "UniProtKB", + "PR", + "ENSEMBL", + "FB", + "UMLS" ], - "broad_mappings": [ - "UMLSSC:T116", - "UMLSST:aapp" + "in_subset": [ + "model_organism_database" ], - "exact_mappings": [ - "PR:000000001", - "SIO:010043", - "WIKIDATA:Q8054", + "narrow_mappings": [ "SO:0000104", + "UMLSSC:T116", + "UMLSST:aapp", "UMLSSC:T087", "UMLSST:amas" + ] + }, + "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", + "thing with taxon" ], "id_prefixes": [ "UniProtKB", "PR", "ENSEMBL", - "FB" + "FB", + "UMLS" ], - "in_subset": [ - "model_organism_database" + "exact_mappings": [ + "PR:000000001", + "SIO:010043", + "WIKIDATA:Q8054" + ], + "narrow_mappings": [ + "UMLSSC:T126", + "UMLSST:enzy", + "UMLSSC:T192", + "UMLSST:rcpt" ] }, "protein isoform": { @@ -6553,7 +8129,7 @@ "orthogroup", "protein family" ], - "is_a": "molecular entity", + "is_a": "biological entity", "exact_mappings": [ "NCIT:C26004", "WIKIDATA:Q2278983" @@ -6564,7 +8140,8 @@ "WIKIDATA:Q417841" ], "mixins": [ - "gene grouping mixin" + "gene grouping mixin", + "chemical entity or gene or gene product" ], "description": "any grouping of multiple genes or gene products related by common descent", "id_prefixes": [ @@ -6599,7 +8176,13 @@ ] }, "genotype": { - "is_a": "genomic entity", + "is_a": "biological entity", + "mixins": [ + "physical essence", + "genomic entity", + "physical essence", + "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" @@ -6620,7 +8203,12 @@ ] }, "haplotype": { - "is_a": "genomic entity", + "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]", "exact_mappings": [ "GENO:0000871", @@ -6635,10 +8223,15 @@ "local_names": { "agr": "allele" }, - "is_a": "genomic entity", + "is_a": "biological entity", + "mixins": [ + "genomic entity", + "physical essence", + "ontology class" + ], "description": "An allele that varies in its sequence from what is considered the reference allele at that locus.", "comments": [ - "This class is for modeling the specific state at a locus.\nA single DBSNP rs ID could correspond to more than one sequence variants\n(e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)" + "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)" ], "broad_mappings": [ "SO:0001060" @@ -6708,10 +8301,21 @@ ] }, "reagent targeted gene": { - "is_a": "genomic entity", + "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 attribute": { @@ -6830,10 +8434,6 @@ "timepoint" ], "description": "A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes", - "broad_mappings": [ - "UMLSSC:T051", - "UMLSST:evnt" - ], "exact_mappings": [ "XCO:0000000" ], @@ -6842,10 +8442,12 @@ ] }, "genomic background exposure": { - "is_a": "genomic entity", "mixins": [ "exposure event", - "gene grouping mixin" + "gene grouping mixin", + "physical essence", + "genomic entity", + "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." }, @@ -6875,11 +8477,10 @@ ] }, "pathological process exposure": { - "is_a": "pathological process", "mixins": [ "exposure event" ], - "description": "A pathological process, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." + "description": "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." }, "pathological anatomical structure": { "description": "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.", @@ -6889,14 +8490,12 @@ ] }, "pathological anatomical exposure": { - "is_a": "pathological anatomical structure", "mixins": [ "exposure event" ], "description": "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." }, "disease or phenotypic feature exposure": { - "is_a": "disease or phenotypic feature", "mixins": [ "exposure event", "pathological entity mixin" @@ -6904,31 +8503,26 @@ "description": "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." }, "chemical exposure": { - "is_a": "chemical substance", "mixins": [ "exposure event" ], - "description": "A chemical exposure is an intake of a particular chemical substance, other than a drug.", + "description": "A chemical exposure is an intake of a particular chemical entity.", "exact_mappings": [ "ECTO:9000000", "SIO:001399" ] }, "complex chemical exposure": { - "description": "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug.", - "is_a": "chemical exposure", - "mixins": [ - "mixture" - ] + "description": "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." }, "drug exposure": { + "is_a": "chemical exposure", "aliases": [ "drug intake", "drug dose", "medication intake" ], "description": "A drug exposure is an intake of a particular drug.", - "is_a": "drug", "mixins": [ "exposure event" ], @@ -6954,7 +8548,7 @@ "is_a": "named thing", "mixins": [ "exposure event", - "chemical or drug or treatement" + "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": [ @@ -6972,35 +8566,31 @@ "viral exposure", "bacterial exposure" ], - "is_a": "organism taxon", "mixins": [ "exposure event" ], "description": "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." }, "geographic exposure": { - "is_a": "geographic location", + "is_a": "environmental exposure", "mixins": [ "exposure event" ], "description": "A geographic exposure is a factor relating to geographic proximity to some impactful entity." }, "environmental exposure": { - "is_a": "environmental process", "mixins": [ "exposure event" ], "description": "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." }, "behavioral exposure": { - "is_a": "behavior", "mixins": [ "exposure event" ], "description": "A behavioral exposure is a factor relating to behavior impacting an individual." }, "socioeconomic exposure": { - "is_a": "behavior", "mixins": [ "exposure event" ], @@ -7017,49 +8607,42 @@ "description": "An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes." }, "pathological process outcome": { - "is_a": "pathological process", "mixins": [ "outcome" ], "description": "An outcome resulting from an exposure event which is the manifestation of a pathological process." }, "pathological anatomical outcome": { - "is_a": "pathological anatomical structure", "mixins": [ "outcome" ], "description": "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure." }, "disease or phenotypic feature outcome": { - "is_a": "disease or phenotypic feature", "mixins": [ "outcome" ], "description": "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype." }, "behavioral outcome": { - "is_a": "behavior", "mixins": [ "outcome" ], "description": "An outcome resulting from an exposure event which is the manifestation of human behavior." }, "hospitalization outcome": { - "is_a": "hospitalization", "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": { - "is_a": "death", "mixins": [ "outcome" ], "description": "An outcome of death from resulting from an exposure event." }, "epidemiological outcome": { - "is_a": "biological entity", "mixins": [ "outcome" ], @@ -7069,7 +8652,6 @@ ] }, "socioeconomic outcome": { - "is_a": "behavior", "mixins": [ "outcome" ], @@ -7360,22 +8942,22 @@ } } }, - "molecular entity to entity association mixin": { - "description": "An interaction between a molecular entity and another entity", + "chemical entity to entity association mixin": { + "description": "An interaction between a chemical entity and another entity", "mixin": true, "defining_slots": [ "subject" ], "slot_usage": { "subject": { - "range": "molecular entity", - "description": "the molecular entity that is an interactor" + "range": "chemical entity", + "description": "the chemical entity that is an interactor" } } }, "drug to entity association mixin": { "description": "An interaction between a drug and another entity", - "is_a": "molecular entity to entity association mixin", + "is_a": "chemical entity to entity association mixin", "mixin": true, "defining_slots": [ "subject" @@ -7389,15 +8971,15 @@ }, "chemical to entity association mixin": { "description": "An interaction between a chemical entity and another entity", - "is_a": "molecular entity to entity association mixin", + "is_a": "chemical entity to entity association mixin", "mixin": true, "defining_slots": [ "subject" ], "slot_usage": { "subject": { - "range": "chemical substance", - "description": "the chemical substance or entity that is an interactor" + "range": "chemical entity", + "description": "the chemical entity or entity that is an interactor" } } }, @@ -7426,13 +9008,41 @@ ], "slot_usage": { "object": { - "range": "chemical substance", + "range": "chemical entity", "description": "the chemical element that is the target of the statement" } } }, + "reaction to participant association": { + "description": null, + "is_a": "chemical to chemical association", + "slots": [ + "stoichiometry", + "reaction direction", + "reaction side" + ], + "slot_usage": { + "subject": { + "range": "molecular entity" + } + }, + "defining_slots": [ + "subject", + "predicate", + "object" + ] + }, + "reaction to catalyst association": { + "description": null, + "is_a": "reaction to participant association", + "slot_usage": { + "object": { + "range": "gene or gene product" + } + } + }, "chemical to chemical derivation association": { - "description": "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF\n R has-input C1 AND\n R has-output C2 AND\n R enabled-by P AND\n R type Reaction\n THEN\n C1 derives-into C2 <>", + "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:\n IF\n R has-input C1 AND\n R has-output C2 AND\n R enabled-by P AND\n R type Reaction\n THEN\n C1 derives-into C2 <>", "is_a": "chemical to chemical association", "defining_slots": [ "subject", @@ -7444,18 +9054,18 @@ ], "slot_usage": { "subject": { - "range": "chemical substance", + "range": "chemical entity", "description": "the upstream chemical entity" }, "object": { - "range": "chemical substance", + "range": "chemical entity", "description": "the downstream chemical entity" }, "predicate": { "subproperty_of": "derives into" }, "catalyst qualifier": { - "description": "this connects the derivation edge to the molecular entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." + "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." } } }, @@ -7636,16 +9246,7 @@ ] }, "exposure event to entity association mixin": { - "description": "An association between some exposure event and some entity.", - "mixin": true, - "defining_slots": [ - "subject" - ], - "slot_usage": { - "subject": { - "range": "exposure event" - } - } + "deprecated": true }, "entity to outcome association mixin": { "description": "An association between some entity and an outcome", @@ -7730,6 +9331,28 @@ "sex qualifier" ] }, + "named thing to information content entity 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": "named thing" + }, + "object": { + "range": "publication" + }, + "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, @@ -7772,18 +9395,6 @@ } } }, - "disease or phenotypic feature association to location association": { - "deprecated": "This association class name is deprecated in favor of the 'disease or phenotypic feature to location association' class.", - "is_a": "association", - "mixins": [ - "disease or phenotypic feature to entity association mixin" - ], - "slot_usage": { - "object": { - "range": "anatomical entity" - } - } - }, "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", @@ -7899,7 +9510,7 @@ ] }, "behavior to behavioral feature association": { - "description": "An association between an aggregate behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior.", + "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", @@ -8314,6 +9925,50 @@ } } }, + "organism to organism association": { + "is_a": "association", + "defining_slots": [ + "subject", + "predicate", + "object" + ], + "slot_usage": { + "subject": { + "range": "individual organism" + }, + "relation": { + "values_from": [ + "ro" + ] + }, + "object": { + "range": "individual organism", + "description": "An association between two individual organisms." + } + } + }, + "taxon to taxon association": { + "is_a": "association", + "defining_slots": [ + "subject", + "predicate", + "object" + ], + "slot_usage": { + "subject": { + "range": "organism taxon" + }, + "relation": { + "values_from": [ + "ro" + ] + }, + "object": { + "range": "organism taxon", + "description": "An association between individuals of different taxa." + } + } + }, "gene has variant that contributes to disease association": { "is_a": "gene to disease association", "defining_slots": [ @@ -8495,7 +10150,7 @@ ], "slot_usage": { "subject": { - "range": "molecular entity", + "range": "gene", "description": "gene, product or macromolecular complex that has the function associated with the GO term", "examples": [ { @@ -8519,25 +10174,47 @@ } } }, + "entity to disease association": { + "is_a": "association", + "exact_mappings": null, + "slots": [ + "FDA approval status" + ], + "defining_slots": [ + "subject", + "object" + ] + }, + "entity to phenotypic feature association": { + "is_a": "association", + "exact_mappings": null, + "slots": [ + "FDA approval status" + ], + "defining_slots": [ + "subject", + "object" + ] + }, "sequence association": { "is_a": "association", - "description": "An association between a sequence feature and a genomic entity it is localized to." + "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 genomic entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig.", + "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": "genomic entity" + "range": "nucleic acid entity" }, "object": { "aliases": [ "reference" ], - "range": "genomic entity" + "range": "nucleic acid entity" }, "predicate": { "subproperty_of": "has sequence location" @@ -8560,10 +10237,10 @@ "description": "For example, a particular exon is part of a particular transcript or gene", "slot_usage": { "subject": { - "range": "genomic entity" + "range": "nucleic acid entity" }, "object": { - "range": "genomic entity" + "range": "nucleic acid entity" } }, "exact_mappings": [ @@ -8794,9 +10471,9 @@ "description": "the environment in which the organism occurs" }, "predicate": { - "description": "predicate describing the relationship between the taxon and the environment" + "description": "predicate describing the relationship between the taxon and the environment\n " } } } } -} \ No newline at end of file +}